mainDir <- koboloadeR::kobo_getMainDirectory()

form_tmp <- paste(mainDir, "data-raw", form, sep = "/", collapse = "/")

tryCatch({

#### Load and test i indicators #############################################################################

#library(readxl)

tried <- try(readxl::read_excel(form_tmp, sheet = "indicator"),

silent = TRUE)

if (inherits(tried, "try-error")) {

writeLines("Note that you have not defined (or defined correctly) indicators within your xlsform file. \n")

} else {

rm(tried)

## load all required data files #########################################

cat("\n\nload all required data files..\n")

dataBeginRepeat <- koboloadeR::kobo_get_begin_repeat(form)

dataBeginRepeat <- dataBeginRepeat$names

## Check if there's a repeat - aka hierarchical structure in the dataset

if (length(dataBeginRepeat) > 0) {

for (dbr in dataBeginRepeat) {

dataFrame <- utils::read.csv(paste(mainDir,"/data/",dbr,"_edited.csv",sep = ""),stringsAsFactors = F)

#load(paste(mainDir,"/data/",dbr,"_edited.rda",sep = ""))

assign(dbr, dataFrame)

}

}

indicator <- readxl::read_excel(form_tmp, sheet = "indicator")

if (nrow(indicator) == 0) {

writeLines("Note that you have not defined (or defined correctly) indicators within your xlsform file. \n")

} else {

## Load data & dico #############################################################################

#form <- "form.xls"

## Run this only after data cleaning

dico <- utils::read.csv(paste0(mainDir,"/data/dico_",form,".csv"), encoding = "UTF-8", na.strings = "")

#load(paste(mainDir,"/data/dico_",form,".rda",sep = ""))

## Create the dicotemp #############################################################################

#names(dico)

dicotemp <- data.frame(c("trigger"))

names(dicotemp)[1] <- "type"

#dicotemp$type <- "trigger"

dicotemp$name <- "trigger"

dicotemp$fullname <- "trigger"

dicotemp$label <- "trigger"

dicotemp$labelReport <- "trigger"

dicotemp$hintReport <- "trigger"

dicotemp$report <- "trigger"

dicotemp$chapter <- "trigger"

dicotemp$disaggregation <- "trigger"

dicotemp$correlate <- "trigger"

dicotemp$anonymise <- "trigger"

dicotemp$clean <- "trigger"

dicotemp$cluster <- "trigger"

dicotemp$predict <- "trigger"

dicotemp$variable <- "trigger"

dicotemp$mappoint <- "trigger"

dicotemp$mappoly <- "trigger"

dicotemp$listname <- "trigger"

dicotemp$qrepeat <- "trigger"

dicotemp$qrepeatlabel <- "trigger"

dicotemp$qlevel <- "trigger"

dicotemp$qgroup <- "trigger"

dicotemp$labelchoice <- "trigger"

dicotemp$variable <- "trigger"

dicotemp$order <- "trigger"

dicotemp$weight <- "trigger"

dicotemp$score <- "trigger"

dicotemp$recategorise <- "trigger"

dicotemp$formpart <- "trigger"

dicotemp$indic <- "trigger"

dicotemp$constraint <- "trigger"

dicotemp$label <- "trigger"

dicotemp$relevant <- "trigger"

dicotemp$repeat_count <- "trigger"

dicotemp$required <- "trigger"

## Need to check that all column are presents...

## Load indicator info #############################################################################

if (file.exists(paste0(mainDir,"/R/build_indicator.R") )) file.remove(paste0(mainDir,"/R/build_indicator.R"))

cat(paste('### Script to generate indicator: ',sep = ""), file = paste0(mainDir,"/R/build_indicator.R") , sep = "\n", append = TRUE)

cat(paste('form <- "',form,'"',sep = ""), file = paste0(mainDir,"/R/build_indicator.R") , sep = "\n", append = TRUE)

cat("mainDir <- koboloadeR::kobo_getMainDirectory()", file = paste0(mainDir,"/R/build_indicator.R") , sep = "\n", append = TRUE)

