In Thaliehln/timci: Data management and visualisation for the TIMCI project

knitr::opts_chunk$set(echo = TRUE)

library(dplyr)
library(readxl)
cdate <- "2022-04-07"
cdate <- "2022-04-21"#Sys.Date()
cdate <- "2022-05-05"#Uasin Gishu only
myxlsx <- paste0("C:/Users/langhe/Documents/Kenya/timci_exports/export_", cdate, "/02_Kenya_main_study/03_Kenya_qualitative/01_Kenya_caregiver_idis/01_cg_idi_participants.xlsx")
set.seed(2021)

Loading data

df <- readxl::read_excel(myxlsx)
df <- df %>%
  mutate(month_category = ifelse(age_mo < 2, 1, ifelse(age_mo < 12, 2, ifelse(age_mo < 24, 3, 4))))
print(nrow(df))

Filter data

facilities <- read_excel("C:/Users/langhe/Documents/Kenya/timci_research_facilities.xlsx") %>% dplyr::distinct(facility_id, .keep_all = TRUE)
df <- df %>%
  merge(y = facilities[,c("facility_id", "training_date", "rollout_date")],
        by.x = 'fid',
        by.y = 'facility_id',
        all.x = TRUE)
post_intervention_df <- df %>%
  dplyr::filter(!is.na(rollout_date) & as.Date(date_visit) >= as.Date(rollout_date)) %>%
  dplyr::mutate(days_since_intervention = as.Date(date_visit) - as.Date(rollout_date))
print(post_intervention_df)

openxlsx::write.xlsx(post_intervention_df, "kenya_qual_post_intervention.xlsx", row.names = FALSE, overwrite = TRUE)

Referred children

referred_df <- post_intervention_df %>% dplyr::filter(referral_cg == 1 | referral_hf == 1)
print(referred_df)

openxlsx::write.xlsx(referred_df, "kenya_qual_referred_post_intervention.xlsx", row.names = FALSE, overwrite = TRUE)

Non-referred children

nonreferred_df <- post_intervention_df %>% dplyr::filter((referral_cg == 0 | is.nan(referral_cg)) & referral_hf == 0)
print(nrow(nonreferred_df))

openxlsx::write.xlsx(nonreferred_df, "kenya_qual_nonreferred_post_intervention.xlsx", row.names = FALSE, overwrite = TRUE)

Split by regions

referred_kitui_df <- referred_df %>% dplyr::filter(district == "Kitui")
referred_kitui_df

referred_ug_df <- referred_df %>% dplyr::filter(district == "Uasin Gishu")
referred_ug_df

referred_kakamega_df <- referred_df %>% dplyr::filter(district == "Kakamega")
referred_kakamega_df

nonreferred_kitui_df <- nonreferred_df %>% dplyr::filter(district == "Kitui")
nonreferred_kitui_df

nonreferred_ug_df <- nonreferred_df %>%
  dplyr::filter(district == "Uasin Gishu") %>%
  dplyr::filter(days_since_intervention >= 10)
nonreferred_ug_df

nonreferred_kakamega_df <- nonreferred_df %>% dplyr::filter(district == "Kakamega")
nonreferred_kakamega_df

Random selection for non-referred children

random_selection_kitui <- nonreferred_kitui_df %>%
  group_by(month_category) %>%
  sample_n(1)
print(random_selection_kitui)

openxlsx::write.xlsx(random_selection_kitui, "kenya_qual_selection_nonreferred_kitui_21.xlsx", row.names = FALSE, overwrite = TRUE)

random_selection_kakamega <- nonreferred_kakamega_df %>%
  group_by(month_category) %>%
  sample_n(1)
print(random_selection_kakamega)

openxlsx::write.xlsx(random_selection_kakamega, "kenya_qual_selection_nonreferred_kakamega_21.xlsx", row.names = FALSE, overwrite = TRUE)

random_selection_ug <- nonreferred_ug_df %>%
  group_by(month_category) %>%
  sample_n(1)
print(random_selection_ug)

openxlsx::write.xlsx(random_selection_ug, "kenya_qual_selection_nonreferred_ug_21.xlsx", row.names = FALSE, overwrite = TRUE)

Random selection for non-referred children (backup)

nonreferred_kitui_df <- nonreferred_kitui_df[!nonreferred_kitui_df$child_id %in% random_selection_kitui$child_id, ]

random_selection_kitui_bkp <- nonreferred_kitui_df %>%
  group_by(month_category) %>%
  sample_n(1)

print(random_selection_kitui_bkp)

openxlsx::write.xlsx(random_selection_kitui_bkp, "kenya_qual_selection_nonreferred_kitui_21_bkp.xlsx", row.names = FALSE, overwrite = TRUE)

nonreferred_kakamega_df <- nonreferred_kakamega_df[!nonreferred_kakamega_df$child_id %in% random_selection_kakamega$child_id, ]

random_selection_kakamega_bkp <- nonreferred_kakamega_df %>%
  group_by(month_category) %>%
  sample_n(1)

print(random_selection_kakamega_bkp)

openxlsx::write.xlsx(random_selection_kakamega_bkp, "kenya_qual_selection_nonreferred_kakamega_21_bkp.xlsx", row.names = FALSE, overwrite = TRUE)

nonreferred_ug_df <- nonreferred_ug_df[!nonreferred_ug_df$child_id %in% random_selection_ug$child_id, ]

random_selection_ug_bkp <- nonreferred_ug_df %>%
  group_by(month_category) %>%
  sample_n(1)

print(random_selection_ug_bkp)

openxlsx::write.xlsx(random_selection_ug_bkp, "kenya_qual_selection_nonreferred_ug_21_bkp.xlsx", row.names = FALSE, overwrite = TRUE)

Random selection for non-referred children (backup)

nonreferred_kitui_df <- nonreferred_kitui_df[!nonreferred_kitui_df$child_id %in% random_selection_kitui_bkp$child_id, ]

random_selection_kitui_bkp2 <- nonreferred_kitui_df %>%
  group_by(month_category) %>%
  sample_n(1)

print(random_selection_kitui_bkp2)

openxlsx::write.xlsx(random_selection_kitui_bkp2, "kenya_qual_selection_nonreferred_kitui_21_bkp2.xlsx", row.names = FALSE, overwrite = TRUE)

nonreferred_kakamega_df <- nonreferred_kakamega_df[!nonreferred_kakamega_df$child_id %in% random_selection_kakamega_bkp$child_id, ]

random_selection_kakamega_bkp2 <- nonreferred_kakamega_df %>%
  group_by(month_category) %>%
  sample_n(1)

print(random_selection_kakamega_bkp2)

openxlsx::write.xlsx(random_selection_kakamega_bkp2, "kenya_qual_selection_nonreferred_kakamega_21_bkp2.xlsx", row.names = FALSE, overwrite = TRUE)

Random selection for non-referred children (backup)

nonreferred_kitui_df <- nonreferred_kitui_df[!nonreferred_kitui_df$child_id %in% random_selection_kitui_bkp2$child_id, ]

random_selection_kitui_bkp3 <- nonreferred_kitui_df %>%
  group_by(month_category) %>%
  sample_n(1)

print(random_selection_kitui_bkp3)

openxlsx::write.xlsx(random_selection_kitui_bkp3,
                     "kenya_qual_selection_nonreferred_kitui_21_bkp3.xlsx",
                     row.names = FALSE,
                     overwrite = TRUE)

Thaliehln/timci documentation built on April 8, 2024, 3:38 p.m.