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workingScript-IndicatorCodeGenerator.R
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166 lines (123 loc) · 10 KB
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# read csv from url
FacilityCodeList <-read.csv("https://www.datim.org/api/sqlViews/DotdxKrNZxG/data.csv?var=dataSets:zL8TlPVzEBZ",stringsAsFactors = F,sep=',')
CommunityCodeList <-read.csv("https://www.datim.org/api/sqlViews/DotdxKrNZxG/data.csv?var=dataSets:TBcmmtoaCBC",stringsAsFactors = F,sep=',')
AGYW_PREV_CodeList <-read.csv("https://www.datim.org/api/sqlViews/DotdxKrNZxG/data.csv?var=dataSets:qHyrHc4zwx4",stringsAsFactors = F,sep=',')
# Add conditional column for reporting frequency
FacilityCodeList$ReportingFreq <- ifelse(grepl("HTS|TX_NEW|TX_CURR|TX_RTT|TX_ML|TX_PVLS|TX_ML|VMMC_CIRC|PMTCT|TB_ART|TB_STAT", FacilityCodeList$dataelement) , "Quarterly",
ifelse(grepl("TX_TB|TB_PREV|KP_PREV|PP_PREV|AGYW_PREV|PrEP_CURR|PrEP_NEW|OVC_SERV|OVC_HIVSTAT|SC_ARVDISP|SC_CURR|CXCA_TX|CXCA_SCRN", FacilityCodeList$dataelement) , "SemiAnnual", "Annual"))
CommunityCodeList$ReportingFreq <- ifelse(grepl("HTS|TX_NEW|TX_CURR|TX_RTT|TX_ML|TX_PVLS|TX_ML|VMMC_CIRC|PMTCT|TB_ART|TB_STAT", CommunityCodeList$dataelement) , "Quarterly",
ifelse(grepl("TX_TB|TB_PREV|KP_PREV|PP_PREV|AGYW_PREV|PrEP_CURR|PrEP_NEW|OVC_SERV|OVC_HIVSTAT|SC_ARVDISP|SC_CURR|CXCA_TX|CXCA_SCRN", CommunityCodeList$dataelement) , "SemiAnnual", "Annual"))
# separate into DSD, TA and NoApp
code_DSD_Facility <- subset(FacilityCodeList, grepl("_DSD", code))
rownames(code_DSD_Facility) <- c()
code_DSD_Community <- subset(CommunityCodeList, grepl("_DSD", code))
rownames(code_DSD_Community) <- c()
#
code_TA_Facility <- subset(FacilityCodeList, grepl("_TA", code))
rownames(code_TA_Facility) <- c()
code_TA_Community <- subset(CommunityCodeList, grepl("_TA", code))
rownames(code_TA_Community) <- c()
code_NoApp_Facility <- subset(FacilityCodeList, grepl("_NoApp", code))
rownames(code_NoApp_Facility) <- c()
code_CS_Facility <- subset(FacilityCodeList, grepl("_CS_", code)) # CS means Centrally Supported
rownames(code_CS_Facility) <- c()
code_CS_Community <- subset(CommunityCodeList, grepl("_CS_", code))
rownames(code_CS_Community) <- c()
## multi find and replace, start
mgsub <-function(pattern, replacement, x, ...) {
if (length(pattern)!=length(replacement)) {
stop("pattern and replacement do not have the same length.")
}
result <- x
for (i in 1:length(pattern)) {
result <- gsub(pattern[i], replacement[i], result, ...)
