Add "start" and "end" to group_vars.PKNCAresults

R/class-PKNCAresults.R

@@ -138,5 +138,5 @@ getGroups.PKNCAresults <- function(object,
 #'   from the PKNCAconc object within
 #' @exportS3Method dplyr::group_vars
 group_vars.PKNCAresults <- function(x) {
-  group_vars.PKNCAconc(as_PKNCAconc(x))
+  c("start","end",group_vars.PKNCAconc(as_PKNCAconc(x))) 
 }

R/class-summary_PKNCAresults.R

@@ -63,7 +63,8 @@ summary.PKNCAresults <- function(object, ...,
                                  summarize.n.per.group = deprecated(),
                                  not.requested.string = deprecated(),
                                  not.calculated.string = deprecated(),
-                                 pretty_names = NULL) {
+                                 pretty_names = NULL,
+                                 caption_prefix = NULL) {
   # Process inputs ####
 
   ## Deprecated inputs ####
@@ -183,7 +184,8 @@ summary.PKNCAresults <- function(object, ...,
       param_names = names(result_values),
       pretty_names = pretty_names,
       footnote_N = "N" %in% names(ret),
-      footnote_n = attr(ret, "footnote_n", exact = TRUE)
+      footnote_n = attr(ret, "footnote_n", exact = TRUE),
+      caption_prefix = caption_prefix
     )
   attr(ret, "footnote_n") <- NULL
   ret_pretty <- rename_summary_PKNCAresults(data = ret, unit_list = unit_list, pretty_names = pretty_names)
@@ -294,7 +296,7 @@ get_summary_PKNCAresults_count_N <- function(data, result_group, subject_col, su
 }
 
 # Provide a clean caption for summarized parameters
-get_summary_PKNCAresults_caption <- function(param_names, pretty_names, footnote_N, footnote_n) {
+get_summary_PKNCAresults_caption <- function(param_names, pretty_names, footnote_N, footnote_n, caption_prefix) {
   # Extract the summarization descriptions for the caption
   summary_descriptions <-
     unlist(
@@ -333,11 +335,17 @@ get_summary_PKNCAresults_caption <- function(param_names, pretty_names, footnote
   if (footnote_n) {
     ret <- c(ret, "n: number of measurements included in summary")
   }
-  paste(ret, collapse = "; ")
+  current_caption <- paste(ret, collapse = "; ")
+
+  if (is.null(caption_prefix)) {
+    current_caption
+  } else {
+    paste(caption_prefix, current_caption)
+  }
 }
 
 #' Clean up the exclusions in the object
-#'
+#' 
 #' @param object The PKNCAresults object to clean
 #' @returns The results data.frame with exclusions set to `NA`
 #' @noRd

tests/testthat/test-class-PKNCAresults.R

@@ -411,14 +411,14 @@ test_that("group_vars.PKNCAresult", {
   o_data_group <- PKNCAdata(o_conc_group, intervals = data.frame(start = 0, end = 1, cmax = TRUE))
   suppressMessages(o_nca_group <- pk.nca(o_data_group))
 
-  expect_equal(dplyr::group_vars(o_nca_group), "Subject")
+  expect_equal(dplyr::group_vars(o_nca_group), c("start", "end", "Subject"))
 
   # Check that it works without groupings as expected [empty]
   o_conc_nongroup <- PKNCAconc(as.data.frame(datasets::Theoph)[datasets::Theoph$Subject == 1,], conc~Time)
   o_data_nogroup <- PKNCAdata(o_conc_nongroup, intervals = data.frame(start = 0, end = 1, cmax = TRUE))
   suppressMessages(o_nca_nogroup <- pk.nca(o_data_nogroup))
 
-  expect_equal(dplyr::group_vars(o_nca_nogroup), character(0))
+  expect_equal(dplyr::group_vars(o_nca_nogroup), c("start","end"))
 })
 
 test_that("as.data.frame.PKNCAresults can filter for only requested parameters", {

tests/testthat/test-class-summary_PKNCAresults.R

@@ -307,6 +307,28 @@ test_that("print.summary_PKNCAresults works", {
   )
 })
 
+test_that("print.summary_PKNCAresults supports caption_prefix", {
+  tmpconc <- generate.conc(2, 1, 0:24)
+  tmpdose <- generate.dose(tmpconc)
+  myconc <- PKNCAconc(tmpconc, formula = conc ~ time | treatment + ID)
+  mydose <- PKNCAdose(tmpdose, formula = dose ~ time | treatment + ID)
+  mydata <- PKNCAdata(myconc, mydose)
+  myresult <- pk.nca(mydata)
+
+  expect_output(
+    print(summary(myresult, caption_prefix = "Summary:")),
+    paste(
+      " start end treatment N     auclast         cmax              tmax   half.life.*",
+      "     0  24     Trt 1 2 13.8 \\[2.51\\]            .                 .           ..*",
+      "     0 Inf     Trt 1 2           . 0.970 \\[4.29\\] 3.00 \\[2.00, 4.00\\] 14.2 \\[2.79\\].*",
+      "",
+      "Caption: Summary: auclast, cmax, aucinf.obs: geometric mean and geometric coefficient of variation; tmax: median and range; half.life: arithmetic mean and standard deviation",
+      sep = "\n"
+    )
+  )
+})
+
+
 test_that("summary pretty_name control", {
   tmpconc <- generate.conc(2, 1, 0:24)
   tmpdose <- generate.dose(tmpconc)