R/HA_CATH_W_ATN.R

In surveyPrev: Mapping the Prevalence of Binary Indicators using Survey Data in Small Areas

##'HA_CATH_W_ATN
#' @param IRdata  data.frame from surveyPrev::getDHSdata
#'
#' @return A partially processed data.frame that will be used in surveyPrev::getDHSindicator. The whole function can be used as a parameter in surveyPrev::getDHSindicator
#'
#' @author Miaolei Bao, Yunhan Wu, Qianyu Dong
#' @examples
#' \dontrun{
#' }
#' @export
##'HA_CATH_W_ATN
#' @param IRdata  data.frame from surveyPrev::getDHSdata
#'
#' @return A partially processed data.frame that will be used in surveyPrev::getDHSindicator. The whole function can be used as a parameter in surveyPrev::getDHSindicator
#'
#' @author Miaolei Bao, Yunhan Wu, Qianyu Dong
#' @examples
#' \dontrun{
#' }
#' @export
##'HA_CATH_W_ATN
#' @param IRdata  data.frame from surveyPrev::getDHSdata
#'
#' @return A partially processed data.frame that will be used in surveyPrev::getDHSindicator. The whole function can be used as a parameter in surveyPrev::getDHSindicator
#'
#' @author Miaolei Bao, Yunhan Wu, Qianyu Dong
#' @examples
#' \dontrun{
#' dhsData <- getDHSdata(country = "Zambia", indicator = "HA_CATH_W_ATN", year = 2018)
#' }
#'
#' @export
HA_CATH_W_ATN <- function(IRdata){
# ******************************************************************************
# Program: 			  HK_TEST_CONSL.R
# Purpose: 			  Code to compute indicators on HIV rior testing and counseling
# Data inputs: 		IR and MR datasets
# Data outputs:		coded variables
# Author:				  Shireen Assaf for code share project
# Translated to R: Courtney Allen
# Date last modified: September 2022 by Courtney Allen 
# ******************************************************************************

# Variables created in this file ------------------------------------------------
# hk_test_where			"Know where to get an HIV test"
# hk_test_prior			"Prior HIV testing status and whether received test result"
# hk_test_ever			"Ever been tested for HIV"
# hk_test_12m				"Tested for HIV in the past 12 months and received results of the last test"
# 
# hk_hiv_selftest_heard	"Ever heard of HIV self-test kits"
# hk_hiv_selftest_use		"Ever used a HIV self-test kit"
#
# 
# FOR WOMEN ONLY
#   hk_hiv_consl_anc		"Received counseling on HIV during ANC visit among women with a birth 2 years before the survey"
#   hk_test_consl_anc		"Received HIV test during ANC visit and received results and post-test counseling among women with a birth 2 years before the survey"
#   hk_test_noconsl_anc		"Received HIV test during ANC visit and received results but no post-test counseling among women with a birth 2 years before the survey"
#   hk_test_noresult_anc	"Received HIV test during ANC visit and did not receive test results among women with a birth 2 years before the survey"
#   hk_hiv_receivedall_anc	"Received HIV counseling, HIV test, and test results during ANC visit among women with a birth 2 years before the survey"
#   hk_test_anclbr_result	"Received HIV test during ANC visit or labor and received results among women with a birth 2 years before the survey"
#   hk_test_anclbr_noresult	"Received HIV test during ANC visit or labor but did not receive results among women with a birth 2 years before the survey"

# SETUP ------------------------------------------------------------------------

# Create yes and no category labels
yesno<- c("Yes" = 1, "No" = 0)


# COVERAGE OF PRIOR HIV TESTING (WOMEN)-----------------------------------------
    
# Know where to get HIV test
IRdata <- IRdata %>% mutate(hk_test_where = case_when(
  v781==1 | v783==1 ~ 1,
  TRUE ~ 0)) %>%
  set_value_labels(hk_test_where = yesno) %>%
  set_variable_labels(hk_test_where = "Know where to get an HIV test")

# Had prior HIV test and whether they received results
IRdata <- IRdata %>% mutate(hk_test_prior = case_when(
  v781==1 & v828==1 ~ 1,
  v781==1 & v828==0 ~ 2,
  v781==0 ~ 3)) %>%
  set_value_labels(hk_test_prior = c("Tested and received results"= 1,
                                   "Tested and did not receive results" = 2,
                                   "Never tested" = 3)) %>%
  set_variable_labels(hk_test_prior = "Prior HIV testing status and whether received test result")

# Ever tested
IRdata <- IRdata %>% mutate(hk_test_ever = case_when(
  v781==1 ~ 1,
  TRUE ~ 0)) %>%
  set_value_labels(hk_test_ever = yesno) %>%
  set_variable_labels(hk_test_ever = "Ever been tested for HIV")

# Tested in last 12 months and received test results
IRdata <- IRdata %>% mutate(hk_test_12m = case_when(
  v828==1 & v826a %in% 0:11 ~ 1,
  TRUE ~ 0)) %>%
    set_value_labels(hk_test_12m = yesno) %>%
    set_variable_labels(hk_test_12m = "Tested for HIV in the past 12 months and received results of the last test")

