Create cleaning logbook

NAMESPACE

@@ -20,6 +20,7 @@ export(check_outliers)
 export(create_audit_list)
 export(create_clean_data)
 export(create_cleaning_log)
+export(create_cleaning_logbook)
 export(create_duration_from_audit_sum_all)
 export(create_duration_from_audit_with_start_end)
 export(create_logic_for_other)

R/create_cleaning_logbook.R

@@ -0,0 +1,111 @@
+
+
+#' Create data_exstract, logbook, deletion_log tables and add them to the cleaning logbook template
+#'
+#' @param raw_data Raw Dataset
+#' @param cleaning_log Cleaning Log
+#' @param col_enum Enumerator column name in both raw_data and cleaning_log. Must be the same and by default NA
+#' @param filename URL link for the location of the updated cleaning logbook
+#' @param uuid uuid column name both in raw_data and cleaning_log
+#'
+#' @return Return a list of 3 tables:
+#'         - "template_data_extract"
+#'         - "template_logbook"
+#'         - "template_deletion_log"
+#' And update the cleaning logbook with the new tables and automatically update the enumerator performance table
+#' @export
+#' @examples
+#' \dontrun{
+#' create_enumerator_performance(
+#' raw_data = cleaningtools::cleaningtools_raw_data,
+#' cleaning_log = cleaningtools::cleaningtools_cleaning_log,
+#' uuid = "X_uuid",
+#' col_enum = "enumerator_num",
+#' filename = "new_cleaning_logbook_draft.xlsx"
+#' )}
+create_cleaning_logbook <- function(raw_data,
+                                          cleaning_log,
+                                          uuid = "X_uuid",
+                                          col_enum = NA,
+                                          # link_cleaning_logbook = NA,
+                                          filename = NA){
+  ## check if col_enum in raw_data and cleaning_log
+  if(!col_enum %in% colnames(raw_data)) stop("Enumerator column not found in raw_data")
+  if(!col_enum %in% colnames(cleaning_log)) stop("Enumerator column not found in cleaning_log")
+
+  ## check if uuid in raw_data and cleaning_log
+  if(!uuid %in% colnames(raw_data)) stop("uuid column not found in raw_data")
+  if(!uuid %in% colnames(cleaning_log)) stop("uuid column not found in cleaning_log")
+
+  ## Create the template_data_extract table
+  template_data_extract <- raw_data %>%
+    dplyr::select(all_of(uuid), all_of(col_enum)) %>%
+    dplyr::rename("enumerator ID"= all_of(col_enum),
+                  "uuid" = all_of(uuid)) %>%
+    as.data.frame()
+
+  ## create a device id df
+  deviceiddf <- raw_data %>%
+    dplyr::select(all_of(uuid), deviceid)
+
+  ## Create the template_logbook table
+  template_logbook <- cleaning_log %>%
+    dplyr::filter(!change_type %in% c("remove_survey")) %>%
+    dplyr::left_join(deviceiddf, by = uuid) %>%
+    dplyr::mutate(`Type of Issue (Select from dropdown list)` = NA,
+                  changed = ifelse(change_type %in% c("change_response","blank_response"),"Yes","No")) %>%
+    dplyr::select(all_of(uuid),all_of(col_enum),deviceid,questions,issue,`Type of Issue (Select from dropdown list)`,
+                  reason,changed,old_value,new_value) %>%
+    dplyr::rename("uuid" = all_of(uuid),
+                  "Enumerator ID" = all_of(col_enum),
+                  "device ID" = deviceid,
+                  "question.name" = questions,
+                  "feedback" = reason,
+                  "old.value" = old_value, "new.value" = new_value) %>%
+    as.data.frame()
+
+  ## Create the template_deletion_log table
+  template_deletion_log <- cleaning_log %>%
+    dplyr::filter(change_type %in% c("remove_survey")) %>%
+    dplyr::left_join(deviceiddf, by = uuid) %>%
+    dplyr::mutate(`Type of Issue (Select from dropdown list)` = NA) %>%
+    dplyr::select(all_of(uuid),all_of(col_enum),deviceid,issue,`Type of Issue (Select from dropdown list)`,reason) %>%
+    dplyr::rename("uuid" = all_of(uuid),
+                  "Enumerator ID" = all_of(col_enum),
+                  "device ID" = deviceid,
+                  "Issue" = issue,
+                  "feedback" = reason)%>%
+    as.data.frame()
+
+  named_table = list("template_data_extract" = template_data_extract,
+                     "template_logbook" = template_logbook,
+                     "template_deletion_log" = template_deletion_log)
+
+  ## Writing tables to cleaning_logbook
+  wb <- openxlsx::loadWorkbook(system.file("extdata","Research_cycle_data_cleaning_logbook_template_v4_202331_AA.xlsx",package = "cleaningtools"))
+
+  openxlsx::writeData(wb = wb,
+                      x = named_table[["template_data_extract"]],
+                      sheet = "01_TEMPLATE_data_extract",
+                      startRow = 1, startCol = 1)
+
+  openxlsx::writeData(wb = wb,
+                           x = named_table[["template_logbook"]],
+                           sheet = "02_TEMPLATE_Logbook",
+                           startRow = 1,startCol = 1)
+
+
+  openxlsx::writeData(wb,
+                           x = named_table[["template_deletion_log"]],
+                           sheet = "03_TEMPLATE_deletion log",
+                           startCol = 1,startRow = 1)
+
+  if(is.na(filename)){
+    cat("Link to where the new cleaning_logbook should be saved is not provided, new cleaning_logbook will be saved in the same directory of the script.")
+    filename <- paste0("data_cleaning_workbook.xlsx")
+  }
+
+  openxlsx::saveWorkbook(wb, filename, overwrite = T)
+
+  return(named_table)
+}

