diff --git a/DESCRIPTION b/DESCRIPTION index dc01edb..748003c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: ALASCA Title: Assorted, Linear ASCA Functions -Version: 1.0.17 +Version: 1.0.19 Authors@R: person(given = "Anders H.", family = "Jarmund", @@ -15,7 +15,7 @@ Encoding: UTF-8 LazyData: true ByteCompile: true Roxygen: list(markdown = TRUE, r6 = TRUE) -RoxygenNote: 7.1.2 +RoxygenNote: 7.3.2 Depends: data.table Imports: diff --git a/NAMESPACE b/NAMESPACE index 59904c6..8aa0a15 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -20,5 +20,6 @@ export(plot_covariate) export(plot_covariates) export(plot_mm) export(plot_val) +export(predict_scores) export(save.AlascaModel) export(screeplot) diff --git a/NEWS.md b/NEWS.md index 70c8266..f1d9189 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,13 @@ +# ALASCA 1.0.19 + +* Bug fix: The prediction plots should now work for models with separated effects too + +# ALASCA 1.0.18 + +* Replacing `aes_string()` due to changes in the `ggplot2` package +* Moved `finalize()` from public to private re changes in the `R6` package +* Bug fix: Plots all variables instead of subset + # ALASCA 1.0.17 * Minor bug fix related to 1.0.16 diff --git a/R/ALASCA.R b/R/ALASCA.R index 7c6d3cb..22b48d4 100644 --- a/R/ALASCA.R +++ b/R/ALASCA.R @@ -1499,43 +1499,43 @@ plot_prediction <- function() { if(self$model$validate) { if (self$black_and_white) { - g <- ggplot2::ggplot(data_to_plot, ggplot2::aes_string(x = "x_data", - y = "pred", - group = "group_data", - linetype = "group_data", - ymin = "low", - ymax = "high")) + g <- ggplot2::ggplot(data_to_plot, ggplot2::aes(x = .data[["x_data"]], + y = .data[["pred"]], + group = .data[["group_data"]], + linetype = .data[["group_data"]], + ymin = .data[["low"]], + ymax = .data[["high"]])) } else { - g <- ggplot2::ggplot(data_to_plot, ggplot2::aes_string(x = "x_data", - y = "pred", - group = "group_data", - color = "group_data", - linetype = "group_data", - ymin = "low", - ymax = "high")) + g <- ggplot2::ggplot(data_to_plot, ggplot2::aes(x = .data[["x_data"]], + y = .data[["pred"]], + group = .data[["group_data"]], + color = .data[["group_data"]], + linetype = .data[["group_data"]], + ymin = .data[["low"]], + ymax = .data[["high"]])) } g <- g + ggplot2::geom_pointrange(position = ggplot2::position_dodge(width = self$dodgewidth)) + ggplot2::geom_line(position = ggplot2::position_dodge(width = self$dodgewidth)) if (self$ribbon && self$black_and_white) { - g <- g + ggplot2::geom_ribbon(ggplot2::aes_string(fill = "group_data"), + g <- g + ggplot2::geom_ribbon(ggplot2::aes(fill = .data[["group_data"]]), alpha = .1, position = ggplot2::position_dodge(width = self$dodgewidth), color = NA ) + ggplot2::scale_fill_manual(values = self$get_plot_palette()) + ggplot2::labs(fill = self$group_label) } } else { if (self$black_and_white) { - g <- ggplot2::ggplot(data_to_plot, ggplot2::aes_string(x = "x_data", - y = "pred", - group = "group_data", - linetype = "group_data")) + g <- ggplot2::ggplot(data_to_plot, ggplot2::aes(x = .data[["x_data"]], + y = .data[["pred"]], + group = .data[["group_data"]], + linetype = .data[["group_data"]])) } else { - g <- ggplot2::ggplot(data_to_plot, ggplot2::aes_string(x = "x_data", - y = "pred", - group = "group_data", - color = "group_data", - linetype = "group_data")) + g <- ggplot2::ggplot(data_to_plot, ggplot2::aes(x = .data[["x_data"]], + y = .data[["pred"]], + group = .data[["group_data"]], + color = .data[["group_data"]], + linetype = .data[["group_data"]])) } g <- g + ggplot2::geom_point() + ggplot2::geom_line() } @@ -1692,7 +1692,7 @@ plot_effect <- function() { } } else { # Return only a single effect/component - gs <- self$plot_effect_score(effect_i = effect_i, component = component) + gs <- self$plot_effect_score(effect_i = effect_i, component = component) gl <- self$plot_effect_loading(effect_i = effect_i, component = component) if (is.null(self$loading_group_column)) { ggpubr::ggarrange(gs, gl, widths = c(2,3), common.legend = TRUE, legend = "bottom", align = "h", labels = self$labels) @@ -1729,48 +1729,48 @@ plot_effect_score <- function(effect_i = 1, component = 1) { if (self$model$method == "LMM") { if (self$black_and_white) { g <- ggplot2::ggplot(data_to_plot, - ggplot2::aes_string(x = "x_data", - y = "score", - group = "group_data", - shape = "group_data", - linetype = "group_data", - ymin = "low", - ymax = "high")) + ggplot2::aes(x = .data[["x_data"]], + y = .data[["score"]], + group = .data[["group_data"]], + shape = .data[["group_data"]], + linetype = .data[["group_data"]], + ymin = .data[["low"]], + ymax = .data[["high"]])) } else { g <- ggplot2::ggplot(data_to_plot, - ggplot2::aes_string(x = "x_data", - y = "score", - group = "group_data", - color = "group_data", - linetype = "group_data", - ymin = "low", - ymax = "high")) + ggplot2::aes(x = .data[["x_data"]], + y = .data[["score"]], + group = .data[["group_data"]], + color = .data[["group_data"]], + linetype = .data[["group_data"]], + ymin = .data[["low"]], + ymax = .data[["high"]])) } g <- g + ggplot2::geom_line(position = ggplot2::position_dodge(width = self$dodgewidth)) } else { if (self$black_and_white) { g <- ggplot2::ggplot(data_to_plot, - ggplot2::aes_string(x = "x_data", - y = "score", - shape = "group_data", - ymin = "low", - ymax = "high")) + ggplot2::aes(x = .data[["x_data"]], + y = .data[["score"]], + shape = .data[["group_data"]], + ymin = .data[["low"]], + ymax = .data[["high"]])) } else { g <- ggplot2::ggplot(data_to_plot, - ggplot2::aes_string(x = "x_data", - y = "score", - color = "group_data", - ymin = "low", - ymax = "high")) + ggplot2::aes(x = .data[["x_data"]], + y = .data[["score"]], + color = .data[["group_data"]], + ymin = .data[["low"]], + ymax = .data[["high"]])) } } g <- g + ggplot2::geom_pointrange(position = ggplot2::position_dodge(width = self$dodgewidth)) if (self$ribbon && !self$black_and_white && self$model$method == "LMM") { - g <- g + ggplot2::geom_ribbon(ggplot2::aes_string(fill = "group_data"), - alpha = .1, + g <- g + ggplot2::geom_ribbon(ggplot2::aes(fill = .data[["group_data"]]), + alpha = .1, position = ggplot2::position_dodge(width = self$dodgewidth), color = NA - ) + ggplot2::scale_fill_manual(values = self$get_plot_palette()) + ggplot2::labs(fill = self$group_label) + ) + ggplot2::scale_fill_manual(values = self$get_plot_palette()) + ggplot2::labs(fill = self$group_label) } } else { @@ -1779,31 +1779,35 @@ plot_effect_score <- function(effect_i = 1, component = 1) { if (self$model$method == "LMM") { if (self$black_and_white) { g <- ggplot2::ggplot(data_to_plot, - ggplot2::aes_string(x = "x_data", - y = "score", - linetype = "group_data", - group = "group_data", - shape = "group_data")) + ggplot2::aes(x = .data[["x_data"]], + y = .data[["score"]], + linetype = .data[["group_data"]], + group = .data[["group_data"]], + shape = .data[["group_data"]]) + ) } else { g <- ggplot2::ggplot(data_to_plot, - ggplot2::aes_string(x = "x_data", - y = "score", - linetype = "group_data", - group = "group_data", - color = "group_data")) + ggplot2::aes(x = .data[["x_data"]], + y = .data[["score"]], + linetype = .data[["group_data"]], + group = .data[["group_data"]], + color = .data[["group_data"]]) + ) } g <- g + ggplot2::geom_line() } else { if (self$black_and_white) { g <- ggplot2::ggplot(data_to_plot, - ggplot2::aes_string(x = "x_data", - y = "score", - shape = "group_data")) + ggplot2::aes(x = .data[["x_data"]], + y = .data[["score"]], + shape = .data[["group_data"]]) + ) } else { g <- ggplot2::ggplot(data_to_plot, - ggplot2::aes_string(x = "x_data", - y = "score", - color = "group_data")) + ggplot2::aes(x = .data[["x_data"]], + y = .data[["score"]], + color = .data[["group_data"]]) + ) } } g <- g + ggplot2::geom_point() @@ -1859,15 +1863,15 @@ plot_effect_loading <- function(effect_i = 1, component = 1) { # Validated model if (is.null(self$loading_group_column)) { - g <- ggplot2::ggplot(data_to_plot, ggplot2::aes_string(x = "covars", y = "loading", ymin = "low", ymax = "high")) + g <- ggplot2::ggplot(data_to_plot, ggplot2::aes(x = .data[["covars"]], y = .data[["loading"]], ymin = .data[["low"]], ymax = .data[["high"]])) } else { if (self$black_and_white) { - g <- ggplot2::ggplot(data_to_plot, ggplot2::aes_string(x = "covars", y = "loading", ymin = "low", ymax = "high", shape = "covargroup")) + g <- ggplot2::ggplot(data_to_plot, ggplot2::aes(x = .data[["covars"]], y = .data[["loading"]], ymin = .data[["low"]], ymax = .data[["high"]], shape = .data[["covargroup"]])) } else { if (self$waterfall == TRUE) { - g <- ggplot2::ggplot(data_to_plot, ggplot2::aes_string(x = "covars", y = "loading", ymin = "low", ymax = "high", shape = "covargroup", fill = "covargroup")) + g <- ggplot2::ggplot(data_to_plot, ggplot2::aes(x = .data[["covars"]], y = .data[["loading"]], ymin = .data[["low"]], ymax = .data[["high"]], shape = .data[["covargroup"]], fill = .data[["covargroup"]])) } else { - g <- ggplot2::ggplot(data_to_plot, ggplot2::aes_string(x = "covars", y = "loading", ymin = "low", ymax = "high", shape = "covargroup", color = "covargroup")) + g <- ggplot2::ggplot(data_to_plot, ggplot2::aes(x = .data[["covars"]], y = .data[["loading"]], ymin = .data[["low"]], ymax = .data[["high"]], shape = .data[["covargroup"]], color = .data[["covargroup"]])) } } } @@ -1885,15 +1889,32 @@ plot_effect_loading <- function(effect_i = 1, component = 1) { # Unvalidated model if (is.null(self$loading_group_column)) { - g <- ggplot2::ggplot(data_to_plot, ggplot2::aes_string(x = "covars", y = "loading")) + g <- ggplot2::ggplot(data_to_plot, + ggplot2::aes(x = .data[["covars"]], + y = .data[["loading"]]) + ) } else { if (self$black_and_white) { - g <- ggplot2::ggplot(data_to_plot, ggplot2::aes_string(x = "covars", y = "loading", shape = "covargroup")) + g <- ggplot2::ggplot(data_to_plot, + ggplot2::aes(x = .data[["covars"]], + y = .data[["loading"]], + shape = .data[["covargroup"]]) + ) } else { if (self$waterfall == TRUE) { - g <- ggplot2::ggplot(data_to_plot, ggplot2::aes_string(x = "covars", y = "loading", shape = "covargroup", fill = "covargroup")) + g <- ggplot2::ggplot(data_to_plot, + ggplot2::aes(x = .data[["covars"]], + y = .data[["loading"]], + shape = .data[["covargroup"]], + fill = .data[["covargroup"]]) + ) } else { - g <- ggplot2::ggplot(data_to_plot, ggplot2::aes_string(x = "covars", y = "loading", shape = "covargroup", color = "covargroup")) + g <- ggplot2::ggplot(data_to_plot, + ggplot2::aes(x = .data[["covars"]], + y = .data[["loading"]], + shape = .data[["covargroup"]], + color = .data[["covargroup"]]) + ) } } } @@ -2043,11 +2064,12 @@ plot_effect_validation_score <- function(effect_i = 1, component = 1) { # Validated model g <- ggplot2::ggplot(data_to_plot[model != 0], - ggplot2::aes_string(x = "x_data", - y = "score", - group = "grouping", - color = "group_data", - linetype = "group_data")) + + ggplot2::aes(x = .data[["x_data"]], + y = .data[["score"]], + group = .data[["grouping"]], + color = .data[["group_data"]], + linetype = .data[["group_data"]]) + ) + ggplot2::geom_point(alpha = 0.5) + ggplot2::geom_line(alpha = 0.5) + ggplot2::geom_point(data = data_to_plot[model == 0], color = "black") + @@ -2055,10 +2077,10 @@ plot_effect_validation_score <- function(effect_i = 1, component = 1) { ggplot2::scale_alpha(range = c(0.1, 1), guide = "none") + ggplot2::scale_color_manual(values = self$get_plot_palette()) + ggplot2::scale_linetype_manual(values = self$get_plot_linetypes()) + - ggplot2::labs(color = self$group_label, + ggplot2::labs(color = self$group_label, linetype = self$group_label, - x = self$x_label, - y = self$get_explained_label(effect_i = effect_i, component = component, type= "Score")) + + x = self$x_label, + y = self$get_explained_label(effect_i = effect_i, component = component, type= "Score")) + self$my_theme + self$xflip(flip = FALSE) return(g) } @@ -2089,9 +2111,19 @@ plot_effect_validation_loading <- function(effect_i = 1, component = 1) { data_to_plot[, nval := as.numeric(covars)] if (is.null(self$loading_group_column)) { - g <- ggplot2::ggplot(data_to_plot[model != 0], ggplot2::aes_string(x = "covars", y = "loading", group = "model")) + g <- ggplot2::ggplot(data_to_plot[model != 0], + ggplot2::aes(x = .data[["covars"]], + y = .data[["loading"]], + group = .data[["model"]]) + ) } else { - g <- ggplot2::ggplot(data_to_plot[model != 0], ggplot2::aes_string(x = "covars", y = "loading", group = "model", shape = "covargroup", color = "covargroup")) + g <- ggplot2::ggplot(data_to_plot[model != 0], + ggplot2::aes(x = .data[["covars"]], + y = .data[["loading"]], + group = .data[["model"]], + shape = .data[["covargroup"]], + color = .data[["covargroup"]]) + ) } g <- g + ggplot2::geom_hline(yintercept = 0, linetype = "dashed") + @@ -2314,20 +2346,21 @@ plot_2D_score <- function() { data_to_plot <- dcast(data = data_to_plot, ...~PC, value.var = "score") g <- ggplot2::ggplot(data_to_plot, - ggplot2::aes_string(x = "PC_1", - y = "PC_2", - shape = "x_data", - color = "group_data")) + + ggplot2::aes(x = .data[["PC_1"]], + y = .data[["PC_2"]], + shape = .data[["x_data"]], + color = .data[["group_data"]]) + ) + ggplot2::geom_point(alpha = 0.8) + ggplot2::geom_line(ggplot2::aes(group = paste(group_data, model)), alpha = 0.3) + ggplot2::stat_ellipse(ggplot2::aes(linetype = x_data)) + ggplot2::scale_color_manual(values = self$get_plot_palette()) + ggplot2::scale_alpha(range = c(0, 1)) + - ggplot2::labs(color = self$group_label, + ggplot2::labs(color = self$group_label, linetype = self$x_label, - shape = self$x_label, - x = self$get_explained_label(effect_i = self$effect_i, component = self$component[[1]], type= "Score"), - y = self$get_explained_label(effect_i = self$effect_i, component = self$component[[2]], type= "Score")) + + shape = self$x_label, + x = self$get_explained_label(effect_i = self$effect_i, component = self$component[[1]], type= "Score"), + y = self$get_explained_label(effect_i = self$effect_i, component = self$component[[2]], type= "Score")) + self$my_theme } @@ -2512,18 +2545,20 @@ plot_participants <- function(effect_i = 1, component = 1) { if(self$model$method == "LMM") { g <- ggplot2::ggplot(data_to_plot, - ggplot2::aes_string(x = "x_data", - y = self$model$formula$lhs, - group = self$model$formula$ID, - color = "group_data", - linetype = "group_data")) + + ggplot2::aes(x = .data[["x_data"]], + y = .data[[self$model$formula$lhs]], + group = .data[[self$model$formula$ID]], + color = .data[["group_data"]], + linetype = .data[["group_data"]]) + ) + ggplot2::geom_point(position = ggplot2::position_dodge(width = self$dodgewidth)) + ggplot2::geom_line(position = ggplot2::position_dodge(width = self$dodgewidth)) } else { g <- ggplot2::ggplot(data_to_plot, - ggplot2::aes_string(x = "x_data", - y = self$model$formula$lhs, - color = "group_data")) + + ggplot2::aes(x = .data[["x_data"]], + y = .data[[self$model$formula$lhs]], + color = .data[["group_data"]]) + ) + ggplot2::geom_point(position = ggplot2::position_dodge(width = self$dodgewidth)) } g <- g + ggplot2::scale_color_manual(values = self$get_plot_palette()) + diff --git a/R/AlascaModel.R