R/make_example_PK_input.R

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

#' Examples for supplying PK parameters to the pk_table or calc_PK_ratios
#' functions for the argument \code{PKparameters}
#'
#' \code{make_example_PK_input} gives examples of how to request specific PK
#' parameters or supply specific PK data to the functions
#' \code{\link{pk_table}}, \code{\link{calc_PK_ratios}}, or
#' \code{\link{calc_PK_ratios_mult}}. You can either just get a printout in the
#' console of the examples or you can get an example csv file to use a as a
#' template.
#'
#'
#' @return saves a csv file of example PK parameters for supplying to the
#'   argument \code{PKparameters}
#' @export
#'
#' @examples
#' # None. This is an interactive function.
#'
#' 
make_example_PK_input <- function(){
   
   # Error catching ----------------------------------------------------------
   # Check whether tidyverse is loaded
   if("package:tidyverse" %in% search() == FALSE){
      stop("The SimcypConsultancy R package also requires the package tidyverse to be loaded, and it doesn't appear to be loaded yet. Please run `library(tidyverse)` and then try again.")
   }
   
   # Main body of function ---------------------------------------------------
   
   Opts_main <- c("1" = "typical dose 1", 
                  "2" = "typical last dose",
                  "3" = "typical DDI", 
                  "4" = "specifying the sheet to use", 
                  "5" = "specifying the compounds to use", 
                  "6" = "specifying the tissues to use", 
                  "7" = "all possible AUCs", 
                  "8" = "all possible clearance types", 
                  "9" = "comparing multiple simulations to the same observed PK", 
                  "10" = "including variability in observed PK")
   
   Opts_ratios <- c("1" = wrapn("everything is the same except the simulation files, e.g., you're comparing fasted vs. fed or healthy vs. hepatic impairment and want standard PK parameters"), 
                    "2" = wrapn("like #1, everything is the same except the simulation files but, unlike #1, you want to specify exactly which PK parameters to get"), 
                    "3" = wrapn("you need to compare one PK parameter in the numerator simulation to a different PK parameter in the denominator simulation, e.g., you want the baseline PK for the denominator simulation and the DDI PK in the numerator simulation"), 
                    "4" = wrapn("the compound you want is in a different position in the two simulations, e.g., you needed some fancy models only available for the substrate for your drug of interest, but you also need to model perpetrator liability and thus had to run one simulation with your drug as the substrate and what's actually the probe substrate in the inhibitor 1 position and a second simulation with the probe substrate alone for the baseline"), 
                    "5" = wrapn("different tissues, e.g., you want to compare blood vs. plasma (this will probably be the same simulation for both)"), 
                    "6" = wrapn("get the data from different sheets for the numerator and denominator sims, e.g., you want to compare the last-dose PK between two simulations but one simulation included a washout period and the other did not, which means you need a user-specified interval sheet for one and the regular last-dose sheet for the other"))
   
   message(str_wrap("Would you like examples for standard PK parameters, e.g., for the function 'pk_table', or for ratios of PK parameters from diferent simulations, e.g., for the function 'calc_PK_ratios?"))
   message("  1) standard PK parameters\n  2) ratios of PK parameters\n")
   MainOrRatios <- switch(readline("   "), 
                          "1" = "main",
                          "2" = "ratios")
   message("\n")
   
   ## Main PK parameters -----------------------------------------------------
   
   if(MainOrRatios == "main"){
      
      
      ### Collecting requests ----------------------------------------------------
      message(str_wrap("\nWhat kind of PK data do you want to include in the PK table you're making? There are examples with or without observed data for comparing to simulated. Options are:"))
      message(paste0("  ", 1:length(Opts_main), ") ", Opts_main, "\n"))
      Q1 <- readline("   ")
      message("\n")
      
      if(Q1 %in% as.numeric(1:length(Opts_main)) == FALSE){
         message(paste0("Please try again. You must enter a number from 1 to ", 
                        length(Opts_main), ".\n"))
         message(str_wrap("What kind of PK data do you want to include in the PK table you're making? There are examples with or without observed data for comparing to simulated. Options are:"))
         message(paste0("  ", 1:length(Opts_main), ") ", Opts_main, "\n"))
         Q1 <- readline("   ")
         message("\n")
         
         if(Q1 %in% as.numeric(1:length(Opts_main)) == FALSE){
            stop("Sorry, we don't know what you want. Please start over.", 
                 call. = FALSE)
         }
      }
      
      repeat{
         Q2 <- readline(paste0("Any others? (Enter a number from 1 to ", 
                               length(Opts_main), " or `n` for no)  "))
         message("\n")
         
