diff --git a/.Rhistory b/.Rhistory
index e57ef8c..3abf73f 100644
--- a/.Rhistory
+++ b/.Rhistory
@@ -1,207 +1,512 @@
-library(devtools)
-load_all(".")
-freq
-freq.data.frame(esoph[, c("alcgp", "agegp")])
-unclass(freq.data.frame(esoph[, c("alcgp", "agegp")]))
-q("no")
-library(devtools)
-args(build)
-build(binary=T)
-q("no")
-args(print)
-cross(cbind(...) ~ agegp, data = esoph, test = T)
-library(biostat2)
-cross(cbind(...) ~ agegp, data = esoph, test = T)
-x = cross(cbind(...) ~ agegp, data = esoph, test = T)
-res
-res
-load_all()
-library(devtools)
-load_all()
-x = cross(cbind(...) ~ agegp, data = esoph, test = T)
-x
-q("no")
-library(devtools)
-load_all()
-x = cross(cbind(...) ~ agegp, data = esoph, test = T)
-x
-class(x)
-load_all()
-x = cross(cbind(...) ~ agegp, data = esoph, test = T)
-)
-load_all()
-x = cross(cbind(...) ~ agegp, data = esoph, test = T)
-x
-x
-x
-library(pander)
-pander(x)
-install.packages("pander")
-library(pander)
-pander(x)
-knitr::kable(x)
-x
-unclass(x)
-x
-x = cross(cbind(...) ~ agegp, data = esoph, test = T)
-x
-as.data.frame(x)
-fun(x)
-length(esoph)
-is.list(x)
-is.data.frame(x)
-x
-x
-x = cross(... ~ agegp, data = esoph, test = T)
+varnames = names(data)
+varnames = names(data)
+parsed = parse_formula(formula, varnames)
+data = parse_data(expand_formula(formula, varnames), data)
+names(data) = remove_blank(names(data))
+varform = names(data)
+if (regroup) {
+numdata = varform[sapply(data, function(x) is.numeric(x) & !is.Surv(x))]
+catdata = varform[sapply(data, is.character.or.factor)]
+survdata = varform[sapply(data, is.Surv)]
+parsed$left = regroup(parsed$left, numdata, catdata, survdata)
+parsed$right = regroup(parsed$right, numdata, catdata, survdata)
+}
+eg = expand.grid(left=parsed$left, right=parsed$right, stringsAsFactors = F)
+comb = eg %>%
+pmap(list) %>%
+modify_depth(2, ~{
+if(.x==".") return(NULL)
+of = .x %>% .[.!="."] %>% elements %>% remove_blank
+data %>% select(one_of(of))
+})
+results = comb %>%
+map(cross_list,
+funs=funs, ..., margin=margin, total=total, digits=digits, showNA=showNA, method=method, times=times, followup=followup, test=test, test.summarize=test.summarize, test.tabular=test.tabular, test.survival=test.survival, show.test=show.test, plim=plim, effect=effect, effect.summarize=effect.summarize, effect.tabular=effect.tabular, effect.survival=effect.survival, conf.level=conf.level, show.method=show.method, label=label)
+results
+comb
+cross_list(comb[[1]], funs=funs, ..., margin=margin, total=total, digits=digits, showNA=showNA, method=method, times=times, followup=followup, test=test, test.summarize=test.summarize, test.tabular=test.tabular, test.survival=test.survival, show.test=show.test, plim=plim, effect=effect, effect.summarize=effect.summarize, effect.tabular=effect.tabular, effect.survival=effect.survival, conf.level=conf.level, show.method=show.method, label=label)
+comb[[1]]
+cross_list
 x
-load_all()
-x = cross(... ~ agegp, data = esoph, test = T)
-load_all()
-load_all()
-x = cross(... ~ agegp, data = esoph, test = T)
-q("no")
-library(devtools);load_all()
-x = cross(... ~ agegp, data = esoph, test = T)
 x
-x = cross(cbind(...) ~ agegp, data = esoph, test = T)
+x()
+eg
+eg
+eg %>%
+pmap(list)
+results = data %>% select(x) %>% cross_list(funs=funs, ..., margin=margin, total=total, digits=digits, showNA=showNA, method=method, times=times, followup=followup, test=test, test.summarize=test.summarize, test.tabular=test.tabular, test.survival=test.survival, show.test=show.test, plim=plim, effect=effect, effect.summarize=effect.summarize, effect.tabular=effect.tabular, effect.survival=effect.survival, conf.level=conf.level, show.method=show.method, label=label)
+vars_select(data, x)
+tidyselect::vars_select(data, x)
+tidyselect::vars_select(names(data), x)
+cross_list
+data %>% select(tidyselect::vars_select(names(data), x))
+tidyselect::vars_select(names(data), x) %>% class
+data %>% select(tidyselect::vars_select(names(data), x)) %>% cross_list(funs=funs, ..., margin=margin, total=total, digits=digits, showNA=showNA, method=method, times=times, followup=followup, test=test, test.summarize=test.summarize, test.tabular=test.tabular, test.survival=test.survival, show.test=show.test, plim=plim, effect=effect, effect.summarize=effect.summarize, effect.tabular=effect.tabular, effect.survival=effect.survival, conf.level=conf.level, show.method=show.method, label=label)
+results = data %>% select(tidyselect::vars_select(names(data), x)) %>% cross_list(data=., funs=funs, ..., margin=margin, total=total, digits=digits, showNA=showNA, method=method, times=times, followup=followup, test=test, test.summarize=test.summarize, test.tabular=test.tabular, test.survival=test.survival, show.test=show.test, plim=plim, effect=effect, effect.summarize=effect.summarize, effect.tabular=effect.tabular, effect.survival=effect.survival, conf.level=conf.level, show.method=show.method, label=label)
+cross_all
+comb
+data
+cross_list
+source('F:/GITHUB/fork_biostat2/R/crosstable.r', encoding = 'UTF-8')
+# Formula parsing *****************************************************
+browser()
+varnames = names(data)
+varnames = names(data)
+parsed = parse_formula(formula, varnames)
+data = parse_data(expand_formula(formula, varnames), data)
+names(data) = remove_blank(names(data))
+varform = names(data)
+if (regroup) {
+numdata = varform[sapply(data, function(x) is.numeric(x) & !is.Surv(x))]
+catdata = varform[sapply(data, is.character.or.factor)]
+survdata = varform[sapply(data, is.Surv)]
+parsed$left = regroup(parsed$left, numdata, catdata, survdata)
+parsed$right = regroup(parsed$right, numdata, catdata, survdata)
+}
+eg = expand.grid(left=parsed$left, right=parsed$right, stringsAsFactors = F)
+comb = eg %>%
+pmap(list) %>%
+modify_depth(2, ~{
+if(.x==".") return(NULL)
+of = .x %>% .[.!="."] %>% elements %>% remove_blank
+data %>% select(one_of(of))
+})
+data %>% select(tidyselect::vars_select(names(data), x))
+cross_list
+comb
+results = data %>% select(tidyselect::vars_select(names(data), x)) %>% cross_all(funs=funs, ..., margin=margin, total=total, digits=digits, showNA=showNA, method=method, times=times, followup=followup, test=test, test.summarize=test.summarize, test.tabular=test.tabular, test.survival=test.survival, show.test=show.test, plim=plim, effect=effect, effect.summarize=effect.summarize, effect.tabular=effect.tabular, effect.survival=effect.survival, conf.level=conf.level, show.method=show.method, label=label)
+results
+by
+data %>% select(tidyselect::vars_select(names(data), by))
+x2 = data %>% select(tidyselect::vars_select(names(data), x))
+y2
+y2=NULL
+cross_all(x2, y2, funs=funs, ..., margin=margin, total=total, digits=digits, showNA=showNA, method=method, times=times, followup=followup, test=test, test.summarize=test.summarize, test.tabular=test.tabular, test.survival=test.survival, show.test=show.test, plim=plim, effect=effect, effect.summarize=effect.summarize, effect.tabular=effect.tabular, effect.survival=effect.survival, conf.level=conf.level, show.method=show.method, label=label)
+?select_
+cross_all
 x
+x=starts_with("Sepal")
 x
-unclass(x)
-as.data.frame(x)
-x
-is.list(x)
-unclass(x)
-data.frame(unclass(x))
-data.frame(x)
-library(devtools);load_all()
-x = cross(cbind(...) ~ agegp, data = esoph, test = T)
-x
-class(x)
-x = cross(... ~ agegp, data = esoph, test = T)
-x
-class(x)
-class(x[[1]])
-check()
-q("no")
-q("no")
-library(devtools)
-document()
-check()
-check()
-rename
-x
-load_all()
-x = cross(... ~ agegp, data = esoph, test = T)
-x
-x = cross(cbind(...) ~ agegp, data = esoph, test = T)
-x
-names(x)
-names(x)[1] <- "modalité"
-x
-load_all()
-x = cross(cbind(...) ~ agegp, data = esoph, test = T)
-names(x)[1] <- "modalité"
-x
-names(x)[1] <- "Variable"
-x
-build()
-build(binary = T)
-install_local("../biostat2_0.1.zip")
-q("no")
-library(devtools)
-build()
-build(binary = TRUE)
-q("no")
-load_all()
-library(devtools)
-load_all()
-library(survival)
-cross(Surv(time, status) ~ x, data = aml, total= T, test = T)
-q("no")
-library(devtools)
-build()
-build(binary = T)
-install.packages("../biostat2_0.2.zip")
-q("no")
-args(t.test)
-?t.test
-?wilcox.test
-sapply(esoph$ncases, esoph$alcgp)
-sapply(esoph$ncases, esoph$alcgp, c)
-tapply(esoph$ncases, esoph$alcgp, c)
-tapply(esoph$ncases, esoph$alcgp, c, simplify = FALSE)
-?wilcox.test
-?t.test
-load.all()
-library(devtools)
-load_all()
-cross(cbind(...) ~ alcgp, data = esoph, test = T)
-esoph$trt <- rep(c("A", "B"), length = nrow(esoph))
-cross(cbind(...) ~ alcgp, data = esoph, test = T)
-esoph$num <- rnorm(nrow(esoph))
-cross(cbind(...) ~ alcgp, data = esoph, test = T)
-cross(cbind(...) ~ trt, data = esoph, test = T)
-?wilcox.test
-kruskal.test(esoph$ncases, esoph$trt)
-kruskal.test(esoph$ncases ~ esoph$trt)
-esoph$trt
-esoph$ncases
-kruskal.test(esoph$ncases, esoph$trt)
-kruskal.test(esoph$ncases, factor(esoph$trt))
-wilcox.test(esoph$ncases ~factor(esoph$trt), correct = F)
-?kruskall
-?kruskall.t
-?kruskal.test
-oneway.test(esoph$num ~ esoph$trt, var.equal = FALSE)
-oneway.test(esoph$num ~ esoph$trt, var.equal = TRUE)
-t.test(esoph$num ~ esoph$trt, var.equal = TRUE)
-t.test(esoph$num ~ esoph$trt, var.equal = FALSE)
-?t.test
-check()
-check()
-load_all()
-cross(cbind(...) ~ trt, data = esoph, test = T)
-cross(cbind(...) ~ trt, data = esoph, test = T, test.summarize = test.summarize.kruskal)
-load_all()
-cross(cbind(...) ~ trt, data = esoph, test = T, test.summarize = test.summarize.kruskal)
-cross(cbind(...) ~ trt, data = esoph, test = T)
-cross(cbind(...) ~ trt, data = esoph, test = T, test.summarize = test.summarize.kruskal)
-cross(cbind(...) ~ trt, data = esoph, test = T, test.summarize = test.summarize.oneway.equal)
-cross(cbind(...) ~ trt, data = esoph, test = T, test.summarize = test.summarize.oneway.equalvar)
-cross(cbind(...) ~ trt, data = esoph, test = T, test.summarize = test.summarize.oneway.unequalvar)
-cross(cbind(...) ~ trt, data = esoph, test = T, test.summarize = test.summarize.kruskal)
-cross(cbind(num) ~ trt, data = esoph, test = T, test.summarize = test.summarize.kruskal)
-cross(cbind(ncases) ~ trt, data = esoph, test = T, test.summarize = test.summarize.kruskal)
-wilcox.test(esoph$num ~ esoph$trt)
-cross(cbind(num) ~ trt, data = esoph, test = T, test.summarize = test.summarize.kruskal)
-cross(cbind(ncases) ~ trt, data = esoph, test = T, test.summarize = test.summarize.kruskal)
-cross(cbind(num) ~ trt, data = esoph, test = T, test.summarize = test.summarize.kruskal)
-cross(cbind(num) ~ alcgp, data = esoph, test = T, test.summarize = test.summarize.kruskal)
-build()
-build(binary = TRUE)
-install.packages("../biostat2_0.5.zip")
-q("no")
-library(devtools)
-document()
-build()
-load_all()
-FlexCrossTable
-?FlexCrossTable
-     library(ReporteRs)
-     mytable <- cross(cbind(...) ~ tobgp, esoph, test = TRUE)
-     CrossFlexTable(mytable)
-
-document()
-load_all()
-     library(ReporteRs)
-     mytable <- cross(cbind(...) ~ tobgp, esoph, test = TRUE)
-     CrossFlexTable(mytable)
-
-load_all()
-     FlexCrossTable(mytable)
-     FlexCrossTable(mytable, TRUE)
-build()
-build(binary = TRUE)
-q("no")
-install.packages("../biostat2_0.6.zip", repos = NULL)
-q("no")
+source('F:/GITHUB/fork_biostat2/R/crosstable.r', encoding = 'UTF-8')
+tidyselect::vars_select(names(data), x) %>% class
+tidyselect::vars_select(names(data), x)
+source('F:/GITHUB/fork_biostat2/R/crosstable.r', encoding = 'UTF-8')
+tidyselect::vars_select(names(data), x)
+y2 = data %>% select(tidyselect::vars_select(names(data), by))
+y2
+x2 = data %>% select(tidyselect::vars_select(names(data), x, -by))
+x2
+results = cross_all(x2, y2, funs=funs, ..., margin=margin, total=total, digits=digits, showNA=showNA, method=method, times=times, followup=followup, test=test, test.summarize=test.summarize, test.tabular=test.tabular, test.survival=test.survival, show.test=show.test, plim=plim, effect=effect, effect.summarize=effect.summarize, effect.tabular=effect.tabular, effect.survival=effect.survival, conf.level=conf.level, show.method=show.method, label=label)
+results
+assert_scalar
+y2
+byname = tidyselect::vars_select(names(data), by)
+byname
+assert_scalar(byname)
+x2
+assert_scalar(y2)
+check_scalar(byname)
+check_scalar(y2)
+test_scalar(y2)
+install.packages("assertive")
+assertive::assert_is_scalar(byname)
+assertive::assert_is_scalar(y2)
+y2
+xname = tidyselect::vars_select(names(data), x, -by)
+assertive::assert_is_scalar(xname)
+assert_scalar(xname)
+assert_scalar(xname, .var.name = "frfrfr")
+cross_all
+##' @export
+##' @import checkmate dplyr purrr
+crosstable = function(data, x=everything(), by=NULL, formula = cbind(...) ~ ., funs = c(" " = cross_summary), ..., margin = c("all", "row", "column", "cell"), total = c("none", "all", "row", "column", "FALSE", "TRUE", 0, 1, 2), digits = 2, showNA = c("no", "ifany", "always"), method = c("pearson", "kendall", "spearman"), times = NULL, followup = FALSE, test = FALSE, test.summarize = test.summarize.auto, test.survival = test.survival.logrank, test.tabular = test.tabular.auto, show.test = display.test, plim = 4, show.method = TRUE, effect = FALSE, effect.summarize = diff.mean.auto, effect.tabular = or.row.by.col, effect.survival = effect.survival.coxph, conf.level = 0.95, label = TRUE, regroup = FALSE) {
+# Arguments checks ****************************************************
+coll = makeAssertCollection()
+# assertFormula(formula, add=coll)
+assertDataFrame(data, add=coll)
+assertCount(digits, add=coll)
+assertLogical(label, add=coll)
+if (!is.character(funs)) {
+nomf = names(funs)
+funs = as.character(as.list(substitute(funs)))
+funs = funs[funs != "c" & funs != "list"]
+names(funs) = nomf
+}
+if (missing(margin)) margin = "all"
+if (is.character(margin)) {
+assertSubset(margin, c("all", "row", "column", "cell"), add=coll)
+if(is.null(margin)) {
+margin=0:2 #defaulting
+} else {
+marginopts = list(all = 0:2,
+row = 1,
+column = 2,
+cell = 0)
+margin = unname(unlist(marginopts[margin]))
+}
+}
+if (missing(total)) total = "none"
+if (is.character(total)) {
+assertChoice(total, c("none", "both", "all", "row", "column"), add=coll)
+if(is.null(total)) {
+total=0 #defaulting
+} else {
+totalopts = list(all = 1:2,
+both = 1:2,
+row = 1,
+column = 2,
+none = 0)
+total = unname(unlist(totalopts[total]))
+}
+}
+if (is_formula(formula))
+formula = paste(deparse(formula, 500), collapse="")
+reportAssertions(coll)
+byname = tidyselect::vars_select(names(data), by)
+xnames = tidyselect::vars_select(names(data), x, -by)
+assert_scalar(byname, .var.name = "by")
+assert_(xnames, .var.name = "x")
+# Formula parsing *****************************************************
+# varnames = names(data)
+# parsed = parse_formula(formula, varnames)
+# # parsed$left = gsub("\\n *", "", parsed$left)
+#
+# data = parse_data(expand_formula(formula, varnames), data)
+# names(data) = remove_blank(names(data))
+# varform = names(data)
+#
+# if (regroup) {
+#     numdata = varform[sapply(data, function(x) is.numeric(x) & !is.Surv(x))]
+#     catdata = varform[sapply(data, is.character.or.factor)]
+#     survdata = varform[sapply(data, is.Surv)]
+#
+#     parsed$left = regroup(parsed$left, numdata, catdata, survdata)
+#     parsed$right = regroup(parsed$right, numdata, catdata, survdata)
+# }
+#
+# eg = expand.grid(left=parsed$left, right=parsed$right, stringsAsFactors = F)
+# #eg (DF) : chaque ligne est une combinaison by en fonction du nombre de +
+#
+#
+# comb = eg %>%
+#     pmap(list) %>%
+#     modify_depth(2, ~{
+#         if(.x==".") return(NULL)
+#         of = .x %>% .[.!="."] %>% elements %>% remove_blank
+#         data %>% select(one_of(of))
+#     })
+#
+#
+# # Results *****************************************************
+#
+# results = comb %>%
+#     map(cross_list, funs=funs, ..., margin=margin, total=total, digits=digits, showNA=showNA, method=method, times=times, followup=followup, test=test, test.summarize=test.summarize, test.tabular=test.tabular, test.survival=test.survival, show.test=show.test, plim=plim, effect=effect, effect.summarize=effect.summarize, effect.tabular=effect.tabular, effect.survival=effect.survival, conf.level=conf.level, show.method=show.method, label=label)
+# browser()
+tidyselect::vars_select(names(data), x)
+y2 = data %>% select(byname)
+x2 = data %>% select(xnames)
+results = cross_all(x2, y2, funs=funs, ..., margin=margin, total=total, digits=digits, showNA=showNA, method=method, times=times, followup=followup, test=test, test.summarize=test.summarize, test.tabular=test.tabular, test.survival=test.survival, show.test=show.test, plim=plim, effect=effect, effect.summarize=effect.summarize, effect.tabular=effect.tabular, effect.survival=effect.survival, conf.level=conf.level, show.method=show.method, label=label)
+if (length(results) == 1) {
+results = results[[1]]
+class(results) = c("crosstable", "data.frame")
+} else {
+results = results[results != "What?"]
+}
+# attr(results, "formula") = formula
+# attr(results, "left") = parsed$left
+# attr(results, "right") = parsed$right
+# attr(results, "by") = parsed$by
+# attr(results, "data") = data
+return(results)
+}
+crosstable(data = iris, x=starts_with("S"), by="Species")
+source('F:/GITHUB/fork_biostat2/R/crosstable.r', encoding = 'UTF-8')
+crosstable(data = iris, x=starts_with("S"), by="Species")
+cross_list
+source('F:/GITHUB/fork_biostat2/R/crosstable.r', encoding = 'UTF-8')
+data
+varnames = names(data)
+parsed = parse_formula(formula, varnames)
+parse_data(expand_formula(formula, varnames), data)
+x2 = data %>% select(xnames)
+y2 = data %>% select(byname)
+x2
+y2
+cross_all(x2, y2, funs=funs, ..., margin=margin, total=total, digits=digits, showNA=showNA, method=method, times=times, followup=followup, test=test, test.summarize=test.summarize, test.tabular=test.tabular, test.survival=test.survival, show.test=show.test, plim=plim, effect=effect, effect.summarize=effect.summarize, effect.tabular=effect.tabular, effect.survival=effect.survival, conf.level=conf.level, show.method=show.method, label=label)
+source('F:/GITHUB/fork_biostat2/R/crosstable.r', encoding = 'UTF-8')
+crosstable(data = iris, x=starts_with("S"), by="Species")
+crosstable(data = iris, x=everything(), by="Species")
+crosstable(data = iris, x=everything())
+source('F:/GITHUB/fork_biostat2/R/crosstable.r', encoding = 'UTF-8')
+by
+tidyselect::vars_select(names(data), x, -by)
+byname = tidyselect::vars_select(names(data), by)
+byname
+tidyselect::vars_select(names(data), x, -byname)
+source('F:/GITHUB/fork_biostat2/R/crosstable.r', encoding = 'UTF-8')
+source('F:/GITHUB/fork_biostat2/R/crosstable.r', encoding = 'UTF-8')
+crosstable(data = iris, x=starts_with("S"))
+crosstable(data = iris, x=everything())
+##' @export
+##' @import checkmate dplyr purrr
+crosstable = function(data, x=everything(), by=NULL, formula = cbind(...) ~ ., funs = c(" " = cross_summary), ..., margin = c("all", "row", "column", "cell"), total = c("none", "all", "row", "column", "FALSE", "TRUE", 0, 1, 2), digits = 2, showNA = c("no", "ifany", "always"), method = c("pearson", "kendall", "spearman"), times = NULL, followup = FALSE, test = FALSE, test.summarize = test.summarize.auto, test.survival = test.survival.logrank, test.tabular = test.tabular.auto, show.test = display.test, plim = 4, show.method = TRUE, effect = FALSE, effect.summarize = diff.mean.auto, effect.tabular = or.row.by.col, effect.survival = effect.survival.coxph, conf.level = 0.95, label = TRUE, regroup = FALSE) {
+# Arguments checks ****************************************************
+coll = makeAssertCollection()
+# assertFormula(formula, add=coll)
+assertDataFrame(data, add=coll)
+assertCount(digits, add=coll)
+assertLogical(label, add=coll)
+if (!is.character(funs)) {
+nomf = names(funs)
+funs = as.character(as.list(substitute(funs)))
+funs = funs[funs != "c" & funs != "list"]
+names(funs) = nomf
+}
+if (missing(margin)) margin = "all"
+if (is.character(margin)) {
+assertSubset(margin, c("all", "row", "column", "cell"), add=coll)
+if(is.null(margin)) {
+margin=0:2 #defaulting
+} else {
+marginopts = list(all = 0:2,
+row = 1,
+column = 2,
+cell = 0)
+margin = unname(unlist(marginopts[margin]))
+}
+}
+if (missing(total)) total = "none"
+if (is.character(total)) {
+assertChoice(total, c("none", "both", "all", "row", "column"), add=coll)
+if(is.null(total)) {
+total=0 #defaulting
+} else {
+totalopts = list(all = 1:2,
+both = 1:2,
+row = 1,
+column = 2,
+none = 0)
+total = unname(unlist(totalopts[total]))
+}
+}
+if (is_formula(formula))
+formula = paste(deparse(formula, 500), collapse="")
+reportAssertions(coll)
+# browser()
+byname = tidyselect::vars_select(names(data), by)
+xnames = tidyselect::vars_select(names(data), x, -byname)
+assert_scalar(byname, .var.name = "by")
+# Formula parsing *****************************************************
+# varnames = names(data)
+# parsed = parse_formula(formula, varnames)
+# # parsed$left = gsub("\\n *", "", parsed$left)
+#
+# data = parse_data(expand_formula(formula, varnames), data)
+# names(data) = remove_blank(names(data))
+# varform = names(data)
+#
+# if (regroup) {
+#     numdata = varform[sapply(data, function(x) is.numeric(x) & !is.Surv(x))]
+#     catdata = varform[sapply(data, is.character.or.factor)]
+#     survdata = varform[sapply(data, is.Surv)]
+#
+#     parsed$left = regroup(parsed$left, numdata, catdata, survdata)
+#     parsed$right = regroup(parsed$right, numdata, catdata, survdata)
+# }
+#
+# eg = expand.grid(left=parsed$left, right=parsed$right, stringsAsFactors = F)
+# #eg (DF) : chaque ligne est une combinaison by en fonction du nombre de +
+#
+#
+# comb = eg %>%
+#     pmap(list) %>%
+#     modify_depth(2, ~{
+#         if(.x==".") return(NULL)
+#         of = .x %>% .[.!="."] %>% elements %>% remove_blank
+#         data %>% select(one_of(of))
+#     })
+#
+#
+# # Results *****************************************************
+#
+# results = comb %>%
+#     map(cross_list, funs=funs, ..., margin=margin, total=total, digits=digits, showNA=showNA, method=method, times=times, followup=followup, test=test, test.summarize=test.summarize, test.tabular=test.tabular, test.survival=test.survival, show.test=show.test, plim=plim, effect=effect, effect.summarize=effect.summarize, effect.tabular=effect.tabular, effect.survival=effect.survival, conf.level=conf.level, show.method=show.method, label=label)
+# browser()
+# tidyselect::vars_select(names(data), x)
+x2 = data %>% select(xnames)
+y2 = data %>% select(byname)
+results = cross_all(x2, y2, funs=funs, ..., margin=margin, total=total, digits=digits, showNA=showNA, method=method, times=times, followup=followup, test=test, test.summarize=test.summarize, test.tabular=test.tabular, test.survival=test.survival, show.test=show.test, plim=plim, effect=effect, effect.summarize=effect.summarize, effect.tabular=effect.tabular, effect.survival=effect.survival, conf.level=conf.level, show.method=show.method, label=label)
+# if (length(results) == 1) {
+#     results = results[[1]]
+# } else {
+#     results = results[results != "What?"]
+# }
+class(results) = c("crosstable", "data.frame")
+# attr(results, "formula") = formula
+# attr(results, "left") = parsed$left
+# attr(results, "right") = parsed$right
+# attr(results, "by") = parsed$by
+# attr(results, "data") = data
+return(results)
+}
+crosstable(data = iris, x=starts_with("S"), by="Species")
+crosstable(data = iris, x=starts_with("S"))
+source('F:/GITHUB/fork_biostat2/R/crosstable.r', encoding = 'UTF-8')
+source('F:/GITHUB/fork_biostat2/R/crosstable.r', encoding = 'UTF-8')
+crosstable(data = iris, x=starts_with("S"), by="Species")
+crosstable(data = iris, x=starts_with("S"))
+crosstable(data = iris, x=everything())
+source('F:/GITHUB/fork_biostat2/R/crosstable.r', encoding = 'UTF-8')
+byname = tidyselect::vars_select(names(data), by)
+byname
+xnames = tidyselect::vars_select(names(data), x, -byname)
+xnames
+assert_scalar(byname, .var.name = "by", null.ok = T)
+byname = tidyselect::vars_select(names(data), by)
+xnames = tidyselect::vars_select(names(data), x, -byname)
+byname
+xnames
+x2 = data %>% select(xnames)
+y2 = data %>% select(byname)
+x2
+y2
+install.packages("assertive")
+ncol(y2)
+source('F:/GITHUB/fork_biostat2/R/crosstable.r', encoding = 'UTF-8')
+##' @export
+##' @import checkmate dplyr purrr
+crosstable = function(data, x=everything(), by=NULL, formula = cbind(...) ~ ., funs = c(" " = cross_summary), ..., margin = c("all", "row", "column", "cell"), total = c("none", "all", "row", "column", "FALSE", "TRUE", 0, 1, 2), digits = 2, showNA = c("no", "ifany", "always"), method = c("pearson", "kendall", "spearman"), times = NULL, followup = FALSE, test = FALSE, test.summarize = test.summarize.auto, test.survival = test.survival.logrank, test.tabular = test.tabular.auto, show.test = display.test, plim = 4, show.method = TRUE, effect = FALSE, effect.summarize = diff.mean.auto, effect.tabular = or.row.by.col, effect.survival = effect.survival.coxph, conf.level = 0.95, label = TRUE, regroup = FALSE) {
+# Arguments checks ****************************************************
+coll = makeAssertCollection()
+# assertFormula(formula, add=coll)
+assertDataFrame(data, add=coll)
+assertCount(digits, add=coll)
+assertLogical(label, add=coll)
+if (!is.character(funs)) {
+nomf = names(funs)
+funs = as.character(as.list(substitute(funs)))
+funs = funs[funs != "c" & funs != "list"]
+names(funs) = nomf
+}
+if (missing(margin)) margin = "all"
+if (is.character(margin)) {
+assertSubset(margin, c("all", "row", "column", "cell"), add=coll)
+if(is.null(margin)) {
+margin=0:2 #defaulting
+} else {
+marginopts = list(all = 0:2,
+row = 1,
+column = 2,
+cell = 0)
+margin = unname(unlist(marginopts[margin]))
+}
+}
+if (missing(total)) total = "none"
+if (is.character(total)) {
+assertChoice(total, c("none", "both", "all", "row", "column"), add=coll)
+if(is.null(total)) {
+total=0 #defaulting
+} else {
+totalopts = list(all = 1:2,
+both = 1:2,
+row = 1,
+column = 2,
+none = 0)
+total = unname(unlist(totalopts[total]))
+}
+}
+if (is_formula(formula))
+formula = paste(deparse(formula, 500), collapse="")
+reportAssertions(coll)
+# browser()
+byname = tidyselect::vars_select(names(data), by)
+xnames = tidyselect::vars_select(names(data), x, -byname)
+assert_scalar(byname, .var.name = "by", null.ok = T)
+# Formula parsing *****************************************************
+# varnames = names(data)
+# parsed = parse_formula(formula, varnames)
+# # parsed$left = gsub("\\n *", "", parsed$left)
+#
+# data = parse_data(expand_formula(formula, varnames), data)
+# names(data) = remove_blank(names(data))
+# varform = names(data)
+#
+# if (regroup) {
+#     numdata = varform[sapply(data, function(x) is.numeric(x) & !is.Surv(x))]
+#     catdata = varform[sapply(data, is.character.or.factor)]
+#     survdata = varform[sapply(data, is.Surv)]
+#
+#     parsed$left = regroup(parsed$left, numdata, catdata, survdata)
+#     parsed$right = regroup(parsed$right, numdata, catdata, survdata)
+# }
+#
+# eg = expand.grid(left=parsed$left, right=parsed$right, stringsAsFactors = F)
+# #eg (DF) : chaque ligne est une combinaison by en fonction du nombre de +
+#
+#
+# comb = eg %>%
+#     pmap(list) %>%
+#     modify_depth(2, ~{
+#         if(.x==".") return(NULL)
+#         of = .x %>% .[.!="."] %>% elements %>% remove_blank
+#         data %>% select(one_of(of))
+#     })
+#
+#
+# # Results *****************************************************
+#
+# results = comb %>%
+#     map(cross_list, funs=funs, ..., margin=margin, total=total, digits=digits, showNA=showNA, method=method, times=times, followup=followup, test=test, test.summarize=test.summarize, test.tabular=test.tabular, test.survival=test.survival, show.test=show.test, plim=plim, effect=effect, effect.summarize=effect.summarize, effect.tabular=effect.tabular, effect.survival=effect.survival, conf.level=conf.level, show.method=show.method, label=label)
+# browser()
+# tidyselect::vars_select(names(data), x)
+x2 = data %>% select(xnames)
+y2 = data %>% select(byname)
+if(ncol(y2)==0) y2=NULL
+results = cross_all(x2, y2, funs=funs, ..., margin=margin, total=total, digits=digits, showNA=showNA, method=method, times=times, followup=followup, test=test, test.summarize=test.summarize, test.tabular=test.tabular, test.survival=test.survival, show.test=show.test, plim=plim, effect=effect, effect.summarize=effect.summarize, effect.tabular=effect.tabular, effect.survival=effect.survival, conf.level=conf.level, show.method=show.method, label=label)
+# if (length(results) == 1) {
+#     results = results[[1]]
+# } else {
+#     results = results[results != "What?"]
+# }
+class(results) = c("crosstable", "data.frame")
+# attr(results, "formula") = formula
+# attr(results, "left") = parsed$left
+# attr(results, "right") = parsed$right
+# attr(results, "by") = parsed$by
+# attr(results, "data") = data
+return(results)
+}
+crosstable(data = iris, x=starts_with("S"), by="Species")
+crosstable(data = iris, x=starts_with("S"))
+source('F:/GITHUB/fork_biostat2/R/crosstable.r', encoding = 'UTF-8')
+crosstable(data = iris, x=starts_with("S"), by="Species")
+crosstable(data = iris, x=starts_with("S"))
+crosstable(data = iris, x=everything())
+crosstable(data = iris, x=Sepal.Length, by="Species")
+select
+dplyr:::select.data.frame
+dplyr:::select_impl
+`!!!`
+?`!!!`
+crosstable(data = iris, x="Sepal.Length", by="Species")
+?mean_by
+??mean_by
+tbl_vars
+dplyr:::tbl_vars.data.frame
+dplyr:::tbl_vars.tbl_cube
+tbl_cube
+?tbl_cube
+nasa
+head(as.data.frame(nasa))
+titanic <- as.tbl_cube(Titanic)
+head(as.data.frame(titanic))
+as.tbl_cube(Titanic) %>% head
+as.tbl_cube(Titanic)
+(Titanic)
+cross_all
+cross_one
+library(gmodels)
+data(infert, package = "datasets")
+CrossTable(infert$education, infert$induced, expected = TRUE)
+library(biostat2)
+library(biostat2)
diff --git a/.gitignore b/.gitignore
index 3b26574..8aae547 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,16 @@
+
+# RStudio internals
+.Rproj.user
+*.RData
+*.Rhistory
+.Rhistory
+
+# MS Word files
+test*.docx
+~*.docx
+
+
+
 # Windows image file caches
 Thumbs.db
 ehthumbs.db
@@ -21,21 +34,18 @@ $RECYCLE.BIN/
 # OSX
 # =========================
 
