README.md

In dyhazard/Phase2.1MultStateModPackage: What the Package Does (One Line, Title Case)

4CE_Phase2.1_MultStateModPackage

R code to run and submit the analysis for the multi-state models project. The code should take about 30 minutes to run. We appreciate your collaboration!

Important details to running the R script

Always RESTART your R session before installing or re-installing the package!

The package uses the Phase 2.1 LocalPatientSummary.csv

Missing values in the LocalPatientSummary.csv should be given "NA"

Make sure R packages listed in the code are already installed

User needs to enter to 4 values noted with "### Enter own value" 1. Local site same ("site_name") 2. Administrative censoring date ("last_date") 3. Directory with the Phase 2.1 LocalPatientSummary.csv file ("dir.LocPatSum") 4. Directory for the output (dir.output)

Note again: Missing values in the LocalPatientSummary.csv should be given "NA"

Run the following script in R

```{r, echo=TRUE, message=FALSE, warning=FALSE ,include=FALSE}

Install packages if not already installed

library(devtools) library(readr) library(mstate) library(dplyr) library(survival) options(kableExtra.latex.load_packages = FALSE) library(kableExtra) library(lubridate) library(tableone) library(papeR) library(rmarkdown)

rm(list=ls())

devtools::install_github("https://github.com/dyhazard/Phase2.1MultStateModPackage", upgrade=FALSE, ref="master", force=T)

Enter own value

Give site name

site_name <- "Freiburg"

Enter own value

Give date of administrative censoring (last date data were collected) in year-month-day

last_date <- "2021-10-31"

Enter own value

Directory with the Phase 2.1 LocalPatientSummary.csv file (should be .csv format)

dir.LocPatSum <- "/Users/dyhazard/Documents/LocalPatientSummary.csv"

Enter own value

Directory for results

dir.output <- "/Users/dyhazard/Documents/Output"

library(Phase2.1MultStateModPackage)

Create pdf Report

render(file.path(system.file("rmd", "4CE_Phase21_MSM.Rmd", package = "Phase2.1MultStateModPackage")), output_file = paste(site_name), output_dir = dir.output, envir = parent.frame(), params = list(dir_LPS = dir.LocPatSum, admin_censor = last_date, site_loc = site_name))

Create object with aggregated results

final_results <- save_results()

Save results in output directory

save(final_results ,file = file.path(dir.output, paste(site_name,"_MSM_Results.Rda")))

```

Submit Results

1. The code produces a pdf report and an R object list of aggregated results Either post on Slack channel or send results to [e-mail]

dyhazard/Phase2.1MultStateModPackage documentation built on Dec. 20, 2021, 2:17 a.m.