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small change in teh save.deletion.request for the IPHRA cleaning part…
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…1 and fix the github readme
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@AbrahamAz
AbrahamAz committed Oct 9, 2024
1 parent 2a926ca commit 5ded5bb
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1 change: 1 addition & 0 deletions README.Rmd
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Expand Up @@ -884,6 +884,7 @@ After running all the line in the run_mort_descriptive_analysis.R, below are the
>`Weight` <- If yes, select the weight column in your data.<br>
>`Died Healthcare` <- Did the died person seek healthcare (Yes/No)<br>
</details>
As you saw in the output folder, you will have another excel file outputed from the analysis script.
<ul>
<li>The Excel file includes 2 sheets. The first 2 are all the tables that you see in the different sections of this HTML output. You can navigate to respective tables through the first sheet "Table of Contents".</li>
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -1266,6 +1266,7 @@ Details
> weighted`<- Question to check if your data is weighted (Yes/No).<br>`Weight`<- If yes, select the weight column in your data.<br>`Died
> Healthcare\` \<- Did the died person seek healthcare (Yes/No)<br>
</details>
As you saw in the output folder, you will have another excel file
outputed from the analysis script.
<ul>
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211 changes: 104 additions & 107 deletions inst/iphra_cleaning/src/utils/utils_cleaning.R
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Expand Up @@ -117,126 +117,123 @@ save.deletion.requests <- function(df, wb_name, use_template = F){
openxlsx::addWorksheet(wb, "Sheet3", visible = F)
openxlsx::writeData(wb, "Sheet3", x = c("Remove","Keep","Change"))
## add roster loop_indexes
dl_uuids_roster <- df %>%
filter(variable == "num_hh" & stringr::str_starts(reason, "hh_roster")) %>%
pull(uuid)
if(length(dl_uuids_roster)>0){
uuid_roster_loops <- raw.hh_roster %>%
filter(uuid %in% dl_uuids_roster) %>%
dplyr::select(uuid, loop_index)
openxlsx::addWorksheet(wb, "Sheet4", visible = F)
openxlsx::writeData(wb, "Sheet4",x = uuid_roster_loops)
}
## add health loop_indexes
dl_uuids_health <- df %>%
filter(variable == "num_hh" & stringr::str_starts(reason, "ind_health")) %>%
pull(uuid)
if(length(dl_uuids_health)>0){
uuid_health_loops <- raw.ind_health %>%
filter(uuid %in% dl_uuids_health) %>%
dplyr::select(uuid, loop_index)
openxlsx::addWorksheet(wb, "Sheet5", visible = F)
openxlsx::writeData(wb, "Sheet5",x = uuid_health_loops)
}

if(!is.null(raw.water_count_loop)){
## add water loop_indexes
dl_uuids_water <- df %>%
filter(variable == "num_containers") %>%
if("variable" %in% names(df)){
dl_uuids_roster <- df %>%
filter(variable == "num_hh" & stringr::str_starts(reason, "hh_roster")) %>%
pull(uuid)
if(length(dl_uuids_water)>0){
uuid_water_loops <- raw.water_count_loop %>%
filter(uuid %in% dl_uuids_water) %>%
if(length(dl_uuids_roster)>0){
uuid_roster_loops <- raw.hh_roster %>%
filter(uuid %in% dl_uuids_roster) %>%
dplyr::select(uuid, loop_index)
openxlsx::addWorksheet(wb, "Sheet6", visible = F)
openxlsx::writeData(wb, "Sheet6",x = uuid_water_loops)
openxlsx::addWorksheet(wb, "Sheet4", visible = F)
openxlsx::writeData(wb, "Sheet4",x = uuid_roster_loops)
}
}

## add child loop_indexes
dl_uuids_child <- df %>%
filter(variable == "num_hh" & stringr::str_starts(reason, "child")) %>%
pull(uuid)
if(length(dl_uuids_child)>0){
uuid_child_loops <- raw.child_nutrition %>%
filter(uuid %in% dl_uuids_child) %>%
dplyr::select(uuid, loop_index)
openxlsx::addWorksheet(wb, "Sheet7", visible = F)
openxlsx::writeData(wb, "Sheet7",x = uuid_child_loops)
}
if(!is.null(raw.women)){
## add water loop_indexes
dl_uuids_women <- df %>%
filter(variable == "num_hh" & stringr::str_starts(reason, "women")) %>%
## add health loop_indexes
dl_uuids_health <- df %>%
filter(variable == "num_hh" & stringr::str_starts(reason, "ind_health")) %>%
pull(uuid)
if(length(dl_uuids_women)>0){
uuid_women_loops <- raw.women %>%
filter(uuid %in% dl_uuids_women) %>%
if(length(dl_uuids_health)>0){
uuid_health_loops <- raw.ind_health %>%
filter(uuid %in% dl_uuids_health) %>%
dplyr::select(uuid, loop_index)
openxlsx::addWorksheet(wb, "Sheet8", visible = F)
openxlsx::writeData(wb, "Sheet8",x = uuid_women_loops)
openxlsx::addWorksheet(wb, "Sheet5", visible = F)
openxlsx::writeData(wb, "Sheet5",x = uuid_health_loops)
}
}