-.DS_Store
-.AppleDouble
-.LSOverride
-
-# Icon must ends with two \r.
-Icon

-
-# Thumbnails
-._*
-
-# Files that might appear on external disk
-.Spotlight-V100
-.Trashes
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must ends with two \r.
+Icon
+
+
+# Thumbnails
+._*
+
+# Files that might appear on external disk
+.Spotlight-V100
+.Trashes
 *~
-*.Rhistory
-*.Rhistory
-*.Rhistory
-.Rproj.user
diff --git a/DESCRIPTION b/DESCRIPTION
index 7c47516..1cd7058 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,19 +1,33 @@
 Package: biostat2
 Title: biostat, mais 2
-Version: 0.9.0
-Authors@R: person("David", "Hajage", email = "david.hajage@lmr.aphp.fr", role =
-    c("aut", "cre"))
-Description: Fonctions facilitant la description et l'analyse
+Encoding: UTF-8
+Version: 0.13.0
+Authors@R: c(
+    person("David", "Hajage", email = "david.hajage@lmr.aphp.fr", role = c("aut", "cre")),
+    person("Dan", "Chaltiel", email = "dan.chaltiel@gmail.com", role = c("ctb")))
+Description: Fonctions facilitant la description et l'analyse.
 Depends:
     R (>= 3.1.0)
 Imports:
     stats,
     plyr,
+    dplyr,
+    purrr,
+    checkmate,
     reshape2,
     Hmisc,
     survival,
-    ReporteRs,
+    methods,
+    gmodels,
+    DescTools,
+    officer,
+    flextable,
+    lifecycle,
     nortest
 License: GPL (>= 2)
 LazyData: true
-RoxygenNote: 6.0.1
+RoxygenNote: 7.1.0
+Suggests: 
+    testthat,
+    ReporteRs
+RdMacros: lifecycle
diff --git a/NAMESPACE b/NAMESPACE
index 1e50824..fa3281f 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,8 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(diff,mean.auto)
+S3method(diff,mean.boot)
+S3method(diff,mean.student)
+S3method(diff,median)
 export(FlexCrossTable)
-export(Max)
-export(Min)
 export(addAlert)
 export(addCode)
 export(addComment)
@@ -13,28 +15,61 @@ export(addNormal)
 export(addPlotlegend)
 export(addTablegend)
 export(addVerbatim)
+export(as.crosstable)
+export(body_add_crosstable)
+export(body_add_crosstable_bak)
+export(body_add_glued)
+export(body_add_normal)
+export(body_add_table_legend)
+export(body_add_title)
+export(compact)
 export(create.report)
 export(cross)
+export(cross_to_flextable)
 export(display.effect)
 export(display.test)
+export(effect.survival.coxph)
 export(expand)
+export(format_fixed)
+export(mediqr)
+export(minmax)
+export(moystd)
 export(n)
 export(na)
+export(nna)
+export(or.col.by.row)
+export(or.row.by.col)
 export(paste.matrix)
 export(plim)
 export(rbind_crosstable)
+export(rd.col.by.row)
+export(rd.row.by.col)
+export(rr.col.by.row)
+export(rr.row.by.col)
 export(simple.table)
 export(test.summarize.auto)
 export(test.summarize.auto.old)
+export(test.summarize.contrasts.lin)
 export(test.summarize.kruskal)
 export(test.summarize.oneway.equalvar)
 export(test.summarize.oneway.unequalvar)
 export(test.survival.logrank)
 export(test.tabular.auto)
 export(test.tabular.fisher)
-import(ReporteRs)
+import(checkmate)
+import(flextable)
+import(gmodels)
+import(officer)
+import(stats)
 import(survival)
+importFrom(DescTools,CochranArmitageTest)
 importFrom(Hmisc,label)
+importFrom(dplyr,"%>%")
+importFrom(dplyr,lead)
+importFrom(dplyr,select)
+importFrom(dplyr,sym)
+importFrom(lifecycle,deprecate_warn)
+importFrom(methods,is)
 importFrom(nortest,ad.test)
 importFrom(plyr,.)
 importFrom(plyr,alply)
diff --git a/R/addCrossTable.r b/R/body_add_crosstable.r
similarity index 55%
rename from R/addCrossTable.r
rename to R/body_add_crosstable.r
index 2d08bef..4ad7ac7 100644
--- a/R/addCrossTable.r
+++ b/R/body_add_crosstable.r
@@ -1,10 +1,13 @@
 ##' Compact the result of cross function
 ##'
-##' @param x x
+##' @param x a crosstable, the result of \code{cross} function
 ##' @author David Hajage
-##' @keywords internal
-##' @importFrom plyr alply
-##' @importFrom plyr dlply
+##' @importFrom plyr alply dlply
+##' @export
+##' 
+##' @examples
+##' mytable <- cross(cbind(...) ~ tobgp, esoph, test = TRUE)
+##' compact(mytable)
 compact <- function(x) {
     ordre <- unique(x$.id)
     if ("p" %in% names(x) | "effect" %in% names(x)) {
@@ -76,35 +79,338 @@ compact <- function(x) {
         res[res[, 1] == "    Effect", which(colnames(res) == "variable")] <- "    Effect"
     }
     
+    res <- as.data.frame(res)
+    attr(res, "noms.col") <- attr(x, "noms.col")
+    attr(res, "labs.col") <- attr(x, "labs.col")
+    class(res) <- c("cross", "data.frame", "compacted")
     res
 }
 
-##' Create a FlexTable object from a table made by the cross function
-##'
-##' @name FlexCrossTable-ReporteRs
-##' @param crosstable the result of \code{cross} function
-##' @param compact compact the table?
-##' @param id name of the 'id' column
-##' @param variable name of the 'variable' column
-##' @param value name of the 'value' column
-##' @param effect name of the 'effect' column
-##' @param p name of the 'p' column
-##' @return
-##'   A \code{FlexTable} object (see \code{ReporteRs} package)
-##' @author David Hajage
-##' @examples
-##' \dontrun{
-##' library(biostat2)
-##' library(ReporteRs)
-##' mytable <- cross(cbind(...) ~ tobgp, esoph, test = TRUE)
-##' FlexCrossTable(mytable)
-##' FlexCrossTable(mytable, TRUE)
-##' }
-##' @keywords univar
-##' @export
-##' @import ReporteRs
-FlexCrossTable <- function(crosstable, compact = FALSE, id = ".id", variable = "variable", value = "value", effect = "effect", p = "p") {
 
+#TODO: implement
+# compact_dataframe = function(data, name_from, name_to, rtn_flextable=T){
+#     tmp=data.frame()
+#     id=(data[[name_from]]!=lag(data[[name_from]])) %>% replace_na(TRUE)
+#     for (i in 1:sum(id)) {
+#         x1=which(id)[i]
+#         x2=which(id)[i+1]-1
+#         if(is.na(x2)) x2=nrow(data)
+#         row = data[1,] %>% mutate_all(~"") %>% mutate(!!sym(name_to):=data[x1,name_from])
+#         tmp=rbind(tmp, row, data[x1:x2,])
+#     }
+#     tmp=tmp %>% select(-!!sym(name_from))
+#     if(rtn_flextable){
+#         id2=which(id)+(0:(sum(id)-1))
+#         tmp = tmp %>% flextable %>% border(id2, border.top = fp_border()) %>% 
+#             bold(id2) %>% align(id2, align="left")
+#     }
+#     tmp
+# }
+
+
+
+
+#' Crosstables output 
+#' @description \code{cross_to_flextable} turns a table made by the cross function into a flextable.
+#'
+#' @param crosstable the result of \code{cross} function
+#' @param compact whether to compact the table
+#' @param auto.fit whether to \code{flextable::autofit} the table
+#' @param id name of the 'id' column
+#' @param variable name of the 'variable' column
+#' @param label name of the 'label' column
+#' @param value name of the 'value' column
+#' @param p name of the 'p' column
+#' @param show.test.name in the p column, show the test name
+#'
+#' @return A \code{rdocx} object
+#' @author Dan Chaltiel
+#' @importFrom dplyr select lead sym %>% 
+#' @importFrom methods is
+#' @import officer flextable 
+#' @export
+#'
+#' @examples 
+#' ### cross_to_flextable
+#' library(dplyr) #for the pipe operator
+#' library(officer)
+#' cross(cbind(...) ~ tobgp, esoph, test = TRUE) %>% cross_to_flextable
+#' cross(cbind(...) ~ Species, iris, test = TRUE) %>% cross_to_flextable
+#' cross(cbind(...) ~ ., esoph) %>% cross_to_flextable
+#' 
+cross_to_flextable = 
+    function (crosstable, compact = FALSE, auto.fit = FALSE, 
+              id = ".id", variable = "variable", label = "label", value = "value", p = "p", effect="effect", total="Total",
+              show.test.name = F, generic.labels=c(id, variable, label, value, p, effect, total)) {
+    stopifnot(is.data.frame(crosstable))    
+    border1 <- fp_border(color = "black", style = "solid", width = 1)
+    border2 <- fp_border(color = "black", style = "solid", width = 1.5)
+    labs.col <- attr(crosstable, "labs.col")
+    labs.names <- crosstable %>% names %>% .[!(. %in% generic.labels)]
+    is_tested = crosstable %>% names %>% grepl(p, .) %>% any
+    is_multiple = crosstable %>% names %>% grepl(value, .) %>% any %>% `!`
+    has_total = crosstable %>% names %>% grepl(total, .) %>% any
+    has_effect = crosstable %>% names %>% grepl(effect, .) %>% any
+    rtn = crosstable
+    if (is_tested && !show.test.name) {
+        rtn$p = rtn$p %>% gsub(" \\(.*\\)", "", .)
+    }
+    if (compact && !is(rtn, "compacted")) {
+        rtn <- compact(rtn)
+    }
+    if (is(rtn, "compacted")) {
+        sep.rows <- which(rtn[, 1] %in% crosstable$label)[-1]
+        rtn <- rtn %>% as.data.frame %>% flextable %>% hline(i=sep.rows - 1, border=border1)
+        if (is_multiple) {
+            header_colwidths = if (is_tested) c(1, ncol(crosstable) - 4)
+            else           c(1, ncol(crosstable) - 3)
+            rtn <- rtn %>% 
+                add_header_row(values=c(variable, labs.col), colwidths=header_colwidths) %>% 
+                merge_v(j = 1, part = "head") %>%
+                merge_h(i = c(1, sep.rows, sep.rows + 1)) %>% 
+                bold(i = c(1, sep.rows))
+        }
+    }
+    else {
+        sep.rows <- which(rtn$label != lead(rtn$label))
+        rtn <- rtn %>% select(-!!sym(id)) %>% flextable %>% hline(i=sep.rows, border=border1)
+        if (is_multiple) {
+            r = labs.names %>% 
+                gsub("([\\\\\\^\\$\\.\\|\\?\\*\\+\\(\\)\\[\\{])", "\\\\\\1", .) %>% 
+                paste(collapse="|")
+            header_values = crosstable %>% select(-id) %>% names %>% 
+                gsub(r, labs.col, .) %>% unique
+            header_colwidths = ifelse(header_values==labs.col, sum(names(crosstable) %in% labs.names), 1)
+            # browser()
+            
+            head_merge = header_values[!header_values %in% labs.col]
+            rtn <- rtn %>% 
+                add_header_row(values = header_values, colwidths = header_colwidths) %>% 
+                merge_v(j = head_merge, part = "head")
+        }
+        body_merge = if (is_tested) c(label, p) else label
+        body_merge = if (has_effect) c(body_merge, effect) else body_merge
+        rtn <- rtn  %>% 
+            merge_v(j = label, target=body_merge, part = "body")
+    }
+    rtn <- rtn %>% 
+        bold(part = "head") %>% 
+        align(align = "left", part = "all") %>% 
+        align(i = 1, align = "center", part = "head") %>% 
+        hline_top(border = border2, part = "head") %>% 
+        hline_bottom(border = border2, part = "head") %>% 
+        border_inner_h(border = border2, part = "head") %>% 
+        fix_border_issues
+    
+    if (auto.fit) {
+        rtn <- autofit(rtn)
+    }
+    return(rtn)
+}
+
+
+#' body_add_crosstable
+#' @description \code{body_add_crosstable2} adds a table made by the cross function into an officer document
+#'
+#' @param doc a \code{rdocx} object created by \code{read_docx} function (see \code{officer} package)
+#' @param ... arguments for \code{cross_to_flextable}
+#'
+#' @export
+#' @rdname cross_to_flextable
+#' 
+#' @examples 
+#' ### body_add_crosstable
+#' #mytable <- cross(cbind(...) ~ tobgp, esoph, test = TRUE)
+#' #mytable <- cross(cbind(...) ~ Species, iris, test = TRUE)
+#' mytable <- cross(cbind(...) ~ ., esoph)
+#' doc <- read_docx() %>% 
+#'     body_add_crosstable(mytable) %>% 
+#'     body_add_break %>% 
+#'     body_add_crosstable(mytable, compact=TRUE)
+#' 
+#' \dontrun{
+#' dfile <- "test_doc.docx"
+#' print(doc, target = dfile)
+#' shell.exec(dfile)
+#' }
+body_add_crosstable = function (doc, ...) {
+    ft = cross_to_flextable(...)
+    doc <- body_add_flextable(doc, ft)
+    return(doc)
+}
+
+
+
+
+
+
+#' Coerce to a Crosstable (for officer docx addition)
+#'
+#' @param df a data.frame
+#' @param labs.col the name of the grouping variable
+#'
+#' @return a cross
+#' @export
+#'
+#' @examples
+#' library(dplyr) #for the pipe operator
+#' library(officer)
+#' mytable = cross(cbind(Sepal.Length, I(Sepal.Width^2)) ~ Species, iris) %>% 
+#'    as.data.frame %>% #loses attributes
+#'    as.crosstable(labs.col = "Species")
+#'    
+#' doc <- read_docx() %>% 
+#'     body_add_crosstable(mytable) 
+#' 
+#' \dontrun{
+#' dfile <- "test_doc.docx"
+#' print(doc, target = dfile)
+#' shell.exec(dfile)
+#' }
+#' 
+as.crosstable = function(df, labs.col = "???"){
+    class(df) = c("cross", "data.frame")
+    attr(df, "labs.col") = labs.col
+    df
+}
+
+
+
+# LEGACY ------------------------------------------------------------------
+
+
+#' OLD: Adds a table made by the cross function into an officer document
+#'
+#' @param doc a \code{rdocx} object created by \code{read_docx} function (see \code{officer} package)
+#' @param crosstable the result of \code{cross} function
+#' @param compact whether to compact the table
+#' @param auto.fit whether to \code{flextable::autofit} the table
+#' @param id name of the 'id' column
+#' @param variable name of the 'variable' column
+#' @param label name of the 'label' column
+#' @param value name of the 'value' column
+#' @param p name of the 'p' column
+#' @param show.test.name in the p column, show the test name
+#'
+#' @return A \code{rdocx} object
+#' @author Dan Chaltiel
+#' @importFrom dplyr select lead sym %>% 
+#' @importFrom methods is
+#' @import officer flextable 
+#' @export
+#'
+#' @examples 
+#' library(dplyr) #for the pipe operator
+#' library(officer)
+#' mytable <- cross(cbind(...) ~ tobgp, esoph, test = TRUE)
+#' mytable <- cross(cbind(...) ~ Species, iris, test = TRUE)
+#' mytable <- cross(cbind(...) ~ ., esoph)
+#' doc <- read_docx() %>% 
+#'     body_add_crosstable(mytable) %>% 
+#'     body_add_break %>% 
+#'     body_add_crosstable(mytable, TRUE)
+#' 
+#' \dontrun{
+#' dfile <- "test_doc.docx"
+#' print(doc, target = dfile)
+#' shell.exec(dfile)
+#' }
+body_add_crosstable_bak = function(doc, crosstable, compact = FALSE, auto.fit = FALSE, id = ".id", variable = "variable", label = "label", value="value", p = "p", show.test.name=F){
+    border1 <- fp_border(color = "black", style = "solid", width = 1)
+    border2 <- fp_border(color = "black", style = "solid", width = 1.5)
+    
+    labs.col <- attr(crosstable, "labs.col")
+    rtn = crosstable
+    
+    is_tested = rtn %>% names %>% grepl(p,.) %>% any
+    is_multiple = rtn %>% names %>% grepl(value,.) %>% any %>% `!`
+    
+    if(is_tested && !show.test.name){
+        rtn$p = rtn$p %>% gsub(" \\(.*\\)","", .)
+    }
+    if(compact && !is(rtn, "compacted")) {
+        rtn <- compact(rtn)
+    }
+    #TODO : si une seule fonction (funs=moystd) et compact  
+    #TODO : implémenter si compact arrive avant la fonction  
+    
+    if(is(rtn, "compacted")) {
+        sep.rows <- which(rtn[,1] %in% crosstable$label)[-1] #$label ou $.id ?
+        
+        rtn <- rtn %>% 
+            as.data.frame %>% 
+            flextable %>% 
+            hline(i=sep.rows-1, border = border1)
+        
+        if(is_multiple){
+            header_colwidths = if(is_tested) c(1, ncol(crosstable)-4) else c(1, ncol(crosstable)-3)
+            rtn <- rtn %>% 
+                add_header_row(values=c(variable, labs.col), colwidths=header_colwidths) %>% 
+                merge_v(j=1, part = "head") %>% 
+                merge_h(i=c(1, sep.rows, sep.rows+1)) %>% 
+                bold(i=c(1, sep.rows))
+        }
+    } else {
+        sep.rows <- which(rtn$label != lead(rtn$label)) #$label ou $.id ?
+        rtn <- rtn %>% 
+            select(-!!sym(id)) %>% 
+            flextable %>% 
+            hline(i=sep.rows, border = border1)
+        if(is_multiple){
+            header_values = if(is_tested) c(label, variable, labs.col, p) else c(label, variable, value)
+            header_colwidths = if(is_tested) c(1, 1, ncol(crosstable)-4, 1) else c(1, 1, ncol(crosstable)-3)
+            body_merge = if(is_tested) c("label", p) else c("label")
+            rtn <- rtn %>% 
+                add_header_row(values=header_values, 
+                               colwidths=header_colwidths) %>% 
+                merge_v(j=c(1,2,ncol(crosstable)-1), part = "head") %>% 
+                merge_v(j = body_merge)
+        }
+    }
+    rtn <- rtn %>% 
+        bold(part="head") %>% 
+        align(align = "left", part="all") %>% 
+        align(i=1, align = "center", part="head") %>% 
+        hline_top(border = border2, part = "head") %>% 
+        hline_bottom(border = border2, part = "head") %>% 
+        border_inner_h(border = border2, part = "head")
+    if(auto.fit){
+        rtn <- autofit(rtn)
+    }
+    doc <- body_add_flextable(doc, rtn)
+    return(doc)
+}
+
+#' Deprecated
+#' Create a FlexTable object from a table made by the cross function
+#'
+#' **Deprecation** : Since \code{ReporteRs} is deprecated and not available on CRAN, please use \code{flextable} and \code{officer} packages instead.
+#'
+#' @name FlexCrossTable-ReporteRs
+#' @param crosstable the result of \code{cross} function
+#' @param compact compact the table?
+#' @param id name of the 'id' column
+#' @param variable name of the 'variable' column
+#' @param value name of the 'value' column
+#' @param effect name of the 'effect' column
+#' @param p name of the 'p' column
+#' @import stats
+#' @return
+#'   A \code{FlexTable} object (see \code{ReporteRs} package)
+#' @author David Hajage
+#' @examples
+#' \dontrun{
+#' library(biostat2)
+#' library(ReporteRs)
+#' mytable <- cross(cbind(...) ~ tobgp, esoph, test = TRUE)
+#' FlexCrossTable(mytable)
+#' FlexCrossTable(mytable, TRUE)
+#' }
+#' @keywords univar
+#' @export
+FlexCrossTable <- function(crosstable, compact = FALSE, id = ".id", variable = "variable", value = "value", effect = "effect", p = "p") {
+    check_reporter_dependency()
+    
     header <- names(crosstable)[names(crosstable) != "label"]
     names(header) <- header
     header[header == ".id"] <- id
@@ -119,7 +425,7 @@ FlexCrossTable <- function(crosstable, compact = FALSE, id = ".id", variable = "
         if ("p" %in% names(crosstable)) {
             ft <- spanFlexTableRows(ft, j = c(1, which(names(crosstable) == "p")-1), runs = crosstable$`.id`)
         }
-         if ("effect" %in% names(crosstable)) {
+        if ("effect" %in% names(crosstable)) {
             ft <- spanFlexTableRows(ft, j = c(1, which(names(crosstable) == "effect")-1), runs = crosstable$`.id`)
         }
         if (length(attr(crosstable, "noms.col")) > 0) {
@@ -141,11 +447,11 @@ FlexCrossTable <- function(crosstable, compact = FALSE, id = ".id", variable = "
             ft <- addHeaderRow(ft, value = c(sapply(attr(crosstable, "labs.col"), function(x) c("", x))), colspan = colspan, par.properties = parProperties(text.align = "center"))
         }
         ft <- addHeaderRow(ft, value = header)
-
+        
         ft <- setFlexTableBorders(ft,
                                   inner.vertical =  borderProperties(width = 0), inner.horizontal = borderProperties(width = 0),
                                   outer.vertical = borderProperties(width = 0), outer.horizontal = borderProperties(width = 3))
-
+        
         if ("p" %in% names(crosstable) | "effect" %in% names(crosstable)) {
             if ("effect" %in% names(crosstable)) {
                 bord <- grep("    Effect", crosstable2[, "variable"])
@@ -156,7 +462,7 @@ FlexCrossTable <- function(crosstable, compact = FALSE, id = ".id", variable = "
             bord2 <- cumsum(table(factor(crosstable$.id, unique(crosstable$.id)))+nb+1) - (table(factor(crosstable$.id, unique(crosstable$.id)))+nb)
             
