Add RM-ANOVA

R/mod_tableGen_fct_methods.R

@@ -72,6 +72,8 @@ app_methods <- function(agg, column, week, group, data, totals, filter = NA) {
     app_freq(column, group, data, totals)
   } else if (agg == "ANOVA") {
     app_anova(column, week, group, data)
+  } else if (agg == "RM_ANOVA") {
+    app_rmanova(column, week, group, data)
   } else if (agg == "NESTED_FREQ_DSC"){
     app_nested_freq(column, week, group, data, totals, sort = "desc_tot")
   } else if (agg == "NESTED_FREQ_ABC"){

R/mod_tableGen_fct_rmanova.R

@@ -0,0 +1,168 @@
+#' Generate RM-ANOVA using table generator blocks
+#'
+#' @param column the variable to perform RM-ANOVA on,
+#' this also contains the class of the column
+#' based on the data file the column came from
+#' @param week filter the variable by certain week
+#' @param group the groups to compare for the RM-ANOVA
+#' @param data the data to use 
+#'
+#' @return an RM-ANOVA table of grouped variables
+#' @family tableGen Functions
+#' @keywords tabGen
+#' 
+#' @noRd
+app_rmanova <- function(column, week, group, data) {
+  UseMethod("app_rmanova", column)
+}
+
+
+#' @return NULL
+#' @rdname app_rmanova
+#' @family tableGen Functions
+#' @noRd
+
+app_rmanova.default <- function(column, week, group, data) {
+  rlang::abort(glue::glue(
+    "Can't calculate mean because data is not classified as ADLB, BDS or OCCDS",
+  ))
+}
+
+#' if ADSL supplied look for the column to take mean of
+#' and look for a grouping variable to group_by
+#' 
+#' @importFrom rlang sym !! 
+#' @import dplyr
+#' @return an RM-ANOVA table of grouped variables
+#' @rdname app_rmanova
+#' @family tableGen Functions
+#' 
+#' @noRd
+
+app_rmanova.ADAE <- app_rmanova.ADSL <- function(column, week, group = NULL, data) {
+
+  column <- as.character(column)
+
+  if (!is.numeric(data[[column]])) {
+    stop(paste("Can't calculate RM-ANOVA, ", column, " is not numeric"))
+  }
+
+  if (is.null(group)) {
+
+    stop(paste("Can't calculate RM-ANOVA without grouping data"))
+
+  } else {
+    group <- rlang::sym(group)
+    column <- rlang::sym(column)
+
+    all_dat <- data %>% dplyr::distinct(!!column, !!group, USUBJID)
+
+    ttest <- summary(aov(all_dat[[paste(column)]] ~ all_dat[[paste(group)]] + Error(factor(USUBJID)), data=all_dat))[[1]][[1]] %>%
+      tidyr::as_tibble()
+
+    group_n <- length(unique(all_dat[[paste(group)]])) + 2
+
+    anova_df <- data.frame(matrix(NA, ncol=group_n, nrow=4))
+
+    anova_df[1,1] <- "p-value"
+    anova_df[2,1] <- "Test Statistic"
+    anova_df[3,1] <- "Mean Sum of Squares"
+    anova_df[4,1] <- "Sum of Squares"
+    anova_df[1, group_n] <- round(ttest$`Pr(>F)`[1], 3)
+    anova_df[2, group_n] <- round(ttest$`F value`[1], 2)
+    anova_df[3, group_n] <- round(ttest$`Mean Sq`[1], 2)
+    anova_df[4, group_n] <- round(ttest$`Sum Sq`[1], 2)
+
+    anova_df <- dplyr::mutate_all(anova_df, as.character) %>%
+      dplyr::mutate_all(dplyr::coalesce, "")
+
+    anova_df
+  }
+
+
+}
+
+
+#' if BDS filter by paramcd and week
+#' We need to calculate the difference in N for this
+#' and report missing values from the mean if any
+#' 
+#' @importFrom rlang sym !!
+#' @import dplyr
+#' @return an ANOVA table of grouped variables
+#' @rdname app_rmanova
+#' @family tableGen Functions
+#' 
+#' @noRd
+
+app_rmanova.BDS <- function(column, week, group = NULL, data) {
+
+  column <- as.character(column)
+
+  if (!column %in% data[["PARAMCD"]]) {
+    stop(paste("Can't calculate RM-ANOVA, ", column, " has no AVAL"))
+  }
+
+  if (week == "NONE") {
+    stop(paste("Select week from dropdown to calculate RM-ANOVA"))
+  }
+
+
+  if (is.null(group)) {
+    stop(paste("Can't calculate RM-ANOVA without grouping data"))
+  } else {
+    group <- sym(group)
+
+    all_dat <- data %>%  filter(PARAMCD == column & AVISIT == week)
+
+    if (length(unique(all_dat[[paste(group)]])) == 1) stop(glue::glue("Only one {group} in data selected, choose another week for RM-ANOVA"))
+
+    ttest <- summary(aov(all_dat$AVAL ~ all_dat[[paste(group)]] + Error(factor(USUBJID)), data=all_dat))[[1]][[1]] %>%
+      tidyr::as_tibble()
+
+    group_n <- length(unique(all_dat[[paste(group)]])) + 2
+
+    anova_df <- data.frame(matrix(NA, ncol=group_n, nrow=4))
+    anova_df[1,1] <- "p-value"
+    anova_df[2,1] <- "Test Statistic"
+    anova_df[3,1] <- "Mean Sum of Squares"
+    anova_df[4,1] <- "Sum of Squares"
+    anova_df[1, group_n] <- round(ttest$`Pr(>F)`[1], 3)
+    anova_df[2, group_n] <- round(ttest$`F value`[1], 2)
+    anova_df[3, group_n] <- round(ttest$`Mean Sq`[1], 2)
+    anova_df[4, group_n] <- round(ttest$`Sum Sq`[1], 2)
+
+    anova_df <- dplyr::mutate_all(anova_df, as.character) %>%
+      dplyr::mutate_all(dplyr::coalesce, "")
+    anova_df
+  }
+
+}
+
+#' @return NULL
+#' @rdname app_rmanova
+#' @family tableGen Functions
+#' 
+#' @noRd
+
+app_rmanova.OCCDS <- function(column, week = NULL, group = NULL, data) {
+  rlang::abort(glue::glue(
+    "Currently no method to perform RM-ANOVA on OCCDS"
+  ))
+}
+
+
+
+
+
+#' @return NULL
+#' @rdname app_rmanova
+#' @family tableGen Functions
+#' 
+#' @noRd
+
+app_rmanova.custom <- function(column, week = NULL, group = NULL, data) {
+  rlang::abort(glue::glue(
+    "Can't calculate RM-ANOVA, data is not classified as ADLB, BDS or OCCDS"
+  ))
+}