cat('form_tmp <- paste(mainDir, "data", form, sep = "/", collapse = "/")', file = paste0(mainDir,"/R/build_indicator.R") , sep = "\n", append = TRUE)

cat('dataBeginRepeat <- koboloadeR::kobo_get_begin_repeat(form)', file = paste0(mainDir,"/R/build_indicator.R") , sep = "\n", append = TRUE)

cat('dataBeginRepeat <- dataBeginRepeat$names', file = paste0(mainDir,"/R/build_indicator.R") , sep = "\n", append = TRUE)

cat('MainDataFrame <- utils::read.csv(paste(mainDir,"/data/MainDataFrame_edited.csv",sep = ""), encoding = "UTF-8", na.strings = "NA")', file = paste0(mainDir,"/R/build_indicator.R") , sep = "\n", append = TRUE)

#cat('load(paste(mainDir,"/data/MainDataFrame_edited.rda",sep = ""))', file = paste0(mainDir,"/R/build_indicator.R") , sep = "\n", append = TRUE)

## Check if there's a repeat - aka hierarchical structure in the dataset

if (length(dataBeginRepeat) > 0) {

cat('for (dbr in dataBeginRepeat) {

assign(paste0(dbr,"_edited"), dataFrame) }', file = paste0(mainDir,"/R/build_indicator.R") , sep = "\n", append = TRUE)

}

for (i in 1:nrow(indicator))

{

# i <- 1

indicator.type <- as.character(indicator[ i, c("type")])

indicator.fullname <- as.character(indicator[ i, c("fullname")])

# indicator.label <- as.character(indicator[ i, c("label")])

indicator.label <- as.character("")

indicator.labelReport <- as.character(indicator[ i, c("labelReport")])

indicator.hintReport <- as.character(indicator[ i, c("hintReport")])

indicator.report <- as.character(indicator[ i, c("report")])

indicator.chapter <- as.character(indicator[ i, c("chapter")])

indicator.disaggregation <- as.character(indicator[ i, c("disaggregation")])

indicator.correlate <- as.character(indicator[ i, c("correlate")])

indicator.anonymise <- as.character(indicator[ i, c("anonymise")])

indicator.frame <- as.character(indicator[ i, c("frame")])

indicator.listname <- as.character(indicator[ i, c("listname")])

indicator.calculation <- as.character(indicator[ i, c("calculation")])

indicator.cluster <- as.character(indicator[ i, c("cluster")])

indicator.predict <- as.character(indicator[ i, c("predict")])

indicator.variable <- as.character(indicator[ i, c("variable")])

indicator.mappoint <- as.character(indicator[ i, c("mappoint")])

indicator.mappoly <- as.character(indicator[ i, c("mappoly")])

cat(paste0(i, "- Load indicator: ", indicator.labelReport," of type: ",indicator.type,"\n"))

## Build and run the formula to insert the indicator in the right frame ###########################

indic.formula <- paste0(indicator.frame,"$",indicator.fullname," <- ",indicator.calculation )

cat(paste('\n \n### Script to generate indicator: ',indicator.labelReport,sep = ""), file = paste0(mainDir,"/R/build_indicator.R") , sep = "\n", append = TRUE)

cat(indic.formula, file = paste0(mainDir,"/R/build_indicator.R") , sep = "\n", append = TRUE)

## do a check on indicator variable type

indicator.type2 <- indicator.type

ifelse(indicator.type == "select_one", indicator.type2 <- "character", indicator.type2 <- indicator.type)

cat(paste0(indicator.frame,"$",indicator.fullname," <- as.",indicator.type2,"(",indicator.frame,"$",indicator.fullname,")"), file = paste0(mainDir,"/R/build_indicator.R") , sep = "\n", append = TRUE)

cat(paste0("str(",indicator.frame,"$",indicator.fullname,")"), file = paste0(mainDir,"/R/build_indicator.R") , sep = "\n", append = TRUE)

cat(paste0("summary(",indicator.frame,"$",indicator.fullname,")"), file = paste0(mainDir,"/R/build_indicator.R") , sep = "\n", append = TRUE)