             bord3 <- grep("    Effect|    Test", crosstable2[, "variable"])
-                
+            
             ft[bord[-length(bord)], , side = "bottom"] = borderProperties(width = 1)
             ft[bord- (nb-1), , side = "top"] = borderProperties(style = "dashed")
             ft[bord2, ] <- textProperties(font.style = "italic")
@@ -184,32 +490,38 @@ FlexCrossTable <- function(crosstable, compact = FALSE, id = ".id", variable = "
 }
 
 
-##' add a table made by the cross function into a ReporteRs document
-##'
-##' @param doc a \code{docx} object created by \code{docx} function (see \code{ReporteRs} package)
-##' @param crosstable the result of \code{cross} function
-##' @param compact compact the table?
-##' @param id name of the 'id' column
-##' @param variable name of the 'variable' column
-##' @param value name of the 'value' column
-##' @param p name of the 'p' column
-##' @return
-##'   A \code{docx} object
-##' @author David Hajage
-##' @examples
-##' \dontrun{
-##' library(biostat2)
-##' library(ReporteRs)
-##' mytable <- cross(cbind(...) ~ tobgp, esoph, test = TRUE)
-##' doc <- docx()
-##' doc <- addCrossTable(doc, mytable)
-##' doc <- addPageBreak(doc)
-##' doc <- addCrossTable(doc, mytable, TRUE)
-##' }
-##' @keywords univar
-##' @export
-##' @import ReporteRs
+#' Deprecated
+#' add a table made by the cross function into a ReporteRs document
+#' 
+#' **Deprecation** : Since \code{ReporteRs} is deprecated and not available on CRAN, please use \code{officer} and \code{biostats2::body_add_crosstable} instead.
+#'
+#' @param doc a \code{docx} object created by \code{docx} function (see \code{ReporteRs} package)
+#' @param crosstable the result of \code{cross} function
+#' @param compact compact the table?
+#' @param id name of the 'id' column
+#' @param variable name of the 'variable' column
+#' @param value name of the 'value' column
+#' @param p name of the 'p' column
+#' @return
+#'   A \code{docx} object
+#' @author David Hajage
+#' @examples
+#' \dontrun{
+#' library(biostat2)
+#' library(ReporteRs)
+#' mytable <- cross(cbind(...) ~ tobgp, esoph, test = TRUE)
+#' doc <- docx()
+#' doc <- addCrossTable(doc, mytable)
+#' doc <- addPageBreak(doc)
+#' doc <- addCrossTable(doc, mytable, TRUE)
+#' dfile <- "test_doc.docx"
+#' print(doc, target = dfile)
+#' shell.exec(dfile)
+#' }
+#' @keywords univar
+#' @export
 addCrossTable <- function(doc, crosstable, compact = FALSE, id = ".id", variable = "variable", value = "value", p = "p") {
+    check_reporter_dependency()
     if (!inherits(crosstable, "FlexTable")) {
         ft <- FlexCrossTable(crosstable, compact, id, variable, value, p)
     } else {
@@ -218,6 +530,13 @@ addCrossTable <- function(doc, crosstable, compact = FALSE, id = ".id", variable
     doc <- addFlexTable(doc, ft)
     return(doc)
 }
+
+
+
+
+
+
+
 # 
 # ##' add_header_list
 # ##'
diff --git a/R/body_add_legend.r b/R/body_add_legend.r
new file mode 100644
index 0000000..57dd974
--- /dev/null
+++ b/R/body_add_legend.r
@@ -0,0 +1,20 @@
+#' Add a table legend
+#'
+#' @param x a docx object
+#' @param legend the table legend
+#' @param legend_style may depend on the docx template
+#' @param style the legend style (strnog, italic...)
+#' @param seqfield to figure this out, in a docx file, insert a table legend, right click on the inserted number and select "Toggle Field Codes". This argument should be the value of the field, with extra escaping.
+#'
+#' @export
+body_add_table_legend = function(x, legend, legend_style="table title", style="strong", 
+                                 seqfield="SEQ Table \\* Arabic"){
+    x %>% 
+        body_add_par(value=legend, style=legend_style) %>% 
+        slip_in_text(str=": ", style=style, pos="before") %>% 
+        slip_in_seqfield(str=seqfield, 
+                         style=style, pos="before") %>% 
+        slip_in_text(str="Table ", style=style,
+                     pos="before") %>%
+        identity
+}
\ No newline at end of file
diff --git a/R/remix.r b/R/cross.r
similarity index 89%
rename from R/remix.r
rename to R/cross.r
index eeafed5..2c24519 100644
--- a/R/remix.r
+++ b/R/cross.r
@@ -1,3 +1,4 @@
+
 ##' test
 ##'
 ##' @param x x
@@ -393,6 +394,8 @@ regroup <- function(vars, numdata, catdata, survdata) {
 ##' group everything in the same table, but only if it is possible...
 ##'
 ##'
+##' \lifecycle{superseded}
+##' \Sexpr[results=rd, stage=render]{lifecycle::badge("superseded")}
 ##' @return
 ##'   A data.frame, or a list of data.frames.
 ##' @author David Hajage, inspired by the design and the code of
@@ -403,34 +406,80 @@ regroup <- function(vars, numdata, catdata, survdata) {
 ##'
 ##' library(biostat2)
 ##' cross(data = iris)
-##' cross(cbind(...) ~ ., iris[, sapply(iris, is.numeric)], funs = c(median, mad, min, max))
-##' cross(cbind(Sepal.Length, I(Sepal.Width^2)) ~ Species, iris, funs = quantile, probs = c(1/3, 2/3))
+##' cross(cbind(...) ~ ., iris[, sapply(iris, is.numeric)], funs=c(median, mad, min, max))
+##' cross(cbind(Sepal.Length, I(Sepal.Width^2)) ~ Species, iris, funs=quantile, probs=c(1/3, 2/3), total="row") #tertiles 1 and 2 by Species
 ##' cross(Sepal.Length + Sepal.Width ~ Petal.Length + Petal.Width, iris)
 ##' cross(cbind(Sepal.Length, Sepal.Width) ~ cbind(Petal.Length, Petal.Width), iris)
-##' cross(... ~ ., esoph)
-##' cross(alcgp ~ tobgp, esoph, test = TRUE)
+##' cross(... ~ ., esoph) #returns a list
+##' cross(alcgp ~ tobgp, esoph, margin="row", total="both", test=TRUE)
+##' cross(cbind(hp, mpg) ~ factor(am), mtcars, effect=TRUE, test=TRUE, show.method=FALSE)
 ##' library(survival)
 ##' cross(Surv(time, status) ~ x, data = aml)
+##' 
 ##' @keywords univar
 ##' @export
-##' @importFrom plyr is.formula
-##' @importFrom plyr llply
-cross <- function(formula = cbind(...) ~ ., data = NULL, funs = c(" " = mysummary), ..., margin = 0:2, total = FALSE, digits = 2, showNA = c("no", "ifany", "always"), method = c("pearson", "kendall", "spearman"), times = NULL, followup = FALSE, test = FALSE, test.summarize = test.summarize.auto, test.survival = test.survival.logrank, test.tabular = test.tabular.auto, show.test = display.test, plim = 4, show.method = TRUE, effect = FALSE, effect.summarize = diff.mean.auto, effect.tabular = or.row.by.col, effect.survival = effect.survival.coxph, conf.level = 0.95, label = FALSE, regroup = FALSE) {
-
+##' @import checkmate
+##' @importFrom plyr llply is.formula
+##' @importFrom lifecycle deprecate_warn
+cross <- function(formula = cbind(...) ~ ., data = NULL, funs = c(" " = cross_summary), ..., margin = c("all", "row", "column", "cell"), total = c("none", "all", "row", "column", "FALSE", "TRUE", 0, 1, 2), digits = 2, showNA = c("no", "ifany", "always"), method = c("pearson", "kendall", "spearman"), times = NULL, followup = FALSE, test = FALSE, test.summarize = test.summarize.auto, test.survival = test.survival.logrank, test.tabular = test.tabular.auto, show.test = display.test, plim = 4, show.method = TRUE, effect = FALSE, effect.summarize = diff.mean.auto, effect.tabular = or.row.by.col, effect.survival = effect.survival.coxph, conf.level = 0.95, label = TRUE, regroup = FALSE) {
+  
+  deprecate_warn("0.13.0", "cross()", 
+                 details="Please use the package `crosstable` instead.")
+  
+  coll = makeAssertCollection()
+  assertFormula(formula, add=coll)
+  assertDataFrame(data, add=coll)
+  assertCount(digits, add=coll)
+  assertLogical(label, add=coll)
+  
   if (is.formula(formula))
     formula <- paste(deparse(formula, 500), collapse = "")
-
+  
   if (!is.character(funs)) {
-      nomf <- names(funs)
-      funs <- as.character(as.list(substitute(funs)))
-      funs <- funs[funs != "c" & funs != "list"]
-      names(funs) <- nomf
+    nomf <- names(funs)
+    funs <- as.character(as.list(substitute(funs)))
+    funs <- funs[funs != "c" & funs != "list"]
+    names(funs) <- nomf
   }
-
+   
+  if (missing(margin)) margin = "all"
+  if (is.character(margin)) {
+    assertSubset(margin, c("all", "row", "column", "cell"), add=coll)
+    if(is.null(margin)) {
+      margin=0:2 #defaulting 
+    } else {
+      marginopts = list(all = 0:2,
+                        row = 1,
+                        column = 2,
+                        cell = 0)
+      margin <- unname(unlist(marginopts[margin]))
+    }
+  }
+  
+  if (missing(total)) total = "none"
+  if (total=="line") total = "row"
+  if (is.character(total)) {
+    assertChoice(total, c("none", "both", "all", "row", "column"), add=coll)
+    if(is.null(total)) {
+      total=0 #defaulting to none
+    } else {
+      totalopts = list(all = 1:2,
+                       both = 1:2,
+                       row = 1,
+                       column = 2,
+                       none = 0)
+      total <- unname(unlist(totalopts[total]))
+    }
+  }
+  
+  reportAssertions(coll)
+  
+  
   varnames <- names(data)
   parsed <- parse_formula(formula, varnames)
-
-  data <-   parse_data(expand_formula(formula, varnames), data)
+  # parsed$left = gsub("\\n *", "", parsed$left) 
+  
+  data <- parse_data(expand_formula(formula, varnames), data)
   names(data) <- remove_blank(names(data))
   varform <- names(data)
 
@@ -453,13 +502,13 @@ cross <- function(formula = cbind(...) ~ ., data = NULL, funs = c(" " = mysummar
       lapply(y, function(z) data[, remove_blank(elements(z)), drop = FALSE])
   })
 
-  # results <- llply(comb, function(x) cross_list(x, funs = funs, margin = margin, total = total, digits = digits, showNA = showNA, method = method, times = times, followup = followup, test = test, test.summarize = test.summarize, test.tabular = test.tabular, test.survival = test.survival, show.test = show.test, plim = plim, effect = effect, effect.summarize = effect.summarize, effect.tabular = effect.tabular, effect.survival = effect.survival, conf.level = conf.level, show.method = show.method, label = label))
-
-  results <- llply(comb, function(x) cross_list(x, funs = funs, ..., margin = margin, total = total, digits = digits, showNA = showNA, method = method, times = times, followup = followup, test = test, test.summarize = test.summarize, test.tabular = test.tabular, test.survival = test.survival, show.test = show.test, plim = plim, effect = effect, effect.summarize = effect.summarize, effect.tabular = effect.tabular, effect.survival = effect.survival, conf.level = conf.level, show.method = show.method, label = label))
+  
+  results <- llply(comb, function(x) 
+    cross_list(x, funs = funs, ..., margin = margin, total = total, digits = digits, showNA = showNA, method = method, times = times, followup = followup, test = test, test.summarize = test.summarize, test.tabular = test.tabular, test.survival = test.survival, show.test = show.test, plim = plim, effect = effect, effect.summarize = effect.summarize, effect.tabular = effect.tabular, effect.survival = effect.survival, conf.level = conf.level, show.method = show.method, label = label))
 
   if (length(results) == 1) {
       results <- results[[1]]
-      ## class(results) <- c("cross", "data.frame")
+      class(results) <- c("cross", "data.frame")
 
   } else {
       results <- results[results != "What?"]
@@ -475,10 +524,18 @@ cross <- function(formula = cbind(...) ~ ., data = NULL, funs = c(" " = mysummar
 
   ## attr(results, "data") <- data
   ## attr(results, "test") <- test
+  
   results
 }
 
 
+
+
+
+# Old ---------------------------------------------------------------------
+
+
+
 ## ##' Print a cross object
 ## ##'
 ## ##' Print cross object using ascii package
diff --git a/R/effect.r b/R/effect.r
index 937edfa..d966be5 100644
--- a/R/effect.r
+++ b/R/effect.r
@@ -5,9 +5,10 @@
 #'
 #' @export
 display.effect <- function(effect, digits = 4) {
-    if (all(sapply(effect, is.null)))
-        "No effect"
-    else {
+    if (all(sapply(effect, is.null))){
+        warning("Could not calculate effect. Is there not 2 groups exactly?", immediate.=T)
+        return("No effect?")
+    }else {
         paste(paste0(effect$effect.type, " (", effect$effect.name, "): ", formatC(effect$effect, format = "f", digits = digits), " CI", effect$conf.level*100, "%[", paste(formatC(effect$ci[, 1], format = "f", digits = digits), formatC(effect$ci[, 2], format = "f", digits = digits), sep = " to "), "]"), collapse = "\n")
     }
 }
@@ -29,7 +30,7 @@ display.effect <- function(effect, digits = 4) {
 # rd.row.by.col <- function (x, y, conf.level = 0.95) {
 #     tab <- table(x, y)
 #     if (ncol(tab) <= 1 | ncol(tab) > 2) {
-#         ## Je ne sais pas quel effet calculer par défaut quand il existe plus de 2 catégories en colonne
+#         ## Je ne sais pas quel effet calculer par d?faut quand il existe plus de 2 cat?gories en colonne
 #         effect <- NULL
 #         ci <- NULL
 #         effect.name <- NULL
@@ -61,7 +62,7 @@ display.effect <- function(effect, digits = 4) {
 # rr.row.by.col <- function (x, y, conf.level = 0.95) {
 #     tab <- table(x, y)
 #     if (ncol(tab) <= 1 | ncol(tab) > 2) {
-#         ## Je ne sais pas quel effet calculer par défaut quand il existe plus de 2 catégories en colonne
+#         ## Je ne sais pas quel effet calculer par d?faut quand il existe plus de 2 cat?gories en colonne
 #         effect <- NULL
 #         ci <- NULL
 #         effect.name <- NULL
@@ -93,7 +94,7 @@ display.effect <- function(effect, digits = 4) {
 # or.row.by.col <- function (x, y, conf.level = 0.95) {
 #     tab <- table(x, y)
 #     if (ncol(tab) <= 1 | ncol(tab) > 2) {
-#         ## Je ne sais pas quel effet calculer par défaut quand il existe plus de 2 catégories en colonne
+#         ## Je ne sais pas quel effet calculer par d?faut quand il existe plus de 2 cat?gories en colonne
 #         effect <- NULL
 #         ci <- NULL
 #         effect.name <- NULL
@@ -309,7 +310,7 @@ rd.col.by.row <- function (x, y, conf.level = 0.95) {
 diff.mean.auto <- function(x, g, conf.level = 0.95, R = 500) {
     ng <- table(g)
     if (length(ng) <= 1 | length(ng) > 2) {
-        ## Je ne sais pas quel effet calculer par défaut quand il existe plus de 2 catégories en colonne
+        ## Je ne sais pas quel effet calculer par d?faut quand il existe plus de 2 cat?gories en colonne
         effect <- NULL
         ci <- NULL
         effect.name <- NULL
@@ -369,7 +370,7 @@ diff.mean.auto <- function(x, g, conf.level = 0.95, R = 500) {
 diff.mean.boot <- function(x, g, conf.level = 0.95, R = 500) {
     ng <- table(g)
     if (length(ng) <= 1 | length(ng) > 2) {
-        ## Je ne sais pas quel effet calculer par défaut quand il existe plus de 2 catégories en colonne
+        ## Je ne sais pas quel effet calculer par d?faut quand il existe plus de 2 cat?gories en colonne
         effect <- NULL
         ci <- NULL
         effect.name <- NULL
@@ -404,7 +405,7 @@ diff.mean.boot <- function(x, g, conf.level = 0.95, R = 500) {
 diff.mean.student <- function(x, g, conf.level = 0.95) {
     ng <- table(g)
     if (length(ng) <= 1 | length(ng) > 2) {
-        ## Je ne sais pas quel effet calculer par défaut quand il existe plus de 2 catégories en colonne
+        ## Je ne sais pas quel effet calculer par d?faut quand il existe plus de 2 cat?gories en colonne
         effect <- NULL
         ci <- NULL
         effect.name <- NULL
@@ -443,7 +444,7 @@ diff.mean.student <- function(x, g, conf.level = 0.95) {
 diff.median <- function(x, g, conf.level = 0.95, R = 500) {
     ng <- table(g)
     if (length(ng) <= 1 | length(ng) > 2) {
-        ## Je ne sais pas quel effet calculer par défaut quand il existe plus de 2 catégories en colonne
+        ## Je ne sais pas quel effet calculer par d?faut quand il existe plus de 2 cat?gories en colonne
         effect <- NULL
         ci <- NULL
         effect.type <- NULL
diff --git a/R/funs.r b/R/funs.r
index d5c2732..3f8b992 100644
--- a/R/funs.r
+++ b/R/funs.r
@@ -1,111 +1,196 @@
-##' Remove blancks at the begining and the end
-##'
-##' @param x x
-##' @author David Hajage
-##' @keywords internal
-trim <- function (x) {
-    x <- sub("^ +", "", x)
-    x <- sub(" +$", "", x)
-    x
-}
 
-##' Concatenate functions
-##'
-##' @param ... functions
-##' @author David Hajage
-##' @keywords internal
-funs2fun <- function(...) {
-  fnames <- as.character(match.call()[-1])
-  fs <- list(...)
-  fnames2 <- names(fs)
 
-  if (!is.null(fnames2)) {
-      fnames[fnames2 != ""] <- fnames2[fnames2 != ""]
-  }
 