         if((Q2 %in% as.numeric(1:length(Opts_main)) == FALSE) &
            (str_sub(tolower(Q2), 1, 2) != "n")){
            message(paste0("Please try again. You must enter a number from 1 to ",
                           length(Opts_main), " or `n`.\n"))
            
            message("What kind of PK data do you want in your table? Options are:   \n  1) typical dose 1\n  2) typical last dose\n  3) typical DDI\n  4) PK from a specific sheet in the output\n  5) PK for specific compounds\n  6) PK for specific tissues\n  7) all possible AUCs\n  8) all possible clearance\n  9) comparing more than one simulation to the same observed PK\n  10) including variability in observed PK\nor `n` for `no more`.")
            
            Q2 <- readline("   ")
            message("\n")
            
            if((Q2 %in% as.numeric(1:length(Opts_main)) == FALSE) &
               (str_sub(tolower(Q2), 1, 2) != "n")){
               stop("Sorry, we don't know what you want. Please start over.", 
                    call. = FALSE)
            }
         }
         
         if(str_sub(tolower(Q2), 1, 2) == "n"){
            break
         } else {
            Q1 <- c(Q1, Q2)
         }
      }
      
      Q1 <- sort(unique(Q1))
      
      ### Pulling examples ------------------------------------------------------
      
      Examples <- list()
      PKexamples <- PKexamples %>% 
         unite(ID, c(File, Tissue, CompoundID, PKparameter),  remove = FALSE)
      
      #### dose 1 ------------------------------------------------------------------
      if("1" %in% Q1){ # dose 1
         Examples[["A1"]] <- 
            PKexamples %>% filter(str_detect(PKparameter, "_dose1"))
      }
      
      #### last dose ------------------------------------------------------------------
      if("2" %in% Q1){ # last dose
         Examples[["A2"]] <- 
            PKexamples %>% filter(str_detect(PKparameter, "_last"))
      }
      
      #### DDI ------------------------------------------------------------------
      if("3" %in% Q1){ # DDI
         
         ExistingIDs <- bind_rows(Examples)
         if("ID" %in% names(ExistingIDs)){ExistingIDs <- ExistingIDs$ID}
         
         if("2" %in% Q1){ # last dose
            # If they asked for DDI parameters AND they asked for last dose, just
            # give them last-dose DDI examples. Otherwise, give them only 1st dose
            # DDI examples.
            Examples[["A3"]] <- 
               PKexamples %>% filter(DDI_MD == TRUE) %>% 
               filter(!ID %in% ExistingIDs) %>% 
               mutate(Notes = "")
            
         } else {
            
            Examples[["A3"]] <- 
               PKexamples %>% filter(DDI_SD == TRUE) %>% 
               filter(!ID %in% ExistingIDs) %>% 
               mutate(Notes = "")
         }
         
         if(nrow(Examples[["A3"]]) > 0){
            Examples[["A3"]]$Notes[1] <- 
               "If it's a DDI parameter, add `_withInhib` to the PKparameter name. If it's the DDI ratio, put `_ratio` before the `_dose1` or `_last` bit."
         }
         
         if("4" %in% Q1){ # specific sheet
            ExistingIDs <- bind_rows(Examples)
            if("ID" %in% names(ExistingIDs)){ExistingIDs <- ExistingIDs$ID}
            
            Examples[["A3.4"]] <- 
               PKexamples %>% filter(DDI_sheet == TRUE) %>% 
               filter(!ID %in% ExistingIDs) %>% 
               mutate(Notes = "")
            
            if(nrow(Examples[["A3.4"]]) > 0){
               Examples[["A3.4"]]$Notes[1] <- 
                  "If it's a DDI parameter for a user-defined interval, still add `_withInhib` to the end of the PKparameter name, and, if it's the DDI ratio, put `_ratio` at the end."
            }
         }
      }
      
      #### Sheet ------------------------------------------------------------------
      
      if("4" %in% Q1){ # specific sheet
         ExistingIDs <- bind_rows(Examples)
         if("ID" %in% names(ExistingIDs)){ExistingIDs <- ExistingIDs$ID}
         
         Examples[["A4"]] <- 
            PKexamples %>% filter(complete.cases(Sheet)) %>% 
            filter(!ID %in% ExistingIDs) %>% 
            mutate(Notes = "")
         
         if(nrow(Examples[["A4"]]) > 0){
            Examples[["A4"]]$Notes[1] <- 
               "Only fill in the `Sheet` column when you have a specific sheet you want and not when it's the standard first or last dose PK. You can specify more than one user-defined tab for the same simulation; put them in separate rows, though."
         }
      } 
      
