curtisScript.R

#!/usr/bin/env Rscript

library(magrittr)
library(reshape2)

d <- read.csv("FINAL LAB DATA Mar 23 2017.csv", colClasses="character", fileEncoding = "UTF-8-BOM")
d <- d[order(d$ID),]

# assign each visit a number (per patient)
visit.numbers <- tapply(d$Collection.Date, d$ID, function (x) 
                        as.integer(as.factor(x)))
visit.numbers <- visit.numbers[match(names(visit.numbers), unique(d$ID))]
d$Visit.Number <- unlist(visit.numbers)

# make columns for visit dates
visits <- dcast(d, ID~Visit.Number, value.var="Collection.Date", fun.aggregate=head, 1, fill="")
colnames(visits)[2:ncol(visits)] <- paste0(colnames(visits)[2:ncol(visits)], "_Collection.Date")

# make columns for test values
tests <- dcast(d, ID~Visit.Number+Lab.Type, value.var="Value", fun.aggregate=head, 1, fill="")

# merge visit dates with test values
pdata <- merge(visits, tests)

# save the file
write.csv(pdata, "out.csv", row.names=FALSE)