}
result
}
#
code_DSD_Facility$de <- mgsub("DSD", "TA",code_DSD_Facility$dataelement) # very important part. connection starts from here
code_DSD_Community$de <- mgsub("DSD", "TA",code_DSD_Community$dataelement) # very important part. connection starts from here
library(dplyr)
code_DSD_Facility <- code_DSD_Facility %>%
# tidyr::unite(Concatenate_1, "Indi_Code","categoryoptioncombouid", sep=";", remove=FALSE) %>%
tidyr::unite(Concatenate_1, "de","categoryoptioncombouid", sep=";", remove=FALSE) %>%
tidyr::unite(RETURN_FIELD_DSD, "dataelementuid","categoryoptioncombouid", sep=";", remove=FALSE)
code_TA_Facility <- code_TA_Facility %>%
#tidyr::unite(Concatenate_1, "Indi_Code","categoryoptioncombouid", sep=";", remove=FALSE) %>%
tidyr::unite(Concatenate_1, "dataelement","categoryoptioncombouid", sep=";", remove=FALSE) %>%
tidyr::unite(RETURN_FIELD_TA, "dataelementuid","categoryoptioncombouid", sep=";", remove=FALSE)
code_DSD_Community <- code_DSD_Community %>%
#tidyr::unite(Concatenate_1, "Indi_Code","categoryoptioncombouid", sep=";", remove=FALSE) %>%
tidyr::unite(Concatenate_1, "de","categoryoptioncombouid", sep=";", remove=FALSE) %>%
tidyr::unite(RETURN_FIELD_DSD, "dataelementuid","categoryoptioncombouid", sep=";", remove=FALSE)
code_TA_Community <- code_TA_Community %>%
#tidyr::unite(Concatenate_1, "Indi_Code","categoryoptioncombouid", sep=";", remove=FALSE) %>%
tidyr::unite(Concatenate_1, "dataelement","categoryoptioncombouid", sep=";", remove=FALSE) %>%
tidyr::unite(RETURN_FIELD_TA, "dataelementuid","categoryoptioncombouid", sep=";", remove=FALSE)
# merge DSD & TA dataframes by a common RowIndex column
code_DSD_TA_Facility<-merge(code_DSD_Facility,code_TA_Facility, by="Concatenate_1")
code_DSD_TA_Community<-merge(code_DSD_Community,code_TA_Community, by="Concatenate_1")
# select wanted columns
code_DSD_TA_Facility <-dplyr::select(code_DSD_TA_Facility,
"dataset.x","dataelement.x","dataelementuid.x","categoryoptioncombo.x","categoryoptioncombouid.x","RETURN_FIELD_DSD","dataelement.y","dataelementuid.y","categoryoptioncombo.y","categoryoptioncombouid.y","RETURN_FIELD_TA", "ReportingFreq.x")
code_DSD_TA_Community <-dplyr::select(code_DSD_TA_Community,
"dataset.x","dataelement.x","dataelementuid.x","categoryoptioncombo.x","categoryoptioncombouid.x","RETURN_FIELD_DSD","dataelement.y","dataelementuid.y","categoryoptioncombo.y","categoryoptioncombouid.y","RETURN_FIELD_TA", "ReportingFreq.x")
#rename columns
code_DSD_TA_Facility <-dplyr::rename(code_DSD_TA_Facility,
dataset=dataset.x,
dataelement.DSD=dataelement.x,
dataelementuid.DSD=dataelementuid.x,
categoryoptioncombo.DSD=categoryoptioncombo.x,
categoryoptioncombouid.DSD=categoryoptioncombouid.x,
dataelement.TA=dataelement.y,
dataelementuid.TA=dataelementuid.y,
categoryoptioncombo.TA=categoryoptioncombo.y,
categoryoptioncombouid.TA=categoryoptioncombouid.y,
ReportingFreq=ReportingFreq.x
)
code_DSD_TA_Community <-dplyr::rename(code_DSD_TA_Community,
dataset=dataset.x,
dataelement.DSD=dataelement.x,
dataelementuid.DSD=dataelementuid.x,
categoryoptioncombo.DSD=categoryoptioncombo.x,
categoryoptioncombouid.DSD=categoryoptioncombouid.x,
dataelement.TA=dataelement.y,
dataelementuid.TA=dataelementuid.y,
categoryoptioncombo.TA=categoryoptioncombo.y,
categoryoptioncombouid.TA=categoryoptioncombouid.y,
ReportingFreq=ReportingFreq.x
)
# Concatenate two string columns with ";"
code_NoApp_Facility$RETURN_FIELD_DSD = paste(code_NoApp_Facility$`dataelementuid`,";",code_NoApp_Facility$`categoryoptioncombouid`)