-  n <- length(fs)
-  function(x, ...) {
-    results <- NULL
-    args <- list(...)
-    namesargs <- names(args)
-    for (i in 1:n) {
-      func <- match.fun(fs[[i]])
-      forms <- formals(func) # Pour min et max (et les autres
-                             # primitives), il faudrait mettre
-                             # 'formals(args(func))'. Le probleme est
-                             # que min et max retourne le minimum de
-                             # tout ce qui n'est pas 'na.rm', donc si
-                             # je met un autre argument (genre probs =
-                             # 1/3), min et max prennent en compte sa
-                             # valeur, d'ou surprises... Je prefere
-                             # laisser comme ca.
-      namesforms <- names(forms)
-      if (all(namesforms != "...")) {
-        finalargs <- c(list(x = x), args[namesargs %in% namesforms])
-      } else {
-        finalargs <- c(list(x = x), args)
-      }
-      tmp <- do.call(func, finalargs)
-      names(tmp) <- trim(paste(fnames[i], names(tmp)))
-      results <- c(results, as.list(tmp))
+#' Format numbers with same number of decimals, including trailing zeros
+#'
+#' @param x a numeric vector to format
+#' @param digits number of decimals
+#' @param zero_digits number of significant digits for values rounded to 0 (set to NULL to keep the original 0 value)
+#' @param only_round util option, to simply return rounded value instead of formatted
+#'
+#' @return a character vector of formatted numbers
+#' @author Dan Chaltiel
+#' @export
+#'
+#' @examples
+#' x = c(1, 1.2, 12.78749, pi, 0.00000012)
+#' format_fixed(x, digits=3)
+#' format_fixed(x, digits=3, zero_digits=2)
+#' format_fixed(x, digits=3, zero_digits=NULL)
+#' x = iris$Sepal.Length/10000
+#' x %>% 
+#' sd(na.rm=na.rm) %>% 
+#'   format_fixed(dig=3, zero_digits=2, only_round=T)
+format_fixed = function(x, digits, zero_digits=1, only_round=FALSE){
+  stopifnot(is.numeric(x), 
+            is.numeric(digits), 
+            is.logical(only_round), 
+            is.null(zero_digits)||is.numeric(zero_digits)
+            )
+  if(only_round) {
+    return(round(x,digits))
+  } else {
+    rtn = formatC(x, format='f', digits=digits)
+    if(!is.null(zero_digits) && !is.na(zero_digits)){
+      rtn = ifelse(as.numeric(rtn)==0, signif(x, digits=zero_digits), rtn)
     }
-    data.frame(results, check.names = FALSE)
+    return(rtn)
   }
 }
 
-## Default summary function
-
-##' Return min and max
-##'
-##' @param x a numeric vector
-##' @param na.rm \code{TRUE} as default
-##' @param dig number of digits
-##' @keywords internal
-minmax <- function(x, na.rm = TRUE, dig = 2) {
-    mi <- ifelse(!all(is.na(x)), round(min(x, na.rm = na.rm), dig), NA)
-    ma <- ifelse(!all(is.na(x)), round(max(x, na.rm = na.rm), dig), NA)
-    paste(mi, "/", ma)
+
+# summary functions --------------------------------------------------------
+
+
+#' Summary functions
+#' 
+#' Summary functions to use with \code{\link{cross}} or anywhere else.
+#'
+#' @section Fixed format:
+#' The use of the \code{fixed_format} argument allows to have trailing zeros after rounded values.
+#' In the case when the output of rounded values is zero, the use of the \code{zero_digits} argument allows to keep some significant digits for this specific case only. 
+#' 
+#' @param x a numeric vector
+#' @param na.rm \code{TRUE} as default
+#' @param dig number of digits
+#' @param fixed_format use \code{\link{format_fixed}} instead of round (default)
+#' @param zero_digits is fixed_format==TRUE, number of significant digits for values rounded to 0 (set to NULL to keep the original 0 value)
+#' 
+#' 
+#' @examples 
+#' moystd(iris$Sepal.Length, dig=3)
+#' minmax(iris$Sepal.Length, dig=3)
+#' mediqr(iris$Sepal.Length, dig=3)
+#' nna(iris$Sepal.Length, dig=3)
+#' 
+#' x = iris$Sepal.Length/10000 #closer to zero 
+#' 
+#' moystd(x, dig=3, fixed_format=T)
+#' moystd(x, dig=3, fixed_format=T, zero_digits=NULL)
+#' options("biostat2_fixed_format"=T)
+#' moystd(x, dig=3, zero_digits=2)
+#' options("biostat2_fixed_format"=NULL)
+#'
+#' @author Dan Chaltiel
+#' @author David Hajage
+#' 
+#' @seealso \code{\link{format_fixed}}
+#' 
+#' @name biostats2SummaryFunctions
+NULL
+
+
+#' @describeIn biostats2SummaryFunctions returns mean and std error
+#' @export
+moystd = function(x, na.rm = TRUE, dig = 2, 
+                  fixed_format=getOption("biostat2_fixed_format", FALSE), zero_digits=1) {
+  moy = x %>% 
+    mean(na.rm=na.rm) %>% 
+    format_fixed(digits=dig, zero_digits=zero_digits, only_round=!fixed_format)
+  std = x %>% 
+    sd(na.rm=na.rm) %>% 
+    format_fixed(digits=dig, zero_digits=zero_digits, only_round=!fixed_format)
+  paste0(moy, " (", std, ")")
 }
 
-##' Return median and IQR
-##'
-##' @param x a numeric vector
-##' @param na.rm \code{TRUE} as default
-##' @param dig number of digits
-##' @keywords internal
-mediqr <- function(x, na.rm = TRUE, dig = 2) {
-    med <- round(median(x, na.rm = na.rm), dig)
-    iqr <- round(quantile(x, probs = c(0.25, 0.75), na.rm = na.rm), dig)
-    paste(med, " [", iqr[1], "-", iqr[2], "]", sep = "")
+#' @describeIn biostats2SummaryFunctions returns median and IQR
+#' @export
+mediqr = function(x, na.rm = TRUE, dig = 2, 
+                   fixed_format=getOption("biostat2_fixed_format", FALSE), zero_digits=1) {
+  med = x %>% 
+    median(na.rm=na.rm) %>% 
+    format_fixed(digits=dig, zero_digits=zero_digits, only_round=!fixed_format)
+  iqr = x %>% 
+    quantile(probs=c(0.25, 0.75), na.rm=na.rm) %>% 
+    format_fixed(digits=dig, zero_digits=zero_digits, only_round=!fixed_format)
+  paste0(med, " [", iqr[1], ";", iqr[2], "]")
 }
 
-##' Return mean and sd
-##'
-##' @param x a numeric vector
-##' @param na.rm \code{TRUE} as default
-##' @param dig number of digits
-##' @keywords internal
-moystd <- function(x, na.rm = TRUE, dig = 2) {
-    moy <- round(mean(x, na.rm = na.rm), dig)
-    std <- round(sd(x, na.rm = na.rm), dig)
-    paste(moy, " (", std, ")", sep = "")
+#' @describeIn biostats2SummaryFunctions returns minimum and maximum
+#' @export
+minmax = function(x, na.rm = TRUE, dig = 2) {
+  mi = ifelse(!all(is.na(x)), round(min(x, na.rm = na.rm), dig), NA)
+  ma = ifelse(!all(is.na(x)), round(max(x, na.rm = na.rm), dig), NA)
+  paste(mi, "/", ma)
 }
 
-##' Return n and na
-##'
-##' @param x a numeric vector
-##' @keywords internal
-nna <- function(x) {
-    paste(n(x), " (", na(x), ")", sep = "")
+#' @describeIn biostats2SummaryFunctions returns  number of observations and number of missing values
+#' @export
+nna = function(x) {
+  paste0(n(x), " (", na(x), ")")
 }
 
-##' Summarize a numeric vector
-##'
-##' @param x a numeric vector
-##' @param na.rm \code{TRUE} as default
-##' @param dig number of digits
-##' @keywords internal
-mysummary <- function(x, na.rm = TRUE, dig = 2) {
-        return(c("Min / Max" = minmax(x), "Med [IQR]" = mediqr(x), "Moy (std)" = moystd(x), "N (NA)" = nna(x)))
+
+#' Summarize a numeric vector
+#'
+#' @param x a numeric vector
+#' @param dig number of digits
+#' @keywords internal
+#' @section Note: 
+#' Function \code{mysummary} is kept for compatibility with old codes. It produces the same exact object than \code{cross_summary}, which should be preferred.
+cross_summary = function(x, dig=2) {
+  return(c("Min / Max" = minmax(x, dig=dig), "Med [IQR]" = mediqr(x, dig=dig), 
+           "Moy (std)" = moystd(x, dig=dig), "N (NA)" = nna(x)))
 }
+#' @rdname cross_summary
+mysummary=cross_summary
+
+# Utils functions ---------------------------------------------------------
 
+
+
+#' Remove blancks at the begining and the end
+#'
+#' @param x x
+#' @author David Hajage
+#' @keywords internal
+trim = function (x) {
+  x = sub("^ +", "", x)
+  x = sub(" +$", "", x)
+  x
+}
+
+
+#' Concatenate functions
+#'
+#' @param ... functions
+#' @author David Hajage
+#' @keywords internal
+funs2fun = function(...) {
+  fnames = as.character(match.call()[-1])
+  fs = list(...)
+  fnames2 = names(fs)
+  
+  if (!is.null(fnames2)) {
+    fnames[fnames2 != ""] = fnames2[fnames2 != ""]
+  }
+  
+  n = length(fs)
+  function(x, ...) {
+    results = NULL
+    args = list(...)
+    namesargs = names(args)
+    for (i in 1:n) {
+      func = match.fun(fs[[i]])
+      forms = formals(func) # Pour min et max (et les autres
+      # primitives), il faudrait mettre
+      # 'formals(args(func))'. Le probleme est
+      # que min et max retourne le minimum de
+      # tout ce qui n'est pas 'na.rm', donc si
+      # je met un autre argument (genre probs =
+      # 1/3), min et max prennent en compte sa
+      # valeur, d'ou surprises... Je prefere
+      # laisser comme ca.
+      namesforms = names(forms)
+      if (all(namesforms != "...")) {
+        finalargs = c(list(x = x), args[namesargs %in% namesforms])
+      } else {
+        finalargs = c(list(x = x), args)
+      }
+      tmp = do.call(func, finalargs)
+      names(tmp) = trim(paste(fnames[i], names(tmp)))
+      results = c(results, as.list(tmp))
+    }
+    data.frame(results, check.names = FALSE)
+  }
+}
\ No newline at end of file
diff --git a/R/na.r b/R/na.r
index 820d8ee..4cd3105 100644
--- a/R/na.r
+++ b/R/na.r
@@ -19,23 +19,3 @@ n <- function(x, na.rm = FALSE) {
 na <- function(x, na.rm = FALSE) {
   sum(is.na(x))
 }
-
-##' Return the min (and have formals)
-##'
-##' @export
-##' @param x a vector
-##' @param na.rm Remove NA?
-##' @author David Hajage
-##' @keywords univar
-Min <- function(x, na.rm = FALSE)
-    min(x, na.rm = na.rm)
-
-##' Return the max (and have formals)
-##'
-##' @export
-##' @param x a vector
-##' @param na.rm Remove NA?
-##' @author David Hajage
-##' @keywords univar
-Max <- function(x, na.rm = FALSE)
-    max(x, na.rm = na.rm)
diff --git a/R/officer.r b/R/officer.r
new file mode 100644
index 0000000..a3c208b
--- /dev/null
+++ b/R/officer.r
@@ -0,0 +1,74 @@
+
+
+#' Add a new paragraph with a Normal style, inserting variables with \code{base::paste}
+#'
+#' @name body_add_normal
+#' @param doc the doc object (created with the \code{read_docx} function of \code{officer} package)
+#' @param ... one or several character strings, collapsed into a paragraph with \code{base::paste}
+#' @return a new doc object
+#' @author Dan Chaltiel
+#' @examples
+#' \dontrun{
+#' library(officer)
+#' library(biostat2)
+#' library(dplyr)
+#' doc = read_docx()
+#' doc = doc %>% body_add_normal("La table iris a ", ncol(iris), " colonnes.")
+#' }
+#' @export
+body_add_normal <- function(doc, ...) {
+    value = paste0(..., collapse = "")
+    body_add_par(doc, value, style = "Normal")
+}
+
+#' Add a new paragraph with a Normal style, inserting variables with \code{glue::glue}
+#'
+#' @name body_add_normal
+#' @param doc the doc object (created with the \code{read_docx} function of \code{officer} package)
+#' @param x the string with \code{glue::glue} patterns (Expressions enclosed by braces will be evaluated as R code)
+#' @param ... parameters to be passed to \code{glue::glue}
+#' @return a new doc object
+#' @author Dan Chaltiel
+#' @examples
+#' \dontrun{
+#' library(officer)
+#' library(biostat2)
+#' library(dplyr)
+#' doc = read_docx()
+#' doc = body_add_glued(doc, "La table iris a {ncol(iris)} colonnes.")
+#' }
+#' @export
+body_add_glued <- function(doc, x, ...) {
+    value = glue::glue(x, ...,.envir = parent.frame())
+    body_add_par(doc, value, style = "Normal")
+    # value
+}
+
+
+#' Add a new title
+#'
+#' @name body_add_title
+#' @param doc the doc object (created with the \code{read_docx} function of \code{officer} package)
+#' @param value a character string
+#' @param level the level of the title. See \code{styles_info(doc)} to know the possibilities.
+#' @return a new doc object
+#' @author Dan Chaltiel
+#' @examples
+#' \dontrun{
+#' library(officer)
+#' library(biostat2)
+#' library(dplyr)
+#' doc = read_docx()
+#' doc = doc %>% 
+#'    body_add_title(doc, "La table iris", 1) %>% 
+#'    body_add_title(doc, "Description", 2) %>% 
+#'    addNormal(doc, "La table iris a ", ncol(iris), " colonnes.")
+#' }
+#' @export
+body_add_title <- function(x, value, level = 1, style = "heading") {
+    style <- paste(style, level)
+    body_add_par(x, value, style = style)
+}
+
+
+#TODO: extends all https://github.com/eusebe/biostat2/blob/master/R/officer.r
diff --git a/R/pretty.r b/R/pretty.r
index 757e011..428375c 100644
--- a/R/pretty.r
+++ b/R/pretty.r
@@ -1,31 +1,31 @@
-rdv <- function(x, ...) {
-    UseMethod("rdv")
-}
-
-remove.term <- function(f, term) {
-    lr <- left_right(f)
-    l <- lr$left
-    r <- lr$right
-    r2 <- r[!grepl(paste("^", term, "$", sep = ""), r) & !grepl(paste("^", term, ":", sep = ""), r) & !grepl(paste(":", term, "$", sep = ""), r) & !grepl(paste(":", term, ":", sep = ""), r)]
-    paste(l, "~", paste(r2, collapse = "+"))
-}
-
-rdv.glm <- function(x, ...) {
-
-}
-
-rdv.coxph <- function(x, ...) {
-
-}
-
-pretty <- function (x, ...) {
-    UseMethod("pretty")
-}
-
-pretty.glm <- function(x, ...) {
-
-}
-
-pretty.coxph <- function(x, ...) {
-
-}
+# rdv <- function(x, ...) {
+#     UseMethod("rdv")
+# }
+# 
+# remove.term <- function(f, term) {
+#     lr <- left_right(f)
+#     l <- lr$left
+#     r <- lr$right
+#     r2 <- r[!grepl(paste("^", term, "$", sep = ""), r) & !grepl(paste("^", term, ":", sep = ""), r) & !grepl(paste(":", term, "$", sep = ""), r) & !grepl(paste(":", term, ":", sep = ""), r)]
+#     paste(l, "~", paste(r2, collapse = "+"))
+# }
+# 
+# rdv.glm <- function(x, ...) {
+# 
+# }
+# 
+# rdv.coxph <- function(x, ...) {
+# 
+# }
+# 
+# pretty <- function (x, ...) {
+#     UseMethod("pretty")
+# }
+# 
+# pretty.glm <- function(x, ...) {
+# 
+# }
+# 
+# pretty.coxph <- function(x, ...) {
+# 
+# }
diff --git a/R/reporters.r b/R/reporters.r
index 760c68e..b58ce3e 100644
--- a/R/reporters.r
+++ b/R/reporters.r
@@ -1,3 +1,11 @@
+
+check_reporter_dependency <- function(){
+    if (!requireNamespace("ReporteRs", quietly = TRUE)) {
+        stop("Package \"ReporteRs\" is deprecated but needed for this function to work. \nIf you really want to use this function, please install it",
+             call. = FALSE)
+    }
+}
+
 ##' Add a new paragraph with a Normal style
 ##'
 ##' @name addNormal
@@ -16,8 +24,8 @@
 ##' }
 ##' @keywords univar
 ##' @export
-##' @import ReporteRs
 addNormal <- function(doc, value, stylename = "Normal", ...) {
+    check_reporter_dependency()
     if (class(value) == "character") {
         value <- do.call("set_of_paragraphs", args = lapply(value, pot))
     }
@@ -42,8 +50,8 @@ addNormal <- function(doc, value, stylename = "Normal", ...) {
 ##' }
 ##' @keywords univar
 ##' @export
-##' @import ReporteRs
 addComment <- function(doc, value, stylename = "Comment", ...) {
+    check_reporter_dependency()
     addParagraph(doc, value, stylename = stylename)
 }
 
@@ -65,8 +73,8 @@ addComment <- function(doc, value, stylename = "Comment", ...) {
 ##' }
 ##' @keywords univar
 ##' @export
-##' @import ReporteRs
 addAlert <- function(doc, value, stylename = "Alert", ...) {
+    check_reporter_dependency()
     addParagraph(doc, value, stylename = stylename)
 }
 
@@ -88,8 +96,8 @@ addAlert <- function(doc, value, stylename = "Alert", ...) {
 ##' }
 ##' @keywords univar
 ##' @export
-##' @import ReporteRs
 addVerbatim <- function(doc, value, stylename = "Verbatim", ...) {
+    check_reporter_dependency()
     addParagraph(doc, value, stylename = stylename, ...)
 }
 
@@ -110,8 +118,8 @@ addVerbatim <- function(doc, value, stylename = "Verbatim", ...) {
 ##' }
 ##' @keywords univar
 ##' @export
-##' @import ReporteRs
 addCode <- function(doc, value, ...) {
+    check_reporter_dependency()
     addRScript(doc, text = value, par.properties = parProperties(shading.color = "#eeeeee"))
 }
 
@@ -133,8 +141,8 @@ addCode <- function(doc, value, ...) {
 ##' }
 ##' @keywords univar
 ##' @export
-##' @import ReporteRs
 addPlotlegend <- function(doc, value, stylename = "figurereference", ...) {
+    check_reporter_dependency()
     addParagraph(doc, value, stylename = stylename)
 }
 
@@ -155,9 +163,9 @@ addPlotlegend <- function(doc, value, stylename = "figurereference", ...) {
 ##' doc <- addTablegend(doc, "Coucou")
 ##' }
 ##' @keywords univar
-##' @export
-##' @import ReporteRs
+##' @export 
 addTablegend <- function(doc, value, stylename = "tablereference", ...) {
+    check_reporter_dependency()
     addParagraph(doc, value, stylename = stylename)
 }
 
@@ -179,8 +187,8 @@ addTablegend <- function(doc, value, stylename = "tablereference", ...) {
 ##' }
 ##' @keywords univar
 ##' @export
-##' @import ReporteRs
 addItemize <- function(doc, value, level = 1, ...) {
+    check_reporter_dependency()
     unordered.list.level1 <- parProperties(list.style = "unordered", level = 1)
     unordered.list.level2 <- parProperties(list.style = "unordered", level = 2)
     unordered.list.level3 <- parProperties(list.style = "unordered", level = 3)
@@ -216,8 +224,8 @@ addItemize <- function(doc, value, level = 1, ...) {
 ##' }
 ##' @keywords univar
 ##' @export
-##' @import ReporteRs
 addEnumerate <- function(doc, value, level = 1, ...) {
+    check_reporter_dependency()
     ordered.list.level1 <- parProperties(list.style = "ordered", level = 1)
     ordered.list.level2 <- parProperties(list.style = "ordered", level = 2)
     ordered.list.level3 <- parProperties(list.style = "ordered", level = 3)
@@ -251,8 +259,8 @@ addEnumerate <- function(doc, value, level = 1, ...) {
 ##' }
 ##' @keywords univar
 ##' @export
-##' @import ReporteRs
 simple.table <- function(dataset, add.rownames = FALSE) {
+    check_reporter_dependency()
     ft = FlexTable(dataset, add.rownames = add.rownames)
     ft[, , to = "header"] = textBold()
     #    ft[, , to = "header"] = parRight()
@@ -315,9 +323,9 @@ simple.table <- function(dataset, add.rownames = FALSE) {
 ##' }
 ##' @keywords univar
 ##' @export
-##' @import ReporteRs
 create.report <- function(template = c("gerc", "urc", "cephepi"), title = "", acronym = "", version = "", npromo = "", nct = "", invest = "", biostat = "", methodo = "", date_lastmodif = "", date_freez = "", date_update = "", history = NULL) {
     
+    check_reporter_dependency()
     URC <- FALSE
     if (template[1] == "urc") {
         template.file <- system.file("templates/template_urc.docx", package = "biostat2")
diff --git a/R/summarize.by.r b/R/summarize.by.r
index 713705f..dc54c03 100644
--- a/R/summarize.by.r
+++ b/R/summarize.by.r
@@ -21,7 +21,6 @@
 summarize.by <- function(x, by, funs = c(mean, sd, quantile, n, na), ..., showNA = c("no", "ifany", "always"), total = FALSE, digits = 2, test = FALSE, test.summarize = test.summarize.auto, show.test = display.test, plim = 4, show.method = TRUE, effect = FALSE, effect.summarize = diff.mean.auto, conf.level = 0.95, show.effect = display.effect) {
 
     showNA <- showNA[1]
-
     by2 <- by
     if (showNA == "always" | (showNA == "ifany" & anyNA(by))) {
         by2 <- addNA(by2)
@@ -53,13 +52,7 @@ summarize.by <- function(x, by, funs = c(mean, sd, quantile, n, na), ..., showNA
   if (identical(total, 1) | identical(total, 1:2) | identical(total, TRUE)) {
         results$Total <- summarize(x, funs = funs, ..., digits = digits)[, 2]
     }
-    ## results <- sapply(results, function(x) if (is.numeric(x)) as.character(round(x, digits)) else as.character(x))
 
-    ## Si NA n'est pas dans le facteur, on met la colonne apres "Total"
-    if ((any(colnames(results) == "NA") & any(colnames(results) == "Total")) & !anyNA(levels(by))) {
-        tmp <- results[, "NA"]
-        results <- cbind(results[, colnames(results) != "NA"], "NA" = tmp)
-    }
 
     if (effect) {
         results <- cbind(results, effect = show.effect(effect.summarize(x, by, conf.level), digits = digits))
diff --git a/R/test.r b/R/test.r
index 9b37c45..29e3187 100644
--- a/R/test.r
+++ b/R/test.r
@@ -6,14 +6,14 @@
 ##' @export
 ##' @author David Hajage
 plim <- function (p, digits = 4) {
-    pround <- round(p, digits)
-    lim <- 10^(-digits)
-    ptxt <- vector("character", length(p))
-    ptxt[pround < lim] <- paste("<", "0.", paste(rep("0", digits -
-        1), collapse = ""), "1", sep = "")
-    ptxt[pround >= lim] <- formatC(pround[pround >= lim], format = "f",
-        digits = digits)
-    return(ptxt)
+  pround <- round(p, digits)
+  lim <- 10^(-digits)
+  ptxt <- vector("character", length(p))
+  ptxt[pround < lim] <- paste("<", "0.", paste(rep("0", digits -
+                                                     1), collapse = ""), "1", sep = "")
+  ptxt[pround >= lim] <- formatC(pround[pround >= lim], format = "f",
+                                 digits = digits)
+  return(ptxt)
 }
 
 ##' Display a test result
@@ -30,9 +30,9 @@ display.test <- function(test, digits = 4, method = TRUE) {
   else {
     p <- plim(test$p.value, digits = digits)
     if (method)
-    paste("p value: ", p, " (", test$method, ")", sep = "")
-  else
-    paste("p value: ", p, sep = "")
+      paste("p value: ", p, " \n(", test$method, ")", sep = "")
+    else
+      p
   }
 }
 
