REDCap metaanalysis data dictionary

biasfig.R

# Download data
token <- readLines("PATH/TO/TOKEN")
library(httr)
url <- "PATH/TO/API"
# data itself
x <- POST(url, 
          config = httr::config(SSL_VERIFYPEER = FALSE),
          body = list(token = token,
                      content = "record", type = "flat",
                      format = "csv"))
x <- as.character(x)
con <- textConnection(x)
dat <- read.csv(con, head = TRUE, na.strings = "", stringsAsFactors = FALSE)

# metadata
x <- POST(url, 
          config = httr::config(SSL_VERIFYPEER = FALSE),
          body = list(token = token,
                      content = "metadata", type = "flat",
                      format = "csv"))
x <- as.character(x)
con <- textConnection(x)
meta <- read.csv(con, head = TRUE, na.strings = "", stringsAsFactors = FALSE)

# filter data
bias <- meta[meta$form_name == "bias_assessment", ]
bias <- bias[bias$field_type == "radio", ]

bias_dat <- dat[is.na(dat$redcap_repeat_instrument), c("record_id", "author_short", bias$field_name)]

N <- nrow(bias_dat)


# function to split string at space after half way  
X <- function(string){
  require(stringr) 
  str <- string
  chars <- nchar(str)
  spaces <- str_locate_all(str, " ")
  mapply(function(str, x, y) {
    l <- x[, 1]
    s <- l[l > y/2][1]
    if(!is.na(s)){ 
      r <- gsub(paste0("^(.{", s, "})(.*)$"), "\\1\n\\2", str)
    } else {
      r <- str
    }
    r
  }, str, spaces, chars)
}

X(bias$field_label)

# plot matrix of colours 
par(mai = c(2,2,.1,.1), xaxt = "n", yaxt = "n")
image(t(as.matrix(bias_dat[, 3:9])), 
      col = c("green", "orange", "red"), 
      bty = "n")
# author labels
text(y = seq(0, 1, length.out = N),
     x = par("usr")[1],
     labels = bias_dat$author_short,
     pos = 2,
     xpd = "n")
# questions
par(lheight=.8)
text(y = par("usr")[3],
     x = seq(0, 1, length.out = 7),
     labels = X(bias$field_label),
     pos = 2,
     xpd = "n", srt = 60)

rc_datadict_metaanalysis.csv

Added field for DOI and fields for units

Forms other than inclusionexclusion and study_details should be set as repeating instruments

inclusion/exclusion/units/endpoints need to be defined for each project

added bias assessment

Added code to show bias assessment results (see fig 1 from here)