# Heard of self-test kits
IRdata <- IRdata %>% mutate(hk_hiv_selftest_heard = case_when(
  v856 %in% 1:3 ~ 1,
  TRUE ~ 0)) %>%
  set_value_labels(hk_hiv_selftest_heard = yesno) %>%
  set_variable_labels(hk_hiv_selftest_heard = "Ever heard of HIV self-test kits")

# Ever used a self-test kit
IRdata <- IRdata %>% mutate(hk_hiv_selftest_use = case_when(
  v856==1 ~ 1,
  TRUE ~ 0)) %>%
  set_value_labels(hk_hiv_selftest_use = yesno) %>%
  set_variable_labels(hk_hiv_selftest_use = "Ever used a HIV self-test kit")



# PREGNANT WOMEN COUNSELED, TESTED FOR HIV -------------------------------------

  
# NOTE - HOW TO CHECK FOR B19 -------------------------  -----------------------
# Indicators are among women with a live birth in the two years preceiding the survey. 

# To make this restriction we need to compute the age of most recent child (agec).
IRdata <- IRdata %>% mutate(agec = v008 - b3_01)

# check if survey has b19, which should be used instead to compute age. 
b19_check <-"b19_01" %in% colnames(IRdata)

# if b19 is present
ifelse(b19_check=="TRUE",
       b19_included <- 1,
       b19_included <- 0)

# check if b19 actually has values or is empty
ifelse(is.na(sd(IRdata$b19_01, na.rm=TRUE)) | sd(IRdata$b19_01) == 0, 
       b19_included <- 0,)
IRdata <- IRdata %>% mutate(b19_included = b19_included)

# if b19 is present or has values, replace agec var created above
IRdata$agec <- ifelse(IRdata$b19_included==1, IRdata$b19_01, IRdata$agec)


# Received counseling on HIV during ANC visit
IRdata <- IRdata %>% mutate(hk_hiv_consl_anc = case_when(
  v838a==1 & v838b==1 & v838c==1 & agec<24 ~ 1,
  agec<24 ~ 0)) %>%
  set_value_labels(hk_hiv_consl_anc = yesno) %>%
  set_variable_labels(hk_hiv_consl_anc = "Received counseling on HIV during ANC visit among women with birth <2yrs before survey")

# Tested for HIV during ANC visit and received results and post-test counseling
IRdata <- IRdata %>% mutate(hk_test_consl_anc = case_when(
  v840==1 & v841==1 & v855==1 & agec<24 ~ 1,
  agec<24 ~ 0)) %>%
  set_value_labels(hk_test_consl_anc = yesno) %>%
  set_variable_labels(hk_test_consl_anc = "Received HIV test during ANC visit and results and post-test counseling among women with birth <2yrs before survey")

# Tested for HIV during ANC visit and received results but no post-test counseling
IRdata <- IRdata %>% mutate(hk_test_noconsl_anc = case_when(
  v840==1 & v841==1 & v855!=1 & agec<24~ 1,
  agec<24 ~ 0)) %>%
  set_value_labels(hk_test_noconsl_anc = yesno) %>%
  set_variable_labels(hk_test_noconsl_anc = "Received HIV test during ANC visit and received results but no post-test counseling among women with birth <2yrs before survey")

# Tested for HIV during ANC visit and did not receive test results
IRdata <- IRdata %>% mutate(hk_test_noresult_anc = case_when(
  v840==1 & v841!=1 & agec<24 ~ 1,
  agec<24 ~ 0)) %>%
  set_value_labels(hk_test_noresult_anc = yesno) %>%
  set_variable_labels(hk_test_noresult_anc = "Received HIV test during ANC visit and did not receive test results among women with birth <2yrs before survey")

# Received HIV counseling, test, and results
IRdata <- IRdata %>% mutate(hk_hiv_receivedall_anc = case_when(
  v838a ==1 & v838b ==1 & v838c ==1 & v840 ==1 & v841 ==1 &  agec<24 ~ 1,
  agec<24 ~ 0)) %>%
  set_value_labels(hk_hiv_receivedall_anc = yesno) %>%
  set_variable_labels(hk_hiv_receivedall_anc = "Received HIV counseling, HIV test, and test results during ANC visit among women with birth <2yrs before survey")

# Received HIV test during ANC or labor and received results
IRdata <- IRdata %>% mutate(hk_test_anclbr_result = case_when(
  (v840==1 | v840a==1) & (v841==1 | v841a==1) & agec<24 ~ 1,
  agec<24 ~ 0)) %>%
  set_value_labels(hk_test_anclbr_result = yesno) %>%
  set_variable_labels(hk_test_anclbr_result	= "Received HIV test during ANC visit or labor and received results among women with birth <2yrs before survey")

# Received HIV test during ANC or labor but did not receive results
IRdata <- IRdata %>% mutate(hk_test_anclbr_noresult = case_when(
  (v840==1 | v840a==1) & (v841!=1 | is.na(v841)) & (v841a!=1 | is.na(v841a)) & agec<24 ~ 1,
  agec<24 ~ 0)) %>%
  set_value_labels(hk_test_anclbr_noresult = yesno) %>%
  set_variable_labels(hk_test_anclbr_noresult = "Received HIV test during ANC visit or labor but no results among women with birth <2yrs before survey")
  


colnames(IRdata)[colnames(IRdata) == 'hk_test_anclbr_noresult'] <- 'value'
return(IRdata)
}