b/R/AlascaModel.R index 848c960..0cd4430 100644 --- a/R/AlascaModel.R +++ b/R/AlascaModel.R @@ -19,9 +19,9 @@ AlascaModel <- R6::R6Class("AlascaModel", #' @field ignore_missing_covars If TRUE, ignore missing covariate values ignore_missing_covars = FALSE, #' @field version Version number - version = "1.0.17", + version = "1.0.19", #' @field update_date Date of latest update - update_date = "2024-09-13", + update_date = "2026-01-16", # Effect matrices #' @field separate_effects If TRUE, try to separate the effects @@ -256,15 +256,6 @@ AlascaModel <- R6::R6Class("AlascaModel", # Build the ALASCA model ---- self$build_model() }, - finalize = function() { - if (self$save_to_disk && !self$minimize_object) { - if (self$db_method == "SQLite") { - DBI::dbDisconnect(self$db_con) - } else { - DBI::dbDisconnect(self$db_con, shutdown = TRUE) - } - } - }, #' @description #' Update the current model (used for validation) update = function() { @@ -446,7 +437,7 @@ AlascaModel <- R6::R6Class("AlascaModel", if (self$equal_baseline) { # Must add baselines for missing interactions (baseline x group) - baseline_to_add <- self$model_prediction[get(self$effect_terms) %in% self$get_ref(self$effect_terms)] + baseline_to_add <- self$model_prediction[self$get_ref(self$effect_terms)] if (length(self$effect_terms) == 2) { # In this case, there are no main effects except time @@ -844,5 +835,15 @@ AlascaModel <- R6::R6Class("AlascaModel", unique(unlist(self$effect_list$terms)) } ), - private = list() + private = list( + finalize = function() { + if (self$save_to_disk && !self$minimize_object) { + if (self$db_method == "SQLite") { + DBI::dbDisconnect(self$db_con) + } else { + DBI::dbDisconnect(self$db_con, shutdown = TRUE) + } + } + } + ) ) diff --git a/R/AlascaPlot.R b/R/AlascaPlot.R index 6a77178..5307be2 100644 --- a/R/AlascaPlot.R +++ b/R/AlascaPlot.R @@ -85,8 +85,7 @@ AlascaPlot <- R6::R6Class("AlascaPlot", #' @field type Plot type type = "effect", initialize = function(model) { - self$model <- model - self$n_limit <- min(self$n_limit / 2, floor(length(self$model$get_levels("variable")) / 2)) + self$model <- model }, call_plot = function(...) { inputs <- list(...) @@ -253,10 +252,10 @@ AlascaPlot <- R6::R6Class("AlascaPlot", if (is.null(self$loading_group_column)) { if (self$model$validate) { - g <- ggplot2::ggplot(data_to_plot, ggplot2::aes_string(x = "covar", y = "estimate", ymin = "low", ymax = "high")) + + g <- ggplot2::ggplot(data_to_plot, ggplot2::aes(x = .data[["covar"]], y = .data[["estimate"]], ymin = .data[["low"]], ymax = .data[["high"]])) + ggplot2::geom_pointrange() } else { - g <- ggplot2::ggplot(data_to_plot, ggplot2::aes_string(x = "covar", y = "estimate")) + + g <- ggplot2::ggplot(data_to_plot, ggplot2::aes(x = .data[["covar"]], y = .data[["estimate"]])) + ggplot2::geom_point() } } else { @@ -266,16 +265,16 @@ AlascaPlot <- R6::R6Class("AlascaPlot", } if (self$model$validate) { if (self$black_and_white) { - g <- ggplot2::ggplot(data_to_plot, ggplot2::aes_string(x = "covar", y = "estimate", ymin = "low", ymax = "high", shape = "covargroup")) + g <- ggplot2::ggplot(data_to_plot, ggplot2::aes(x = .data[["covar"]], y = .data[["estimate"]], ymin = .data[["low"]], ymax = .data[["high"]], shape = .data[["covargroup"]])) } else { - g <- ggplot2::ggplot(data_to_plot, ggplot2::aes_string(x = "covar", y = "estimate", ymin = "low", ymax = "high", shape = "covargroup", color = "covargroup")) + g <- ggplot2::ggplot(data_to_plot, ggplot2::aes(x = .data[["covar"]], y = .data[["estimate"]], ymin = .data[["low"]], ymax = .data[["high"]], shape = .data[["covargroup"]], color = .data[["covargroup"]])) } g <- g + ggplot2::geom_pointrange() } else { if (self$black_and_white) { - g <- ggplot2::ggplot(data_to_plot, ggplot2::aes_string(x = "covar", y = "estimate", shape = "covargroup")) + g <- ggplot2::ggplot(data_to_plot, ggplot2::aes(x = .data[["covar"]], y = .data[["estimate"]], shape = .data[["covargroup"]])) } else { - g <- ggplot2::ggplot(data_to_plot, ggplot2::aes_string(x = "covar", y = "estimate", shape = "covargroup", color = "covargroup")) + g <- ggplot2::ggplot(data_to_plot, ggplot2::aes(x = .data[["covar"]], y = .data[["estimate"]], shape = .data[["covargroup"]], color = .data[["covargroup"]])) } g <- g + ggplot2::geom_point() diff --git a/man/AlascaModel.Rd b/man/AlascaModel.Rd index 21f18a0..b52efe5 100644 --- a/man/AlascaModel.Rd +++ b/man/AlascaModel.Rd @@ -41,6 +41,8 @@ The object builds the ALASCA model and contains the data \item{\code{optimize_score}}{If TRUE, test all combinations of signs for the most important loadings, and choose the combination being the best fit} +\item{\code{optimize_PCs}}{If TRUE, test if principal components have to be re-ordered during validation} + \item{\code{validate}}{If TRUE, validate the model} \item{\code{validate_regression}}{If TRUE, validate get marginal means} @@ -111,59 +113,60 @@ The object builds the ALASCA model and contains the data \section{Methods}{ \subsection{Public methods}{ \itemize{ -\item \href{#method-remove_embedded_data}{\code{AlascaModel$remove_embedded_data()}} -\item \href{#method-get_default_scaling_function}{\code{AlascaModel$get_default_scaling_function()}} -\item \href{#method-get_scaling_function}{\code{AlascaModel$get_scaling_function()}} -\item \href{#method-get_pca_function}{\code{AlascaModel$get_pca_function()}} -\item \href{#method-build_model}{\code{AlascaModel$build_model()}} -\item \href{#method-run_regression}{\code{AlascaModel$run_regression()}} -\item \href{#method-get_regression_coefficients}{\code{AlascaModel$get_regression_coefficients()}} -\item \href{#method-remove_covars}{\code{AlascaModel$remove_covars()}} -\item \href{#method-get_effect_matrix}{\code{AlascaModel$get_effect_matrix()}} -\item \href{#method-do_pca}{\code{AlascaModel$do_pca()}} -\item \href{#method-do_reduce_dimensions}{\code{AlascaModel$do_reduce_dimensions()}} -\item \href{#method-clean_pca}{\code{AlascaModel$clean_pca()}} -\item \href{#method-clean_alasca}{\code{AlascaModel$clean_alasca()}} -\item \href{#method-do_validate}{\code{AlascaModel$do_validate()}} -\item \href{#method-get_validation_percentiles}{\code{AlascaModel$get_validation_percentiles()}} -\item \href{#method-get_validation_percentiles_regression}{\code{AlascaModel$get_validation_percentiles_regression()}} -\item \href{#method-get_validation_percentiles_covars}{\code{AlascaModel$get_validation_percentiles_covars()}} -\item \href{#method-get_validation_percentiles_loading}{\code{AlascaModel$get_validation_percentiles_loading()}} -\item \href{#method-get_validation_scores}{\code{AlascaModel$get_validation_scores()}} -\item \href{#method-get_validation_loadings}{\code{AlascaModel$get_validation_loadings()}} -\item \href{#method-get_validation_percentiles_score}{\code{AlascaModel$get_validation_percentiles_score()}} -\item \href{#method-get_regression_predictions}{\code{AlascaModel$get_regression_predictions()}} -\item \href{#method-get_validation_ids}{\code{AlascaModel$get_validation_ids()}} -\item \href{#method-prepare_validation_run}{\code{AlascaModel$prepare_validation_run()}} -\item \href{#method-get_bootstrap_data}{\code{AlascaModel$get_bootstrap_data()}} -\item \href{#method-new}{\code{AlascaModel$new()}} -\item \href{#method-finalize}{\code{AlascaModel$finalize()}} -\item \href{#method-update}{\code{AlascaModel$update()}} -\item \href{#method-log}{\code{AlascaModel$log()}} -\item \href{#method-plot}{\code{AlascaModel$plot()}} -\item \href{#method-get_residuals}{\code{AlascaModel$get_residuals()}} -\item \href{#method-set_effect_terms}{\code{AlascaModel$set_effect_terms()}} -\item \href{#method-set_design_matrices}{\code{AlascaModel$set_design_matrices()}} -\item \href{#method-flip}{\code{AlascaModel$flip()}} -\item \href{#method-get_ref}{\code{AlascaModel$get_ref()}} -\item \href{#method-get_levels}{\code{AlascaModel$get_levels()}} -\item \href{#method-get_PCs}{\code{AlascaModel$get_PCs()}} -\item \href{#method-get_predictions}{\code{AlascaModel$get_predictions()}} -\item \href{#method-get_scores}{\code{AlascaModel$get_scores()}} -\item \href{#method-get_loadings}{\code{AlascaModel$get_loadings()}} -\item \href{#method-get_covars}{\code{AlascaModel$get_covars()}} -\item \href{#method-print_version}{\code{AlascaModel$print_version()}} -\item \href{#method-save_validation}{\code{AlascaModel$save_validation()}} -\item \href{#method-save_to_csv}{\code{AlascaModel$save_to_csv()}} -\item \href{#method-save_model}{\code{AlascaModel$save_model()}} -\item \href{#method-rotate_matrix_optimize_score}{\code{AlascaModel$rotate_matrix_optimize_score()}} -\item \href{#method-rotate_matrix}{\code{AlascaModel$rotate_matrix()}} -\item \href{#method-clone}{\code{AlascaModel$clone()}} -} -} -\if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-remove_embedded_data}{}}} +\item \href{#method-AlascaModel-remove_embedded_data}{\code{AlascaModel$remove_embedded_data()}} +\item \href{#method-AlascaModel-get_default_scaling_function}{\code{AlascaModel$get_default_scaling_function()}} +\item \href{#method-AlascaModel-get_scaling_function}{\code{AlascaModel$get_scaling_function()}} +\item \href{#method-AlascaModel-get_pca_function}{\code{AlascaModel$get_pca_function()}} +\item \href{#method-AlascaModel-build_model}{\code{AlascaModel$build_model()}} +\item \href{#method-AlascaModel-run_regression}{\code{AlascaModel$run_regression()}} +\item \href{#method-AlascaModel-get_regression_coefficients}{\code{AlascaModel$get_regression_coefficients()}} +\item \href{#method-AlascaModel-remove_covars}{\code{AlascaModel$remove_covars()}} +\item \href{#method-AlascaModel-get_effect_matrix}{\code{AlascaModel$get_effect_matrix()}} +\item \href{#method-AlascaModel-do_pca}{\code{AlascaModel$do_pca()}} +\item \href{#method-AlascaModel-do_reduce_dimensions}{\code{AlascaModel$do_reduce_dimensions()}} +\item \href{#method-AlascaModel-clean_pca}{\code{AlascaModel$clean_pca()}} +\item \href{#method-AlascaModel-clean_alasca}{\code{AlascaModel$clean_alasca()}} +\item \href{#method-AlascaModel-do_validate}{\code{AlascaModel$do_validate()}} +\item \href{#method-AlascaModel-get_validation_percentiles}{\code{AlascaModel$get_validation_percentiles()}} +\item \href{#method-AlascaModel-get_validation_percentiles_regression}{\code{AlascaModel$get_validation_percentiles_regression()}} +\item \href{#method-AlascaModel-get_validation_percentiles_covars}{\code{AlascaModel$get_validation_percentiles_covars()}} +\item \href{#method-AlascaModel-get_validation_percentiles_loading}{\code{AlascaModel$get_validation_percentiles_loading()}} +\item \href{#method-AlascaModel-get_validation_scores}{\code{AlascaModel$get_validation_scores()}} +\item \href{#method-AlascaModel-get_validation_loadings}{\code{AlascaModel$get_validation_loadings()}} +\item \href{#method-AlascaModel-get_validation_percentiles_score}{\code{AlascaModel$get_validation_percentiles_score()}} +\item \href{#method-AlascaModel-get_regression_predictions}{\code{AlascaModel$get_regression_predictions()}} +\item \href{#method-AlascaModel-get_validation_ids}{\code{AlascaModel$get_validation_ids()}} +\item \href{#method-AlascaModel-prepare_validation_run}{\code{AlascaModel$prepare_validation_run()}} +\item \href{#method-AlascaModel-get_bootstrap_data}{\code{AlascaModel$get_bootstrap_data()}} +\item \href{#method-AlascaModel-predict_scores}{\code{AlascaModel$predict_scores()}} +\item \href{#method-AlascaModel-new}{\code{AlascaModel$new()}} +\item \href{#method-AlascaModel-update}{\code{AlascaModel$update()}} +\item \href{#method-AlascaModel-log}{\code{AlascaModel$log()}} +\item \href{#method-AlascaModel-plot}{\code{AlascaModel$plot()}} +\item \href{#method-AlascaModel-get_residuals}{\code{AlascaModel$get_residuals()}} +\item \href{#method-AlascaModel-set_effect_terms}{\code{AlascaModel$set_effect_terms()}} +\item \href{#method-AlascaModel-set_design_matrices}{\code{AlascaModel$set_design_matrices()}} +\item \href{#method-AlascaModel-flip}{\code{AlascaModel$flip()}} +\item \href{#method-AlascaModel-get_ref}{\code{AlascaModel$get_ref()}} +\item \href{#method-AlascaModel-get_levels}{\code{AlascaModel$get_levels()}} +\item \href{#method-AlascaModel-get_PCs}{\code{AlascaModel$get_PCs()}} +\item \href{#method-AlascaModel-get_predictions}{\code{AlascaModel$get_predictions()}} +\item \href{#method-AlascaModel-get_scores}{\code{AlascaModel$get_scores()}} +\item \href{#method-AlascaModel-get_loadings}{\code{AlascaModel$get_loadings()}} +\item \href{#method-AlascaModel-get_covars}{\code{AlascaModel$get_covars()}} +\item \href{#method-AlascaModel-print_version}{\code{AlascaModel$print_version()}} +\item \href{#method-AlascaModel-save_validation}{\code{AlascaModel$save_validation()}} +\item \href{#method-AlascaModel-save_to_csv}{\code{AlascaModel$save_to_csv()}} +\item \href{#method-AlascaModel-save_model}{\code{AlascaModel$save_model()}} +\item \href{#method-AlascaModel-rotate_matrix_optimize_score}{\code{AlascaModel$rotate_matrix_optimize_score()}} +\item \href{#method-AlascaModel-optimize_components}{\code{AlascaModel$optimize_components()}} +\item \href{#method-AlascaModel-rotate_matrix}{\code{AlascaModel$rotate_matrix()}} +\item \href{#method-AlascaModel-clone}{\code{AlascaModel$clone()}} +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-remove_embedded_data}{}}} \subsection{Method \code{remove_embedded_data()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$remove_embedded_data()}\if{html}{\out{
}} @@ -171,8 +174,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_default_scaling_function}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_default_scaling_function}{}}} \subsection{Method \code{get_default_scaling_function()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$get_default_scaling_function()}\if{html}{\out{
}} @@ -180,8 +183,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_scaling_function}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_scaling_function}{}}} \subsection{Method \code{get_scaling_function()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$get_scaling_function()}\if{html}{\out{
}} @@ -189,8 +192,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_pca_function}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_pca_function}{}}} \subsection{Method \code{get_pca_function()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$get_pca_function()}\if{html}{\out{
}} @@ -198,8 +201,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-build_model}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-build_model}{}}} \subsection{Method \code{build_model()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$build_model()}\if{html}{\out{
}} @@ -207,8 +210,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-run_regression}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-run_regression}{}}} \subsection{Method \code{run_regression()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$run_regression()}\if{html}{\out{
}} @@ -216,8 +219,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_regression_coefficients}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_regression_coefficients}{}}} \subsection{Method \code{get_regression_coefficients()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$get_regression_coefficients()}\if{html}{\out{
