Re: [R] Function with large nested list

Michael Dewey Mon, 18 Dec 2023 08:31:11 -0800

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 finalparenthesis 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

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R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Function with large nested list

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