# if (indicator.frame == "MainDataFrame_edited") {

# }else{

# cat(paste('dbr<-"',indicator.frame,'"',sep = ""))

# cat('utils::write.csv(eval(as.name(dbr)),paste(mainDir,"/data/",dbr,".csv",sep = ""), row.names = FALSE, na = "")', file = paste0(mainDir,"/R/build_indicator.R") , sep = "\n", append = TRUE)

# }

# source(paste0(mainDir,"/R/build_indicator.R"))

# cat(paste0(i, "- Executed indicator: ", indicator.labelReport,"\n"))

# if (file.exists(paste0(mainDir,"/R/build_indicator.R"))) file.remove(paste0(mainDir,"/R/build_indicator.R"))

## Insert the indicator in a temp dico frame to be appended to the full dico ######################

dicotemp1 <- data.frame(c("trigger"))

names(dicotemp1)[1] <- "type"

dicotemp1$type <- indicator.type

dicotemp1$name <- indicator.fullname

dicotemp1$fullname <- indicator.fullname

dicotemp1$label <- indicator.label

dicotemp1$labelReport <- indicator.labelReport

dicotemp1$hintReport <- indicator.hintReport

dicotemp1$report <- indicator.report

dicotemp1$chapter <- indicator.chapter

dicotemp1$disaggregation <- indicator.disaggregation

dicotemp1$correlate <- indicator.correlate

dicotemp1$anonymise <- indicator.anonymise

dicotemp1$clean <- " "

dicotemp1$cluster <- indicator.cluster

dicotemp1$predict <- indicator.predict

dicotemp1$variable <- indicator.variable

dicotemp1$mappoint <- indicator.mappoint

dicotemp1$mappoly <- indicator.mappoly

dicotemp1$listname <- indicator.listname

dicotemp1$qrepeat <- " "

dicotemp1$qrepeatlabel <- indicator.frame

dicotemp1$qlevel <- " "

dicotemp1$qgroup <- " "

dicotemp1$labelchoice <- " "

dicotemp1$order <- " "

dicotemp1$weight <- " "

dicotemp1$score <- " "

dicotemp1$recategorise <- " "

dicotemp1$formpart <- " "

dicotemp1$indic <- "feature"

dicotemp1$constraint <- " "

dicotemp1$label <- " "

dicotemp1$relevant <- " "

dicotemp1$repeat_count <- " "

dicotemp1$required <- " "

dicotemp <- rbind(dicotemp,dicotemp1)

}

cat('utils::write.csv(MainDataFrame, paste(mainDir,"/data/MainDataFrame_edited.csv",sep = ""), row.names = FALSE, na = "")', file = paste0(mainDir,"/R/build_indicator.R") , sep = "\n", append = TRUE)

#cat('save(MainDataFrame, file = paste(mainDir,"/data/MainDataFrame_edited.rda",sep = ""))', file = paste0(mainDir,"/R/build_indicator.R") , sep = "\n", append = TRUE)

source(paste0(mainDir,"/R/build_indicator.R"))

## Append indicators in the dico #############################################################################

## removing first line

dicotemp <- dicotemp[ 2:nrow(dicotemp), ]

### Merging choices from the newly created indicators #################################################################

cat("\n\n\n It's assumed that the modalities for newly calculated categoric indicators are in the same xlsform - choices worksheet \n\n\n\n")

choices <- readxl::read_excel(form_tmp, sheet = "choices")

#rm(choices)

#names(choices)[names(choices) == "labelReport"] <- "label"

names(choices)[names(choices) == "label::english"] <- "label"

names(choices)[names(choices) == "label::English"] <- "label"

names(choices)[names(choices) == "label::English (en)"] <- "label"

names(choices)[names(choices) == "list name"] <- "listname"

names(choices)[names(choices) == "list_name"] <- "listname"

