The goal of the iteval-sims GitHub repository is to enable replication of the simulation study in Hoogland et al. DOI 10.1002/sim.10186. The R scripts are not meant to be used for other purposes and are not annotated. R package iteval is available for application of the methods in practice and contains example illustrations and help for all functions.
This README file describes the contents of the iteval-sims repository and the required steps for replication of the simulations, tables, and figures. Note that this repository does not have the structure of an R package and does not have to be installed.
First, population.R simulates the population data and stores the
required representations in population.RData. Second, sim.RData
performs the simulation study. Note that this script depends on R
package Hmisc, rms, MatchIt and iteval and sources
support_functions.R (which only contains helper functions specific to
the simulation).
Just running sim.RData for a number of simulation provides some
replications to check against the pre-computed results in the
replicate folder. Note that the simulations take a considerable amount
of time, and that all results are available in pre-computed form. The
replicate.R script provides exact replicates of the Figures and Tables
in Hoogland et al. DOI 10.1002/sim.10186. Results have been checked on R
version 4.2.0 and using the following package versions.
Supplementary simulations on model misspecification have also been added
in the sup folder, where the sim*.R scripts can run the simulations,
replicate_suppl.R again provides replication of key figures, and the
supple_sim_* folders contain pre-computed simulation results.
library(Hmisc)
#>
#> Attaching package: 'Hmisc'
#> The following objects are masked from 'package:base':
#>
#> format.pval, units
library(rms)
library(MatchIt)
library(iteval)
library(ggplot2)
sessionInfo()
#> R version 4.2.0 (2022-04-22)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur/Monterey 10.16
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
#>
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] ggplot2_3.5.0 iteval_0.1.0 MatchIt_4.5.5 rms_6.7-1 Hmisc_5.1-1
#>
#> loaded via a namespace (and not attached):
#> [1] zoo_1.8-12 tidyselect_1.2.0 xfun_0.42 splines_4.2.0
#> [5] lattice_0.20-45 colorspace_2.1-0 vctrs_0.6.5 generics_0.1.3
#> [9] htmltools_0.5.7 yaml_2.3.8 base64enc_0.1-3 utf8_1.2.4
#> [13] survival_3.4-0 rlang_1.1.3 pillar_1.9.0 withr_3.0.0
#> [17] foreign_0.8-84 glue_1.7.0 multcomp_1.4-25 lifecycle_1.0.4
#> [21] stringr_1.5.1 MatrixModels_0.5-3 munsell_0.5.0 gtable_0.3.4
#> [25] mvtnorm_1.2-3 htmlwidgets_1.6.4 codetools_0.2-18 evaluate_0.23
#> [29] knitr_1.45 fastmap_1.1.1 SparseM_1.81 quantreg_5.97
#> [33] fansi_1.0.6 htmlTable_2.4.2 Rcpp_1.0.12 TH.data_1.1-2
#> [37] scales_1.3.0 backports_1.4.1 checkmate_2.3.1 gridExtra_2.3
#> [41] digest_0.6.34 stringi_1.8.3 polspline_1.1.23 dplyr_1.1.4
#> [45] grid_4.2.0 cli_3.6.2 tools_4.2.0 sandwich_3.1-0
#> [49] magrittr_2.0.3 tibble_3.2.1 Formula_1.2-5 cluster_2.1.4
#> [53] pkgconfig_2.0.3 MASS_7.3-58.1 Matrix_1.6-5 data.table_1.15.2
#> [57] rmarkdown_2.26 rstudioapi_0.15.0 R6_2.5.1 rpart_4.1.19
#> [61] nnet_7.3-18 nlme_3.1-163 compiler_4.2.0