R/mod_tableGen_ui.R

@@ -77,6 +77,10 @@ mod_tableGen_ui <- function(id){
                                    class = "ui-state-default agg", id = "anova",
                                    div(tippy(div("ANOVA"), "ANOVA"))
                                  ),
+                                 tags$li(
+                                   class = "ui-state-default agg", id = "rm_anova",
+                                   div(tippy(div("RM-ANOVA"), "Repeated Measures ANOVA"))
+                                 ),
                                  tags$li(
                                    class = "ui-state-default agg", id = "chg",
                                    div(tippy(div("CHG"), "Change from Baseline"))

data-raw/internal-data.R

@@ -1,7 +1,8 @@
 pretty_blocks <- tidyr::tibble(
-  Pattern = c("MEAN", "FREQ", "CHG", "Y_FREQ", "MAX_FREQ", "NON_MISSING",
+  Pattern = c("RM_ANOVA", "MEAN", "FREQ", "CHG", "Y_FREQ", "MAX_FREQ", "NON_MISSING",
               "NESTED_FREQ_DSC", "NESTED_FREQ_ABC"),
-  Replacement = c("Descriptive Statistics", 
+  Replacement = c("Repeated Measures ANOVA",
+                  "Descriptive Statistics", 
                   "Summary Counts", 
                   "Descriptive Statistics of Change from Baseline",
                   "Subject Count for those with 'Y' values",

inst/app/www/js/script.js

@@ -167,8 +167,10 @@ $(function() {
       var draggableId = ui.draggable.attr("id");
       var newid = getNewId(draggableId);
       if (weeks_array) {
-        if (draggableId.includes("anova")) {
+        if (draggableId === "anova") {
           $(this).append(selectBlock(newid, "ANOVA", week_opts));
+        } else if (draggableId === "rm_anova") {
+          $(this).append(selectBlock(newid, "RM_ANOVA", week_opts));
         } else if (draggableId.includes("chg")) {
           $(this).append(selectBlock(newid, "CHG", week_opts));
         } else if (draggableId.includes("mean")) {