[R] Function with large nested list

[Michael Dewey]

Dear Emily

Comment in-line

On 18/12/2023 09:56, Emily Bakker wrote:
> Hello list,
> 
> I want to make a large rulebased algorithm, to provide decision support for drug prescriptions. I have defined the algorithm in a function, with a for loop and many if statements. The structure should be as follows:
> 1. Iterate over a list of drug names. For each drug:
> 2. Get some drug related data (external dataset). Row of a dataframe.
> 3.  Check if adaptions should be made to standard dosage and safety information in case of contraindications. If patient has an indication, update current dosage and safety information with the value from the dataframe row.
> 4. Save dosage and safety information in some lists and continue to the next drug.
> 5. When the iteration over all drugs is done, return the lists.
> 
> ISSUE:
> So it is a very large function with many nested if statements. I have checked the code structure multiple times, but i run into some issues. When i try to run the function definiton, the command never "completes" in de console. Instead of ">", the console shows "+". No errors are raised.

When my console returns a + is usually means I have left off the final 
parenthesis or given it an incomplete line.

Michael
> 
> As I said, i have checked the structure multiple times, but cant find an error. I have tried rebuilding it and testing each time i add a part. Each part functions isolated, but not together in the same function. I can't find any infinite loops either.
> I suspect the function may be too large, and i have to define functions for each part separately. That isn't an issue necessarily, but i would still like to know why my code won't run. And whether there are any downsides or considerations for using many small functions.
> 
> Below is my code. I have left part of it out. There are six more parts like the diabetes part that are similar.
> I also use a lot of data/variabeles not included here, to try and keep things compact. But I can provide additional information if helpful.
> Thanks it advance for thinking along!!
> Kind regards,
> Emily
> 
> The code:
> 
> decision_algorithm <- function(AB_list, dataset_ab = data.frame(), diagnose = 'cystitis', diabetes_status = "nee", katheter_status = "nee",
>                                 lang_QT_status = "nee", obesitas_status = "nee", zwangerschap_status = "nee",
>                                 medicatie_actief = data.frame(dict[["med_AB"]]), geslacht = "man", gfr=90){
>    
>    
>    
>    # vars
>    list_AB_status <- setNames(as.list(rep("green", length(AB_list))), names(AB_list)) #make a dict of all AB's and assign status green as deafault for status
>    list_AB_remarks <- setNames(as.list(rep("Geen opmerkingen", length(AB_list))), names(AB_list)) #make a dict of all AB's and assign "Geen" as default for remarks #Try empty list
>    list_AB_dosering <- setNames(as.list(rep("Geen informatie", length(AB_list))), names(AB_list)) # make named list of all AB's and assign "Geen informatie", will be replaced with actual information in algorithm
>    list_AB_duur <- setNames(as.list(rep("Geen informatie", length(AB_list))), names(AB_list)) # make named list of all AB's and assign "Geen informatie", will be replaced with actual information in algorithm
>    
>    ##### CULTURES #####
>    for (i in names(AB_list)) {
>      
>      ab_data <- dataset_ab[dataset_ab$middel == i,] #get info for this AB from dataset_ab
>      
>      # Extract and split the diagnoses, dosering, and duur info for the current antibiotic
>      ab_diagnoses <- str_split(ab_data$diagnoses, pattern = " \\| ")[[1]]
>      ab_diagnose_dosering <- str_split(ab_data$`diagnose dosering`, pattern = " \\| ")[[1]]
>      ab_diagnose_duur <- str_split(ab_data$`diagnose duur`, pattern = " \\| ")[[1]]
>      
>      # Find the index of the current diagnose in the ab_diagnoses list
>      diagnose_index <- match(diagnose, ab_diagnoses)
>      
>      # Determine dosering and duur based on the diagnose_index
>      if (!is.na(diagnose_index)) {
>        dosering <- ifelse(ab_diagnose_dosering[diagnose_index] == "standaard", ab_data$dosering, ab_diagnose_dosering[diagnose_index])
>        duur <- ifelse(ab_diagnose_duur[diagnose_index] == "standaard", ab_data$duur, ab_diagnose_duur[diagnose_index])
>      } else {
>        # Use general dosering and duur as fallback if diagnose is not found
>        dosering <- ab_data$dosering
>        duur <- ab_data$duur
>      }
>      
>      list_AB_dosering[[i]] <- dosering
>      list_AB_duur[[i]] <- duur
>      
>      if ((!is.null(AB_list[[i]]) && AB_list[[i]] == "I")) {
>        list_AB_status[[i]] <- "yellow"
>          list_AB_remarks[[i]] <- "Kweek verminderd gevoelig"
>      } else if ((!is.null(AB_list[[i]]) && AB_list[[i]] == "R")) {
>        list_AB_status[[i]] <- "red"
>          list_AB_remarks[[i]] <- "Kweek resistent"
>      }else if ((!is.null(AB_list[[i]]) && AB_list[[i]] == "S")) {
>        next
>      } else {
>        list_AB_status[[i]] <- "yellow"
>          list_AB_remarks[[i]] <- "Geen kweekgegevens"
>      }
>    
>      
>      # counters, for check if dosering / duur are updated more than once
>      dosering_update_count <- 0
>      duur_update_count <- 0
>      
>      ##### DIABETES #####
>      if (diabetes_status == "ja") {
>        if (ab_data$'diabetes veiligheid' == "ja") {
>          list_AB_status[[i]] <- "red"
>            list_AB_remarks[[i]] <- paste(list_AB_remarks[[i]], "Niet veilig met diabetes")
>        }
> 
>        if (ab_data$'diabetes effectiviteit' == "aanpassing") {
>          dosering <- ifelse(ab_data$'diabetes dosering' != "standaard", ab_data$'diabetes dosering', dosering) # if dosering does not equal standaard, apply dosering in column, otherwise keep initial dosering
>          duur <- ifelse(ab_data$'diabetes duur' != "standaard", ab_data$'diabetes duur', duur) # if dosering does not equal standaard, apply dosering in column, otherwise keep initial dosering
>          dosering_update_count <- dosering_update_count + 1
>          duur_update_count <- duur_update_count + 1
>          list_AB_remarks[[i]] <- paste(list_AB_remarks[[i]], ab_data$'diabetes opmerkingen')
>        }
> 
>      } else if (diabetes_status == "?") {
>        if (ab_data$'diabetes veiligheid' == "ja") {
>          list_AB_remarks[[i]] <- paste(list_AB_remarks[[i]], "Waarschuwing: Dit middel kan veiligheidsimplicaties hebben bij diabetes.")
>        }
>        if (ab_data$'diabetes effectiviteit' == "aanpassing") {
>          list_AB_remarks[[i]] <- paste(list_AB_remarks[[i]], "Waarschuwing: Dit middel kan dosisaanpassingen vereisen bij diabetes.")
>        }
>      }
> 
>      list_AB_dosering[[i]] <- dosering
>      list_AB_duur[[i]] <- duur
>      
>      # within for loop
>      
>    }
>    # within function
>    return(list(status = list_AB_status, remarks = list_AB_remarks, duur = list_AB_duur, dosering = list_AB_dosering))
> }
>      
> 
> 
> 
> 
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-- 
Michael