Merge pull request #66 from unhcr/gh-pages

merge
unhcr · Nov 14, 2020 · 18872d5 · 18872d5
2 parents 20e3216 b185865
commit 18872d5
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7  1,7 @@
 Type: Package
 Package: koboloadeR
 Title: A Metapackage for Survey Data Crunching
-Version: 0.1.7
 Version: 0.1.8
 Authors@R: 
     c(person(given = "Edouard",
              family = "Legoupil",
@@ -11,6  11,10 @@ Authors@R:
              family = "Daoud",
              role = "aut",
              email = "[email protected]"),
       person(given = "Hisham",
              family = "Galal",
              role = "aut",
              email = "[email protected]"),
       person(given = "Elliott",
              family = "Messeiller",
              role = "ctb",
@@ -58,6  62,7 @@ Imports:
     pander,
     pls,
     plyr,
     qpdf,
     randomForest,
     rattle,
     RColorBrewer,
@@ -82,14  87,19 @@ Imports:
     stringi,
     stringr,
     survey,
-    tidyverse,
     tools,
     truncnorm,
     tidyverse,
     VIM,
     viridis,
     xgboost,
-    xlsx
     jsonlite,
     magrittr,
     tibble,
     miniUI,
     ckanr,
     openxlsx,
     fs
 Suggests:
     testthat (>= 2.1.0)
 VignetteBuilder: 

diff --git a/NAMESPACE b/NAMESPACE
@@ -22,6  22,7 @@ export(kobo_ddi)
 export(kobo_dico)
 export(kobo_dummy)
 export(kobo_edit_form)
 export(kobo_edit_ridl_metadata)
 export(kobo_encode)
 export(kobo_encode_repeat)
 export(kobo_form)
@@ -49,6  50,9 @@ export(kobo_samplingframe)
 export(kobo_shiny)
 export(kobo_split_multiple)
 export(kobo_submission_count)
 export(kobo_submit_ridl_package)
 export(kobo_submit_ridl_resource)
 export(kobo_submit_to_ridl)
 export(kobo_time_parser_UTC)
 export(kobo_to_xlsform)
 export(kobo_unhcr_style_bar)
@@ -68,3  72,4 @@ import(RCurl)
 import(httr)
 import(plyr)
 import(readxl)
 importFrom(magrittr,"%>%")
diff --git a/NEWS.md b/NEWS.md
@@ -1,3  1,12 @@
 ## koboloadeR 0.1.8
 
   *  Refactored the koboloadeR project structure so that it looks like a data package - R, data-raw, data - applying suggestions made here: https://raw.githubusercontent.com/statnmap/prez/master/2019-07_useR_Toulouse.pdf 
 
   *  Included dependency to unhcRstyle package where all the brand style is managed - used now an argument to crunching report function
 
   *  Saving now all intermediary file as binary rda -- not yet tested fully...
 
 
 ## koboloadeR 0.1.7
 
   *  Added different output for the crunching report - docx, pptx, html, aspx

diff --git a/R/kobo_aggregate.R b/R/kobo_aggregate.R
@@ -21,7  21,7 @@
 #' }
 #'
 
-kobo_aggregate <- function( form = "form.xls", 
 kobo_aggregate <- function( form = "form.xlsx", 
                             aggregVar = "admin1") {
 
   # aggregVar = mapref

diff --git a/R/kobo_anonymisation_report.R b/R/kobo_anonymisation_report.R
@@ -16,14  16,14 @@
 #'
 #' @examples
 #' \dontrun{
-#' kobo_anonymisation_report(frame, form = "form.xls")
 #' kobo_anonymisation_report(frame, form = "form.xlsx")
 #' }
 #'
 #' @export kobo_anonymisation_report
 #'
 #'
 
-kobo_anonymisation_report <- function(frame, form = "form.xls", app = "console") {
 kobo_anonymisation_report <- function(frame, form = "form.xlsx", app = "console") {
   tryCatch({
     if (app == "shiny") {
       progress <- shiny::Progress$new()

diff --git a/R/kobo_anonymise.R b/R/kobo_anonymise.R
@@ -41,11  41,11 @@
 #'
 #' @examples
 #' \dontrun{
-#' kobo_anonymise(frame,  form = "form.xls")
 #' kobo_anonymise(frame,  form = "form.xlsx")
 #' }
 #'
 
-kobo_anonymise <- function(frame, form = "form.xls", app = "console") {
 kobo_anonymise <- function(frame, form = "form.xlsx", app = "console") {
 
   mainDir <- kobo_getMainDirectory()
   form_tmp <- paste(mainDir, "data", form, sep = "/", collapse = "/")

diff --git a/R/kobo_atlas_report.R b/R/kobo_atlas_report.R
@@ -24,7  24,7 @@
 #' }
 #'
 