}} @@ -225,8 +228,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-remove_covars}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-remove_covars}{}}} \subsection{Method \code{remove_covars()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$remove_covars()}\if{html}{\out{
}} @@ -234,8 +237,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_effect_matrix}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_effect_matrix}{}}} \subsection{Method \code{get_effect_matrix()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$get_effect_matrix()}\if{html}{\out{
}} @@ -243,8 +246,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-do_pca}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-do_pca}{}}} \subsection{Method \code{do_pca()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$do_pca()}\if{html}{\out{
}} @@ -252,8 +255,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-do_reduce_dimensions}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-do_reduce_dimensions}{}}} \subsection{Method \code{do_reduce_dimensions()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$do_reduce_dimensions()}\if{html}{\out{
}} @@ -261,8 +264,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-clean_pca}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-clean_pca}{}}} \subsection{Method \code{clean_pca()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$clean_pca()}\if{html}{\out{
}} @@ -270,8 +273,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-clean_alasca}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-clean_alasca}{}}} \subsection{Method \code{clean_alasca()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$clean_alasca()}\if{html}{\out{
}} @@ -279,8 +282,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-do_validate}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-do_validate}{}}} \subsection{Method \code{do_validate()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$do_validate()}\if{html}{\out{
}} @@ -288,8 +291,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_validation_percentiles}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_validation_percentiles}{}}} \subsection{Method \code{get_validation_percentiles()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$get_validation_percentiles(objectlist)}\if{html}{\out{
}} @@ -297,8 +300,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_validation_percentiles_regression}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_validation_percentiles_regression}{}}} \subsection{Method \code{get_validation_percentiles_regression()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$get_validation_percentiles_regression(objectlist)}\if{html}{\out{
}} @@ -306,8 +309,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_validation_percentiles_covars}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_validation_percentiles_covars}{}}} \subsection{Method \code{get_validation_percentiles_covars()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$get_validation_percentiles_covars(objectlist)}\if{html}{\out{
}} @@ -315,8 +318,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_validation_percentiles_loading}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_validation_percentiles_loading}{}}} \subsection{Method \code{get_validation_percentiles_loading()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$get_validation_percentiles_loading(objectlist)}\if{html}{\out{
}} @@ -324,8 +327,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_validation_scores}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_validation_scores}{}}} \subsection{Method \code{get_validation_scores()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$get_validation_scores(objectlist = NULL, effect_i = 1)}\if{html}{\out{
}} @@ -333,8 +336,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_validation_loadings}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_validation_loadings}{}}} \subsection{Method \code{get_validation_loadings()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$get_validation_loadings(objectlist = NULL, effect_i = 1)}\if{html}{\out{
}} @@ -342,8 +345,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_validation_percentiles_score}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_validation_percentiles_score}{}}} \subsection{Method \code{get_validation_percentiles_score()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$get_validation_percentiles_score(objectlist)}\if{html}{\out{
}} @@ -351,8 +354,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_regression_predictions}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_regression_predictions}{}}} \subsection{Method \code{get_regression_predictions()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$get_regression_predictions()}\if{html}{\out{
}} @@ -360,8 +363,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_validation_ids}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_validation_ids}{}}} \subsection{Method \code{get_validation_ids()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$get_validation_ids()}\if{html}{\out{
}} @@ -369,8 +372,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-prepare_validation_run}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-prepare_validation_run}{}}} \subsection{Method \code{prepare_validation_run()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$prepare_validation_run(runN)}\if{html}{\out{
}} @@ -378,8 +381,8 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_bootstrap_data}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_bootstrap_data}{}}} \subsection{Method \code{get_bootstrap_data()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$get_bootstrap_data(df_raw, participants_in_bootstrap, modmat)}\if{html}{\out{
}} @@ -387,26 +390,26 @@ The object builds the ALASCA model and contains the data } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-new}{}}} -\subsection{Method \code{new()}}{ +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-predict_scores}{}}} +\subsection{Method \code{predict_scores()}}{ \subsection{Usage}{ -\if{html}{\out{
}}\preformatted{AlascaModel$new(df, formula, effects, ...)}\if{html}{\out{
}} +\if{html}{\out{
}}\preformatted{AlascaModel$predict_scores(data, effect_i = 1, component = 1)}\if{html}{\out{
}} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-finalize}{}}} -\subsection{Method \code{finalize()}}{ +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-new}{}}} +\subsection{Method \code{new()}}{ \subsection{Usage}{ -\if{html}{\out{
}}\preformatted{AlascaModel$finalize()}\if{html}{\out{
}} +\if{html}{\out{
}}\preformatted{AlascaModel$new(df, formula, effects, ...)}\if{html}{\out{
}} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-update}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-update}{}}} \subsection{Method \code{update()}}{ Update the current model (used for validation) \subsection{Usage}{ @@ -415,8 +418,8 @@ Update the current model (used for validation) } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-log}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-log}{}}} \subsection{Method \code{log()}}{ Function for logging messages using the log4r package \subsection{Usage}{ @@ -434,8 +437,8 @@ Function for logging messages using the log4r package } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-plot}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-plot}{}}} \subsection{Method \code{plot()}}{ Main function for plots \subsection{Usage}{ @@ -453,18 +456,19 @@ Main function for plots } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_residuals}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_residuals}{}}} \subsection{Method \code{get_residuals()}}{ Resample participants for validation +TODO: There is a bug when the order of the terms in \code{self$effect_list$expr} differs from \code{t1:t2:t3} in a three-way interaction \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$get_residuals(variable = NULL)}\if{html}{\out{
}} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-set_effect_terms}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-set_effect_terms}{}}} \subsection{Method \code{set_effect_terms()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$set_effect_terms()}\if{html}{\out{
}} @@ -472,8 +476,8 @@ Resample participants for validation } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-set_design_matrices}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-set_design_matrices}{}}} \subsection{Method \code{set_design_matrices()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$set_design_matrices()}\if{html}{\out{
}} @@ -481,8 +485,8 @@ Resample participants for validation } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-flip}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-flip}{}}} \subsection{Method \code{flip()}}{ Switch the sign of scores and loadings \subsection{Usage}{ @@ -500,8 +504,8 @@ Switch the sign of scores and loadings } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_ref}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_ref}{}}} \subsection{Method \code{get_ref()}}{ Returns the reference level of a given column \subsection{Usage}{ @@ -520,8 +524,8 @@ The reference level } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_levels}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_levels}{}}} \subsection{Method \code{get_levels()}}{ Returns all the levels of a given column \subsection{Usage}{ @@ -542,8 +546,8 @@ A vector with factor levels } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_PCs}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_PCs}{}}} \subsection{Method \code{get_PCs()}}{ Returns the most interesting principal components (i.e., components explaining more than a given limit of variance: \code{explanatory_limit}) \subsection{Usage}{ @@ -562,8 +566,8 @@ A vector with principal components } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_predictions}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_predictions}{}}} \subsection{Method \code{get_predictions()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$get_predictions()}\if{html}{\out{
}} @@ -571,8 +575,8 @@ A vector with principal components } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_scores}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_scores}{}}} \subsection{Method \code{get_scores()}}{ Return scores \subsection{Usage}{ @@ -590,8 +594,8 @@ Return scores } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_loadings}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_loadings}{}}} \subsection{Method \code{get_loadings()}}{ Return loadings \subsection{Usage}{ @@ -611,8 +615,8 @@ Return loadings } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_covars}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-get_covars}{}}} \subsection{Method \code{get_covars()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaModel$get_covars(n_limit = 0)}\if{html}{\out{
}} @@ -627,8 +631,8 @@ Return loadings } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-print_version}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-print_version}{}}} \subsection{Method \code{print_version()}}{ Print ALASCA version \subsection{Usage}{ @@ -640,8 +644,8 @@ String with version number and date of latest update } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-save_validation}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-save_validation}{}}} \subsection{Method \code{save_validation()}}{ Write scores, loadings, covars and predictions from validation run to database and remove data from memory \subsection{Usage}{ @@ -657,8 +661,8 @@ Write scores, loadings, covars and predictions from validation run to database a } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-save_to_csv}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-save_to_csv}{}}} \subsection{Method \code{save_to_csv()}}{ Save scores, loading, covars, and predictions to csv files \subsection{Usage}{ @@ -667,8 +671,8 @@ Save scores, loading, covars, and predictions to csv files } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-save_model}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-save_model}{}}} \subsection{Method \code{save_model()}}{ Save model to RDS and scores, loading, covars, and predictions to csv files \subsection{Usage}{ @@ -677,8 +681,8 @@ Save model to RDS and scores, loading, covars, and predictions to csv files } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-rotate_matrix_optimize_score}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-rotate_matrix_optimize_score}{}}} \subsection{Method \code{rotate_matrix_optimize_score()}}{ Rotate model loadings and scores with procrustes. This function checks all combinations of signs to minimize variation \subsection{Usage}{ @@ -694,8 +698,25 @@ Rotate model loadings and scores with procrustes. This function checks all combi } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-rotate_matrix}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-optimize_components}{}}} +\subsection{Method \code{optimize_components()}}{ +Check if components have to be re-ordered to better match the target +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{AlascaModel$optimize_components(target)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{target}}{Compare components of the model (\code{self}) with this as target} +} +\if{html}{\out{
}} +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-rotate_matrix}{}}} \subsection{Method \code{rotate_matrix()}}{ Rotate model loadings and scores with procrustes \subsection{Usage}{ @@ -711,8 +732,8 @@ Rotate model loadings and scores with procrustes } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-clone}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaModel-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{ diff --git a/man/AlascaPlot.Rd b/man/AlascaPlot.Rd index e547fab..805f36f 100644 --- a/man/AlascaPlot.Rd +++ b/man/AlascaPlot.Rd @@ -25,6 +25,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume \item{\code{n_bins}}{Number of bins for histograms} +\item{\code{sort_loadings}}{String: loading, alpha, vector} + \item{\code{ribbon}}{Boolean. Plot ribbons for uncertainties} \item{\code{bw}}{Boolean. Plot in gray scale} @@ -47,7 +49,7 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume \item{\code{sort_by_loading_group}}{Boolean. Sort loadings within loading group} -\item{\code{palette_end}}{Improve contrast by not using the full color space. See \code{\link[scales:viridis_pal]{scales::viridis_pal()}}} +\item{\code{palette_end}}{Improve contrast by not using the full color space. See \code{\link[scales:pal_viridis]{scales::viridis_pal()}}} \item{\code{effect_i}}{Effect(s) to plot} @@ -72,42 +74,42 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume \section{Methods}{ \subsection{Public methods}{ \itemize{ -\item \href{#method-plot_prediction}{\code{AlascaPlot$plot_prediction()}} -\item \href{#method-plot_effect}{\code{AlascaPlot$plot_effect()}} -\item \href{#method-plot_effect_score}{\code{AlascaPlot$plot_effect_score()}} -\item \href{#method-plot_effect_loading}{\code{AlascaPlot$plot_effect_loading()}} -\item \href{#method-plot_effect_validation}{\code{AlascaPlot$plot_effect_validation()}} -\item \href{#method-plot_effect_validation_score}{\code{AlascaPlot$plot_effect_validation_score()}} -\item \href{#method-plot_effect_validation_loading}{\code{AlascaPlot$plot_effect_validation_loading()}} -\item \href{#method-plot_2D_advanced}{\code{AlascaPlot$plot_2D_advanced()}} -\item \href{#method-plot_2D}{\code{AlascaPlot$plot_2D()}} -\item \href{#method-plot_2D_score}{\code{AlascaPlot$plot_2D_score()}} -\item \href{#method-plot_2D_loading_1}{\code{AlascaPlot$plot_2D_loading_1()}} -\item \href{#method-plot_2D_loading_2}{\code{AlascaPlot$plot_2D_loading_2()}} -\item \href{#method-plot_histogram_score}{\code{AlascaPlot$plot_histogram_score()}} -\item \href{#method-plot_histogram_loading}{\code{AlascaPlot$plot_histogram_loading()}} -\item \href{#method-plot_histogram}{\code{AlascaPlot$plot_histogram()}} -\item \href{#method-plot_participants}{\code{AlascaPlot$plot_participants()}} -\item \href{#method-new}{\code{AlascaPlot$new()}} -\item \href{#method-call_plot}{\code{AlascaPlot$call_plot()}} -\item \href{#method-plot_scree}{\code{AlascaPlot$plot_scree()}} -\item \href{#method-plot_residuals}{\code{AlascaPlot$plot_residuals()}} -\item \href{#method-plot_covars}{\code{AlascaPlot$plot_covars()}} -\item \href{#method-capitalize}{\code{AlascaPlot$capitalize()}} -\item \href{#method-prettify_covar}{\code{AlascaPlot$prettify_covar()}} -\item \href{#method-get_plot_linetypes}{\code{AlascaPlot$get_plot_linetypes()}} -\item \href{#method-get_plot_shapes}{\code{AlascaPlot$get_plot_shapes()}} -\item \href{#method-get_plot_palette}{\code{AlascaPlot$get_plot_palette()}} -\item \href{#method-get_explained_label}{\code{AlascaPlot$get_explained_label()}} -\item \href{#method-get_levels}{\code{AlascaPlot$get_levels()}} -\item \href{#method-get_ref}{\code{AlascaPlot$get_ref()}} -\item \href{#method-xflip}{\code{AlascaPlot$xflip()}} -\item \href{#method-clone}{\code{AlascaPlot$clone()}} +\item \href{#method-AlascaPlot-plot_prediction}{\code{AlascaPlot$plot_prediction()}} +\item \href{#method-AlascaPlot-plot_effect}{\code{AlascaPlot$plot_effect()}} +\item \href{#method-AlascaPlot-plot_effect_score}{\code{AlascaPlot$plot_effect_score()}} +\item \href{#method-AlascaPlot-plot_effect_loading}{\code{AlascaPlot$plot_effect_loading()}} +\item \href{#method-AlascaPlot-plot_effect_validation}{\code{AlascaPlot$plot_effect_validation()}} +\item \href{#method-AlascaPlot-plot_effect_validation_score}{\code{AlascaPlot$plot_effect_validation_score()}} +\item \href{#method-AlascaPlot-plot_effect_validation_loading}{\code{AlascaPlot$plot_effect_validation_loading()}} +\item \href{#method-AlascaPlot-plot_2D_advanced}{\code{AlascaPlot$plot_2D_advanced()}} +\item \href{#method-AlascaPlot-plot_2D}{\code{AlascaPlot$plot_2D()}} +\item \href{#method-AlascaPlot-plot_2D_score}{\code{AlascaPlot$plot_2D_score()}} +\item \href{#method-AlascaPlot-plot_2D_loading_1}{\code{AlascaPlot$plot_2D_loading_1()}} +\item \href{#method-AlascaPlot-plot_2D_loading_2}{\code{AlascaPlot$plot_2D_loading_2()}} +\item \href{#method-AlascaPlot-plot_histogram_score}{\code{AlascaPlot$plot_histogram_score()}} +\item \href{#method-AlascaPlot-plot_histogram_loading}{\code{AlascaPlot$plot_histogram_loading()}} +\item \href{#method-AlascaPlot-plot_histogram}{\code{AlascaPlot$plot_histogram()}} +\item \href{#method-AlascaPlot-plot_participants}{\code{AlascaPlot$plot_participants()}} +\item \href{#method-AlascaPlot-new}{\code{AlascaPlot$new()}} +\item \href{#method-AlascaPlot-call_plot}{\code{AlascaPlot$call_plot()}} +\item \href{#method-AlascaPlot-plot_scree}{\code{AlascaPlot$plot_scree()}} +\item \href{#method-AlascaPlot-plot_residuals}{\code{AlascaPlot$plot_residuals()}} +\item \href{#method-AlascaPlot-plot_covars}{\code{AlascaPlot$plot_covars()}} +\item \href{#method-AlascaPlot-capitalize}{\code{AlascaPlot$capitalize()}} +\item \href{#method-AlascaPlot-prettify_covar}{\code{AlascaPlot$prettify_covar()}} +\item \href{#method-AlascaPlot-get_plot_linetypes}{\code{AlascaPlot$get_plot_linetypes()}} +\item \href{#method-AlascaPlot-get_plot_shapes}{\code{AlascaPlot$get_plot_shapes()}} +\item \href{#method-AlascaPlot-get_plot_palette}{\code{AlascaPlot$get_plot_palette()}} +\item \href{#method-AlascaPlot-get_explained_label}{\code{AlascaPlot$get_explained_label()}} +\item \href{#method-AlascaPlot-get_levels}{\code{AlascaPlot$get_levels()}} +\item \href{#method-AlascaPlot-get_ref}{\code{AlascaPlot$get_ref()}} +\item \href{#method-AlascaPlot-xflip}{\code{AlascaPlot$xflip()}} +\item \href{#method-AlascaPlot-clone}{\code{AlascaPlot$clone()}} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-plot_prediction}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-plot_prediction}{}}} \subsection{Method \code{plot_prediction()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$plot_prediction()}\if{html}{\out{
}} @@ -115,8 +117,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-plot_effect}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-plot_effect}{}}} \subsection{Method \code{plot_effect()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$plot_effect()}\if{html}{\out{
}} @@ -124,8 +126,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-plot_effect_score}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-plot_effect_score}{}}} \subsection{Method \code{plot_effect_score()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$plot_effect_score(effect_i = 1, component = 1)}\if{html}{\out{
}} @@ -133,8 +135,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-plot_effect_loading}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-plot_effect_loading}{}}} \subsection{Method \code{plot_effect_loading()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$plot_effect_loading(effect_i = 1, component = 1)}\if{html}{\out{
}} @@ -142,8 +144,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-plot_effect_validation}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-plot_effect_validation}{}}} \subsection{Method \code{plot_effect_validation()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$plot_effect_validation()}\if{html}{\out{
}} @@ -151,8 +153,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-plot_effect_validation_score}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-plot_effect_validation_score}{}}} \subsection{Method \code{plot_effect_validation_score()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$plot_effect_validation_score(effect_i = 1, component = 1)}\if{html}{\out{
}} @@ -160,8 +162,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-plot_effect_validation_loading}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-plot_effect_validation_loading}{}}} \subsection{Method \code{plot_effect_validation_loading()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$plot_effect_validation_loading(effect_i = 1, component = 1)}\if{html}{\out{
}} @@ -169,8 +171,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-plot_2D_advanced}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-plot_2D_advanced}{}}} \subsection{Method \code{plot_2D_advanced()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$plot_2D_advanced()}\if{html}{\out{