      #### CompoundID ------------------------------------------------------------------
      if("5" %in% Q1){ # specific compounds 
         ExistingIDs <- bind_rows(Examples)
         if("ID" %in% names(ExistingIDs)){ExistingIDs <- ExistingIDs$ID}
         
         Examples[["A5"]] <- 
            PKexamples %>% filter(CompoundID != "substrate") %>% 
            filter(!ID %in% ExistingIDs) %>% 
            mutate(Notes = "")
         
         if(nrow(Examples[["A5"]]) > 0){
            Examples[["A5"]]$Notes[1] <- 
               paste("All the possible compounds:", 
                     str_comma(AllCompounds$CompoundID))
         }
      }
      
      #### Tissue ------------------------------------------------------------------
      if("6" %in% Q1){ # specific tissues 
         ExistingIDs <- bind_rows(Examples)
         if("ID" %in% names(ExistingIDs)){ExistingIDs <- ExistingIDs$ID}
         
         Examples[["A6"]] <- 
            PKexamples %>% filter(Tissue != "plasma") %>% 
            filter(!ID %in% ExistingIDs) %>% 
            mutate(Notes = "")
         
         if(nrow(Examples[["A6"]]) > 0){
            Examples[["A6"]]$Notes[1] <- 
               "All the possible tissues: plasma (default), unbound plasma, blood, unbound blood, peripheral plasma, or peripheral blood."
         }
      }
      
      #### All AUCs ------------------------------------------------------------------
      if("7" %in% Q1){ # all AUCs
         ExistingIDs <- bind_rows(Examples)
         if("ID" %in% names(ExistingIDs)){ExistingIDs <- ExistingIDs$ID}
         
         Examples[["A7"]] <- 
            PKexamples %>% filter(AUC == TRUE) %>% 
            filter(!ID %in% ExistingIDs) %>% 
            mutate(Notes = "")
         
         if(nrow(Examples[["A7"]]) > 0){
            Examples[["A7"]]$Notes[1] <- 
               "AUCinf_dose1 is only for dose 1. AUCt (whether it's AUCt alone or AUCt_dose1) means there was no extrapolation beyond the end of the specified interval. AUCtau_last is the AUC to time t."
         }
      }
      
      #### All CL ------------------------------------------------------------------
      if("8" %in% Q1){ # all CL
         ExistingIDs <- bind_rows(Examples)
         if("ID" %in% names(ExistingIDs)){ExistingIDs <- ExistingIDs$ID}
         
         Examples[["A8"]] <- 
            PKexamples %>% filter(AUC == TRUE) %>% 
            filter(!ID %in% ExistingIDs) %>% 
            mutate(Notes = "")
         
         if(nrow(Examples[["A8"]]) > 0){
            Examples[["A8"]]$Notes[1] <- 
               "When dose 1 clearance was calculated as dose / AUCinf, it is `CLinf_dose1`. If it were calculated as dose / AUC to time t, it will be `CLt_dose1` for dose 1 or `CLt` for a user-defined interval. CLtau_last is for the dose for the AUCtau for the last dose."
         }
      }
      
      #### multiple sims ------------------------------------------------------------------
      if("9" %in% Q1){ # mult sims
         ExistingIDs <- bind_rows(Examples)
         if("ID" %in% names(ExistingIDs)){ExistingIDs <- ExistingIDs$ID}
         
         Examples[["A9"]] <- 
            PKexamples %>% filter(str_detect(File, ", ")) %>% 
            filter(!ID %in% ExistingIDs) %>% 
            mutate(Notes = "")
         
         if(nrow(Examples[["A9"]]) > 0){
            Examples[["A9"]]$Notes[1] <- 
               "To compare the same values for multiple simulation files, you can use a new row for each or just separate the simulation file names by a comma and a space."
         }
      }
      
      #### obs variability ------------------------------------------------------------------
      if("10" %in% Q1){ # variability in obs PK
         ExistingIDs <- bind_rows(Examples)
         if("ID" %in% names(ExistingIDs)){ExistingIDs <- ExistingIDs$ID}
         
         Examples[["A10"]] <- 
            PKexamples %>% filter(complete.cases(ObsVariability)) %>% 
            filter(!ID %in% ExistingIDs) %>% 
            mutate(Notes = "")
         
         if(nrow(Examples[["A10"]]) > 0){
            Examples[["A10"]]$Notes[1] <- 
               "List variability as a fraction when it's the CV, e.g., 0.5 for `50 percent`, and as the minimum to the maximum when it's a range. CAUTION: Excel will convert things like `1-4` to a date, so list ranges as, e.g., `1 to 4`."
         }
      }
      
