read_alex_database_med_log: function used to clear up the medication log data, keep only...

In reny1/alexdata: Import subject, sample, and medication data for the tobacco project

Description

function used to clear up the medication log data, keep only the medication in the medList, remove the unused records.

Usage

read_alex_database_med_log(dataFrame, medList)

Arguments

dataFrame

the raw medication log data frame contains the data from baseline_antibiotics.csv and medication_log.csv and a column of collect date time

Value

medRaw return a data frame that contains only the medications in the medList

Examples

medList <- as.list(read.xlsx("/Users/yue/Dropbox/Joy/tabacco_grant/data/data_fromsarah/IBD Medication List_2.17.2017.xls", sheetIndex = 1,stringsAsFactors = F))
medList <- sapply(medList, function(x) x = x[!is.na(x)])
names(medList)[which(names(medList) == "Other")] = "Other.med"
names(medList)[which(names(medList) == "X5.ASA")] = "5.ASA"
alex_medication_log <- read_alex_database(fileName = "/Users/yue/Dropbox/Joy/tabacco_grant/data/data_fromalex/database/database10052017/medication_log.csv")
alex_medication_log %<>% mutate(start_date = as.Date(start_date)) %>%
mutate(stop_date = as.Date(stop_date)) %>%
mutate(duration = stop_date - start_date)
a <- read_alex_database(fileName = "/Users/yue/Dropbox/Joy/tabacco_grant/data/data_fromalex/database/database10052017/sample_redcap.csv") %>%
rename(collect_date_time = Collected_Time)
alex_medication_log %<>% left_join(a, by = c("ehb_id")) %>%
rename(SampleType = Sample.Type)
remove(a)
medRaw = read_alex_database_med_log(dataFrame = alex_medication_log, medList = medList)

reny1/alexdata documentation built on May 29, 2019, 8:06 a.m.