Plot fixes for censoring

nlmixr2 · Sep 21, 2022 · c819d63 · c819d63
1 parent cef4e2c
commit c819d63
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Showing 2 changed files with 10 additions and 10 deletions.
diff --git a/R/plot.nlmixr2.R b/R/plot.nlmixr2.R
@@ -1,6 +1,6 @@
 .setupPlotData <- function(data) {
   .dat <- as.data.frame(data)
-  .dat <- .dat[!is.na(.dat$RES),]
+  .dat <- .dat[!is.na(.dat$RES), ]
   .doCmt <- FALSE
   if (any(names(.dat) == "CMT")) {
     if (length(levels(.dat$CMT)) > 1) {
@@ -37,7 +37,7 @@
   if (any(names(.dat0) == "CENS")) {
     dataPlot <- data.frame(DV = .dat0$DV, CENS = .dat0$CENS, utils::stack(.dat0[, vars, drop = FALSE]))
     .aes <- ggplot2::aes(.data$values, .data$DV, color = .data$CENS)
-    if (length(levels(.data$CENS)) == 3) {
+    if (length(levels(.dat0$CENS)) == 3) {
       .color <- ggplot2::scale_color_manual(values = c("blue", "black", "red"))
     } else {
       .color <- ggplot2::scale_color_manual(values = c("black", "red"))

diff --git a/tests/testthat/test-plots-cens.R b/tests/testthat/test-plots-cens.R
@@ -1,26 +1,26 @@
 test_that("plot censoring", {
   skip_on_cran()
 
-  dat <- xgxr::case1_pkpd %>%
-    dplyr::rename(DV=LIDV) %>%
-    dplyr::filter(CMT %in% 1:2) %>%
+  dat <- xgxr::case1_pkpd |>
+    dplyr::rename(DV=LIDV) |>
+    dplyr::filter(CMT %in% 1:2) |>
     dplyr::filter(TRTACT != "Placebo")
 
   doses <- unique(dat$DOSE)
   nid <- 10 # 7 ids per dose group
   dat2 <- do.call("rbind",
                   lapply(doses, function(x) {
-                    ids <- dat %>%
-                      dplyr::filter(DOSE == x) %>%
-                      dplyr::summarize(ids=unique(ID)) %>%
+                    ids <- dat |>
+                      dplyr::filter(DOSE == x) |>
+                      dplyr::summarize(ids=unique(ID)) |>
                       dplyr::pull()
                     ids <- ids[seq(1, nid)]
-                    dat %>%
+                    dat |>
                       dplyr::filter(ID %in% ids)
                   }))
 
   ## Use 2 compartment model
-  cmt2 <- function(){
+  cmt2 <- function() {
     ini({
       lka <- log(0.1) # log Ka
       lv <- log(10) # Log Vc