if(!is.null(raw.died_member)){
## add died loop_indexes
dl_uuids_died <- df %>%
filter(variable == "num_died") %>%
if(!is.null(raw.water_count_loop)){
## add water loop_indexes
dl_uuids_water <- df %>%
filter(variable == "num_containers") %>%
pull(uuid)
if(length(dl_uuids_water)>0){
uuid_water_loops <- raw.water_count_loop %>%
filter(uuid %in% dl_uuids_water) %>%
dplyr::select(uuid, loop_index)
openxlsx::addWorksheet(wb, "Sheet6", visible = F)
openxlsx::writeData(wb, "Sheet6",x = uuid_water_loops)
}
}
## add child loop_indexes
dl_uuids_child <- df %>%
filter(variable == "num_hh" & stringr::str_starts(reason, "child")) %>%
pull(uuid)
if(length(dl_uuids_died)>0){
uuid_died_loops <- raw.died_member %>%
filter(uuid %in% dl_uuids_died) %>%
if(length(dl_uuids_child)>0){
uuid_child_loops <- raw.child_nutrition %>%
filter(uuid %in% dl_uuids_child) %>%
dplyr::select(uuid, loop_index)
openxlsx::addWorksheet(wb, "Sheet9", visible = F)
openxlsx::writeData(wb, "Sheet9",x = uuid_died_loops)
openxlsx::addWorksheet(wb, "Sheet7", visible = F)
openxlsx::writeData(wb, "Sheet7",x = uuid_child_loops)
}
}

