riseR:

# OBJECTIVE 3 CHILD SAMPLING IN FIJI - 26 SEPTEMBER 2019 TO ??? 2019

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

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

# CHILD SAMPLING
child <- read_csv (file="O3_child_sample_FJ_v1.csv")

# FECES COLLECTION
feces <- read_csv (file="O3_feces_FJ_v1.csv")
feces.sample <- read_csv (file="O3_feces_FJ_v1-feces_collection.csv")

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

#infill gender - not required
table(child$child_gender)

child$starttime <- as.Date(child$starttime, format = '%B %d, %Y')
feces$starttime <- as.Date(feces$starttime, format = '%B %d, %Y')

#############################################
# CORRECTIONS
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-corrections.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")

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

#MERGE CHILD SAMPLING - don't need merge for Fiji as only one child per survey
child.merge <- child %>%
  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 WEEKLY REPORT ##
#############################################
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_data_check.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")

#############################################
##  RUN LIMS CHECKS ##
#############################################
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")
source("O3_T1_FJ-LIMS_QC.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")