Update Issue_194 branch

DESCRIPTION

@@ -16,7 +16,7 @@ Description: A simple way of fitting detection functions to distance sampling
     Horvitz-Thompson-like estimator) if survey area information is provided. See
     Miller et al. (2019) <doi:10.18637/jss.v089.i01> for more information on
     methods and <https://examples.distancesampling.org/> for example analyses.
-Version: 2.0.0.9003
+Version: 2.0.0.9004
 URL: https://github.com/DistanceDevelopment/Distance/
 BugReports: https://github.com/DistanceDevelopment/Distance/issues
 Language: en-GB

NEWS.md

@@ -2,7 +2,8 @@
 
 * Fixes issue with print dht2 when multipliers are a data.frame (Issue #179)
 * Fixes bug when including a uniform with no adjustment terms in the summarize_ds_models function (Issue #180)
-* Users to pass a list of models to summarize_ds_models rather than passing them individually. (Issue #)
+* Users to pass a list of models to summarize_ds_models rather than passing them individually. (Issue #149)
+* Truncation distances greater than the largest cutpoint value for binned data are no longer permitted as these cause fitting issues. (Issue #175)
 
 # Distance 2.0.0
 

R/get_truncation.R

@@ -54,5 +54,15 @@ get_truncation <- function(truncation, cutpoints, data){
       stop("Truncation must be supplied as a single number/string or a list with elements \"left\" and \"right\".")
     }
   }
+
+  # Final check that truncation is not greater than largest cutpoint
+  if(!is.null(cutpoints)){
+    if(width > cutpoints[length(cutpoints)]){
+      warning(paste("Truncation width is greater than the largest bin distance, re-setting truncation to be largest cutpoint value: ", cutpoints[length(cutpoints)], sep = ""), immediate. = TRUE, call. = FALSE)
+      # Make truncation largest cutpoint
+      width <- cutpoints[length(cutpoints)]
+    }
+  }
+
   list(left=left, width=width)
 }

R/summarize_ds_models.R

@@ -9,7 +9,9 @@
 #' the resulting `data.frame` in R, you may wish to rename the columns for
 #' ease of access.
 #'
-#' @param ... models to be summarised
+#' @param ... models to be summarised (to be deprecated)
+#' @param models a named list of models to be summarised. If the list is not
+#' named then default names of 'model 1', 'model 2' etc. are used.  
 #' @param sort column to sort by (default `"AIC"`)
 #' @param output should the output be given in `"latex"` compatible format
 #' or as `"plain"` text?

tests/testthat/test_ds.R

@@ -56,6 +56,12 @@ test_that("binning works", {
   # first cutpoint not zero when no left truncation
   expect_error(ds(egdata,4,cutpoints=c(2,3,4)),
                "The first cutpoint must be 0 or the left truncation distance!")
+
+  expect_warning(ds.obj <- ds(egdata,list(left = 2, right = 5),cutpoints=c(2,3,4)),
+               "Truncation width is greater than the largest bin distance, re-setting truncation to be largest cutpoint value: 4")
+
+  # Check that the width has been modified correctly
+  expect_equal(ds.obj$ddf$meta.data$width, 4)
 
   tst_distances <- data.frame(distance = c(0, 0, 0, 10, 50, 70, 110))
   expect_equal(as.vector(table(create_bins(tst_distances,

tests/testthat/test_summarize.R

@@ -85,4 +85,8 @@ test_that("Passing in models via a list",{
   test3 <- summarize_ds_models(list(ds.model, ds.model.cos, ds.model.hr))
 
   expect_identical(test1[,2:7], test3[,2:7])
+  expect_identical(test3[,1], c("\\texttt{model 1}", "\\texttt{model 2}", "\\texttt{model 3}"))
+
+  test4 <- summarize_ds_models(list(m1 = ds.model, m2 = ds.model.cos, m3 = ds.model.hr))
+  expect_identical(test4[,1], c("\\texttt{m1}", "\\texttt{m2}", "\\texttt{m3}"))
 })