@@ -57,7 +57,7 @@ test.tabular.auto <- function(x, y) {
   ##   test <- suppressWarnings(chisq.test(x, y, correct = TRUE))
   else
     test <- fisher.test(x, y)
-
+  
   p <- test$p.value
   method <- test$method
   list(p.value = p, method = method)
@@ -77,7 +77,7 @@ test.tabular.fisher <- function(x, y) {
     test <- list(p.value = NULL, method = NULL)
   else
     test <- fisher.test(x, y)
-
+  
   p <- test$p.value
   method <- test$method
   list(p.value = p, method = method)
@@ -95,18 +95,18 @@ test.tabular.fisher <- function(x, y) {
 ##' @export
 test.summarize.auto.old <- function(x, g) {
   ng <- table(g)
-
+  
   if (length(ng) <= 1) {
     p <- NULL
     method <- NULL
   } else {
     shapirog <- tapply(x, g, function(x) shapiro.test(x)$p.value)
     if (any(ng < 30) | any(shapirog < 0.05)) {
-        if (length(ng) == 2) {
-            type <- "wilcox"
-        } else {
-            type <- "kruskal"
-        }
+      if (length(ng) == 2) {
+        type <- "wilcox"
+      } else {
+        type <- "kruskal"
+      }
     } else {
       bartlettg <- bartlett.test(x, g)$p.value
       if (bartlettg < 0.05 & length(ng) == 2) {
@@ -144,46 +144,46 @@ test.summarize.auto.old <- function(x, g) {
 ##' @importFrom nortest ad.test
 ##' @export
 test.summarize.auto <- function(x, g) {
-    ng <- table(g)
-    
-    if (length(ng) <= 1) {
-        p <- NULL
-        method <- NULL
+  ng <- table(g)
+  
+  if (length(ng) <= 1) {
+    p <- NULL
+    method <- NULL
+  } else {
+    if (any(ng < 50)) {
+      normg <- tapply(x, g, function(x) shapiro.test(x)$p.value)
     } else {
-        if (any(ng < 50)) {
-            normg <- tapply(x, g, function(x) shapiro.test(x)$p.value)
-        } else {
-            normg <- tapply(x, g, function(x) ad.test(x)$p.value)
-        }
-        if (any(normg < 0.05)) {
-            if (length(ng) == 2) {
-                type <- "wilcox"
-            } else {
-                type <- "kruskal"
-            }
-        } else {
-            bartlettg <- bartlett.test(x, g)$p.value
-            if (bartlettg < 0.05 & length(ng) == 2) {
-                type <- "t.unequalvar"
-            } else if (bartlettg < 0.05 & length(ng) > 2) {
-                type <- "a.unequalvar"
-            } else if (bartlettg > 0.05 & length(ng) == 2) {
-                type <- "t.equalvar"
-            } else if (bartlettg > 0.05 & length(ng) > 2) {
-                type <- "a.equalvar"
-            }
-        }
-        test <- switch(type,
-                       wilcox = wilcox.test(x ~ g, correct = FALSE),
-                       kruskal = kruskal.test(x, g),
-                       t.unequalvar = t.test(x ~  g, var.equal = FALSE),
-                       t.equalvar = t.test(x ~  g, var.equal = TRUE),
-                       a.unequalvar = oneway.test(x ~  g, var.equal = FALSE),
-                       a.equalvar = oneway.test(x ~ g, var.equal = TRUE))
-        p <- test$p.value
-        method <- test$method
+      normg <- tapply(x, g, function(x) ad.test(x)$p.value)
     }
-    list(p.value = p, method = method)
+    if (any(normg < 0.05)) {
+      if (length(ng) == 2) {
+        type <- "wilcox"
+      } else {
+        type <- "kruskal"
+      }
+    } else {
+      bartlettg <- bartlett.test(x, g)$p.value
+      if (bartlettg < 0.05 & length(ng) == 2) {
+        type <- "t.unequalvar"
+      } else if (bartlettg < 0.05 & length(ng) > 2) {
+        type <- "a.unequalvar"
+      } else if (bartlettg >= 0.05 & length(ng) == 2) {
+        type <- "t.equalvar"
+      } else if (bartlettg >= 0.05 & length(ng) > 2) {
+        type <- "a.equalvar"
+      }
+    }
+    test <- switch(type,
+                   wilcox = wilcox.test(x ~ g, correct = FALSE),
+                   kruskal = kruskal.test(x, g),
+                   t.unequalvar = t.test(x ~  g, var.equal = FALSE),
+                   t.equalvar = t.test(x ~  g, var.equal = TRUE),
+                   a.unequalvar = oneway.test(x ~  g, var.equal = FALSE),
+                   a.equalvar = oneway.test(x ~ g, var.equal = TRUE))
+    p <- test$p.value
+    method <- test$method
+  }
+  list(p.value = p, method = method)
 }
 
 ##' test for mean comparison
@@ -198,16 +198,16 @@ test.summarize.auto <- function(x, g) {
 test.summarize.kruskal <- function(x, g) {
   ng <- table(g)
   if (length(ng) <= 1) {
-      p <- NULL
-      method <- NULL
+    p <- NULL
+    method <- NULL
   } else if (length(ng) == 2) {
-      test <- wilcox.test(x ~ g, correct = FALSE)
-      p <- test$p.value
-      method <- test$method
+    test <- wilcox.test(x ~ g, correct = FALSE)
+    p <- test$p.value
+    method <- test$method
   } else if (length(ng) > 2) {
-      test <- kruskal.test(x, g)
-      p <- test$p.value
-      method <- test$method
+    test <- kruskal.test(x, g)
+    p <- test$p.value
+    method <- test$method
   }
   list(p.value = p, method = method)
 }
@@ -280,3 +280,104 @@ test.survival.logrank <- function(formula) {
   list(p.value = p, method = "Logrank test")
 }
 
+
+
+
+# DAN ---------------------------------------------------------------------
+
+
+#' Test for linear trend across ordered factor with contrasts
+#'
+#' @param x vector
+#' @param y ordered factor
+#'
+#' @return a list with two componments: p.value and method
+#' @author Dan Chaltiel
+#' @export
+#' @import gmodels
+#' @importFrom DescTools CochranArmitageTest
+#'
+#' @examples
+#' library(dplyr)
+#' iris %>% 
+#'   mutate(Petal.Width.qt = paste0("Q", ntile(Petal.Width, 5)) %>% ordered()) %>% 
+#'   cross(Petal.Length ~ Petal.Width.qt, data=., test=T, test.summarize = test.summarize.contrasts.lin)
+test.summarize.contrasts.lin = function(x, y){
+  stopifnot(is.ordered(y))
+  levels_seq = 1:length(levels(y))
+  contr = levels_seq - mean(levels_seq)  #centered on 0, step of 1
+  m = lm(x ~ y)
+  t = gmodels::fit.contrast(m, y, coeff=contr)
+  list(p.value=t[,"Pr(>|t|)"], method="Contrast test for linear trend")
+}
+
+
+#TODO faire tout ça !
+
+test.summarize.auto.dan = function (x, g) {
+  ng <- table(g)
+  if (length(ng) <= 1) {
+    p <- NULL
+    method <- NULL
+  } else {
+    if(length(x)<3){ #shapiro.test throws an error if n<3
+      shapirog=0
+    } else if(length(x)<5000){ 
+      shapirog <- tapply(x, g, function(x) shapiro.test(x)$p.value)
+    } else { #on large samples, shapiro.test is not relevant
+      shapirog=1
+    }
+    
+    if (any(ng < 30) | any(shapirog < 0.05)) {
+      if (length(ng) == 2) {
+        type <- "wilcox"
+      } else {
+        type <- "kruskal"
+      }
+    }
+    else {
+      bartlettg <- bartlett.test(x, g)$p.value
+      if (bartlettg < 0.05 & length(ng) == 2) {
+        type <- "t.unequalvar"
+      }
+      else if (bartlettg < 0.05 & length(ng) > 2) {
+        type <- "a.unequalvar"
+      }
+      else if (bartlettg >= 0.05 & length(ng) == 2) {#DAN ajoute un egal au cas où bartlettg==0.05!
+        type <- "t.equalvar"
+      }
+      else if (bartlettg >= 0.05 & length(ng) > 2) {
+        type <- "a.equalvar"
+      }
+    }
+    test <- switch(type, 
+                   wilcox = wilcox.test(x ~ g, correct = FALSE), 
+                   kruskal = kruskal.test(x, g), 
+                   t.unequalvar = t.test(x ~ g, var.equal = FALSE), 
+                   t.equalvar = t.test(x ~ g, var.equal = TRUE), 
+                   a.unequalvar = oneway.test(x ~ g, var.equal = FALSE), 
+                   a.equalvar = oneway.test(x ~ g, var.equal = TRUE))
+    p <- test$p.value
+    method <- test$method
+  }
+  list(p.value = p, method = method)
+}
+
+test.tabular.auto.dan = function (x, y) {
+  tab <- table(x, y)
+  if(is.ordered(x) & is.ordered(y)){
+    test <- cor.test(as.numeric(x), as.numeric(y), method = "spearman", exact = FALSE)
+  } else if((is.ordered(x) | is.ordered(y)) & any(dim(tab)==2)){
+    test <- DescTools::CochranArmitageTest(tab, alternative = "two.sided")
+  } else{
+    exp <- rowSums(tab) %*% t(colSums(tab))/sum(tab)
+    if (any(dim(table(x, y)) == 1)) 
+      test <- list(p.value = NULL, method = NULL)
+    else if (all(exp >= 5)) 
+      test <- suppressWarnings(chisq.test(x, y, correct = FALSE))
+    else test <- fisher.test(x, y)
+  }
+  p <- test$p.value
+  method <- test$method
+  list(p.value = p, method = method)
+}
diff --git a/README.Rmd b/README.Rmd
new file mode 100644
index 0000000..d5cdd62
--- /dev/null
+++ b/README.Rmd
@@ -0,0 +1,170 @@
+---
+    output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(
+    collapse=TRUE,
+    comment="#>",
+    fig.path="man/figures/README-",
+    out.width="100%"
+)
+options(Encoding="UTF-8")
+library(knitr)
+library(biostat2)
+library(Hmisc)
+library(officer)
+library(dplyr)
+# cross(cbind(agegp, ncases) ~ tobgp, esoph, margin="row", test = TRUE) %>% cross_to_flextable %>% autofit %>% save_as_image("img/cross_esoph.png", zoom=30)
+# cross(cbind(Sepal.Length, Sepal.Width) ~ Species, iris, test = TRUE, total="column") %>% cross_to_flextable %>% autofit %>% save_as_image("img/cross_iris.png", zoom=30)
+# cross(cbind(mpg, qsec) ~ factor(am), mtcars2, effect=T, test=TRUE, show.method=F) %>% cross_to_flextable %>% autofit %>% save_as_image("img/cross_mtcars.png", zoom=30)
+```
+
+# biostat2
+
+[![Lifecycle: superseded](https://img.shields.io/badge/lifecycle-superseded-blue.svg)](https://www.tidyverse.org/lifecycle/#superseded)
+
+Ceci est un fork du super package [`biostat2`](https://github.com/eusebe/biostat2) de David Hajage.
+
+Il est centré sur la fonction `cross` qui permet de générer très facilement les *statistiques descriptives* d'une étude et s'intègre naturellement au package `officer` permettant de faire un rapport automatisé.
+
+# Important
+
+Ce fork a été totalement réécrit et optimisé dans un nouveau package :[`crosstable`](https://github.com/DanChaltiel/crosstable). Celui-ci permet une nouvelle syntaxe plus efficace avec l'utilisation des helpers de `tidyselect`, des fonctions predicates, et l'output (`flextable`) a été amélioré. Aucune mise-à-jour ne sera effectuée sur ce fork, je vous conseille donc vivement d'utiliser soit le package [`biostat2`](https://github.com/eusebe/biostat2) original, soit le nouveau package [`crosstable`](https://github.com/DanChaltiel/crosstable).
+
+## Installation
+
+```{r install, eval=FALSE}
+install.packages("devtools")
+remotes::install_github("DanChaltiel/biostat2")
+library(biostat2)
+# cross=biostat2::cross #lancer si purrr est chargé pour overrider purrr::cross
+```
+
+## Utilisation
+
+### Description
+
+On décrit une table avec une formule. On utilise `cbind` pour récupérer une dataframe en sortie, mais on pourrait aussi utiliser des `+` et récupérer une liste de descriptions par variable. A droite du `~` on trouve la variable de groupe ou un `.` sinon. Par défaut, `cross` donnera la moyenne, écart-type, médiane, IQR, min, max, nombre d'observations et nombre de manquants.
+
+```{r cross1, echo=TRUE}
+cross(cbind(Sepal.Length, Petal.Length) ~ Species, data=iris)
+
+cross(cbind(Sepal.Length, Petal.Length, Species) ~ ., data=iris)
+```
+
+On peut spécifier des calculs spécifiques dans la formule avec la fonction `I()`, on peut utiliser n'importe quelle fonction de description (ajouter les arguments à la suite, comme l'argument `probs` de la fonction `quantile` ici) et on peut demander des totaux en ligne, en colonne ou les deux.
+
+```{r cross2, echo=TRUE}
+cross(cbind(Sepal.Length, I(Sepal.Width^2)) ~ Species, iris, funs=quantile, probs=c(1/3, 2/3), total="row") #T1 & T2 by Species
+```
+
+Les pourcentages sont donnés par défaut par ligne, colonne et cellule, mais on peut restreindre avec l'argument `margin`. L'argument `test` permet de faire le test adéquat en fonction de règles définies.
+
+```{r cross3, echo=TRUE}
+cross(alcgp ~ tobgp, esoph, margin="row", total="both", test=TRUE)
+```
+
+Si le groupement n'a que deux niveau, il est possible de calculer un effet grâce à l'argument `effect`.
+```{r cross4, echo=TRUE}
+cross(cbind(mpg, qsec) ~ factor(am), mtcars, effect=T, test=TRUE, show.method=F)
+```
+
+Enfin, si la variable de groupe est numérique, `cross` sortira les coefficients de corrélation.
+```{r cross5, echo=TRUE}
+cross(cbind(Sepal.Length, Sepal.Width) ~ cbind(Petal.Length, Petal.Width), iris)
+```
+
+### Labels
+
+`cross` est interfacé avec la fonction `label` du package `Hmisc`, ce qui permet d'avoir des tableaux plus clairs.
+```{r cross6, echo=TRUE}
+library(Hmisc)
+# ?mtcars
+mtcars2=mtcars
+label(mtcars2$mpg) = "Miles/(US) gallon"
+label(mtcars2$qsec) = "1/4 mile time in seconds"
+mtcars2$am = factor(mtcars2$am, levels=0:1, labels=c("automatic", "manual"))
+cross(cbind(mpg, qsec) ~ am, mtcars2)
+```
+
+
+## Reporting
+
+### Tableaux HTML
+
+Il est possible de transformer une table en HTML via la fonction `cross_to_flextable())`.
+
+```{r packages2, message=FALSE, warning=FALSE, include=FALSE}
+library(flextable)
+library(dplyr) #for the pipe operator
+```
+
+```{r flextable1, echo=TRUE, eval=FALSE}
+cross(cbind(agegp, ncases) ~ tobgp, esoph, margin="row", test = TRUE) %>% cross_to_flextable
+```
+<center><img src="img/cross_esoph.png" height="300px"/></center>
+
+```{r flextable2, echo=TRUE, eval=FALSE}
+cross(cbind(Sepal.Length, Sepal.Width) ~ Species, iris, test = TRUE, total="column") %>% cross_to_flextable
+```
+<center><img src="img/cross_iris.png" height="250px"/></center>
+
+```{r flextable3, echo=TRUE, eval=FALSE}
+cross(cbind(mpg, qsec) ~ factor(am), mtcars2, effect=T, test=TRUE, show.method=F) %>% cross_to_flextable
+```
+<center><img src="img/cross_mtcars.png" height="250px"/></center>
+
+### Intégration avec `officer`
+
+Grâce au package `officer`, il est possible de réaliser des fichiers MS Word. On peut ajouter des tableaux `cross` de cette façon :
+    
+    ```{r officer, echo=TRUE, eval=FALSE}
+    library(officer)
+    library(dplyr) #for the pipe operator
+    c1 = cross(cbind(Sepal.Length, Petal.Length) ~ Species, test=TRUE, show.method=F, data=iris)
+    c2 = cross(cbind(mpg, qsec) ~ factor(am), mtcars2, test=TRUE, show.method=F)
+    read_docx() %>% 
+        body_add_title("Cross + officer = <3", 1) %>% 
+        body_add_title("Premier exemple : iris", 2) %>% 
+        body_add_crosstable(c1) %>% 
+        body_add_title("Deuxième exemple : mtcars", 2) %>% 
+        body_add_crosstable(c2, auto.fit=T) %>% 
+        print("exemples/cross_officer.docx")
+    ```
+
+A noter toutefois que les tableaux devront être agrandis avec l'ajustement automatique de Word, l'argument `auto.fit` pouvant largement dépasser les marges de la page. Le fichier de sortie est donc disponible ici : [cross_officer.docx](exemples/cross_officer.docx)
+
+### Intégration avec `Rmarkdown`
+
+<!-- Intégration Rmd in Rmd : la coloration syntaxique RStudio est mauvaise mais le code est bon ! -->
+<!-- https://stackoverflow.com/questions/53226493/add-markdown-code-chunk-to-r-markdown-document#comment104859956_53226493 -->
+Tricoter (`knitr::knit()` ou via **RStudio**) ce code `Rmd` produit un fichier MS Word. L'avantage ici est l'utilisation de `bookdown` pour générer la numérotation automatique des tableaux.
+
+````markdown
+
+---
+title: "Iris"
+output: bookdown::word_document2
+---
+    
+`r ''````{r setup, include=FALSE}
+library(biostat2)
+library(flextable)
+library(dplyr) #pour le pipe %>% 
+```
+
+Table iris is given in Table \@ref(tab:irisTable).
+
+`r ''````{r description, echo=FALSE, results='asis'}
+cat("<caption> (\\#tab:irisTable) Table Iris </caption> \n\r ")
+cross(cbind(Sepal.Length, Sepal.Width) ~ Species, iris, test = TRUE, total="column") %>% cross_to_flextable %>% autofit
+```
+
+````
+
+Le fichier `Rmarkdown` est disponible ici : [cross_markdown.Rmd](exemples/cross_markdown.Rmd) et le fichier de sortie est disponible ici : [cross_markdown.docx](exemples/cross_markdown.docx)
+
+
diff --git a/README.md b/README.md
index b079d9c..a123f49 100644
--- a/README.md
+++ b/README.md
@@ -1 +1,297 @@
-For now, the package implements `cross` (a partial rewrite of `remix`)
\ No newline at end of file
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# biostat2
+
+[![Lifecycle:
+superseded](https://img.shields.io/badge/lifecycle-superseded-blue.svg)](https://www.tidyverse.org/lifecycle/#superseded)
+
+Ceci est un fork du super package
+[`biostat2`](https://github.com/eusebe/biostat2) de David Hajage.
+
+Il est centré sur la fonction `cross` qui permet de générer très
+facilement les *statistiques descriptives* d’une étude et s’intègre
+naturellement au package `officer` permettant de faire un rapport
+automatisé.
+
+# Important
+
+Ce fork a été totalement réécrit et optimisé dans un nouveau package
+:[`crosstable`](https://github.com/DanChaltiel/crosstable). Celui-ci
+permet une nouvelle syntaxe plus efficace avec l’utilisation des helpers
+de `tidyselect`, des fonctions predicates, et l’output (`flextable`) a
+été amélioré. Aucune mise-à-jour ne sera effectuée sur ce fork, je vous
+conseille donc vivement d’utiliser soit le package
+[`biostat2`](https://github.com/eusebe/biostat2) original, soit le
+nouveau package
+[`crosstable`](https://github.com/DanChaltiel/crosstable).
+
+## Installation
+
+``` r
+install.packages("devtools")
+remotes::install_github("DanChaltiel/biostat2")
+library(biostat2)
+# cross=biostat2::cross #lancer si purrr est chargé pour overrider purrr::cross
+```
+
+## Utilisation
+
+### Description
+
+On décrit une table avec une formule. On utilise `cbind` pour récupérer
+une dataframe en sortie, mais on pourrait aussi utiliser des `+` et
+récupérer une liste de descriptions par variable. A droite du `~` on
+trouve la variable de groupe ou un `.` sinon. Par défaut, `cross`
+donnera la moyenne, écart-type, médiane, IQR, min, max, nombre
+d’observations et nombre de manquants.
+
+``` r
+cross(cbind(Sepal.Length, Petal.Length) ~ Species, data=iris)
+#>            .id        label  variable         setosa    versicolor
+#> 1 Sepal.Length Sepal.Length Min / Max      4.3 / 5.8       4.9 / 7
+#> 2 Sepal.Length Sepal.Length Med [IQR]    5 [4.8;5.2] 5.9 [5.6;6.3]
+#> 3 Sepal.Length Sepal.Length Moy (std)    5.01 (0.35)   5.94 (0.52)
+#> 4 Sepal.Length Sepal.Length    N (NA)         50 (0)        50 (0)
+#> 5 Petal.Length Petal.Length Min / Max        1 / 1.9       3 / 5.1
+#> 6 Petal.Length Petal.Length Med [IQR] 1.5 [1.4;1.58]  4.35 [4;4.6]
+#> 7 Petal.Length Petal.Length Moy (std)    1.46 (0.17)   4.26 (0.47)
+#> 8 Petal.Length Petal.Length    N (NA)         50 (0)        50 (0)
+#>         virginica
+#> 1       4.9 / 7.9
+#> 2  6.5 [6.23;6.9]
+#> 3     6.59 (0.64)
+#> 4          50 (0)
+#> 5       4.5 / 6.9
+#> 6 5.55 [5.1;5.88]
+#> 7     5.55 (0.55)
+#> 8          50 (0)
+
+cross(cbind(Sepal.Length, Petal.Length, Species) ~ ., data=iris)
+#>             .id        label   variable          value
+#> 1  Sepal.Length Sepal.Length  Min / Max      4.3 / 7.9
+#> 2  Sepal.Length Sepal.Length  Med [IQR]  5.8 [5.1;6.4]
+#> 3  Sepal.Length Sepal.Length  Moy (std)    5.84 (0.83)
+#> 4  Sepal.Length Sepal.Length     N (NA)        150 (0)
+#> 5  Petal.Length Petal.Length  Min / Max        1 / 6.9
+#> 6  Petal.Length Petal.Length  Med [IQR] 4.35 [1.6;5.1]
+#> 7  Petal.Length Petal.Length  Moy (std)    3.76 (1.77)
+#> 8  Petal.Length Petal.Length     N (NA)        150 (0)
+#> 9       Species      Species     setosa    50 (33.33%)
+#> 10      Species      Species versicolor    50 (33.33%)
+#> 11      Species      Species  virginica    50 (33.33%)
+```
+
+On peut spécifier des calculs spécifiques dans la formule avec la
+fonction `I()`, on peut utiliser n’importe quelle fonction de
+description (ajouter les arguments à la suite, comme l’argument `probs`
+de la fonction `quantile` ici) et on peut demander des totaux en ligne,
+en colonne ou les deux.
+
+``` r
+cross(cbind(Sepal.Length, I(Sepal.Width^2)) ~ Species, iris, funs=quantile, probs=c(1/3, 2/3), total="row") #T1 & T2 by Species
+#>                .id            label           variable setosa versicolor
+#> 1     Sepal.Length     Sepal.Length quantile 33.33333%    4.9        5.7
+#> 2     Sepal.Length     Sepal.Length quantile 66.66667%    5.1        6.1
+#> 3 I(Sepal.Width^2) I(Sepal.Width^2) quantile 33.33333%  10.46       7.29
+#> 4 I(Sepal.Width^2) I(Sepal.Width^2) quantile 66.66667%  12.25       8.41
+#>   virginica Total
+#> 1       6.3   5.4
+#> 2      6.77   6.3
+#> 3      7.84  8.41
+#> 4      9.41 10.24
+```
+
+Les pourcentages sont donnés par défaut par ligne, colonne et cellule,
+mais on peut restreindre avec l’argument `margin`. L’argument `test`
+permet de faire le test adéquat en fonction de règles définies.
+
+``` r
+cross(alcgp ~ tobgp, esoph, margin="row", total="both", test=TRUE)
+#>     .id label  variable    0-9g/day       10-19       20-29         30+
+#> 1 alcgp alcgp 0-39g/day  6 (26.09%)  6 (26.09%)  5 (21.74%)  6 (26.09%)
+#> 2 alcgp alcgp     40-79  6 (26.09%)  6 (26.09%)  6 (26.09%)  5 (21.74%)
+#> 3 alcgp alcgp    80-119  6 (28.57%)  6 (28.57%)  4 (19.05%)  5 (23.81%)
+#> 4 alcgp alcgp      120+  6 (28.57%)  6 (28.57%)  5 (23.81%)  4 (19.05%)
+#> 5 alcgp alcgp     Total 24 (27.27%) 24 (27.27%) 20 (22.73%) 20 (22.73%)
+#>         Total                                                      p
+#> 1 23 (26.14%) p value: 0.9999 \n(Fisher's Exact Test for Count Data)
+#> 2 23 (26.14%) p value: 0.9999 \n(Fisher's Exact Test for Count Data)
+#> 3 21 (23.86%) p value: 0.9999 \n(Fisher's Exact Test for Count Data)
+#> 4 21 (23.86%) p value: 0.9999 \n(Fisher's Exact Test for Count Data)
+#> 5   88 (100%) p value: 0.9999 \n(Fisher's Exact Test for Count Data)
+```
+
+Si le groupement n’a que deux niveau, il est possible de calculer un
+effet grâce à l’argument `effect`.
+
+``` r
+cross(cbind(mpg, qsec) ~ factor(am), mtcars, effect=T, test=TRUE, show.method=F)
+#>    .id label  variable                   0                   1
+#> 1  mpg   mpg Min / Max         10.4 / 24.4           15 / 33.9
+#> 2  mpg   mpg Med [IQR]   17.3 [14.95;19.2]      22.8 [21;30.4]
+#> 3  mpg   mpg Moy (std)        17.15 (3.83)        24.39 (6.17)
+#> 4  mpg   mpg    N (NA)              19 (0)              13 (0)
+#> 5 qsec  qsec Min / Max        15.41 / 22.9         14.5 / 19.9
+#> 6 qsec  qsec Med [IQR] 17.82 [17.18;19.17] 17.02 [16.46;18.61]
+#> 7 qsec  qsec Moy (std)        18.18 (1.75)        17.36 (1.79)
+#> 8 qsec  qsec    N (NA)              19 (0)              13 (0)
+#>                                                                      effect
+#> 1 Difference in means (t-test CI) (0 minus 1): -7.24 CI95%[-10.85 to -3.64]
+#> 2 Difference in means (t-test CI) (0 minus 1): -7.24 CI95%[-10.85 to -3.64]
+#> 3 Difference in means (t-test CI) (0 minus 1): -7.24 CI95%[-10.85 to -3.64]
+#> 4 Difference in means (t-test CI) (0 minus 1): -7.24 CI95%[-10.85 to -3.64]
+#> 5    Difference in means (t-test CI) (0 minus 1): 0.82 CI95%[-0.48 to 2.12]
+#> 6    Difference in means (t-test CI) (0 minus 1): 0.82 CI95%[-0.48 to 2.12]
+#> 7    Difference in means (t-test CI) (0 minus 1): 0.82 CI95%[-0.48 to 2.12]
+#> 8    Difference in means (t-test CI) (0 minus 1): 0.82 CI95%[-0.48 to 2.12]
+#>        p
+#> 1 0.0003
+#> 2 0.0003
+#> 3 0.0003
+#> 4 0.0003
+#> 5 0.2057
+#> 6 0.2057
+#> 7 0.2057
+#> 8 0.2057
+```
+
+Enfin, si la variable de groupe est numérique, `cross` sortira les
+coefficients de corrélation.
+
+``` r
+cross(cbind(Sepal.Length, Sepal.Width) ~ cbind(Petal.Length, Petal.Width), iris)
+#>            .id        label variable Petal.Length variable Petal.Width
+#> 1 Sepal.Length Sepal.Length  pearson         0.87  pearson        0.82
+#> 2  Sepal.Width  Sepal.Width  pearson        -0.43  pearson       -0.37
+```
+
+### Labels
+
+`cross` est interfacé avec la fonction `label` du package `Hmisc`, ce
+qui permet d’avoir des tableaux plus clairs.
+
+``` r
+library(Hmisc)
+# ?mtcars
+mtcars2=mtcars
+label(mtcars2$mpg) = "Miles/(US) gallon"
+label(mtcars2$qsec) = "1/4 mile time in seconds"
+mtcars2$am = factor(mtcars2$am, levels=0:1, labels=c("automatic", "manual"))
+cross(cbind(mpg, qsec) ~ am, mtcars2)
+#>    .id                    label  variable           automatic
+#> 1  mpg        Miles/(US) gallon Min / Max         10.4 / 24.4
+#> 2  mpg        Miles/(US) gallon Med [IQR]   17.3 [14.95;19.2]
+#> 3  mpg        Miles/(US) gallon Moy (std)        17.15 (3.83)
+#> 4  mpg        Miles/(US) gallon    N (NA)              19 (0)
+#> 5 qsec 1/4 mile time in seconds Min / Max        15.41 / 22.9
+#> 6 qsec 1/4 mile time in seconds Med [IQR] 17.82 [17.18;19.17]
+#> 7 qsec 1/4 mile time in seconds Moy (std)        18.18 (1.75)
+#> 8 qsec 1/4 mile time in seconds    N (NA)              19 (0)
+#>                manual
+#> 1           15 / 33.9
+#> 2      22.8 [21;30.4]
+#> 3        24.39 (6.17)
+#> 4              13 (0)
+#> 5         14.5 / 19.9
+#> 6 17.02 [16.46;18.61]
+#> 7        17.36 (1.79)
+#> 8              13 (0)
+```
+
+## Reporting
+
+### Tableaux HTML
+
+Il est possible de transformer une table en HTML via la fonction
+`cross_to_flextable())`.
+
+``` r
+cross(cbind(agegp, ncases) ~ tobgp, esoph, margin="row", test = TRUE) %>% cross_to_flextable
+```
+
+<center>
+
+<img src="img/cross_esoph.png" height="300px"/>
+
+</center>
+
+``` r
+cross(cbind(Sepal.Length, Sepal.Width) ~ Species, iris, test = TRUE, total="column") %>% cross_to_flextable
+```
+
+<center>
+
+<img src="img/cross_iris.png" height="250px"/>
+
+</center>
+
+``` r
+cross(cbind(mpg, qsec) ~ factor(am), mtcars2, effect=T, test=TRUE, show.method=F) %>% cross_to_flextable
+```
+
+<center>
+
+<img src="img/cross_mtcars.png" height="250px"/>
+
+</center>
+
+### Intégration avec `officer`
+
+Grâce au package `officer`, il est possible de réaliser des fichiers MS
+Word. On peut ajouter des tableaux `cross` de cette façon :
+
+    ```r
+    library(officer)
+    library(dplyr) #for the pipe operator
+    c1 = cross(cbind(Sepal.Length, Petal.Length) ~ Species, test=TRUE, show.method=F, data=iris)
+    c2 = cross(cbind(mpg, qsec) ~ factor(am), mtcars2, test=TRUE, show.method=F)
+    read_docx() %>% 
+        body_add_title("Cross + officer = <3", 1) %>% 
+        body_add_title("Premier exemple : iris", 2) %>% 
+        body_add_crosstable(c1) %>% 
+        body_add_title("Deuxième exemple : mtcars", 2) %>% 
+        body_add_crosstable(c2, auto.fit=T) %>% 
+        print("exemples/cross_officer.docx")
+    ```
+
+A noter toutefois que les tableaux devront être agrandis avec
+l’ajustement automatique de Word, l’argument `auto.fit` pouvant
+largement dépasser les marges de la page. Le fichier de sortie est donc
+disponible ici : [cross\_officer.docx](exemples/cross_officer.docx)
+
+### Intégration avec `Rmarkdown`
+
+<!-- Intégration Rmd in Rmd : la coloration syntaxique RStudio est mauvaise mais le code est bon ! -->
+
+<!-- https://stackoverflow.com/questions/53226493/add-markdown-code-chunk-to-r-markdown-document#comment104859956_53226493 -->
+
+Tricoter (`knitr::knit()` ou via **RStudio**) ce code `Rmd` produit un
+fichier MS Word. L’avantage ici est l’utilisation de `bookdown` pour
+générer la numérotation automatique des tableaux.
+
+```` markdown
+
+---
+title: "Iris"
+output: bookdown::word_document2
+---
+    
+```{r setup, include=FALSE}
+library(biostat2)
+library(flextable)
+library(dplyr) #pour le pipe %>% 
+```
+
+Table iris is given in Table \@ref(tab:irisTable).
+
+```{r description, echo=FALSE, results='asis'}
+cat("<caption> (\\#tab:irisTable) Table Iris </caption> \n\r ")
+cross(cbind(Sepal.Length, Sepal.Width) ~ Species, iris, test = TRUE, total="column") %>% cross_to_flextable %>% autofit
+```
+````
+
+Le fichier `Rmarkdown` est disponible ici :
+[cross\_markdown.Rmd](exemples/cross_markdown.Rmd) et le fichier de
+sortie est disponible ici :
+[cross\_markdown.docx](exemples/cross_markdown.docx)
diff --git a/biostat2.Rproj b/biostat2.Rproj
index 4fa70f0..828602d 100644
--- a/biostat2.Rproj
+++ b/biostat2.Rproj
@@ -7,7 +7,7 @@ AlwaysSaveHistory: Default
 EnableCodeIndexing: Yes
 UseSpacesForTab: Yes
 NumSpacesForTab: 4
-Encoding: ISO8859-1
+Encoding: UTF-8
 