for (i in 1:nrow(df)){
if(!is.na(df$variable[i]) & df$variable[i] == "num_died"){
uuid <- df$uuid[i]
range_min <- min(which(uuid_died_loops$uuid %in% uuid)) + 1
range_max <- max(which(uuid_died_loops$uuid %in% uuid)) + 1
validate <- paste0("'Sheet9'!$B",range_min,":$B",range_max)
openxlsx::dataValidation(wb, "Sheet2", cols = ncol(df)-1, rows = 1 + i, type = "list", value = validate)
}
if(!is.na(df$variable[i]) & df$variable[i] == "num_containers"){
uuid <- df$uuid[i]
range_min <- min(which(uuid_water_loops$uuid %in% uuid)) + 1
range_max <- max(which(uuid_water_loops$uuid %in% uuid)) + 1
validate <- paste0("'Sheet6'!$B",range_min,":$B",range_max)
openxlsx::dataValidation(wb, "Sheet2", cols = ncol(df)-1, rows = 1 + i, type = "list", value = validate)
}
if(!is.na(df$variable[i]) & df$variable[i] == "num_hh" & stringr::str_starts(df$reason[i], "child")){
uuid <- df$uuid[i]
range_min <- min(which(uuid_child_loops$uuid %in% uuid)) + 1
range_max <- max(which(uuid_child_loops$uuid %in% uuid)) + 1
validate <- paste0("'Sheet7'!$B",range_min,":$B",range_max)
openxlsx::dataValidation(wb, "Sheet2", cols = ncol(df)-1, rows = 1 + i, type = "list", value = validate)
}
if(!is.na(df$variable[i]) & df$variable[i] == "num_hh" & stringr::str_starts(df$reason[i], "women")){
uuid <- df$uuid[i]
range_min <- min(which(uuid_women_loops$uuid %in% uuid)) + 1
range_max <- max(which(uuid_women_loops$uuid %in% uuid)) + 1
validate <- paste0("'Sheet8'!$B",range_min,":$B",range_max)
openxlsx::dataValidation(wb, "Sheet2", cols = ncol(df)-1, rows = 1 + i, type = "list", value = validate)
if(!is.null(raw.women)){
## add water loop_indexes
dl_uuids_women <- df %>%
filter(variable == "num_hh" & stringr::str_starts(reason, "women")) %>%
pull(uuid)
if(length(dl_uuids_women)>0){
uuid_women_loops <- raw.women %>%
filter(uuid %in% dl_uuids_women) %>%
dplyr::select(uuid, loop_index)
openxlsx::addWorksheet(wb, "Sheet8", visible = F)
openxlsx::writeData(wb, "Sheet8",x = uuid_women_loops)
}
}
if(!is.na(df$variable[i]) & df$variable[i] == "num_hh" & stringr::str_starts(df$reason[i], "ind_health")){
uuid <- df$uuid[i]
range_min <- min(which(uuid_health_loops$uuid %in% uuid)) + 1
range_max <- max(which(uuid_health_loops$uuid %in% uuid)) + 1
validate <- paste0("'Sheet5'!$B",range_min,":$B",range_max)
openxlsx::dataValidation(wb, "Sheet2", cols = ncol(df)-1, rows = 1 + i, type = "list", value = validate)
if(!is.null(raw.died_member)){
## add died loop_indexes
dl_uuids_died <- df %>%
filter(variable == "num_died") %>%
pull(uuid)
if(length(dl_uuids_died)>0){
uuid_died_loops <- raw.died_member %>%
filter(uuid %in% dl_uuids_died) %>%
dplyr::select(uuid, loop_index)
openxlsx::addWorksheet(wb, "Sheet9", visible = F)
openxlsx::writeData(wb, "Sheet9",x = uuid_died_loops)
}
}
if(!is.na(df$variable[i]) & df$variable[i] == "num_hh" & stringr::str_starts(df$reason[i], "hh_roster")){
uuid <- df$uuid[i]
range_min <- min(which(uuid_roster_loops$uuid %in% uuid)) + 1
range_max <- max(which(uuid_roster_loops$uuid %in% uuid)) + 1
validate <- paste0("'Sheet4'!$B",range_min,":$B",range_max)
openxlsx::dataValidation(wb, "Sheet2", cols = ncol(df)-1, rows = 1 + i, type = "list", value = validate)
for (i in 1:nrow(df)){
if(!is.na(df$variable[i]) & df$variable[i] == "num_died"){
uuid <- df$uuid[i]
range_min <- min(which(uuid_died_loops$uuid %in% uuid)) + 1
range_max <- max(which(uuid_died_loops$uuid %in% uuid)) + 1
validate <- paste0("'Sheet9'!$B",range_min,":$B",range_max)
openxlsx::dataValidation(wb, "Sheet2", cols = ncol(df)-1, rows = 1 + i, type = "list", value = validate)
}
if(!is.na(df$variable[i]) & df$variable[i] == "num_containers"){
uuid <- df$uuid[i]
range_min <- min(which(uuid_water_loops$uuid %in% uuid)) + 1
range_max <- max(which(uuid_water_loops$uuid %in% uuid)) + 1
validate <- paste0("'Sheet6'!$B",range_min,":$B",range_max)
openxlsx::dataValidation(wb, "Sheet2", cols = ncol(df)-1, rows = 1 + i, type = "list", value = validate)
}
if(!is.na(df$variable[i]) & df$variable[i] == "num_hh" & stringr::str_starts(df$reason[i], "child")){
uuid <- df$uuid[i]
range_min <- min(which(uuid_child_loops$uuid %in% uuid)) + 1
range_max <- max(which(uuid_child_loops$uuid %in% uuid)) + 1
validate <- paste0("'Sheet7'!$B",range_min,":$B",range_max)
openxlsx::dataValidation(wb, "Sheet2", cols = ncol(df)-1, rows = 1 + i, type = "list", value = validate)
}
if(!is.na(df$variable[i]) & df$variable[i] == "num_hh" & stringr::str_starts(df$reason[i], "women")){
uuid <- df$uuid[i]
range_min <- min(which(uuid_women_loops$uuid %in% uuid)) + 1
range_max <- max(which(uuid_women_loops$uuid %in% uuid)) + 1
validate <- paste0("'Sheet8'!$B",range_min,":$B",range_max)
openxlsx::dataValidation(wb, "Sheet2", cols = ncol(df)-1, rows = 1 + i, type = "list", value = validate)
}
if(!is.na(df$variable[i]) & df$variable[i] == "num_hh" & stringr::str_starts(df$reason[i], "ind_health")){
uuid <- df$uuid[i]
range_min <- min(which(uuid_health_loops$uuid %in% uuid)) + 1
range_max <- max(which(uuid_health_loops$uuid %in% uuid)) + 1
validate <- paste0("'Sheet5'!$B",range_min,":$B",range_max)
openxlsx::dataValidation(wb, "Sheet2", cols = ncol(df)-1, rows = 1 + i, type = "list", value = validate)
}
if(!is.na(df$variable[i]) & df$variable[i] == "num_hh" & stringr::str_starts(df$reason[i], "hh_roster")){
uuid <- df$uuid[i]
range_min <- min(which(uuid_roster_loops$uuid %in% uuid)) + 1
range_max <- max(which(uuid_roster_loops$uuid %in% uuid)) + 1
validate <- paste0("'Sheet4'!$B",range_min,":$B",range_max)
openxlsx::dataValidation(wb, "Sheet2", cols = ncol(df)-1, rows = 1 + i, type = "list", value = validate)
}
}
}

##Adding data validation
for (i in 1:nrow(df)){
validate <- paste0("'Sheet3'!$A1:$A3")
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