tests/testthat/test-create_cleaning_logbook.R

@@ -0,0 +1,66 @@
+testthat::test_that("Create Cleaning Logbook", {
+  raw_data <- cleaningtools_raw_data
+  cleaning_log <- cleaningtools_cleaning_log
+
+  testthat::expect_error(create_cleaning_logbook(raw_data,cleaning_log,uuid = "X_uuid", col_enum = "absd"))
+  testthat::expect_equal(length(create_cleaning_logbook(raw_data,cleaning_log,uuid = "X_uuid", col_enum = "enumerator_num")), 3)
+
+## TESTING First Table
+test_data_raw <- data.frame(X_uuid = c("abcd","eeds","eedt","sdks"),
+                            deviceid = c(1,2,3,4),
+                            enumerator_num = c(1,2,4,4))
+
+expected_output <- data.frame(uuid = c("abcd","eeds","eedt","sdks"),
+                              `enumerator ID` = c(1,2,4,4)) %>%
+  dplyr::rename("enumerator ID" = enumerator.ID)
+actual_ouput <- create_cleaning_logbook(test_data_raw,cleaning_log,uuid = "X_uuid", col_enum = "enumerator_num")
+
+testthat::expect_equal(actual_ouput[[1]],
+                       expected_output)
+
+  ## TESTING Second Table
+  test_cleaning_log <- data.frame(X_uuid = c("abcd","eeds","eedt","sdks"),
+                                  enumerator_num = c(1,2,4,4),
+                                  questions = c("q1","q2","q3","q3"),
+                                  reason = c("f1","f2","f4","f3"),
+                                  issue = c("duplicate","duplicate","outlier",
+                                            "other_responses"),
+                                  change_type = c("remove_survey","remove_survey","no_action",
+                                                  "change_response"),
+                                  old_value= c(1,1,1,1), new_value = c(2,2,2,2))
+
+  expected_output <- data.frame(uuid = c("eedt","sdks"),
+                                `Enumerator ID` = c(4,4),
+                                `device ID` = c(3,4),
+                                question.name = c("q3","q3"),
+                                issue = c("outlier","other_responses"),
+                                `Type of Issue (Select from dropdown list)` = c(NA,NA),
+                                feedback = c("f4","f3"),
+                                changed = c("No","Yes"),
+                                old.value = c(1,1), new.value = c(2,2)) %>%
+    dplyr::rename("Enumerator ID" = Enumerator.ID,
+                  "device ID" = device.ID,
+                  "Type of Issue (Select from dropdown list)" = Type.of.Issue..Select.from.dropdown.list.)
+
+  actual_ouput <- create_cleaning_logbook(test_data_raw,test_cleaning_log,uuid = "X_uuid", col_enum = "enumerator_num")
+
+  testthat::expect_equal(actual_ouput[[2]],
+                         expected_output)
+
+  ## TESTING Third Table
+  expected_output <- data.frame(uuid = c("abcd","eeds"),
+                                `Enumerator ID` = c(1,2),
+                                `device ID` = c(1,2),
+                                Issue = c("duplicate","duplicate"),
+                                `Type of Issue (Select from dropdown list)` = c(NA,NA),
+                                feedback = c("f1","f2")) %>%
+    dplyr::rename("Enumerator ID" = Enumerator.ID,
+                  "device ID" = device.ID,
+                  "Type of Issue (Select from dropdown list)" = Type.of.Issue..Select.from.dropdown.list.)
+  actual_ouput <- create_cleaning_logbook(test_data_raw,test_cleaning_log, col_enum = "enumerator_num")
+
+  testthat::expect_equal(actual_ouput[[3]],
+                         expected_output)
+
+
+})