code_CS_Facility$RETURN_FIELD_DSD = paste(code_CS_Facility$`dataelementuid`,";",code_CS_Facility$`categoryoptioncombouid`)
code_CS_Community$RETURN_FIELD_DSD = paste(code_CS_Community$`dataelementuid`,";",code_CS_Community$`categoryoptioncombouid`)
AGYW_PREV_CodeList$RETURN_FIELD_DSD = paste(AGYW_PREV_CodeList$`dataelementuid`,";",AGYW_PREV_CodeList$`categoryoptioncombouid`)
# check for duplicates
code_DSD_TA_Facility %>%
group_by(dataset,dataelement.DSD,dataelementuid.DSD,categoryoptioncombo.DSD,categoryoptioncombouid.DSD,RETURN_FIELD_DSD,dataelement.TA,dataelementuid.TA,categoryoptioncombo.TA,categoryoptioncombouid.TA,RETURN_FIELD_TA,ReportingFreq) %>%
dplyr::filter(n()>1)
# add column for Row indexes, i.e CODE column having incrementing numbers
code_DSD_TA_Facility$Indicator_code <- seq.int(nrow(code_DSD_TA_Facility))
code_DSD_TA_Community$Indicator_code <- seq.int(from=nrow(code_DSD_TA_Facility)+1, to=(nrow(code_DSD_TA_Facility)+1+nrow(code_DSD_TA_Community)-1)) # 2875 ## manually indicate the custom from and to ranges
code_NoApp_Facility$Indicator_code <- seq.int(nrow(code_NoApp_Facility))
code_CS_Facility$Indicator_code <- seq.int(nrow(code_CS_Facility))
code_CS_Community$Indicator_code <- seq.int(from=nrow(code_CS_Facility)+1, to=(nrow(code_CS_Facility)+1+nrow(code_CS_Community)-1))
AGYW_PREV_CodeList$Indicator_code <- seq.int(nrow(AGYW_PREV_CodeList))
# remove white spaces in a string
code_DSD_TA_Facility$RETURN_FIELD_DSD <-gsub(" ", "", code_DSD_TA_Facility$RETURN_FIELD_DSD, fixed = TRUE)
code_DSD_TA_Facility$RETURN_FIELD_TA <-gsub(" ", "", code_DSD_TA_Facility$RETURN_FIELD_TA, fixed = TRUE)
code_DSD_TA_Community$RETURN_FIELD_DSD <-gsub(" ", "", code_DSD_TA_Community$RETURN_FIELD_DSD, fixed = TRUE)
code_DSD_TA_Community$RETURN_FIELD_TA <-gsub(" ", "", code_DSD_TA_Community$RETURN_FIELD_TA, fixed = TRUE)
code_NoApp_Facility$RETURN_FIELD_DSD <-gsub(" ", "", code_NoApp_Facility$RETURN_FIELD_DSD, fixed = TRUE)
code_CS_Facility$RETURN_FIELD_DSD <-gsub(" ", "", code_CS_Facility$RETURN_FIELD_DSD, fixed = TRUE)
code_CS_Community$RETURN_FIELD_DSD <-gsub(" ", "", code_CS_Community$RETURN_FIELD_DSD, fixed = TRUE)
AGYW_PREV_CodeList$RETURN_FIELD_DSD <-gsub(" ", "", AGYW_PREV_CodeList$RETURN_FIELD_DSD, fixed = TRUE)
# saving the file
# row bind facility and community code list
code_DSD_TA_Facility_and_Community <-rbind(code_DSD_TA_Facility,code_DSD_TA_Community)
code_CS_Facility_and_Community <-rbind(code_CS_Facility,code_CS_Community)
#
write.csv(code_DSD_TA_Facility_and_Community,file=paste0("/home/fred/Downloads/DATIM4U/FY2021/Q1/Metadata/Coding/DATIM4U_IndicatorCodeList_Facility_and_Community_FY2021Q1_DSDTA_", format(Sys.time(), format = "%F_%R_%Z", tz = "Africa/Kampala"), ".csv"), row.names = FALSE)
write.csv(code_NoApp_Facility,file=paste0("/home/fred/Downloads/DATIM4U/FY2021/Q1/Metadata/Coding/DATIM4U_IndicatorCodeList_NoApp_FY2021_", format(Sys.time(), format = "%F_%R_%Z", tz = "Africa/Kampala"), ".csv"), row.names = FALSE)
write.csv(code_CS_Facility_and_Community,file=paste0("/home/fred/Downloads/DATIM4U/FY2021/Q2/Metadata/Coding/DATIM4U_IndicatorCodeList_CS_FY2021Q1_", format(Sys.time(), format = "%F_%R_%Z", tz = "Africa/Kampala"), ".csv"), row.names = FALSE)
write.csv(AGYW_PREV_CodeList,file=paste0("/home/fred/Downloads/DATIM4U/FY2021/Q1/Metadata/Coding/DATIM4U_IndicatorCodeList_AGYW_PREV_FY2021_", format(Sys.time(), format = "%F_%R_%Z", tz = "Africa/Kampala"), ".csv"), row.names = FALSE)