 RnwWeave: Sweave
 LaTeX: pdfLaTeX
@@ -15,3 +15,4 @@ LaTeX: pdfLaTeX
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace
diff --git a/exemples/cross_markdown.Rmd b/exemples/cross_markdown.Rmd
new file mode 100644
index 0000000..d46316f
--- /dev/null
+++ b/exemples/cross_markdown.Rmd
@@ -0,0 +1,19 @@
+---
+    title: "Iris"
+    output: bookdown::word_document2
+    output_file: "cross_markdown.docx"
+---
+
+
+```{r setup, include=FALSE}
+library(biostat2)
+library(flextable)
+library(dplyr) #pour le pipe %>% 
+```
+
+Table iris is given in Table \@ref(tab:irisTable).
+
+```{r description, echo=FALSE, results='asis'}
+cat("<caption> (\\#tab:irisTable) Table Iris </caption> \n\r ")
+cross(cbind(Sepal.Length, Sepal.Width) ~ Species, iris, test = TRUE, total="column") %>% cross_to_flextable %>% autofit
+```
\ No newline at end of file
diff --git a/exemples/cross_markdown.docx b/exemples/cross_markdown.docx
new file mode 100644
index 0000000..3ab6473
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diff --git a/exemples/cross_officer.docx b/exemples/cross_officer.docx
new file mode 100644
index 0000000..38b319c
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diff --git a/img/cross_esoph.png b/img/cross_esoph.png
new file mode 100644
index 0000000..e098c53
Binary files /dev/null and b/img/cross_esoph.png differ
diff --git a/img/cross_iris.png b/img/cross_iris.png
new file mode 100644
index 0000000..9ab9a16
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diff --git a/img/cross_mtcars.png b/img/cross_mtcars.png
new file mode 100644
index 0000000..2704dd4
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diff --git a/man/FlexCrossTable-ReporteRs.Rd b/man/FlexCrossTable-ReporteRs.Rd
index 08cf156..633f567 100644
--- a/man/FlexCrossTable-ReporteRs.Rd
+++ b/man/FlexCrossTable-ReporteRs.Rd
@@ -1,12 +1,20 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/addCrossTable.r
+% Please edit documentation in R/body_add_crosstable.r
 \name{FlexCrossTable-ReporteRs}
 \alias{FlexCrossTable-ReporteRs}
 \alias{FlexCrossTable}
-\title{Create a FlexTable object from a table made by the cross function}
+\title{Deprecated
+Create a FlexTable object from a table made by the cross function}
 \usage{
-FlexCrossTable(crosstable, compact = FALSE, id = ".id",
-  variable = "variable", value = "value", effect = "effect", p = "p")
+FlexCrossTable(
+  crosstable,
+  compact = FALSE,
+  id = ".id",
+  variable = "variable",
+  value = "value",
+  effect = "effect",
+  p = "p"
+)
 }
 \arguments{
 \item{crosstable}{the result of \code{cross} function}
@@ -27,7 +35,7 @@ FlexCrossTable(crosstable, compact = FALSE, id = ".id",
 A \code{FlexTable} object (see \code{ReporteRs} package)
 }
 \description{
-Create a FlexTable object from a table made by the cross function
+**Deprecation** : Since \code{ReporteRs} is deprecated and not available on CRAN, please use \code{flextable} and \code{officer} packages instead.
 }
 \examples{
 \dontrun{
diff --git a/man/Max.Rd b/man/Max.Rd
deleted file mode 100644
index 25d9138..0000000
--- a/man/Max.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/na.r
-\name{Max}
-\alias{Max}
-\title{Return the max (and have formals)}
-\usage{
-Max(x, na.rm = FALSE)
-}
-\arguments{
-\item{x}{a vector}
-
-\item{na.rm}{Remove NA?}
-}
-\description{
-Return the max (and have formals)
-}
-\author{
-David Hajage
-}
-\keyword{univar}
diff --git a/man/Min.Rd b/man/Min.Rd
deleted file mode 100644
index d96ddcf..0000000
--- a/man/Min.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/na.r
-\name{Min}
-\alias{Min}
-\title{Return the min (and have formals)}
-\usage{
-Min(x, na.rm = FALSE)
-}
-\arguments{
-\item{x}{a vector}
-
-\item{na.rm}{Remove NA?}
-}
-\description{
-Return the min (and have formals)
-}
-\author{
-David Hajage
-}
-\keyword{univar}
diff --git a/man/addCrossTable.Rd b/man/addCrossTable.Rd
index e530373..c9927c5 100644
--- a/man/addCrossTable.Rd
+++ b/man/addCrossTable.Rd
@@ -1,11 +1,19 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/addCrossTable.r
+% Please edit documentation in R/body_add_crosstable.r
 \name{addCrossTable}
 \alias{addCrossTable}
-\title{add a table made by the cross function into a ReporteRs document}
+\title{Deprecated
+add a table made by the cross function into a ReporteRs document}
 \usage{
-addCrossTable(doc, crosstable, compact = FALSE, id = ".id",
-  variable = "variable", value = "value", p = "p")
+addCrossTable(
+  doc,
+  crosstable,
+  compact = FALSE,
+  id = ".id",
+  variable = "variable",
+  value = "value",
+  p = "p"
+)
 }
 \arguments{
 \item{doc}{a \code{docx} object created by \code{docx} function (see \code{ReporteRs} package)}
@@ -26,7 +34,7 @@ addCrossTable(doc, crosstable, compact = FALSE, id = ".id",
 A \code{docx} object
 }
 \description{
-add a table made by the cross function into a ReporteRs document
+**Deprecation** : Since \code{ReporteRs} is deprecated and not available on CRAN, please use \code{officer} and \code{biostats2::body_add_crosstable} instead.
 }
 \examples{
 \dontrun{
@@ -37,6 +45,9 @@ doc <- docx()
 doc <- addCrossTable(doc, mytable)
 doc <- addPageBreak(doc)
 doc <- addCrossTable(doc, mytable, TRUE)
+dfile <- "test_doc.docx"
+print(doc, target = dfile)
+shell.exec(dfile)
 }
 }
 \author{
diff --git a/man/as.crosstable.Rd b/man/as.crosstable.Rd
new file mode 100644
index 0000000..619139b
--- /dev/null
+++ b/man/as.crosstable.Rd
@@ -0,0 +1,36 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/body_add_crosstable.r
+\name{as.crosstable}
+\alias{as.crosstable}
+\title{Coerce to a Crosstable (for officer docx addition)}
+\usage{
+as.crosstable(df, labs.col = "???")
+}
+\arguments{
+\item{df}{a data.frame}
+
+\item{labs.col}{the name of the grouping variable}
+}
+\value{
+a cross
+}
+\description{
+Coerce to a Crosstable (for officer docx addition)
+}
+\examples{
+library(dplyr) #for the pipe operator
+library(officer)
+mytable = cross(cbind(Sepal.Length, I(Sepal.Width^2)) ~ Species, iris) \%>\% 
+   as.data.frame \%>\% #loses attributes
+   as.crosstable(labs.col = "Species")
+   
+doc <- read_docx() \%>\% 
+    body_add_crosstable(mytable) 
+
+\dontrun{
+dfile <- "test_doc.docx"
+print(doc, target = dfile)
+shell.exec(dfile)
+}
+
+}
diff --git a/man/biostats2SummaryFunctions.Rd b/man/biostats2SummaryFunctions.Rd
new file mode 100644
index 0000000..e9c8c01
--- /dev/null
+++ b/man/biostats2SummaryFunctions.Rd
@@ -0,0 +1,84 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/funs.r
+\name{biostats2SummaryFunctions}
+\alias{biostats2SummaryFunctions}
+\alias{moystd}
+\alias{mediqr}
+\alias{minmax}
+\alias{nna}
+\title{Summary functions}
+\usage{
+moystd(
+  x,
+  na.rm = TRUE,
+  dig = 2,
+  fixed_format = getOption("biostat2_fixed_format", FALSE),
+  zero_digits = 1
+)
+
+mediqr(
+  x,
+  na.rm = TRUE,
+  dig = 2,
+  fixed_format = getOption("biostat2_fixed_format", FALSE),
+  zero_digits = 1
+)
+
+minmax(x, na.rm = TRUE, dig = 2)
+
+nna(x)
+}
+\arguments{
+\item{x}{a numeric vector}
+
+\item{na.rm}{\code{TRUE} as default}
+
+\item{dig}{number of digits}
+
+\item{fixed_format}{use \code{\link{format_fixed}} instead of round (default)}
+
+\item{zero_digits}{is fixed_format==TRUE, number of significant digits for values rounded to 0 (set to NULL to keep the original 0 value)}
+}
+\description{
+Summary functions to use with \code{\link{cross}} or anywhere else.
+}
+\section{Functions}{
+\itemize{
+\item \code{moystd}: returns mean and std error
+
+\item \code{mediqr}: returns median and IQR
+
+\item \code{minmax}: returns minimum and maximum
+
+\item \code{nna}: returns  number of observations and number of missing values
+}}
+
+\section{Fixed format}{
+
+The use of the \code{fixed_format} argument allows to have trailing zeros after rounded values.
+In the case when the output of rounded values is zero, the use of the \code{zero_digits} argument allows to keep some significant digits for this specific case only.
+}
+
+\examples{
+moystd(iris$Sepal.Length, dig=3)
+minmax(iris$Sepal.Length, dig=3)
+mediqr(iris$Sepal.Length, dig=3)
+nna(iris$Sepal.Length, dig=3)
+
+x = iris$Sepal.Length/10000 #closer to zero 
+
+moystd(x, dig=3, fixed_format=T)
+moystd(x, dig=3, fixed_format=T, zero_digits=NULL)
+options("biostat2_fixed_format"=T)
+moystd(x, dig=3, zero_digits=2)
+options("biostat2_fixed_format"=NULL)
+
+}
+\seealso{
+\code{\link{format_fixed}}
+}
+\author{
+Dan Chaltiel
+
+David Hajage
+}
diff --git a/man/body_add_crosstable_bak.Rd b/man/body_add_crosstable_bak.Rd
new file mode 100644
index 0000000..91f77ed
--- /dev/null
+++ b/man/body_add_crosstable_bak.Rd
@@ -0,0 +1,66 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/body_add_crosstable.r
+\name{body_add_crosstable_bak}
+\alias{body_add_crosstable_bak}
+\title{OLD: Adds a table made by the cross function into an officer document}
+\usage{
+body_add_crosstable_bak(
+  doc,
+  crosstable,
+  compact = FALSE,
+  auto.fit = FALSE,
+  id = ".id",
+  variable = "variable",
+  label = "label",
+  value = "value",
+  p = "p",
+  show.test.name = F
+)
+}
+\arguments{
+\item{doc}{a \code{rdocx} object created by \code{read_docx} function (see \code{officer} package)}
+
+\item{crosstable}{the result of \code{cross} function}
+
+\item{compact}{whether to compact the table}
+
+\item{auto.fit}{whether to \code{flextable::autofit} the table}
+
+\item{id}{name of the 'id' column}
+
+\item{variable}{name of the 'variable' column}
+
+\item{label}{name of the 'label' column}
+
+\item{value}{name of the 'value' column}
+
+\item{p}{name of the 'p' column}
+
+\item{show.test.name}{in the p column, show the test name}
+}
+\value{
+A \code{rdocx} object
+}
+\description{
+OLD: Adds a table made by the cross function into an officer document
+}
+\examples{
+library(dplyr) #for the pipe operator
+library(officer)
+mytable <- cross(cbind(...) ~ tobgp, esoph, test = TRUE)
+mytable <- cross(cbind(...) ~ Species, iris, test = TRUE)
+mytable <- cross(cbind(...) ~ ., esoph)
+doc <- read_docx() \%>\% 
+    body_add_crosstable(mytable) \%>\% 
+    body_add_break \%>\% 
+    body_add_crosstable(mytable, TRUE)
+
+\dontrun{
+dfile <- "test_doc.docx"
+print(doc, target = dfile)
+shell.exec(dfile)
+}
+}
+\author{
+Dan Chaltiel
+}
diff --git a/man/body_add_normal.Rd b/man/body_add_normal.Rd
new file mode 100644
index 0000000..57d931d
--- /dev/null
+++ b/man/body_add_normal.Rd
@@ -0,0 +1,49 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/officer.r
+\name{body_add_normal}
+\alias{body_add_normal}
+\alias{body_add_glued}
+\title{Add a new paragraph with a Normal style, inserting variables with \code{base::paste}}
+\usage{
+body_add_normal(doc, ...)
+
+body_add_glued(doc, x, ...)
+}
+\arguments{
+\item{doc}{the doc object (created with the \code{read_docx} function of \code{officer} package)}
+
+\item{...}{parameters to be passed to \code{glue::glue}}
+
+\item{x}{the string with \code{glue::glue} patterns (Expressions enclosed by braces will be evaluated as R code)}
+}
+\value{
+a new doc object
+
+a new doc object
+}
+\description{
+Add a new paragraph with a Normal style, inserting variables with \code{base::paste}
+
+Add a new paragraph with a Normal style, inserting variables with \code{glue::glue}
+}
+\examples{
+\dontrun{
+library(officer)
+library(biostat2)
+library(dplyr)
+doc = read_docx()
+doc = doc \%>\% body_add_normal("La table iris a ", ncol(iris), " colonnes.")
+}
+\dontrun{
+library(officer)
+library(biostat2)
+library(dplyr)
+doc = read_docx()
+doc = body_add_glued(doc, "La table iris a {ncol(iris)} colonnes.")
+}
+}
+\author{
+Dan Chaltiel
+
+Dan Chaltiel
+}
diff --git a/man/body_add_table_legend.Rd b/man/body_add_table_legend.Rd
new file mode 100644
index 0000000..5008f8b
--- /dev/null
+++ b/man/body_add_table_legend.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/body_add_legend.r
+\name{body_add_table_legend}
+\alias{body_add_table_legend}
+\title{Add a table legend}
+\usage{
+body_add_table_legend(
+  x,
+  legend,
+  legend_style = "table title",
+  style = "strong",
+  seqfield = "SEQ Table \\\\* Arabic"
+)
+}
+\arguments{
+\item{x}{a docx object}
+
+\item{legend}{the table legend}
+
+\item{legend_style}{may depend on the docx template}
+
+\item{style}{the legend style (strnog, italic...)}
+
+\item{seqfield}{to figure this out, in a docx file, insert a table legend, right click on the inserted number and select "Toggle Field Codes". This argument should be the value of the field, with extra escaping.}
+}
+\description{
+Add a table legend
+}
diff --git a/man/body_add_title.Rd b/man/body_add_title.Rd
new file mode 100644
index 0000000..a05a3f9
--- /dev/null
+++ b/man/body_add_title.Rd
@@ -0,0 +1,36 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/officer.r
+\name{body_add_title}
+\alias{body_add_title}
+\title{Add a new title}
+\usage{
+body_add_title(x, value, level = 1, style = "heading")
+}
+\arguments{
+\item{value}{a character string}
+
+\item{level}{the level of the title. See \code{styles_info(doc)} to know the possibilities.}
+
+\item{doc}{the doc object (created with the \code{read_docx} function of \code{officer} package)}
+}
+\value{
+a new doc object
+}
+\description{
+Add a new title
+}
+\examples{
+\dontrun{
+library(officer)
+library(biostat2)
+library(dplyr)
+doc = read_docx()
+doc = doc \%>\% 
+   body_add_title(doc, "La table iris", 1) \%>\% 
+   body_add_title(doc, "Description", 2) \%>\% 
+   addNormal(doc, "La table iris a ", ncol(iris), " colonnes.")
+}
+}
+\author{
+Dan Chaltiel
+}
diff --git a/man/compact.Rd b/man/compact.Rd
index c3b83a8..ce11408 100644
--- a/man/compact.Rd
+++ b/man/compact.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/addCrossTable.r
+% Please edit documentation in R/body_add_crosstable.r
 \name{compact}
 \alias{compact}
 \title{Compact the result of cross function}
@@ -7,12 +7,15 @@
 compact(x)
 }
 \arguments{
-\item{x}{x}
+\item{x}{a crosstable, the result of \code{cross} function}
 }
 \description{
 Compact the result of cross function
 }
+\examples{
+mytable <- cross(cbind(...) ~ tobgp, esoph, test = TRUE)
+compact(mytable)
+}
 \author{
 David Hajage
 }
-\keyword{internal}
diff --git a/man/correlation.data.frame.Rd b/man/correlation.data.frame.Rd
index 275dd36..10b6190 100644
--- a/man/correlation.data.frame.Rd
+++ b/man/correlation.data.frame.Rd
@@ -4,8 +4,13 @@
 \alias{correlation.data.frame}
 \title{Compute correlation (data.frame input)}
 \usage{
-correlation.data.frame(dfx, dfy, method = c("pearson", "kendall", "spearman"),
-  digits = 2, label = FALSE)
+correlation.data.frame(
+  dfx,
+  dfy,
+  method = c("pearson", "kendall", "spearman"),
+  digits = 2,
+  label = FALSE
+)
 }
 \arguments{
 \item{dfx}{data.frame}
diff --git a/man/create.report.Rd b/man/create.report.Rd
index ec27db0..655aaf1 100644
--- a/man/create.report.Rd
+++ b/man/create.report.Rd
@@ -4,10 +4,21 @@
 \alias{create.report}
 \title{Create a docx object with a specific template and informations already inserted}
 \usage{
-create.report(template = c("gerc", "urc", "cephepi"), title = "",
-  acronym = "", version = "", npromo = "", nct = "", invest = "",
-  biostat = "", methodo = "", date_lastmodif = "", date_freez = "",
-  date_update = "", history = NULL)
+create.report(
+  template = c("gerc", "urc", "cephepi"),
+  title = "",
+  acronym = "",
+  version = "",
+  npromo = "",
+  nct = "",
+  invest = "",
+  biostat = "",
+  methodo = "",
+  date_lastmodif = "",
+  date_freez = "",
+  date_update = "",
+  history = NULL
+)
 }
 \arguments{
 \item{template}{either 'gerc', 'urc', or 'cephepi'}
diff --git a/man/cross.Rd b/man/cross.Rd
index 35aa9b1..b02957b 100644
--- a/man/cross.Rd
+++ b/man/cross.Rd
@@ -1,19 +1,36 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/remix.r
+% Please edit documentation in R/cross.r
 \name{cross}
 \alias{cross}
 \title{Describe everything}
 \usage{
-cross(formula = cbind(...) ~ ., data = NULL, funs = c(` ` = mysummary),
-  ..., margin = 0:2, total = FALSE, digits = 2, showNA = c("no",
-  "ifany", "always"), method = c("pearson", "kendall", "spearman"),
-  times = NULL, followup = FALSE, test = FALSE,
+cross(
+  formula = cbind(...) ~ .,
+  data = NULL,
+  funs = c(` ` = cross_summary),
+  ...,
+  margin = c("all", "row", "column", "cell"),
+  total = c("none", "all", "row", "column", "FALSE", "TRUE", 0, 1, 2),
+  digits = 2,
+  showNA = c("no", "ifany", "always"),
+  method = c("pearson", "kendall", "spearman"),
+  times = NULL,
+  followup = FALSE,
+  test = FALSE,
   test.summarize = test.summarize.auto,
-  test.survival = test.survival.logrank, test.tabular = test.tabular.auto,
-  show.test = display.test, plim = 4, show.method = TRUE,
-  effect = FALSE, effect.summarize = diff.mean.auto,
-  effect.tabular = or.row.by.col, effect.survival = effect.survival.coxph,
-  conf.level = 0.95, label = FALSE, regroup = FALSE)
+  test.survival = test.survival.logrank,
+  test.tabular = test.tabular.auto,
+  show.test = display.test,
+  plim = 4,
+  show.method = TRUE,
+  effect = FALSE,
+  effect.summarize = diff.mean.auto,
+  effect.tabular = or.row.by.col,
+  effect.survival = effect.survival.coxph,
+  conf.level = 0.95,
+  label = TRUE,
+  regroup = FALSE
+)
 }
 \arguments{
 \item{formula}{a formula (see Details).}
@@ -147,19 +164,25 @@ grouped in the same table. \code{cbind(...)} works (ie regroups
 all variables of the data.frame together). When a \code{cbind} is
 in both sides of the formula, \code{cross} will do its best to
 group everything in the same table, but only if it is possible...
+
+
+\lifecycle{superseded}
+\Sexpr[results=rd, stage=render]{lifecycle::badge("superseded")}
 }
 \examples{
 
