riseR:

# OBJECTIVE 3&4 ANNUAL SURVEY IN INDONESIA - NOVEMBER 2019 TO ??? 2019/2020

library (tidyverse)
library (lubridate)
library (stringr)
library (readxl)
library (zscorer)

rm(list = ls())
setwd("Z:/Data Files/Practice Data/ID_T4_annual_v1")
#setwd("S:/R-MNHS-SPHPM-EPM-IDEpi/RISE/4. Surveys/3. Objectives/1. FJ/3/20190930_child sampling/3. Data/1. raw data")

# ANNUAL SURVEY
annual <- read_csv (file="T4_ID_annual_v1.csv")
annual_feces_kit <- read_csv (file="T4_ID_annual_v1-feces_kit.csv")
annual_hhd_members_departed <- read_csv (file="T4_ID_annual_v1-hhd_members-reason_departed.csv")
annual_hhd_members_filters <- read_csv (file ="T4_ID_annual_v1-hhd_members-filters_revise.csv")
annual_household_depart <- read_csv (file="T4_ID_annual_v1-household-hhds_depart.csv")
annual_new_people <- read_csv (file="T4_ID_annual_v1-new_people-new_people_info.csv")
annual_person_details <- read_csv (file="T4_ID_annual_v1-person_details1.csv")
annual_child <- read_csv (file="T4_ID_annual_v1-child_loop.csv")

# FECES COLLECTION
feces <- read_csv (file="T4_ID_feces_v4.csv")
feces.sample <- read_csv (file="T4_ID_feces_v4-feces_collection.csv")

#############################################
# coding fixes
#############################################

annual$starttime <- as.Date(annual$starttime, format = '%B %d, %Y')
feces$starttime <- as.Date(feces$starttime, format = '%B %d, %Y')
feces$extract_house_no <- as.numeric(as.character(feces$extract_house_no))

#############################################
# CORRECTIONS
setwd("C:/Users/RISE Fiji/Documents/GitHub/riseR/RISE_ID/T4_annual_survey")
#setwd("S:/R-MNHS-SPHPM-EPM-IDEpi/RISE/4. Surveys/3. Objectives/1. FJ/3/20190930_child sampling/3. Data/2. code/Jeff's finalised scripts/20191002")
source("O3_T4_ID-corrections.R")
setwd("C:/Users/RISE Fiji/Documents/GitHub/riseR/RISE_ID/T4_annual_survey")
#setwd("S:/R-MNHS-SPHPM-EPM-IDEpi/RISE/4. Surveys/3. Objectives/1. FJ/3/20190930_child sampling/3. Data")

#############################################
# MERGE
#############################################

#MERGE ANNUAL SURVEY - don't need merge for ID as only one child per survey
annual.merge <- full_join (annual, annual_feces_kit, by = c("KEY" = "PARENT_KEY"))
annual.departed <- full_join (annual, annual_hhd_members_departed, by = c("KEY" = "PARENT_KEY"))
#annual.merge <- full_join (annual.merge, annual_hhd_members_filters, by = c("KEY" = "PARENT_KEY"))
#annual.merge <- full_join (annual.merge, annual_household_depart, by = c("KEY" = "PARENT_KEY"))
annual.new_people <- full_join (annual, annual_new_people, by = c("KEY" = "PARENT_KEY"))
#annual.merge <- full_join (annual.merge, annual_person_details, by = c("KEY" = "PARENT_KEY"))


#  select (settlement_barcode, extract_house_no, today, starttime,
#          caregiver_present,	home_yn, child_name, child_dob, child_gender,
#          signedyn_pl, feces_pl, blood_pl, height_pl, blood_check2, height_check2,
#          survey_check2, survey_status, endtime, barcode_edta, barcode_edta_text,
#          barcode_serum,barcode_serum_text,	barcode_bloodspot, blood_hb,
#          barcode_bloodspot_text, blood_check2, survey_check2, feces_kit_barcode,
#          feces_kit_barcode_note) %>%
#  mutate (edta = ifelse (is.na(barcode_edta), barcode_edta_text, barcode_edta),
#          serum = ifelse (is.na(barcode_serum), barcode_serum_text, barcode_serum),
#          bloodspot = ifelse (is.na(barcode_bloodspot), barcode_bloodspot_text, barcode_bloodspot),
#          feces = ifelse (is.na(feces_kit_barcode), feces_kit_barcode_note, feces_kit_barcode)) %>%
#  select (-barcode_edta,	-barcode_edta_text, -barcode_serum, -barcode_serum_text,
#          -barcode_bloodspot,	-barcode_bloodspot_text, -feces_kit_barcode, -feces_kit_barcode_note)