}} @@ -178,8 +180,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-plot_2D}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-plot_2D}{}}} \subsection{Method \code{plot_2D()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$plot_2D()}\if{html}{\out{
}} @@ -187,8 +189,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-plot_2D_score}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-plot_2D_score}{}}} \subsection{Method \code{plot_2D_score()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$plot_2D_score()}\if{html}{\out{
}} @@ -196,8 +198,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-plot_2D_loading_1}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-plot_2D_loading_1}{}}} \subsection{Method \code{plot_2D_loading_1()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$plot_2D_loading_1()}\if{html}{\out{
}} @@ -205,8 +207,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-plot_2D_loading_2}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-plot_2D_loading_2}{}}} \subsection{Method \code{plot_2D_loading_2()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$plot_2D_loading_2()}\if{html}{\out{
}} @@ -214,8 +216,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-plot_histogram_score}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-plot_histogram_score}{}}} \subsection{Method \code{plot_histogram_score()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$plot_histogram_score()}\if{html}{\out{
}} @@ -223,8 +225,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-plot_histogram_loading}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-plot_histogram_loading}{}}} \subsection{Method \code{plot_histogram_loading()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$plot_histogram_loading()}\if{html}{\out{
}} @@ -232,8 +234,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-plot_histogram}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-plot_histogram}{}}} \subsection{Method \code{plot_histogram()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$plot_histogram()}\if{html}{\out{
}} @@ -241,8 +243,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-plot_participants}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-plot_participants}{}}} \subsection{Method \code{plot_participants()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$plot_participants(effect_i = 1, component = 1)}\if{html}{\out{
}} @@ -250,8 +252,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-new}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-new}{}}} \subsection{Method \code{new()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$new(model)}\if{html}{\out{
}} @@ -259,8 +261,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-call_plot}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-call_plot}{}}} \subsection{Method \code{call_plot()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$call_plot(...)}\if{html}{\out{
}} @@ -268,8 +270,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-plot_scree}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-plot_scree}{}}} \subsection{Method \code{plot_scree()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$plot_scree()}\if{html}{\out{
}} @@ -277,8 +279,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-plot_residuals}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-plot_residuals}{}}} \subsection{Method \code{plot_residuals()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$plot_residuals()}\if{html}{\out{
}} @@ -286,8 +288,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-plot_covars}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-plot_covars}{}}} \subsection{Method \code{plot_covars()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$plot_covars()}\if{html}{\out{
}} @@ -295,8 +297,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-capitalize}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-capitalize}{}}} \subsection{Method \code{capitalize()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$capitalize(txt)}\if{html}{\out{
}} @@ -304,8 +306,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-prettify_covar}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-prettify_covar}{}}} \subsection{Method \code{prettify_covar()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$prettify_covar(effect, txt)}\if{html}{\out{
}} @@ -313,8 +315,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_plot_linetypes}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-get_plot_linetypes}{}}} \subsection{Method \code{get_plot_linetypes()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$get_plot_linetypes()}\if{html}{\out{
}} @@ -322,8 +324,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_plot_shapes}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-get_plot_shapes}{}}} \subsection{Method \code{get_plot_shapes()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$get_plot_shapes()}\if{html}{\out{
}} @@ -331,8 +333,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_plot_palette}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-get_plot_palette}{}}} \subsection{Method \code{get_plot_palette()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$get_plot_palette()}\if{html}{\out{
}} @@ -340,8 +342,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_explained_label}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-get_explained_label}{}}} \subsection{Method \code{get_explained_label()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$get_explained_label(effect_i = 1, component = 1, type = "Score")}\if{html}{\out{
}} @@ -349,8 +351,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_levels}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-get_levels}{}}} \subsection{Method \code{get_levels()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$get_levels(x)}\if{html}{\out{
}} @@ -358,8 +360,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-get_ref}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-get_ref}{}}} \subsection{Method \code{get_ref()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$get_ref(x)}\if{html}{\out{
}} @@ -367,8 +369,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-xflip}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-xflip}{}}} \subsection{Method \code{xflip()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{AlascaPlot$xflip(flip = TRUE)}\if{html}{\out{
}} @@ -376,8 +378,8 @@ Note: The object is typically accessed by \code{plot(obj, ...)} where the argume } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-clone}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-AlascaPlot-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{ diff --git a/man/get_regression_predictions.Rd b/man/get_regression_predictions.Rd index 21ad277..2879721 100644 --- a/man/get_regression_predictions.Rd +++ b/man/get_regression_predictions.Rd @@ -13,5 +13,5 @@ get_regression_predictions() An ALASCA object } \description{ -This function calcuates predictions from each regression model +This function calculates predictions from each regression model } diff --git a/man/predict_scores.Rd b/man/predict_scores.Rd new file mode 100644 index 0000000..f4b19ff --- /dev/null +++ b/man/predict_scores.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/ALASCA.R +\name{predict_scores} +\alias{predict_scores} +\title{Calculate scores for a new data set} +\usage{ +predict_scores(data, effect_i = 1, component = 1) +} +\arguments{ +\item{data}{A new data set} + +\item{effect_i}{The effect to look at} + +\item{component}{The PCA components to look at} +} +\value{ +A data table with new scores +} +\description{ +Calculate scores for a new data set +}