From c717703b91b276944515b572a81ce56306d55803 Mon Sep 17 00:00:00 2001 From: "Omair A. Khan" Date: Wed, 25 Aug 2021 12:59:21 -0500 Subject: [PATCH] updates biospecimen code to be consistent with other binary (No/Yes) variables --- R/process_biospecimen_availability.R | 28 ++++++++++++++++++---------- 1 file changed, 18 insertions(+), 10 deletions(-) diff --git a/R/process_biospecimen_availability.R b/R/process_biospecimen_availability.R index 48f829d..197d818 100644 --- a/R/process_biospecimen_availability.R +++ b/R/process_biospecimen_availability.R @@ -6,20 +6,28 @@ process_biospecimen_availability <- function(path = "~/box/VMAC BIOSTAT/DATA/MAP biospecimen.list[[epoch.i]]$epoch <- epoch.i } - biospecimen.df <- dplyr::bind_rows(biospecimen.list) + biospecimen.df <- dplyr::bind_rows(biospecimen.list) %>% + format_id() - biospecimen.df$plasma <- ifelse(biospecimen.df$plasma == "y", TRUE, FALSE) - biospecimen.df$serum <- ifelse(biospecimen.df$serum == "y", TRUE, FALSE) - biospecimen.df$DNA <- ifelse(biospecimen.df$DNA == "y", TRUE, FALSE) - biospecimen.df$PAXGene <- ifelse(biospecimen.df$PAXGene == "y", TRUE, FALSE) - biospecimen.df$csf <- ifelse(biospecimen.df$csf == "y", TRUE, FALSE) + biospecimen.df$plasma <- ifelse(biospecimen.df$plasma == "y", "Yes", "No") + biospecimen.df$serum <- ifelse(biospecimen.df$serum == "y", "Yes", "No") + biospecimen.df$DNA <- ifelse(biospecimen.df$DNA == "y", "Yes", "No") + biospecimen.df$PAXGene <- ifelse(biospecimen.df$PAXGene == "y", "Yes", "No") + biospecimen.df$csf <- ifelse(biospecimen.df$csf == "y", "Yes", "No") names(biospecimen.df) <- c("map.id", "plasma.availability", "serum.availability", - "dna.availability", "paxgene.availability", "csf.availability", "epoch") + "dna.availability", "paxgene.availability", "csf.availability", + "epoch") - biospecimen.df <- format_id(biospecimen.df) - - biospecimen.df <- as.data.frame(biospecimen.df) + biospecimen.df <- biospecimen.df %>% + mutate( + plasma.availability = factor(plasma.availability, levels = c("No", "Yes")), + serum.availability = factor(serum.availability, levels = c("No", "Yes")), + dna.availability = factor(dna.availability, levels = c("No", "Yes")), + paxgene.availability = factor(paxgene.availability, levels = c("No", "Yes")), + csf.availability = factor(csf.availability, levels = c("No", "Yes")), + ) %>% + as.data.frame() return(biospecimen.df) }