## Remove trailing space

choices$listname <- trimws(choices$listname)

choices$label <- trimws(choices$label)

if ("order" %in% colnames(choices))

{

cat(" Good: You have a column `order` in your `choices` worksheet.\n");

} else

{cat(" No column `order` in your `choices` worksheet. Creating a dummy one for the moment...\n");

choices$order <- ""}

if ("weight" %in% colnames(choices))

{

cat(" Good: You have a column `weight` in your `choices` worksheet.\n");

} else

{cat(" No column `weight` in your `choices` worksheet. Creating a dummy one for the moment...\n");

choices$weight <- ""}

if ("recategorise" %in% colnames(choices))

{

cat(" Good: You have a column `recategorise` in your `choices` worksheet.\n");

} else

{cat(" No column `recategorise` in your `choices` worksheet. Creating a dummy one for the moment...\n");

choices$recategorise <- ""}

if ("score" %in% colnames(choices))

{

cat(" Good: You have a column `score` in your `choices` worksheet.\n");

} else

{

cat(" No column `score` in your `choices` worksheet. Creating a dummy one for the moment...\n");

choices$score <- ""

}

choices <- choices[,c("listname", "name", "labelReport", "order", "weight","score","recategorise")]

names(choices)[names(choices) == "labelReport"] <- "labelchoice"

# names(choices)[names(choices) == "label"] <- "labelchoice"

#rm(choices)

dicotemp.choice <- dicotemp[ !(is.na(dicotemp$listname)), c( "type", "name",

"fullname","labelReport","hintReport","report","chapter",

"disaggregation","correlate","anonymise",

# "structuralequation.risk","structuralequation.coping","structuralequation.resilience",

"clean","cluster","predict","variable","mappoint","mappoly",

"listname","qrepeat","qrepeatlabel","qlevel","qgroup",

# "order","weight","score","recategorise",

"formpart","indic","constraint","label","relevant","repeat_count","required" )]

choices2 <- plyr::join(x = dicotemp.choice, y = choices, by = "listname", type = "left")

choices2$type <- with(choices2, ifelse(grepl("select_one", ignore.case = TRUE, fixed = FALSE, useBytes = FALSE, choices2$type),

paste0("select_one_d"),choices2$type))

choices2$type <- with(choices2, ifelse(grepl("select_multiple_d", ignore.case = TRUE, fixed = FALSE, useBytes = FALSE, choices2$type),

paste0("select_multiple"),choices2$type))

names(choices2)[2] <- "nameq"

names(choices2)[3] <- "nameqfull"

names(choices2)[4] <- "labelq"

# choices$labelchoice

# View(choices2[ , c("labelchoice")])

#choices2$labelchoice <- as.factor(choices2$labelchoice)

#str(choices2$labelchoice)

#names(choices2)

# choices2$labelq

choices2$labelfull <- paste(choices2$labelq, choices2$labelchoice, sep = ": ")

choices2$namefull <- paste(choices2$nameqfull, choices2$name, sep = ".")

# names(choices2)

#### Now Row bind questions & choices########################################################################################################

choices3 <- choices2[ ,c("type", "name", "namefull", "labelfull","hintReport",

"report", "chapter", "disaggregation","correlate", "anonymise",

# "structuralequation.risk","structuralequation.coping","structuralequation.resilience",

"clean", "cluster", "predict",

"variable", "mappoint", "mappoly", "listname",

"qrepeat", "qrepeatlabel","qlevel","qgroup",

"labelchoice", "order", "weight","score",

"recategorise",

"formpart","indic","constraint","label","relevant","repeat_count","required")]

names(choices3)[names(choices3) == "namefull"] <- "fullname"

names(choices3)[names(choices3) == "labelfull"] <- "labelReport"

#names(choices3)[names(choices3) == "labelfull"] <- "label"

dicotemp <- dicotemp[,c( "type", "name", "fullname", #"label",

"labelReport","hintReport",

"report", "chapter", "disaggregation","correlate", "anonymise",

#"structuralequation.risk","structuralequation.coping","structuralequation.resilience",