 library(biostat2)
 cross(data = iris)
-cross(cbind(...) ~ ., iris[, sapply(iris, is.numeric)], funs = c(median, mad, min, max))
-cross(cbind(Sepal.Length, I(Sepal.Width^2)) ~ Species, iris, funs = quantile, probs = c(1/3, 2/3))
+cross(cbind(...) ~ ., iris[, sapply(iris, is.numeric)], funs=c(median, mad, min, max))
+cross(cbind(Sepal.Length, I(Sepal.Width^2)) ~ Species, iris, funs=quantile, probs=c(1/3, 2/3), total="row") #tertiles 1 and 2 by Species
 cross(Sepal.Length + Sepal.Width ~ Petal.Length + Petal.Width, iris)
 cross(cbind(Sepal.Length, Sepal.Width) ~ cbind(Petal.Length, Petal.Width), iris)
-cross(... ~ ., esoph)
-cross(alcgp ~ tobgp, esoph, test = TRUE)
+cross(... ~ ., esoph) #returns a list
+cross(alcgp ~ tobgp, esoph, margin="row", total="both", test=TRUE)
+cross(cbind(hp, mpg) ~ factor(am), mtcars, effect=TRUE, test=TRUE, show.method=FALSE)
 library(survival)
 cross(Surv(time, status) ~ x, data = aml)
+
 }
 \seealso{
 \code{cast} (reshape) and \code{summary.formula} (Hmisc).
diff --git a/man/cross_all.Rd b/man/cross_all.Rd
index 3b5f0ce..6c9d96c 100644
--- a/man/cross_all.Rd
+++ b/man/cross_all.Rd
@@ -1,19 +1,35 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/remix.r
+% Please edit documentation in R/cross.r
 \name{cross_all}
 \alias{cross_all}
 \title{Cross all x with all y}
 \usage{
-cross_all(x, y = NULL, funs = c(mean, sd, quantile, n, na), ...,
-  margin = 0:2, total = FALSE, digits = 2, showNA = c("no", "ifany",
-  "always"), method = c("pearson", "kendall", "spearman"), times = NULL,
-  followup = FALSE, test = FALSE, test.tabular = test.tabular.auto,
+cross_all(
+  x,
+  y = NULL,
+  funs = c(mean, sd, quantile, n, na),
+  ...,
+  margin = 0:2,
+  total = FALSE,
+  digits = 2,
+  showNA = c("no", "ifany", "always"),
+  method = c("pearson", "kendall", "spearman"),
+  times = NULL,
+  followup = FALSE,
+  test = FALSE,
+  test.tabular = test.tabular.auto,
   test.summarize = test.summarize.auto,
-  test.survival = test.survival.logrank, show.test = display.test,
-  plim = 4, show.method = TRUE, effect = FALSE,
-  effect.summarize = diff.mean.auto, effect.tabular = or.row.by.col,
-  effect.survival = effect.survival.coxph, conf.level = 0.95,
-  label = FALSE)
+  test.survival = test.survival.logrank,
+  show.test = display.test,
+  plim = 4,
+  show.method = TRUE,
+  effect = FALSE,
+  effect.summarize = diff.mean.auto,
+  effect.tabular = or.row.by.col,
+  effect.survival = effect.survival.coxph,
+  conf.level = 0.95,
+  label = FALSE
+)
 }
 \arguments{
 \item{x}{x}
diff --git a/man/cross_list.Rd b/man/cross_list.Rd
index d197327..bda09b5 100644
--- a/man/cross_list.Rd
+++ b/man/cross_list.Rd
@@ -1,18 +1,34 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/remix.r
+% Please edit documentation in R/cross.r
 \name{cross_list}
 \alias{cross_list}
 \title{Cross variables in a list}
 \usage{
-cross_list(l, funs = c(mean, sd, quantile, n, na), ..., margin = 0:2,
-  total = FALSE, digits = 2, showNA = c("no", "ifany", "always"),
-  method = c("pearson", "kendall", "spearman"), times = NULL,
-  followup = FALSE, test = FALSE, test.summarize = test.summarize.auto,
-  test.survival = test.survival.logrank, test.tabular = test.tabular.auto,
-  show.test = display.test, plim = 4, show.method = TRUE,
-  effect = FALSE, effect.summarize = diff.mean.auto,
-  effect.tabular = or.row.by.col, effect.survival = effect.survival.coxph,
-  conf.level = 0.95, label = FALSE)
+cross_list(
+  l,
+  funs = c(mean, sd, quantile, n, na),
+  ...,
+  margin = 0:2,
+  total = FALSE,
+  digits = 2,
+  showNA = c("no", "ifany", "always"),
+  method = c("pearson", "kendall", "spearman"),
+  times = NULL,
+  followup = FALSE,
+  test = FALSE,
+  test.summarize = test.summarize.auto,
+  test.survival = test.survival.logrank,
+  test.tabular = test.tabular.auto,
+  show.test = display.test,
+  plim = 4,
+  show.method = TRUE,
+  effect = FALSE,
+  effect.summarize = diff.mean.auto,
+  effect.tabular = or.row.by.col,
+  effect.survival = effect.survival.coxph,
+  conf.level = 0.95,
+  label = FALSE
+)
 }
 \arguments{
 \item{l}{l}
diff --git a/man/cross_one.Rd b/man/cross_one.Rd
index d56fb21..dc48e55 100644
--- a/man/cross_one.Rd
+++ b/man/cross_one.Rd
@@ -1,19 +1,35 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/remix.r
+% Please edit documentation in R/cross.r
 \name{cross_one}
 \alias{cross_one}
 \title{Cross one x and one y}
 \usage{
-cross_one(x, y = NULL, funs = c(mean, sd, quantile, n, na), ...,
-  margin = 0:2, total = FALSE, digits = 2, showNA = c("no", "ifany",
-  "always"), method = c("pearson", "kendall", "spearman"), times = NULL,
-  followup = FALSE, test = FALSE, test.tabular = test.tabular.auto,
+cross_one(
+  x,
+  y = NULL,
+  funs = c(mean, sd, quantile, n, na),
+  ...,
+  margin = 0:2,
+  total = FALSE,
+  digits = 2,
+  showNA = c("no", "ifany", "always"),
+  method = c("pearson", "kendall", "spearman"),
+  times = NULL,
+  followup = FALSE,
+  test = FALSE,
+  test.tabular = test.tabular.auto,
   test.summarize = test.summarize.auto,
-  test.survival = test.survival.logrank, show.test = display.test,
-  plim = 4, show.method = TRUE, effect = FALSE,
-  effect.summarize = diff.mean.auto, effect.tabular = or.row.by.col,
-  effect.survival = effect.survival.coxph, conf.level = 0.95,
-  label = FALSE)
+  test.survival = test.survival.logrank,
+  show.test = display.test,
+  plim = 4,
+  show.method = TRUE,
+  effect = FALSE,
+  effect.summarize = diff.mean.auto,
+  effect.tabular = or.row.by.col,
+  effect.survival = effect.survival.coxph,
+  conf.level = 0.95,
+  label = FALSE
+)
 }
 \arguments{
 \item{x}{x}
diff --git a/man/mysummary.Rd b/man/cross_summary.Rd
similarity index 51%
rename from man/mysummary.Rd
rename to man/cross_summary.Rd
index ec3ca05..4c62ee7 100644
--- a/man/mysummary.Rd
+++ b/man/cross_summary.Rd
@@ -1,19 +1,25 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/funs.r
-\name{mysummary}
+\name{cross_summary}
+\alias{cross_summary}
 \alias{mysummary}
 \title{Summarize a numeric vector}
 \usage{
-mysummary(x, na.rm = TRUE, dig = 2)
+cross_summary(x, dig = 2)
+
+mysummary(x, dig = 2)
 }
 \arguments{
 \item{x}{a numeric vector}
 
