doseresNMA antidep/data.prep.R

In htx-r/doseresNMA:

require(readxl)
source('data.clean.R')
data.prep <- function(){
  # load data
  X2020_01_20_MASTER_dataset <- read_excel("2020-01-20 MASTER dataset.xlsx",col_names = TRUE, skip = 2)
  antidep <- as.data.frame(X2020_01_20_MASTER_dataset)

  # include only the needed columns
  includedColumns <- c('Study_No','Study_year','Drug','Responders...56','No_randomised','Dose_delivered_mean', # 'Responders',
                       'Overall_study_RoB','Dose_range','Age_mean')
  antidep <- antidep[,includedColumns]

  # change column names
  names(antidep) <- c('studyid','study_year','drug','r','n','dose','ROB','dose_range','age')

  # after 522 we have empty cells in the excel file
  antidep <- antidep[antidep$studyid%in%1:522,]

  # change variables class
  antidep$study_year <- as.numeric(antidep$study_year)
  antidep$drug <- as.factor(antidep$drug)
  antidep$r <- round(as.numeric(antidep$r))
  antidep$n <- as.numeric(antidep$n)
  antidep$dose <- as.numeric(antidep$dose)
  antidep$ROB <- as.factor(antidep$ROB)
  antidep$dose_range <- as.factor(antidep$dose_range)
  antidep$age <- as.numeric(antidep$age)

  # clean rows with NA's in r, n and dose & studies that report the same dose
  antidep <- removeNAdosresdata.fun(antidep)$dataset
  antidep <- antidep[antidep$exclude==FALSE,]

  # exclude single-arm trials
  antidep <- exludesinglearmsdata.fun(antidep,studyid = studyid)

  # order doses within each study - start from 0
  antidep_to_order <- sapply(unique(antidep$studyid), function(i) antidep[antidep$studyid==i,][order(antidep$dose[antidep$studyid==i]),],simplify = FALSE)
  antidep <- do.call(rbind, antidep_to_order)
  return(antidep)
}