"clean", "cluster", "predict",

"variable", "mappoint", "mappoly", "listname",

"qrepeat", "qrepeatlabel","qlevel","qgroup",

"labelchoice", "order", "weight","score",

"recategorise",

"formpart","indic","constraint","label","relevant","repeat_count","required")]

### Check -- normally there should not be duplicate

dicotemp$formpart <- "questions"

choices3$formpart <- "answers"

# test1 <- as.data.frame(names(dicotemp))

# test2 <- as.data.frame(names(choices3))

dicotemp <- rbind(dicotemp,choices3)

dicotemp$label <- dicotemp$labelReport

dicotemp$indic <- "feature"

dico$indic <- "data"

dicotemp$relevant <- ""

dicotemp$required <- ""

dicotemp$constraint <- ""

dicotemp$repeat_count <- ""

#names(dico)

#names(dicotemp)

dico <- dico[ , c( "type", "name", "fullname", "label", "labelReport","hintReport",

"report","chapter", "disaggregation","correlate", "anonymise",

#"structuralequation.risk","structuralequation.coping","structuralequation.resilience",

"anonymise", "clean", "cluster", "predict", "variable", "mappoint", "mappoly",

"relevant", "required", "constraint", "repeat_count",

"listname","qrepeat", "qrepeatlabel","qlevel","qgroup",

"labelchoice", "order", "weight","score",

"recategorise", "formpart", "indic" )]

dicotemp <- dicotemp[ , c("type", "name", "fullname", "label", "labelReport","hintReport",

"report", "chapter", "disaggregation","correlate", "anonymise",

# "structuralequation.risk","structuralequation.coping","structuralequation.resilience",

"anonymise", "clean", "cluster", "predict", "variable", "mappoint", "mappoly",

"relevant", "required", "constraint", "repeat_count",

"listname","qrepeat", "qrepeatlabel","qlevel","qgroup",

"labelchoice", "order", "weight","score",

"recategorise", "formpart", "indic" )]

dico <- rbind(dico,dicotemp)

rm(dicotemp,dicotemp1, choices, choices2, choices3, dicotemp.choice)

MainDataFrame <- utils::read.csv(paste(mainDir,"/data/MainDataFrame_edited.csv",sep = ""), encoding = "UTF-8", na.strings = "NA")

#load(paste(mainDir,"/data/MainDataFrame_edited.rda",sep = ""))

## label Variables

cat("\n\n quick check on labeling\n")

MainDataFrame <- koboloadeR::kobo_label(MainDataFrame , dico)

## Check if there's a repeat - aka hierarchical structure in the dataset

if (length(dataBeginRepeat) > 0) {

for (dbr in dataBeginRepeat) {

dataFrame <- utils::read.csv(paste(mainDir,"/data/",dbr,"_edited.csv",sep = ""),stringsAsFactors = F)

#load(paste(mainDir,"/data/",dbr,"_edited.rda",sep = ""))

dataFrame <- koboloadeR::kobo_label(dataFrame, dico)

utils::write.csv(dataFrame,paste(mainDir,"/data/",dbr,"_edited.csv",sep = ""), row.names = FALSE, na = "")

#save(dataFrame , file = paste(mainDir,"/data/",dbr,"_edited.rda",sep = ""))

}

}

cat("\n\nWrite dico\n")

utils::write.csv(dico, paste0(mainDir,"/data/dico_",form,".csv"), row.names = FALSE, na = "")

# save(dico, file = paste0(mainDir,"/data/dico_",form,".rda"))

utils::write.csv(MainDataFrame, paste(mainDir,"/data/MainDataFrame_edited.csv",sep = ""), row.names = FALSE, na = "")

#save(MainDataFrame, file = paste(mainDir,"/data/MainDataFrame_edited.rda",sep = ""))

}

}

}, error = function(err) {

print("There was an error in the indicator creation step!!! \n\n")

return(structure(err, class = "try-error"))

})