#FECES PICKUP
feces.merge <- merge(x = feces, y = feces.sample, by.x = "KEY", by.y = "PARENT_KEY")  %>%
  mutate (barcode = ifelse (is.na(barcode_feces), barcode_feces_text, barcode_feces)) %>%
  select (-barcode_feces, -barcode_feces_text) #merges only those with a sample picked up

feces.merge2 <- full_join (feces, feces.sample, by = c("KEY" = "PARENT_KEY")) %>%
  mutate (barcode = ifelse (is.na(barcode_feces), barcode_feces_text, barcode_feces)) %>%
  select (-barcode_feces, -barcode_feces_text) # merges all feces surveys started

#############################################
# PULL TOGETHER CONSENT LISTS
#############################################
# PULL TOGETHER FINAL LIST OF CONSENTS
#setwd("C:/Users/RISE Fiji/Documents/GitHub/riseR/RISE_FJ/T1_child_sampling")
#setwd("S:/R-MNHS-SPHPM-EPM-IDEpi/RISE/4. Surveys/3. Objectives/1. FJ/3/20190930_child sampling/3. Data/2. code/Jeff's finalised scripts/20191002")
#source("O3_T1_FJ_consent_update.R")
#setwd("C:/Users/RISE Fiji/Documents/GitHub/riseR/RISE_FJ/T1_child_sampling")
#setwd("S:/R-MNHS-SPHPM-EPM-IDEpi/RISE/4. Surveys/3. Objectives/1. FJ/3/20190930_child sampling/3. Data")

# this includes corrections to consent
#############################################

#############################################
##  DATA CHECKING FOR DAILY REPORT ##
#############################################
setwd("C:/Users/RISE Fiji/Documents/GitHub/riseR/RISE_ID/T4_annual_survey")
#setwd("S:/R-MNHS-SPHPM-EPM-IDEpi/RISE/4. Surveys/3. Objectives/1. FJ/3/20190930_child sampling/3. Data/2. code/Jeff's finalised scripts/20191002")
source("O3_T4_ID-data_check.R")
setwd("C:/Users/RISE Fiji/Documents/GitHub/riseR/RISE_ID/T4_annual_survey")
#setwd("S:/R-MNHS-SPHPM-EPM-IDEpi/RISE/4. Surveys/3. Objectives/1. FJ/3/20190930_child sampling/3. Data")

#############################################
##  RUN LIMS CHECKS ##
#############################################
setwd("C:/Users/RISE Fiji/Documents/GitHub/riseR/RISE_ID/T4_annual_survey")
#setwd("S:/R-MNHS-SPHPM-EPM-IDEpi/RISE/4. Surveys/3. Objectives/1. FJ/3/20190930_child sampling/3. Data/2. code")
source("O3_T4_ID-LIMS_QC.R")
setwd("C:/Users/RISE Fiji/Documents/GitHub/riseR/RISE_ID/T4_annual_survey")
#setwd("S:/R-MNHS-SPHPM-EPM-IDEpi/RISE/4. Surveys/3. Objectives/1. FJ/3/20190930_child sampling/3. Data")


# then run weekly report .Rmd - Jeff to do this end of each week


#############################################
##  Get household identifiers - don't need for fiji      ##
#############################################
# setwd("S:/R-MNHS-SPHPM-EPM-IDEpi/RISE/4. Surveys/3. Objectives/1. FJ/3/20190930_child sampling/3. Data/1. raw data")
# source("O3_T1_ID-hhd_id_corrections.R")
# setwd("S:/R-MNHS-SPHPM-EPM-IDEpi/RISE/4. Surveys/3. Objectives/2. ID/3/20190225_child sampling/3. ID/2. Data")
# #this adds hhd_id to ***??????????????

#############################################
## generate person ids - no new people yet (FIONA WILL DO THIS) ??????????  ##
#############################################
#setwd("C:/Users/RISE Fiji/Documents/GitHub/riseR/RISE_FJ/T1_child_sampling")
# source("O3_T1_ID-person_list.R")
#setwd("C:/Users/RISE Fiji/Documents/GitHub/riseR/RISE_FJ/T1_child_sampling")
# this feeds into R script that generates person_ids
# ID_201903_O3_participants_list.R??????????????


#############################################
## create data files for users / analysis ##
# and for use in next survey              ##
#############################################
#setwd("C:/Users/RISE Fiji/Documents/GitHub/riseR/RISE_FJ/T1_child_sampling")
# source("O3_T1_ID-data_extract.R")
#setwd("C:/Users/RISE Fiji/Documents/GitHub/riseR/RISE_FJ/T1_child_sampling")