-kobo_atlas_report <- function(form = "form.xls", 
 kobo_atlas_report <- function(form = "form.xlsx", 
                               app = "console", 
                               output ="html", 
                               render = "TRUE", 

diff --git a/R/kobo_check_analysis_plan.R b/R/kobo_check_analysis_plan.R
@@ -14,13  14,13 @@
 #'
 #' @examples
 #' \dontrun{
-#' kobo_check_analysis_plan("myform.xls")
 #' kobo_check_analysis_plan("form.xlsx")
 #' }
 #'
 #' @export kobo_check_analysis_plan
 #'
 
-kobo_check_analysis_plan <- function(form = "form.xls") {
 kobo_check_analysis_plan <- function(form = "form.xlsx") {
   tryCatch({
     result <- list()
     result$flag <- T

diff --git a/R/kobo_check_project_configuration.R b/R/kobo_check_project_configuration.R
@@ -14,13  14,13 @@
 #'
 #' @examples
 #' \dontrun{
-#' kobo_check_project_configuration("myform.xls")
 #' kobo_check_project_configuration("myform.xlsx")
 #' }
 #'
 #' @export kobo_check_project_configuration
 #'
 
-kobo_check_project_configuration <- function(form = "form.xls") {
 kobo_check_project_configuration <- function(form = "form.xlsx") {
   tryCatch({
     result <- list()
     result$flag <- T

diff --git a/R/kobo_clean.R b/R/kobo_clean.R
@@ -20,19  20,24 @@
 #'
 #' @examples
 #' \dontrun{
-#' kobo_clean(frame, form = "form.xls")
 #' kobo_clean(frame, form = "form.xlsx")
 #' }
 #'
 #'
 
-kobo_clean <- function(frame, form = "form.xls", app = "console") {
 kobo_clean <- function(frame, form = "form.xlsx", app = "console") {
 
   mainDir <- kobo_getMainDirectory()
   form <- as.character(form)
   #cat(paste0(form,"\n"))
   formpath <- as.character(paste0(mainDir,"/data/dico_",form,".csv"))
   #cat(paste0(formpath,"\n"))
   dico <- utils::read.csv(formpath, encoding = "UTF-8", na.strings = "")
 
 
   #formpath <- as.character(paste0(mainDir,"/data/dico_",form,".rda"))
   #cat(paste0(formpath,"\n"))
   #load(formpath)
 
   # frame <- MainDataFrame
   # frame <- household
@@ -49,7  54,8 @@ kobo_clean <- function(frame, form = "form.xls", app = "console") {
      dico.clean <- dico[ !(is.na(dico[, c("clean")])) ,  ]
       if (nrow(dico.clean) > 0) {
         cat(paste0(nrow(dico.clean), " potential variables to clean\n"))
-
 
         if (file.exists("R/apply_clean.R")) file.remove("R/apply_clean.R")
           for (i in 1:nrow(dico.clean)) {
            # i <- 1
             cat(paste0(i, "- Clean through an external table, if exists, the value of question: ", as.character(dico.clean[ i, c("label")]),"\n"))
@@ -58,7  64,7 @@ kobo_clean <- function(frame, form = "form.xls", app = "console") {
             variable <- paste0(as.character(dico.clean[ i, c("fullname")]))
             cleanfile <- paste0(as.character(dico.clean[ i, c("clean")]))
             cleanframe <- paste0(substr(as.character(dico.clean[ i, c("clean")]), 1, nchar(cleanfile) - 4))
-            formula1 <-  paste0(cleanframe," <- utils::read.csv(\"data/", cleanfile,"\", encoding = \"UTF-8\", na.strings = \"\")" )
             formula1 <-  paste0(cleanframe," <- utils::read.csv(\"data-raw/", cleanfile,"\", encoding = \"UTF-8\", na.strings = \"\")" )
             formula2 <- paste0("names(",cleanframe,")[1] <- \"",dico.clean[ i, c("fullname")],"\"" )
             formula3 <- paste0("names(",cleanframe,")[2] <- \"",dico.clean[ i, c("fullname")],".clean\"" )
             formula4 <- paste0("colname <- which(colnames(",framename,") == \"", variable,"\")")
@@ -69,20  75,20 @@ kobo_clean <- function(frame, form = "form.xls", app = "console") {
             formula9 <- paste0("round( nrow(", framename ,"[ !(is.na(", framename ,"$", variable ,".clean)), ]) / nrow(", framename ,") *100,digits = 1),\"%\n\n\"))")
 
