In shirewoman2/Consultancy: Standardized tools for using R within the Simcyp Consultancy Team

knitr::opts_chunk$set(echo = FALSE, message = FALSE, warning = FALSE, 
                      dpi = 600, 
                      fig.width = 6, 
                      fig.height = 5)

# Name of subfolder: pksummarymult

Observedincluded <- any(str_detect(MyPKResults$Statistic, "S/O"))
MeanType <- ifelse(is.na(mean_type), "geometric", mean_type)

if(FromCalcPKRatios){

   highlight_so_cutoffs = NA
   highlight_so_colors = "yellow to red"

   if(paired){
      OptionalSection <- knitr::knit_child(
         system.file("rmarkdown/templates/pairedci/skeleton/skeleton.Rmd",
                     package="SimcypConsultancy"), 
         envir = environment(), 
         quiet = TRUE)

      cat(OptionalSection, sep = "\n")

   } else {
      OptionalSection <- knitr::knit_child(
         system.file("rmarkdown/templates/unpairedci/skeleton/skeleton.Rmd",
                     package="SimcypConsultancy"), 
         envir = environment(), 
         quiet = TRUE)

      cat(OptionalSection, sep = "\n")

   }

   # calc_PK_ratios only has a single tissue option for now, so need to set
   # tissues to tissue. Same w/compounds. 
   tissues <- tissue
   compoundsToExtract <- compoundToExtract
   PKpulled <- expand_grid(PKpulled = PKToPull, 
                           File = MyPKResults$File, 
                           Tissue = unique(MyPKResults$Tissue), 
                           CompoundID = compoundToExtract)

} 

if(single_table){

   CapText1 <- ifelse(any(str_detect(names(MyPKResults), "tmax")), 
                      paste("the", MeanType, "means, except for t~max~, which is median, minimum, and maximum"),
                      paste("the", MeanType, "means"))

   CapText2a <- paste0(ifelse(any(str_detect(MyPKResults$Statistic, "CV")),
                              "CV: coefficient of variation; ", ""), 
                       ifelse(any(str_detect(MyPKResults$Statistic, " CI")),
                              "CI: confidence interval; ", ""))

   CapText2 <- paste0(sub("; $", ".", CapText2a), 
                      ifelse(Observedincluded, 
                             " S/O: simulated/observed; source observed data: Clinical Study XXX; ",
                             ""))

   AllFiles <- switch(
      as.character(exists("sim_data_file_pairs", inherits = FALSE)), 
      "TRUE" = # from calc_PK_ratios_mult
         str_comma(unique(unlist(str_split(MyPKResults$File, " / ")))),

      "FALSE" = # from pk_table
         str_comma(basename(unique(MyPKResults$File))))

   Annotations <- list(
      "table_heading" = paste0("***Table XXX.*** *Simulated ", 
                              ifelse(Observedincluded, "and observed ", ""), 
                              MeanType, " mean ", str_comma(tissues),
                              " PK parameters.*"),
      "table_caption" = paste0("*Simulated values listed are ",
                              CapText1, ". ", CapText2, 
                              " Source simulated data: ", AllFiles, "*"))
} else {
   Annotations <- list("table_heading" = "", 
                       "table_caption" = "")
}

r Annotations[["table_heading"]]

if("File" %in% names(MyPKResults)){
   MyPKResults <- MyPKResults %>% 
      relocate(File, .after = last_col())
}

if(single_table){

   # If they only wanted 1 tissue, don't include a column for that in the table.
   # It'll be listed in the text and takes up room needlessly.
   if(length(tissues) == 1){
      MyPKResults <- MyPKResults %>% 
         select(-any_of("Tissue"))
   }

   # Similarly, if they only wanted 1 compoundID, don't include a column for that
   # in the table.
   if(length(compoundsToExtract) == 1){
      MyPKResults <- MyPKResults %>% 
         select(-any_of("CompoundID"))
   }

   include_dose_num <- check_include_dose_num(MyPKResults, 
                                              include_dose_num)

   if(include_dose_num == FALSE){
      names(MyPKResults) <- sub("Dose 1 |Last dose ", "", names(MyPKResults))
   }

   formatTable_Simcyp(MyPKResults,
                      shading_column = File, 
                      merge_shaded_cells = TRUE, 
                      fontsize = fontsize,
                      prettify_columns = prettify_columns, 
                      add_header_for_DDI = add_header_for_DDI, 
                      highlight_gmr_colors = highlight_gmr_colors, 
                      highlight_so_cutoffs = highlight_so_cutoffs, 
                      highlight_so_colors = highlight_so_colors)
}

if(single_table == FALSE){

   MyPKResults <- 
      split(MyPKResults, f = list(MyPKResults$File, 
                                  MyPKResults$CompoundID, 
                                  MyPKResults$Tissue))
   PKpulled <- 
      split(PKpulled, f = list(PKpulled$File, 
                               PKpulled$CompoundID, 
                               PKpulled$Tissue))

   MyPKResults <- MyPKResults[which(lapply(MyPKResults, nrow) > 0)]

   for(i in names(MyPKResults)){
      # assign("ITERATION_STEP", value = i, envir = global_env())