      #### Assembling ------------------------------------------------------------
      Examples <- bind_rows(Examples) %>% unique() %>% 
         arrange(SortOrder) %>% 
         select(File, CompoundID, Tissue, Sheet, PKparameter, ObsValue, ObsVariability,
                any_of("Notes")) %>% 
         mutate(across(.cols = any_of("Notes"), 
                       .fns = \(x) ifelse(is.na(x), "", x)))
      
      # If they didn't request specific compounds, only include substrate. 
      if("5" %in% Q1 == FALSE){
         Examples <- Examples %>% filter(CompoundID == "substrate")
      }
      
      # If they didn't request specific sheets, only include NA for sheet. 
      if("4" %in% Q1 == FALSE){
         Examples <- Examples %>% filter(is.na(Sheet))
      }
      
      # If they didn't request specific tissues, only include plasma. 
      if("6" %in% Q1 == FALSE){
         Examples <- Examples %>% filter(Tissue == "plasma")
      }
      
      Examples <- unique(Examples)
      
      
      ### Returning ------------------------------------------------------------
      
      message(str_wrap("Do you want to just see the R code names for these PK parameters or do you want to make a csv file with examples for how to enter data for the pk_table function argument 'PKparameters'?\n"))
      message("Options are:\n  1) just show me the names to use right here in the console\n  2) make me a csv file example\n")
      Q3 <- readline("    ")
      message("\n")
      
      if(Q3 %in% c("1", "2") == FALSE){
         
         message("You entered something other than 1 or 2. Please try again.\n")   
         message(str_wrap("Do you want to just see the R code names for these PK parameters or do you want to make a csv file with examples for how to enter data for the pk_table function argument 'PKparameters'?\n"))
         message("Options are:\n  1) just show me the names to use right here in the console\n  2) make me a csv file example\n")
         Q3 <- readline("    ")
         message("\n")
         
         if(Q3 %in% c("1", "2") == FALSE){
            message("You entered something other than 1 or 2 again, so we'll assume you want to just see these names in the console.\n")
            Q3 <- "1"
         }
      }
      
      if(any(c("1", "2", "3") %in% Q1)){
         Q1subset <- Q1[Q1 %in% c("1", "2", "3")]
         Q1 <- setdiff(Q1, Q1subset)
         
         if(length(Q1) == 0){
            OutPK <- paste(str_comma(Opts_main[Q1subset]), "regimens")
         } else {
            OutPK <- str_comma(c(paste(str_comma(Opts_main[Q1subset]), "regimens"), 
                                 str_comma(Opts_main[Q1])))
         }
      } else {
         OutPK <- str_comma(Opts_main[Q1])
      }
      
      
      if(Q3 == "1"){
         message(str_wrap(paste0("Here are examples for the coded PK parameters for ", 
                                 OutPK, ".")))
         
         print(Examples %>% pull(PKparameter) %>% unique())
         
      } else {
         
         MyFile <- "PK examples for SimcypConsultancy package.csv"
         if(file.exists(MyFile)){
            message(str_wrap(paste0("There is already a file with the same name that we're trying to use for saving your examples (`", 
                                    MyFile, 
                                    "`. Please specify what you would like the file to be called instead:\n")))
            MyFile <- readline("    ")
            
            # If they supplied quotes here, that messes things up. Removing. 
            MyFile <- gsub("\"", "", MyFile)
            
            # If they didn't include ".csv" at the end, add that.
            MyFile <- paste0(sub("\\.wksz$|\\.dscw$|\\.xlsx$|\\.docx$|\\.csv$", "", MyFile), ".csv")
         }
         
         write.csv(Examples, file = MyFile, row.names = FALSE, na = "")
         message(wrapn(paste0(
            "We've made you an example csv file called `", MyFile, 
            "` with PK for ", OutPK, ".")))
         