-\item{na.rm}{\code{TRUE} as default}
-
 \item{dig}{number of digits}
 }
 \description{
 Summarize a numeric vector
 }
+\section{Note}{
+ 
+Function \code{mysummary} is kept for compatibility with old codes. It produces the same exact object than \code{cross_summary}, which should be preferred.
+}
+
 \keyword{internal}
diff --git a/man/cross_to_flextable.Rd b/man/cross_to_flextable.Rd
new file mode 100644
index 0000000..3149852
--- /dev/null
+++ b/man/cross_to_flextable.Rd
@@ -0,0 +1,81 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/body_add_crosstable.r
+\name{cross_to_flextable}
+\alias{cross_to_flextable}
+\alias{body_add_crosstable}
+\title{Crosstables output}
+\usage{
+cross_to_flextable(
+  crosstable,
+  compact = FALSE,
+  auto.fit = FALSE,
+  id = ".id",
+  variable = "variable",
+  label = "label",
+  value = "value",
+  p = "p",
+  effect = "effect",
+  total = "Total",
+  show.test.name = F,
+  generic.labels = c(id, variable, label, value, p, effect, total)
+)
+
+body_add_crosstable(doc, ...)
+}
+\arguments{
+\item{crosstable}{the result of \code{cross} function}
+
+\item{compact}{whether to compact the table}
+
+\item{auto.fit}{whether to \code{flextable::autofit} the table}
+
+\item{id}{name of the 'id' column}
+
+\item{variable}{name of the 'variable' column}
+
+\item{label}{name of the 'label' column}
+
+\item{value}{name of the 'value' column}
+
+\item{p}{name of the 'p' column}
+
+\item{show.test.name}{in the p column, show the test name}
+
+\item{doc}{a \code{rdocx} object created by \code{read_docx} function (see \code{officer} package)}
+
+\item{...}{arguments for \code{cross_to_flextable}}
+}
+\value{
+A \code{rdocx} object
+}
+\description{
+\code{cross_to_flextable} turns a table made by the cross function into a flextable.
+
+\code{body_add_crosstable2} adds a table made by the cross function into an officer document
+}
+\examples{
+### cross_to_flextable
+library(dplyr) #for the pipe operator
+library(officer)
+cross(cbind(...) ~ tobgp, esoph, test = TRUE) \%>\% cross_to_flextable
+cross(cbind(...) ~ Species, iris, test = TRUE) \%>\% cross_to_flextable
+cross(cbind(...) ~ ., esoph) \%>\% cross_to_flextable
+
+### body_add_crosstable
+#mytable <- cross(cbind(...) ~ tobgp, esoph, test = TRUE)
+#mytable <- cross(cbind(...) ~ Species, iris, test = TRUE)
+mytable <- cross(cbind(...) ~ ., esoph)
+doc <- read_docx() \%>\% 
+    body_add_crosstable(mytable) \%>\% 
+    body_add_break \%>\% 
+    body_add_crosstable(mytable, compact=TRUE)
+
+\dontrun{
+dfile <- "test_doc.docx"
+print(doc, target = dfile)
+shell.exec(dfile)
+}
+}
+\author{
+Dan Chaltiel
+}
diff --git a/man/diff.mean.auto.Rd b/man/diff.mean.auto.Rd
new file mode 100644
index 0000000..9739227
--- /dev/null
+++ b/man/diff.mean.auto.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/effect.r
+\name{diff.mean.auto}
+\alias{diff.mean.auto}
+\title{Effect measure for association between one continuous and one categorical variable}
+\usage{
+\method{diff}{mean.auto}(x, g, conf.level = 0.95, R = 500)
+}
+\arguments{
+\item{x}{vector}
+
+\item{conf.level}{confidence interval level}
+
+\item{R}{number of bootstrap replication}
+
+\item{y}{another vector}
+}
+\value{
+a list with five componments
+}
+\description{
+Effect measure for association between one continuous and one categorical variable
+}
diff --git a/man/diff.mean.boot.Rd b/man/diff.mean.boot.Rd
new file mode 100644
index 0000000..1424189
--- /dev/null
+++ b/man/diff.mean.boot.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/effect.r
+\name{diff.mean.boot}
+\alias{diff.mean.boot}
+\title{Effect measure for association between one continuous and one categorical variable}
+\usage{
+\method{diff}{mean.boot}(x, g, conf.level = 0.95, R = 500)
+}
+\arguments{
+\item{x}{vector}
+
+\item{conf.level}{confidence interval level}
+
+\item{R}{number of bootstrap replication}
+
+\item{y}{another vector}
+}
+\value{
+a list with five componments
+}
+\description{
+Effect measure for association between one continuous and one categorical variable
+}
diff --git a/man/diff.mean.student.Rd b/man/diff.mean.student.Rd
new file mode 100644
index 0000000..a273bab
--- /dev/null
+++ b/man/diff.mean.student.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/effect.r
+\name{diff.mean.student}
+\alias{diff.mean.student}
+\title{Effect measure for association between one continuous and one categorical variable}
+\usage{
+\method{diff}{mean.student}(x, g, conf.level = 0.95)
+}
+\arguments{
+\item{x}{vector}
+
+\item{conf.level}{confidence interval level}
+
+\item{y}{another vector}
+}
+\value{
+a list with five componments
+}
+\description{
+Effect measure for association between one continuous and one categorical variable
+}
diff --git a/man/diff.median.Rd b/man/diff.median.Rd
new file mode 100644
index 0000000..b1f5b86
--- /dev/null
+++ b/man/diff.median.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/effect.r
+\name{diff.median}
+\alias{diff.median}
+\title{Effect measure for association between one continuous and one categorical variable}
+\usage{
+\method{diff}{median}(x, g, conf.level = 0.95, R = 500)
+}
+\arguments{
+\item{x}{vector}
+
+\item{conf.level}{confidence interval level}
+
+\item{R}{number of bootstrap replication}
+
+\item{y}{another vector}
+}
+\value{
+a list with five componments
+}
+\description{
+Effect measure for association between one continuous and one categorical variable
+}
diff --git a/man/effect.survival.coxph.Rd b/man/effect.survival.coxph.Rd
new file mode 100644
index 0000000..f8f6116
--- /dev/null
+++ b/man/effect.survival.coxph.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/effect.r
+\name{effect.survival.coxph}
+\alias{effect.survival.coxph}
+\title{Effect measure for association between one consored variable and one categorical variable}
+\usage{
+effect.survival.coxph(formula, conf.level = 0.95)
+}
+\arguments{
+\item{formula}{a formula}
+}
+\value{
+a list with two componments: p.value and method
+}
+\description{
+Effect measure for association between one consored variable and one categorical variable
+}
+\author{
+David Hajage
+}
diff --git a/man/figures/lifecycle-archived.svg b/man/figures/lifecycle-archived.svg
new file mode 100644
index 0000000..48f72a6
--- /dev/null
+++ b/man/figures/lifecycle-archived.svg
@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="110" height="20"><linearGradient id="b" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="a"><rect width="110" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#a)"><path fill="#555" d="M0 0h53v20H0z"/><path fill="#e05d44" d="M53 0h57v20H53z"/><path fill="url(#b)" d="M0 0h110v20H0z"/></g><g fill="#fff" text-anchor="middle" font-family="DejaVu Sans,Verdana,Geneva,sans-serif" font-size="110"> <text x="275" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="430">lifecycle</text><text x="275" y="140" transform="scale(.1)" textLength="430">lifecycle</text><text x="805" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="470">archived</text><text x="805" y="140" transform="scale(.1)" textLength="470">archived</text></g> </svg>
\ No newline at end of file
diff --git a/man/figures/lifecycle-defunct.svg b/man/figures/lifecycle-defunct.svg
new file mode 100644
index 0000000..01452e5
--- /dev/null
+++ b/man/figures/lifecycle-defunct.svg
@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="104" height="20"><linearGradient id="b" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="a"><rect width="104" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#a)"><path fill="#555" d="M0 0h53v20H0z"/><path fill="#e05d44" d="M53 0h51v20H53z"/><path fill="url(#b)" d="M0 0h104v20H0z"/></g><g fill="#fff" text-anchor="middle" font-family="DejaVu Sans,Verdana,Geneva,sans-serif" font-size="110"><text x="275" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="430">lifecycle</text><text x="275" y="140" transform="scale(.1)" textLength="430">lifecycle</text><text x="775" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="410">defunct</text><text x="775" y="140" transform="scale(.1)" textLength="410">defunct</text></g> </svg>
\ No newline at end of file
diff --git a/man/figures/lifecycle-deprecated.svg b/man/figures/lifecycle-deprecated.svg
new file mode 100644
index 0000000..4baaee0
--- /dev/null
+++ b/man/figures/lifecycle-deprecated.svg
@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="124" height="20"><linearGradient id="b" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="a"><rect width="124" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#a)"><path fill="#555" d="M0 0h53v20H0z"/><path fill="#fe7d37" d="M53 0h71v20H53z"/><path fill="url(#b)" d="M0 0h124v20H0z"/></g><g fill="#fff" text-anchor="middle" font-family="DejaVu Sans,Verdana,Geneva,sans-serif" font-size="110"><text x="275" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="430">lifecycle</text><text x="275" y="140" transform="scale(.1)" textLength="430">lifecycle</text><text x="875" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="610">deprecated</text><text x="875" y="140" transform="scale(.1)" textLength="610">deprecated</text></g> </svg>
\ No newline at end of file
diff --git a/man/figures/lifecycle-experimental.svg b/man/figures/lifecycle-experimental.svg
new file mode 100644
index 0000000..d1d060e
--- /dev/null
+++ b/man/figures/lifecycle-experimental.svg
@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="136" height="20"><linearGradient id="b" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="a"><rect width="136" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#a)"><path fill="#555" d="M0 0h53v20H0z"/><path fill="#fe7d37" d="M53 0h83v20H53z"/><path fill="url(#b)" d="M0 0h136v20H0z"/></g><g fill="#fff" text-anchor="middle" font-family="DejaVu Sans,Verdana,Geneva,sans-serif" font-size="110"><text x="275" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="430">lifecycle</text><text x="275" y="140" transform="scale(.1)" textLength="430">lifecycle</text><text x="935" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="730">experimental</text><text x="935" y="140" transform="scale(.1)" textLength="730">experimental</text></g> </svg>
\ No newline at end of file
diff --git a/man/figures/lifecycle-maturing.svg b/man/figures/lifecycle-maturing.svg
new file mode 100644
index 0000000..df71310
--- /dev/null
+++ b/man/figures/lifecycle-maturing.svg
@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="114" height="20"><linearGradient id="b" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="a"><rect width="114" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#a)"><path fill="#555" d="M0 0h53v20H0z"/><path fill="#007ec6" d="M53 0h61v20H53z"/><path fill="url(#b)" d="M0 0h114v20H0z"/></g><g fill="#fff" text-anchor="middle" font-family="DejaVu Sans,Verdana,Geneva,sans-serif" font-size="110"><text x="275" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="430">lifecycle</text><text x="275" y="140" transform="scale(.1)" textLength="430">lifecycle</text><text x="825" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="510">maturing</text><text x="825" y="140" transform="scale(.1)" textLength="510">maturing</text></g> </svg>
\ No newline at end of file
diff --git a/man/figures/lifecycle-questioning.svg b/man/figures/lifecycle-questioning.svg
new file mode 100644
index 0000000..08ee0c9
--- /dev/null
+++ b/man/figures/lifecycle-questioning.svg
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/man/figures/lifecycle-soft-deprecated.svg b/man/figures/lifecycle-soft-deprecated.svg
new file mode 100644
index 0000000..9f014fd
--- /dev/null
+++ b/man/figures/lifecycle-soft-deprecated.svg
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/man/figures/lifecycle-stable.svg b/man/figures/lifecycle-stable.svg
new file mode 100644
index 0000000..e015dc8
--- /dev/null
+++ b/man/figures/lifecycle-stable.svg
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/man/figures/lifecycle-superseded.svg b/man/figures/lifecycle-superseded.svg
new file mode 100644
index 0000000..75f24f5
--- /dev/null
+++ b/man/figures/lifecycle-superseded.svg
@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="128" height="20"><linearGradient id="b" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="a"><rect width="128" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#a)"><path fill="#555" d="M0 0h55v20H0z"/><path fill="#007ec6" d="M55 0h73v20H55z"/><path fill="url(#b)" d="M0 0h128v20H0z"/></g><g fill="#fff" text-anchor="middle" font-family="DejaVu Sans,Verdana,Geneva,sans-serif" font-size="110"> <text x="285" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="450">lifecycle</text><text x="285" y="140" transform="scale(.1)" textLength="450">lifecycle</text><text x="905" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="630">superseded</text><text x="905" y="140" transform="scale(.1)" textLength="630">superseded</text></g> </svg>
\ No newline at end of file
diff --git a/man/format_fixed.Rd b/man/format_fixed.Rd
new file mode 100644
index 0000000..ebec969
--- /dev/null
+++ b/man/format_fixed.Rd
@@ -0,0 +1,36 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/funs.r
+\name{format_fixed}
+\alias{format_fixed}
+\title{Format numbers with same number of decimals, including trailing zeros}
+\usage{
+format_fixed(x, digits, zero_digits = 1, only_round = FALSE)
+}
+\arguments{
+\item{x}{a numeric vector to format}
+
+\item{digits}{number of decimals}
+
+\item{zero_digits}{number of significant digits for values rounded to 0 (set to NULL to keep the original 0 value)}
+
+\item{only_round}{util option, to simply return rounded value instead of formatted}
+}
+\value{
+a character vector of formatted numbers
+}
+\description{
+Format numbers with same number of decimals, including trailing zeros
+}
+\examples{
+x = c(1, 1.2, 12.78749, pi, 0.00000012)
+format_fixed(x, digits=3)
+format_fixed(x, digits=3, zero_digits=2)
+format_fixed(x, digits=3, zero_digits=NULL)
+x = iris$Sepal.Length/10000
+x \%>\% 
+sd(na.rm=na.rm) \%>\% 
+  format_fixed(dig=3, zero_digits=2, only_round=T)
+}
+\author{
+Dan Chaltiel
+}
diff --git a/man/freq.data.frame.Rd b/man/freq.data.frame.Rd
index 818b6d0..03bc137 100644
--- a/man/freq.data.frame.Rd
+++ b/man/freq.data.frame.Rd
@@ -4,8 +4,13 @@
 \alias{freq.data.frame}
 \title{Compute frequencies (data.frame input)}
 \usage{
-freq.data.frame(df, showNA = c("no", "ifany", "always"), total = FALSE,
-  digits = 2, label = FALSE)
+freq.data.frame(
+  df,
+  showNA = c("no", "ifany", "always"),
+  total = FALSE,
+  digits = 2,
+  label = FALSE
+)
 }
 \arguments{
 \item{df}{data.frame}
diff --git a/man/is.character.or.factor.Rd b/man/is.character.or.factor.Rd
index 2204a2e..5c37645 100644
--- a/man/is.character.or.factor.Rd
+++ b/man/is.character.or.factor.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/remix.r
+% Please edit documentation in R/cross.r
 \name{is.character.or.factor}
 \alias{is.character.or.factor}
 \title{test}
diff --git a/man/is.numeric.and.not.surv.Rd b/man/is.numeric.and.not.surv.Rd
index 8d00cde..3d1fb41 100644
--- a/man/is.numeric.and.not.surv.Rd
+++ b/man/is.numeric.and.not.surv.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/remix.r
+% Please edit documentation in R/cross.r
 \name{is.numeric.and.not.surv}
 \alias{is.numeric.and.not.surv}
 \title{test}
diff --git a/man/mediqr.Rd b/man/mediqr.Rd
deleted file mode 100644
index a846143..0000000
--- a/man/mediqr.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/funs.r
-\name{mediqr}
-\alias{mediqr}
-\title{Return median and IQR}
-\usage{
-mediqr(x, na.rm = TRUE, dig = 2)
-}
-\arguments{
-\item{x}{a numeric vector}
-
-\item{na.rm}{\code{TRUE} as default}
-
-\item{dig}{number of digits}
-}
-\description{
-Return median and IQR
-}
-\keyword{internal}
diff --git a/man/minmax.Rd b/man/minmax.Rd
deleted file mode 100644
index ae2f729..0000000
--- a/man/minmax.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/funs.r
-\name{minmax}
-\alias{minmax}
-\title{Return min and max}
-\usage{
-minmax(x, na.rm = TRUE, dig = 2)
-}
-\arguments{
-\item{x}{a numeric vector}
-
-\item{na.rm}{\code{TRUE} as default}
-
-\item{dig}{number of digits}
-}
-\description{
-Return min and max
-}
-\keyword{internal}
diff --git a/man/moystd.Rd b/man/moystd.Rd
deleted file mode 100644
index 2c502e8..0000000
--- a/man/moystd.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/funs.r
-\name{moystd}
-\alias{moystd}
-\title{Return mean and sd}
-\usage{
-moystd(x, na.rm = TRUE, dig = 2)
-}
-\arguments{
-\item{x}{a numeric vector}
-
-\item{na.rm}{\code{TRUE} as default}
-
-\item{dig}{number of digits}
-}
-\description{
-Return mean and sd
-}
-\keyword{internal}
diff --git a/man/nna.Rd b/man/nna.Rd
deleted file mode 100644
index cf72c8b..0000000
--- a/man/nna.Rd
+++ /dev/null
@@ -1,15 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/funs.r
-\name{nna}
-\alias{nna}
-\title{Return n and na}
-\usage{
-nna(x)
-}
-\arguments{
-\item{x}{a numeric vector}
-}
-\description{
-Return n and na
-}
-\keyword{internal}
diff --git a/man/or.col.by.row.Rd b/man/or.col.by.row.Rd
new file mode 100644
index 0000000..0df1f35
--- /dev/null
+++ b/man/or.col.by.row.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/effect.r
+\name{or.col.by.row}
+\alias{or.col.by.row}
+\title{Effect measure for association between two factors}
+\usage{
+or.col.by.row(x, y, conf.level = 0.95)
+}
+\arguments{
+\item{x}{vector}
+
+\item{y}{another vector}
+
+\item{conf.level}{confidence interval level}
+}
+\value{
+a list with five componments
+}
+\description{
+Effect measure for association between two factors
+}
diff --git a/man/or.row.by.col.Rd b/man/or.row.by.col.Rd
new file mode 100644
index 0000000..8ba1724
--- /dev/null
+++ b/man/or.row.by.col.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/effect.r
+\name{or.row.by.col}
+\alias{or.row.by.col}
+\title{Effect measure for association between two factors}
+\usage{
+or.row.by.col(x, y, conf.level = 0.95)
+}
+\arguments{
+\item{x}{vector}
+
+\item{y}{another vector}
+
+\item{conf.level}{confidence interval level}
+}
+\value{
+a list with five componments
+}
+\description{
+Effect measure for association between two factors
+}
diff --git a/man/paste.matrix.Rd b/man/paste.matrix.Rd
index 9447ee6..460aa53 100644
--- a/man/paste.matrix.Rd
+++ b/man/paste.matrix.Rd
@@ -4,8 +4,13 @@
 \alias{paste.matrix}
 \title{paste.matrix}
 \usage{
-paste.matrix(..., sep = " ", transpose.vector = FALSE, collapse = NULL,
-  byrow = FALSE)
+paste.matrix(
+  ...,
+  sep = " ",
+  transpose.vector = FALSE,
+  collapse = NULL,
+  byrow = FALSE
+)
 }
 \arguments{
 \item{...}{...}
diff --git a/man/rd.col.by.row.Rd b/man/rd.col.by.row.Rd
new file mode 100644
index 0000000..f4f48dc
--- /dev/null
+++ b/man/rd.col.by.row.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/effect.r
+\name{rd.col.by.row}
+\alias{rd.col.by.row}
+\title{Effect measure for association between two factors}
+\usage{
+rd.col.by.row(x, y, conf.level = 0.95)
+}
+\arguments{
+\item{x}{vector}
+
+\item{y}{another vector}
+
+\item{conf.level}{confidence interval level}
+}
+\value{
+a list with five componments
+}
+\description{
+Effect measure for association between two factors
+}
diff --git a/man/rd.row.by.col.Rd b/man/rd.row.by.col.Rd
new file mode 100644
index 0000000..7568896
--- /dev/null
+++ b/man/rd.row.by.col.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/effect.r
+\name{rd.row.by.col}
+\alias{rd.row.by.col}
+\title{Effect measure for association between two factors}
+\usage{
+rd.row.by.col(x, y, conf.level = 0.95)
+}
+\arguments{
+\item{x}{vector}
+
+\item{y}{another vector}
+
+\item{conf.level}{confidence interval level}
+}
+\value{
+a list with five componments
+}
+\description{
+Effect measure for association between two factors
+}
diff --git a/man/regroup.Rd b/man/regroup.Rd
index 4dd9846..a890e9f 100644
--- a/man/regroup.Rd
+++ b/man/regroup.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/remix.r
+% Please edit documentation in R/cross.r
 \name{regroup}
 \alias{regroup}
 \title{Regroup factors with factors, and numerical variables with numerical variables}
diff --git a/man/rr.col.by.row.Rd b/man/rr.col.by.row.Rd
new file mode 100644
index 0000000..86a8dcc
--- /dev/null
+++ b/man/rr.col.by.row.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/effect.r
+\name{rr.col.by.row}
+\alias{rr.col.by.row}
+\title{Effect measure for association between two factors}
+\usage{
+rr.col.by.row(x, y, conf.level = 0.95)
+}
+\arguments{
+\item{x}{vector}
+
+\item{y}{another vector}
+
+\item{conf.level}{confidence interval level}
+}
+\value{
+a list with five componments
+}
+\description{
+Effect measure for association between two factors
+}
diff --git a/man/rr.row.by.col.Rd b/man/rr.row.by.col.Rd
new file mode 100644
index 0000000..35adc36
--- /dev/null
+++ b/man/rr.row.by.col.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/effect.r
+\name{rr.row.by.col}
+\alias{rr.row.by.col}
+\title{Effect measure for association between two factors}
+\usage{
+rr.row.by.col(x, y, conf.level = 0.95)
+}
+\arguments{
+\item{x}{vector}
+
+\item{y}{another vector}
+
+\item{conf.level}{confidence interval level}
+}
+\value{
+a list with five componments
+}
+\description{
+Effect measure for association between two factors
+}
diff --git a/man/summarize.by.Rd b/man/summarize.by.Rd
index 50619e8..f0d987e 100644
--- a/man/summarize.by.Rd
+++ b/man/summarize.by.Rd
@@ -4,12 +4,24 @@
 \alias{summarize.by}
 \title{Compute summary statistics according to a factor}
 \usage{
-summarize.by(x, by, funs = c(mean, sd, quantile, n, na), ...,
-  showNA = c("no", "ifany", "always"), total = FALSE, digits = 2,
-  test = FALSE, test.summarize = test.summarize.auto,
-  show.test = display.test, plim = 4, show.method = TRUE,
-  effect = FALSE, effect.summarize = diff.mean.auto, conf.level = 0.95,
-  show.effect = display.effect)
+summarize.by(
+  x,
+  by,
+  funs = c(mean, sd, quantile, n, na),
+  ...,
+  showNA = c("no", "ifany", "always"),
+  total = FALSE,
+  digits = 2,
+  test = FALSE,
+  test.summarize = test.summarize.auto,
+  show.test = display.test,
+  plim = 4,
+  show.method = TRUE,
+  effect = FALSE,
+  effect.summarize = diff.mean.auto,
+  conf.level = 0.95,
+  show.effect = display.effect
+)
 }
 \arguments{
 \item{x}{numeric object}
diff --git a/man/summarize.data.frame.Rd b/man/summarize.data.frame.Rd
index e089ddb..bda6d14 100644
--- a/man/summarize.data.frame.Rd
+++ b/man/summarize.data.frame.Rd
@@ -4,8 +4,13 @@
 \alias{summarize.data.frame}
 \title{Compute summary statistics (data.frame input)}
 \usage{
-summarize.data.frame(df, funs = c(mean, sd, quantile, n, na), ...,
-  digits = 2, label = FALSE)
+summarize.data.frame(
+  df,
+  funs = c(mean, sd, quantile, n, na),
+  ...,
+  digits = 2,
+  label = FALSE
+)
 }
 \arguments{
 \item{df}{a data.frame}
diff --git a/man/summarize.data.frame.by.Rd b/man/summarize.data.frame.by.Rd
index f9097b7..af64165 100644
--- a/man/summarize.data.frame.by.Rd
+++ b/man/summarize.data.frame.by.Rd
@@ -4,12 +4,25 @@
 \alias{summarize.data.frame.by}
 \title{Compute summary statistics according to a factor (data.frame input)}
 \usage{
-summarize.data.frame.by(df, by, funs = c(mean, sd, quantile, n, na), ...,
-  showNA = c("no", "ifany", "always"), total = FALSE, digits = 2,
-  test = FALSE, test.summarize = test.summarize.auto,
-  show.test = display.test, plim = 4, show.method = TRUE, label = FALSE,
-  effect = FALSE, effect.summarize = diff.mean.auto, conf.level = 0.95,
-  show.effect = display.effect)
+summarize.data.frame.by(
+  df,
+  by,
+  funs = c(mean, sd, quantile, n, na),
+  ...,
+  showNA = c("no", "ifany", "always"),
+  total = FALSE,
+  digits = 2,
+  test = FALSE,
+  test.summarize = test.summarize.auto,
+  show.test = display.test,
+  plim = 4,
+  show.method = TRUE,
+  label = FALSE,
+  effect = FALSE,
+  effect.summarize = diff.mean.auto,
+  conf.level = 0.95,
+  show.effect = display.effect
+)
 }
 \arguments{
 \item{df}{data.frame}
diff --git a/man/survival.Rd b/man/survival.Rd
index ee44307..cd86ae2 100644
--- a/man/survival.Rd
+++ b/man/survival.Rd
@@ -4,11 +4,24 @@
 \alias{survival}
 \title{Compute survival}
 \usage{
-survival(surv, by = NULL, times = NULL, followup = FALSE, total = FALSE,
-  digits = 2, test = FALSE, test.survival = test.survival.logrank,
-  show.test = display.test, plim = 4, show.method = TRUE,
-  effect = FALSE, effect.survival = effect.survival.coxph,
-  show.effect = display.effect, conf.level = 0.95, label = FALSE)
+survival(
+  surv,
+  by = NULL,
+  times = NULL,
+  followup = FALSE,
+  total = FALSE,
+  digits = 2,
+  test = FALSE,
+  test.survival = test.survival.logrank,
+  show.test = display.test,
+  plim = 4,
+  show.method = TRUE,
+  effect = FALSE,
+  effect.survival = effect.survival.coxph,
+  show.effect = display.effect,
+  conf.level = 0.95,
+  label = FALSE
+)
 }
 \arguments{
 \item{surv}{a Surv object}
diff --git a/man/survival.data.frame.Rd b/man/survival.data.frame.Rd
index 743a12e..13e53bc 100644
--- a/man/survival.data.frame.Rd
+++ b/man/survival.data.frame.Rd
@@ -4,8 +4,13 @@
 \alias{survival.data.frame}
 \title{Compute survival (data.frame input)}
 \usage{
-survival.data.frame(df, times = NULL, digits = 2, followup = FALSE,
-  label = FALSE)
+survival.data.frame(
+  df,
+  times = NULL,
+  digits = 2,
+  followup = FALSE,
+  label = FALSE
+)
 }
 \arguments{
 \item{df}{df}
diff --git a/man/survival.data.frame.by.Rd b/man/survival.data.frame.by.Rd
index 51cc2d2..217d5b0 100644
--- a/man/survival.data.frame.by.Rd
+++ b/man/survival.data.frame.by.Rd
@@ -4,12 +4,24 @@
 \alias{survival.data.frame.by}
 \title{Compute survival according to a factor (data.frame input)}
 \usage{
-survival.data.frame.by(df, by, times = NULL, followup = FALSE,
-  total = FALSE, digits = 2, test = FALSE,
-  test.survival = test.survival.logrank, show.test = display.test,
-  plim = 4, show.method = TRUE, effect = FALSE,
-  effect.survival = effect.survival.coxph, show.effect = display.effect,
-  conf.level = 0.95, label = FALSE)
+survival.data.frame.by(
+  df,
+  by,
+  times = NULL,
+  followup = FALSE,
+  total = FALSE,
+  digits = 2,
+  test = FALSE,
+  test.survival = test.survival.logrank,
+  show.test = display.test,
+  plim = 4,
+  show.method = TRUE,
+  effect = FALSE,
+  effect.survival = effect.survival.coxph,
+  show.effect = display.effect,
+  conf.level = 0.95,
+  label = FALSE
+)
 }
 \arguments{
 \item{df}{df}
diff --git a/man/tabular.Rd b/man/tabular.Rd
index c297bad..32cb6f0 100644
--- a/man/tabular.Rd
+++ b/man/tabular.Rd
@@ -4,11 +4,23 @@
 \alias{tabular}
 \title{Compute a contingency table}
 \usage{
-tabular(x, y, showNA = c("no", "ifany", "always"), margin = 0:2,
-  total = FALSE, digits = 2, test = FALSE,
-  test.tabular = test.tabular.auto, show.test = display.test, plim = 4,
-  show.method = TRUE, effect = FALSE, effect.tabular = or.row.by.col,
-  conf.level = 0.95, show.effect = display.effect)
+tabular(
+  x,
+  y,
+  showNA = c("no", "ifany", "always"),
+  margin = 0:2,
+  total = FALSE,
+  digits = 2,
+  test = FALSE,
+  test.tabular = test.tabular.auto,
+  show.test = display.test,
+  plim = 4,
+  show.method = TRUE,
+  effect = FALSE,
+  effect.tabular = or.row.by.col,
+  conf.level = 0.95,
+  show.effect = display.effect
+)
 }
 \arguments{
 \item{x}{x}
diff --git a/man/tabular.data.frame.Rd b/man/tabular.data.frame.Rd
index 4689891..080c420 100644
--- a/man/tabular.data.frame.Rd
+++ b/man/tabular.data.frame.Rd
@@ -4,11 +4,24 @@
 \alias{tabular.data.frame}
 \title{Compute a contingency table (data.frame input)}
 \usage{
-tabular.data.frame(dfx, dfy, margin = 0:2, showNA = c("no", "ifany",
-  "always"), total = FALSE, digits = 2, test = FALSE,
-  test.tabular = test.tabular.auto, show.test = display.test, plim = 4,
-  show.method = TRUE, effect = FALSE, effect.tabular = or.row.by.col,
-  conf.level = 0.95, show.effect = display.effect, label = FALSE)
+tabular.data.frame(
+  dfx,
+  dfy,
+  margin = 0:2,
+  showNA = c("no", "ifany", "always"),
+  total = FALSE,
+  digits = 2,
+  test = FALSE,
+  test.tabular = test.tabular.auto,
+  show.test = display.test,
+  plim = 4,
+  show.method = TRUE,
+  effect = FALSE,
+  effect.tabular = or.row.by.col,
+  conf.level = 0.95,
+  show.effect = display.effect,
+  label = FALSE
+)
 }
 \arguments{
 \item{dfx}{data.frame}
diff --git a/man/test.summarize.contrasts.lin.Rd b/man/test.summarize.contrasts.lin.Rd
new file mode 100644
index 0000000..2ae091a
--- /dev/null
+++ b/man/test.summarize.contrasts.lin.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/test.r
+\name{test.summarize.contrasts.lin}
+\alias{test.summarize.contrasts.lin}
+\title{Test for linear trend across ordered factor with contrasts}
+\usage{
+test.summarize.contrasts.lin(x, y)
+}
+\arguments{
+\item{x}{vector}
+
+\item{y}{ordered factor}
+}
+\value{
+a list with two componments: p.value and method
+}
+\description{
+Test for linear trend across ordered factor with contrasts
+}
+\examples{
+library(dplyr)
+iris \%>\% 
+  mutate(Petal.Width.qt = paste0("Q", ntile(Petal.Width, 5)) \%>\% ordered()) \%>\% 
+  cross(Petal.Length ~ Petal.Width.qt, data=., test=T, test.summarize = test.summarize.contrasts.lin)
+}
+\author{
+Dan Chaltiel
+}
diff --git a/tests/testthat.R b/tests/testthat.R
new file mode 100644
index 0000000..785b9df
--- /dev/null
+++ b/tests/testthat.R
@@ -0,0 +1,4 @@
+library(testthat)
+library(biostat2)
+
+test_check("biostat2")
diff --git a/tests/testthat/test-cross.R b/tests/testthat/test-cross.R
new file mode 100644
index 0000000..57f0614
--- /dev/null
+++ b/tests/testthat/test-cross.R
@@ -0,0 +1,56 @@
+context("cross tables")
+
+library(Hmisc)
+label(iris$Species) = "Espèce"
+label(iris$Sepal.Length) = "Longueur du Sépale"
+label(iris$Sepal.Width) = "Longueur du Sépale"
+label(iris$Petal.Length) = "Longueur du Pétale"
+label(iris$Petal.Width) = "Largeur du Pétale"
+
+
+
+test_that("cross OK", {
+    mytable <- cross(cbind(...) ~ tobgp, esoph, test = TRUE)
+    
+    expect_equal(dim(mytable), c(18,8)) #Maybe not the most clever test...
+    expect_is(mytable, c("data.frame"))
+    expect_is(mytable, c("cross"))
+})
+
+test_that("compact OK", {
+    mytable <- cross(cbind(...) ~ tobgp, esoph, test = TRUE) %>% 
+        compact
+    
+    expect_equal(dim(mytable), c(26,5))
+    expect_is(mytable, c("data.frame"))
+    expect_is(mytable, c("compacted"))
+    expect_is(mytable, c("cross"))
+})
+
+
+test_that("Long formula OK", {
+    
+    mytable <- cross(cbind(Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, 
+                           Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, 
+                           Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, 
+                           Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Width, Sepal.Length, Sepal.Length, Sepal.Length, 
+                           Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, 
+                           Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, I(Sepal.Width^2), Sepal.Length, Sepal.Length, 
+                           Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, I(Sepal.Width^2), Sepal.Length, Sepal.Length, 
+                           Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, 
+                           I(Sepal.Width^2), Sepal.Length, Sepal.Length, Sepal.Width, Sepal.Length, Sepal.Length, Sepal.Length, 
+                           Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length, 
+                           Sepal.Length, Sepal.Length, Sepal.Length, Sepal.Length) ~ Species, iris)
+    
+    expect_equal(dim(mytable), c(296,6))
+    expect_is(mytable, c("data.frame"))
+    expect_is(mytable, c("cross"))
+})
+
+
+
+# cross(cbind(Petal.Length, Species) ~ cbind(Petal.Length, Petal.Width), iris)
+# cross(Petal.Length + Species ~ Petal.Length + Petal.Width, iris)
+
+# crosstable(cbind(mpg, factor(vs)) + cbind(drat, hp) ~ cbind(cyl, factor(am)), mtcars) #boss de fin
+
diff --git a/tests/testthat/test-officer.R b/tests/testthat/test-officer.R
new file mode 100644
index 0000000..557574e
--- /dev/null
+++ b/tests/testthat/test-officer.R
@@ -0,0 +1,104 @@
+context("officer")
+
+crosstables = list(
+    simple_test = cross(cbind(...) ~ ., esoph, test = TRUE),
+    double_test = cross(cbind(mpg,cyl,disp) ~ factor(am), mtcars, test = TRUE),
+    triple_test = cross(cbind(...) ~ Species, iris, test = TRUE),
+    simple_no_test = cross(cbind(...) ~ ., esoph, test = F),
+    double_no_test = cross(cbind(mpg,cyl,disp) ~ factor(am), mtcars, test = F),
+    triple_no_test = cross(cbind(...) ~ Species, iris, test = F)
+    #des warnings sur wilcoxon mais OSEF
+)
+
+#TODO body_add_crosstable when compacted before function
+
+test_that("crosstables don't throw errors in officer", {
+    doc <- read_docx()
+    #test with compact=F et compact=T
+    for (i in names(crosstables)) {
+        # print(i)
+        crosstable = crosstables[[i]]
+        expect_is(crosstable, c("cross"))
+        doc = doc %>% 
+            body_add_title(i, 1) %>%
+            body_add_title("Not compacted", 2) %>%
+            body_add_crosstable(crosstable, show.test.name = F, auto.fit = T) %>%
+            body_add_break %>%
+            body_add_title("Compacted in function", 2) %>%
+            body_add_crosstable(crosstable, TRUE, show.test.name = F, auto.fit = T) %>% 
+            body_add_break %>% 
+            body_add_title("Compacted before function", 2) %>%
+            body_add_normal("TODO") %>% 
+            # body_add_crosstable(compact(crosstable), show.test.name = F, auto.fit = T) %>% 
+            body_add_break 
+    }
+    print(doc, "test_cross_officer.docx")
+})
+
+
+
+test_that("crosstables are OK as flextables", {
+    library(purrr)
+    cross=biostat2::cross
+    library(dplyr)
+    library(officer)
+    library(Hmisc)
+    showNA = c("no", "ifany")
+    test = c(T,F)
+    effect = c(T,F)
+    label = T
+    total = list(F,T,1,2)
+    
+    #TODO: si total et (NA dans variable BY), mettre un footer "les chiffres sont pas bons"
+    #TODO: no effect for categorical variables
+    mtcars2 = mtcars %>% 
+        mutate(
+            gear=ifelse(row_number() %in% 17:18, NA, gear),
+            gear=as.factor(gear), 
+            drat=ifelse(between(drat, 3.5, 3.7), NA, drat),
+            qsec=ifelse(between(qsec, 17, 17.5), NA, drat),
+            am=ifelse(am==0, "automatic", "manual"),
+            am=ifelse(row_number() %in% 3:4, NA, am)
+        )
+    label(mtcars2$drat) = "Rear axle ratio"
+    label(mtcars2$gear) = "Number of forward gears"
+    label(mtcars2$qsec) = "Time for a quarter mile"
+    label(mtcars2$am) = "Transmission"
+    
+    x = expand.grid(showNA, test, effect, label, total, stringsAsFactors = F) %>% 
+        set_names(c("showNA", "test", "effect", "label", "total")) %>% 
+        arrange #32 possibilities
+    
+    cross_tables = x %>% pmap(~{
+        # print(paste(..1, ..2, ..3, ..4, ..5))
+        rtn=cross(
+            cbind(gear, qsec) ~ am,
+            data=mtcars2,
+            showNA = ..1,
+            margin = 2,
+            test=..2,
+            effect=..3,
+            label=..4,
+            total=..5
+        )
+        expect_is(rtn, c("cross"))
+        rtn
+    })
+    
+    # # Une table au hasard
+    # x %>% sample_n(1) %>% pmap(~{
+    #     print(paste(..1, ..2, ..3, ..4, ..5, sep=" -- "))
+    #     cross(
+    #         cbind(drat, gear) ~ am,
+    #         data=mtcars2,
+    #         margin = 2,
+    #         show.method = F,
+    #         showNA = ..1,
+    #         test=..2,
+    #         effect=..3,
+    #         label=..4,
+    #         total=..5
+    #     )
+    # }) %>% first %>% cross_to_flextable
+    
+})