Phase2.1MissingRPackage

R code to run, validate, and submit the analysis for the Missing project.

*** We are stratifying analyses by three time periods:

1/01/2020 to 07/30/2020 ("phase_1")
08/01/2020 to 09/30/2021 ("phase_2")
1/01/2020 to 09/30/2021 ("all")

Please run three times with each time period specified in either the runAnalysis function (for docker users) or the runAnalysis_nodocker (for non-docker users).

*** You might want to restart R before running each time point

To run the package:

For docker users:

docker run \
  --name missing4ce \
  --volume your_path_here:/4ceData \
  --rm -it \
  dbmi/4ce-analysis:version-2.4.0 R

While in R terminal:

(Change siteid to reflect your site name)

devtools::install_github("https://github.com/covidclinical/Phase2.1MissingRPackage", subdir="FourCePhase2.1Missing", upgrade=FALSE)
library(FourCePhase2.1Missing)

siteid = 'your site id'

runAnalysis(dateFormat="%d-%b-%y",time = "phase_1",siteid)
submitAnalysis()
runAnalysis(dateFormat="%d-%b-%y",time = "phase_2",siteid)
submitAnalysis()
runAnalysis(dateFormat="%d-%b-%y",time = "all",siteid)
submitAnalysis()

For non-docker users:

install.packages('stm')
library(stm)
devtools::install_github("https://github.com/covidclinical/Phase2.1DataRPackage", subdir="FourCePhase2.1Data", upgrade=FALSE)
library(Phase2.1Data)

devtools::install_github("https://github.com/covidclinical/Phase2.1MissingRPackage", subdir="FourCePhase2.1Missing", upgrade=FALSE)
library(FourCePhase2.1Missing)

data_dir = '/Your directory here /'
siteid = 'your site id'

runAnalysis_nodocker(data_dir,dateFormat="%d-%b-%y",time = "phase_1",siteid)
runAnalysis_nodocker(data_dir,dateFormat="%d-%b-%y",time = "phase_2",siteid)
runAnalysis_nodocker(data_dir,dateFormat="%d-%b-%y",time = "all",siteid)

Please send your results files to us via slack if not using the docker image! They will pop up in your working directory.

Please note that each run will take some time! This is normal.

Dependency: stm package