This repository contains data and code necessary to reproduce analysis from the article: Jarosław Chilimoniuk, Alicja Gosiewska, Jadwiga Słowik, Romano Weiss, Stefan Rödiger, and Michał Burdukiewicz. countfitteR: count data analysis for precision medicine.
The analysis conducted in this article resulted in a framework for the automatic selection of the appropriate count distribution CountfitteR, available as an R package (https://CRAN.R-project.org/package=countfitteR) and a web server (TO DO).
Run scripts/countfitter_simulations.R and scripts/two_step_simulations.R. The first script performs simulations for countfitteR, the second script performs simulations for Two-Step-Procedure.
Run scripts/plots.R to generate plots included in the article and supplementary articles.
Run scripts/supplementary_tables.R to generate tables included in the supplementary materials.
Run scripts/mean_power_table.R to generate Table 2.
All scripts are in the folder scripts.
Partial results saved as binary R data files are in the folder data.
Data and plots are in the folder files.
All scripts used in this study are compatible with following version of R:
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale: LC_COLLATE=Polish_Poland.1250, LC_CTYPE=Polish_Poland.1250, LC_MONETARY=Polish_Poland.1250, LC_NUMERIC=C and LC_TIME=Polish_Poland.1250
attached base packages: stats, graphics, grDevices, datasets, utils, methods and base
other attached packages: MASS(v.7.3-51.6), pscl(v.1.5.5), pbapply(v.1.4-2), countfitteR(v.1.2), gt(v.0.2.1), xtable(v.1.8-4), patchwork(v.1.0.1), latex2exp(v.0.4.0), tidyr(v.1.0.2), dplyr(v.0.8.5), ggh4x(v.0.1.0.9000), ggplot2(v.3.3.2) and readr(v.1.3.1)
loaded via a namespace (and not attached): Rcpp(v.1.0.4.6), later(v.1.0.0), pillar(v.1.4.4), compiler(v.3.6.1), tools(v.3.6.1), digest(v.0.6.25), lifecycle(v.0.2.0), tibble(v.3.0.1), gtable(v.0.3.0), pkgconfig(v.2.0.3), rlang(v.0.4.6), shiny(v.1.4.0.2), rstudioapi(v.0.11), parallel(v.3.6.1), fastmap(v.1.0.1), withr(v.2.2.0), stringr(v.1.4.0), vctrs(v.0.3.1), hms(v.0.5.3), grid(v.3.6.1), tidyselect(v.1.0.0), glue(v.1.4.1), R6(v.2.4.1), pander(v.0.6.3), purrr(v.0.3.3), magrittr(v.1.5), promises(v.1.1.0), htmltools(v.0.4.0), scales(v.1.1.1), ellipsis(v.0.3.1), assertthat(v.0.2.1), mime(v.0.9), colorspace(v.1.4-1), httpuv(v.1.5.2), renv(v.0.11.0), stringi(v.1.4.6), munsell(v.0.5.0) and crayon(v.1.3.4)