R/extractObsConcTime_XML.R

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

#' INTERNAL - Extract observed conc-time data from an xml file
#'
#' @param obs_data_file xml file used for observed data in a workspace
#'
#' @return a data.frame of observed conc time data
#'

extractObsConcTime_XML <- function(obs_data_file){
   
   obs_data_xml <- Simcyp::ReadPEData(path = obs_data_file)
   
   obs_data <- obs_data_xml$Observations
   
   NewNames <- ObsColNames %>% bind_rows() %>% 
      select(PEColName, ColName) %>% unique() %>% 
      mutate(DBColName = str_replace_all(PEColName, " ", ""), 
             DBColName = case_match(DBColName, 
                                    "Age(year)" ~ "Age(years)", 
                                    "PhenotypeCYP2D6" ~ "Phenotype(CYP2D6)", 
                                    .default = DBColName)) %>% 
      filter(DBColName %in% names(obs_data))
   # WARNING: This will drop column names that are not matched. 
   obs_data <- obs_data[, NewNames$DBColName]
   names(obs_data) <- NewNames$ColName
   
   obs_data <- obs_data %>%
      left_join(obs_data_xml$DVInfo %>% 
                   mutate(DVID = as.numeric(DVID)), by = "DVID") %>% 
      mutate(DVID = DV, 
             TimeUnits = tolower(TimeUnits), 
             across(.cols = everything(), 
                    .fns = \(x) case_when(x == "" ~ NA, .default = x))) %>% 
      left_join(ObsDVoptions, by = "DVID") %>% 
      rename(Time_units = TimeUnits, 
             Conc_units = DVUnit) %>% 
      mutate(Simulated = FALSE,
             Trial = "obs",
             # SmokingStatus = Smoke[SmokingStatus], # Not available from Simcyp package, apparently
             ObsFile = obs_data_file)
   
   dose_data <-
      obs_data_xml$DosingEvent
   
   # Filling in some values when they're not present, which is apparently the
   # case for really old simulator versions
   if("Compound" %in% names(dose_data) == FALSE){
      dose_data$Compound <- "substrate" # just guessing here!!!
   }
   if("Dose_units" %in% names(dose_data) == FALSE){
      dose_data$Dose_units <- "mg" # just guessing here!!!
   }
   
   # Need to rename things but account for the fact that some columns might not
   # be present
   NewNames_ch <- NewNames %>% filter(DBColName %in% names(dose_data)) %>% 
      pull(ColName)
   names(NewNames_ch) <- NewNames %>% filter(DBColName %in% names(dose_data)) %>% 
      pull(DBColName)
   
   dose_data <- dose_data %>% 
      rename_with(~ str_replace_all(., NewNames_ch)) %>% 
      mutate(ObsFile = obs_data_file, 
             CompoundID = tolower(Compound), 
             Dose_units = case_when(Dose_units == "mg/mL" ~ "mg", # Bug in Simcyp package
                                    .default = Dose_units),
             across(.cols = everything(), 
                    .fn = as.character)) %>% 
      pivot_longer(cols = any_of(c("DoseAmount", "DoseRoute", "Dose_units", 
                                   "InfDuration", "InjectionSite")), 
                   names_to = "Parameter", 
                   values_to = "Value") %>% 
      left_join(AllCompounds %>% select(CompoundID, Suffix), by = "CompoundID") %>% 
      mutate(Parameter = paste0(Parameter, Suffix)) %>% 
      select(-Suffix, -Compound) %>%
      pivot_wider(names_from = Parameter, 
                  values_from = Value) %>% 
      mutate(across(.cols = c(Time, matches("DoseAmount|InfDuration")), 
                    .fns = as.numeric))
   
   return(list("obs_data" = obs_data, 
               "dose_data" = dose_data))
   
}