      TableSettings <- c(Tissue = length(tissues) > 1, 
                         CompoundID = length(compoundsToExtract) > 1, 
                         File = TRUE)
      TableSettings <- str_c(names(TableSettings)[TableSettings == TRUE], 
                             collapse = " ")

      Heading <- switch(TableSettings, 
                        "Tissue CompoundID File" = paste0(
                           str_to_title(unique(MyPKResults[[i]]$Tissue)), 
                           " PK for the ", 
                           unique(MyPKResults[[i]]$CompoundID), 
                           " for the file '", 
                           unique(MyPKResults[[i]]$File), "'"), 

                        "CompoundID File" = paste0(
                           "PK for the ", 
                           unique(MyPKResults[[i]]$CompoundID), 
                           " for the file '", 
                           unique(MyPKResults[[i]]$File), "'"), 

                        "Tissue File" = paste0(
                           str_to_title(unique(MyPKResults[[i]]$Tissue)), 
                           " PK for the file '", 
                           unique(MyPKResults[[i]]$File), "'"), 

                        "File" = paste0(
                           "PK for the file '", 
                           unique(MyPKResults[[i]]$File), "'"))

      Heading <- ifelse(FromCalcPKRatios, 
                        sub("for the file", "for the file pair", Heading), 
                        Heading)

      TableSection <- knitr::knit_child(
         system.file("rmarkdown/templates/pktablesection/skeleton/skeleton.Rmd",
                     package="SimcypConsultancy"), 
         envir = environment(), 
         quiet = TRUE)

      cat(TableSection, sep = "\n")

      rm(Heading, Deets, MyPerpetrator, MyFiles, MyAnnotations, PKpulled_i)

   }

   MyPKResults <- bind_rows(MyPKResults)

}

r Annotations[["table_caption"]]

if(any(complete.cases(highlight_gmr_colors))){
   TableKeyText_gmr <- "**Key for color-coded GMR values:**"
} else {
   TableKeyText_gmr <- ""
}

r TableKeyText_gmr

if(any(complete.cases(highlight_gmr_colors))){

   highlight_gmr_colors <- set_boundary_colors(color_set = highlight_gmr_colors, 
                       boundaries = c(1, 1.25, 2, 5), 
                       break_type = "GMR")

   tibble(`Interaction level` = names(highlight_gmr_colors)) %>% 
      flextable::flextable() %>% 
      flextable::bold(part = "header") %>% 
      flextable::bg(i = 1, 
                    bg = highlight_gmr_colors["negligible"]) %>% 
      flextable::bg(i = 2, 
                    bg = highlight_gmr_colors["weak"]) %>% 
      flextable::bg(i = 3, 
                    bg = highlight_gmr_colors["moderate"]) %>% 
      flextable::bg(i = 4, 
                    bg = highlight_gmr_colors["strong"]) %>% 
      flextable::width(width = 1.5) %>% 
      flextable::align(align = "center", part = "all")

} 

if(any(complete.cases(highlight_so_cutoffs))){
   TableKeyText_so <- "**Key for color-coded S/O values:**"
} else {
   TableKeyText_so <- ""
}

r TableKeyText_so

if(any(complete.cases(highlight_so_cutoffs))){

   highlight_so_colors <- set_boundary_colors(color_set = highlight_so_colors, 
                                              boundaries = highlight_so_cutoffs, 
                                              break_type = "SO")

   SOkey <- data.frame(UpperA = highlight_so_cutoffs[1:(length(highlight_so_cutoffs)-1)], 
                       UpperB = highlight_so_cutoffs[2:(length(highlight_so_cutoffs))], 
                       LowerA = 1/highlight_so_cutoffs[2:(length(highlight_so_cutoffs))], 
                       LowerB = 1/highlight_so_cutoffs[1:(length(highlight_so_cutoffs)-1)]) %>% 
      bind_rows(data.frame(UpperA = NA, 
                           UpperB = highlight_so_cutoffs[length(highlight_so_cutoffs)], 
                           LowerA = NA, 
                           LowerB = 1/highlight_so_cutoffs[length(highlight_so_cutoffs)])) %>% 
      mutate(across(.fns = round_consultancy), 
             Text = paste(LowerA, "to", LowerB, "fold or", UpperA, "to", UpperB, "fold"))

   SOkey$Text[1] <- paste(SOkey$LowerA[1], "to", SOkey$UpperB[1], "fold")
   SOkey$Text[nrow(SOkey)] <- paste("<", SOkey$LowerB[nrow(SOkey)], 
                                    "fold or >", SOkey$UpperB[nrow(SOkey)], "fold")

   SOkey <- SOkey %>% select(Text) %>% 
      rename(`S/O cutoff` = Text) %>% 
      flextable::flextable() %>% 
      flextable::bold(part = "header") %>% 
      flextable::width(width = 3.5) %>% 
      flextable::align(align = "center", part = "all")

   for(i in 1:length(highlight_so_cutoffs)){
      SOkey <- SOkey %>% 
         flextable::bg(i = i, 
                       bg = highlight_so_colors[i])
   }

   SOkey 


} 

shirewoman2/Consultancy documentation built on Feb. 18, 2025, 10 p.m.