 
-            if (file.exists("code/temp-clean.R")) file.remove("code/temp-clean.R")
-            cat(paste0("if (\"", as.character(dico.clean[ i, c("fullname")]) , "\" %in% names(", framename, ")) {" ), file = "code/temp-clean.R" , sep = "\n", append = TRUE)
-            cat(paste0(formula1, ""), file = "code/temp-clean.R" , sep = "\n", append = TRUE)
-            cat(paste0(formula2, ""), file = "code/temp-clean.R" , sep = "\n", append = TRUE)
-            cat(paste0(formula3, ""), file = "code/temp-clean.R" , sep = "\n", append = TRUE)
-            cat(paste0(formula4, ""), file = "code/temp-clean.R" , sep = "\n", append = TRUE)
-            cat(paste0(formula5, ""), file = "code/temp-clean.R" , sep = "\n", append = TRUE)
-            cat(paste0(formula6, ""), file = "code/temp-clean.R" , sep = "\n", append = TRUE)
-            cat(paste0(formula7, ""), file = "code/temp-clean.R" , sep = "\n", append = TRUE)
-            cat(paste0(formula8, ""), file = "code/temp-clean.R" , sep = "\n", append = TRUE)
-            cat(paste0(formula9, "} else {cat(\" That variable is not in that frame...\n\") } "), file = "code/temp-clean.R" , sep = "\n", append = TRUE)
-            source("code/temp-clean.R")
-            if (file.exists("code/temp-clean.R")) file.remove("code/temp-clean.R")
-          }
             cat(paste0("if (\"", as.character(dico.clean[ i, c("fullname")]) , "\" %in% names(", framename, ")) {" ), file = "R/apply_clean.R" , sep = "\n", append = TRUE)
             cat(paste0(formula1, ""), file = "R/apply_clean.R" , sep = "\n", append = TRUE)
             cat(paste0(formula2, ""), file = "R/apply_clean.R" , sep = "\n", append = TRUE)
             cat(paste0(formula3, ""), file = "R/apply_clean.R" , sep = "\n", append = TRUE)
             cat(paste0(formula4, ""), file = "R/apply_clean.R" , sep = "\n", append = TRUE)
             cat(paste0(formula5, ""), file = "R/apply_clean.R" , sep = "\n", append = TRUE)
             cat(paste0(formula6, ""), file = "R/apply_clean.R" , sep = "\n", append = TRUE)
             cat(paste0(formula7, ""), file = "R/apply_clean.R" , sep = "\n", append = TRUE)
             cat(paste0(formula8, ""), file = "R/apply_clean.R" , sep = "\n", append = TRUE)
             cat(paste0(formula9, "} else {cat(\" That variable is not in that frame...\n\") } "), file = "R/apply_clean.R" , sep = "\n", append = TRUE)
 
           } 
         source("R/apply_clean.R")
         #if (file.exists("R/apply_clean.R")) file.remove("R/apply_clean.R")
       }
   }
   return(frame)

diff --git a/R/kobo_cluster_report.R b/R/kobo_cluster_report.R
@@ -19,12  19,12 @@
 #'
 #' @examples
 #' \dontrun{
-#' kobo_cluster_report(frame =  MainDataFrame , form = "form.xls")
 #' kobo_cluster_report(frame =  MainDataFrame , form = "form.xlsx")
 #' }
 #'
 
 kobo_cluster_report <- function(frame =  MainDataFrame , 
-                                form = "form.xls", 
                                 form = "form.xlsx", 
                                 output ="html", 
                                 app = "console") {
   tryCatch({

diff --git a/R/kobo_consolidateone.R b/R/kobo_consolidateone.R
@@ -14,13  14,13 @@
 #'
 #' @examples
 #' \dontrun{
-#' kobo_consolidateone(frame , form = "form.xls")
 #' kobo_consolidateone(frame , form = "form.xlsx")
 #' }
 #'
 #'
 #' @return data
 
-kobo_consolidateone <- function(frame , form = "form.xls") {
 kobo_consolidateone <- function(frame , form = "form.xlsx") {
 
   configInfo <- kobo_get_config()
   mainDir <- kobo_getMainDirectory()

diff --git a/R/kobo_correlation_analysis.R b/R/kobo_correlation_analysis.R
@@ -22,7  22,7 @@
 #' @export kobo_correlation_analysis
 #'
 
-kobo_correlation_analysis <- function(form = "form.xls", frame, target, app = "console") {
 kobo_correlation_analysis <- function(form = "form.xlsx", frame, target, app = "console") {
   tryCatch({
     if (nrow(frame) == 0) {
       return(structure("Error: the frame is empty", class = "try-error"))