      }
      
      message("\nA few notes:\n")
      message(paste0(str_wrap("- If you made a csv file here, we recommend replacing the numbers and the file names with your own data and using that csv file as input to the argument 'PKparameters'.", 
                              indent = 3, exdent = 5), "\n"))
      message(paste0(str_wrap("- If you don't have any observed PK values for comparisons but you want to specify exactly what PK parameters you want from which simulation file or which tab or which tissue, etc., you can specify that information in a csv file, laid out like in this example, and supply that file for the argument `PKparameters`. For any row where the `ObsValue` column is empty, we'll supply only the simulated results.", 
                              indent = 3, exdent = 5), "\n"))
      message(paste0(str_wrap("- We recommend saving the results from running pk_table to a Word file rather than csv because csv files drop trailing zeroes, so they mess up your rounding in that manner.", 
                              indent = 3, exdent = 5), "\n"))
      message(paste0(str_wrap("- If you want a standard PK parameter for dose 1 or the last dose, leave the `Sheet` column blank; you should only list the sheet when it's a user-defined AUC interval.",
                              indent = 3, exdent = 5), "\n"))
      
   }
   
   
   ## Ratios of PK parameters -----------------------------------------------------
   
   if(MainOrRatios == "ratios"){
      
      ### Collecting requests ----------------------------------------------------
      message(str_wrap("What kind of PK data do you want to include in the PK table you're making? Options are:"))
      message(paste0("  ", 1:length(Opts_ratios), ") ", Opts_ratios, "\n"))
      Q1 <- readline("   ")
      message("\n")
      
      if(Q1 %in% as.numeric(1:length(Opts_ratios)) == FALSE){
         message(paste0("Please try again. You must enter a number from 1 to ", 
                        length(Opts_ratios), ".\n"))
         
         message(str_wrap("What kind of PK data do you want to include in the PK table you're making? Options are:"))
         message(paste0("  ", 1:length(Opts_ratios), ") ", Opts_ratios, "\n"))
         Q1 <- readline("   ")
         message("\n")
         
         if(Q1 %in% as.numeric(1:length(Opts_ratios)) == FALSE){
            stop("Sorry, we don't know what you want. Please start over.", 
                 call. = FALSE)
         }
      }
      
      ### Pulling examples ------------------------------------------------------
      
      Examples <- PKexamples_ratios %>% 
         filter(Opts_ratios == as.numeric(Q1)) %>% 
         select(-matches("^Diff|^Opts|SortOrder")) %>% 
         purrr::discard(~all(is.na(.)))
      
      ### Returning ------------------------------------------------------------
      
      message(str_wrap("Do you want to see the example as a data.frame here in the console or as a csv file?"))
      message("Options are:\n  1) data.frame in the console\n  2) make me a csv file example\n")
      Q3 <- readline("    ")
      message("\n")
      
      if(Q3 %in% c("1", "2") == FALSE){
         
         message("You entered something other than 1 or 2. Please try again.\n")   
         message(wrapn("Do you want to see the example as a data.frame here in the console or as a csv file?"))
         message("Options are:\n  1) data.frame in the console\n  2) make me a csv file example\n")
         Q3 <- readline("    ")
         message("\n")
         
         if(Q3 %in% c("1", "2") == FALSE){
            message("You entered something other than 1 or 2 again, so we'll assume you want to just see this example in the console.\n")
            Q3 <- "1"
         }
      }
      
      if(Q3 == "1"){
         
         print(Examples)
         # paste(capture.output(print(Examples)), collapse = "\n")
         
      } else {
         
         MyFile <- "PK ratio examples for SimcypConsultancy package.csv"
         if(file.exists(MyFile)){
            message(str_wrap(paste0("There is already a file with the same name that we're trying to use for saving your examples (`", 
                                    MyFile, 
                                    "`. Please specify what you would like the file to be called instead:\n")))
            MyFile <- readline("    ")
            
            # If they supplied quotes here, that messes things up. Removing. 
            MyFile <- gsub("\"", "", MyFile)
            
            # If they didn't include ".csv" at the end, add that.
            MyFile <- paste0(sub("\\.wksz$|\\.dscw$|\\.xlsx$|\\.docx$|\\.csv$", "", MyFile), ".csv")
         }
         
         write.csv(Examples, file = MyFile, row.names = FALSE, na = "")
         message(wrapn(paste0(
            "We've made you an example csv file called `", MyFile, ".")))
         
      }
      
      message("\nA few notes:\n")
      message(paste0(str_wrap("- If you made a csv file here, we recommend replacing the numbers and the file names with your own data and using that csv file as input to the argument 'PKparameters'.", 
                              indent = 3, exdent = 5), "\n"))
      message(paste0(str_wrap("- We recommend saving the results from running calc_PK_ratios to a Word file rather than csv because csv files drop trailing zeroes, so they mess up your rounding in that manner.", 
                              indent = 3, exdent = 5), "\n"))
      message(paste0(str_wrap("- If you want a standard PK parameter for dose 1 or the last dose, leave the `Sheet` column blank; you should only list the sheet when it's a user-defined AUC interval.",
                              indent = 3, exdent = 5), "\n"))
      
   }
   
   
}