The dessert package
The dessert package allows you to automatically generate
methodological appendices for your research workflows. Just supply a
data or model object, and dessert will cook up something
sweet! The package is still under development, so please contribute your
own dessert recipe if you’re missing one. The resulting
reports can be exported in different document formats (e.g., HTML or
PDF) and are easy to share. Let’s open up your research workflow and
whip up a dessert!
Set-up
The development version of the dessert package can be
installed from GitHub with:
# install.packages("devtools")
devtools::install_github("gerkovink/dessert")After installing dessert, you can load the package into
your R workspace:
The data we’ll use in this vignette is the boys dataset
from the mice package. This is an incomplete dataset (\(n = 748\)) with cross-sectional data on
\(9\) growth-related variables. We load
the incomplete data with:
library(mice)
str(boys)
#> 'data.frame': 748 obs. of 9 variables:
#> $ age: num 0.035 0.038 0.057 0.06 0.062 0.068 0.068 0.071 0.071 0.073 ...
#> $ hgt: num 50.1 53.5 50 54.5 57.5 55.5 52.5 53 55.1 54.5 ...
#> $ wgt: num 3.65 3.37 3.14 4.27 5.03 ...
#> $ bmi: num 14.5 11.8 12.6 14.4 15.2 ...
#> $ hc : num 33.7 35 35.2 36.7 37.3 37 34.9 35.8 36.8 38 ...
#> $ gen: Ord.factor w/ 5 levels "G1"<"G2"<"G3"<..: NA NA NA NA NA NA NA NA NA NA ...
#> $ phb: Ord.factor w/ 6 levels "P1"<"P2"<"P3"<..: NA NA NA NA NA NA NA NA NA NA ...
#> $ tv : int NA NA NA NA NA NA NA NA NA NA ...
#> $ reg: Factor w/ 5 levels "north","east",..: 4 4 4 4 4 4 4 3 3 2 ...This is an incomplete dataset. Therefore, we’ll request a missing
data dessert.
This is the end of the vignette. This document was generated using:
sessionInfo()
#> R version 4.2.3 (2023-03-15)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.2 LTS
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so
#>
#> locale:
#> [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
#> [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
#> [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
#> [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] dessert_0.0.0.9001 mice_3.15.0
#>
#> loaded via a namespace (and not attached):
#> [1] Rcpp_1.0.10 bslib_0.4.2 compiler_4.2.3 pillar_1.9.0
#> [5] jquerylib_0.1.4 tools_4.2.3 digest_0.6.31 lattice_0.20-45
#> [9] jsonlite_1.8.4 evaluate_0.20 memoise_2.0.1 lifecycle_1.0.3
#> [13] tibble_3.2.1 pkgconfig_2.0.3 rlang_1.1.0 cli_3.6.1
#> [17] yaml_2.3.7 pkgdown_2.0.7 xfun_0.38 fastmap_1.1.1
#> [21] stringr_1.5.0 dplyr_1.1.1 knitr_1.42 desc_1.4.2
#> [25] generics_0.1.3 fs_1.6.1 vctrs_0.6.1 sass_0.4.5
#> [29] systemfonts_1.0.4 grid_4.2.3 rprojroot_2.0.3 tidyselect_1.2.0
#> [33] glue_1.6.2 R6_2.5.1 textshaping_0.3.6 fansi_1.0.4
#> [37] rmarkdown_2.21 tidyr_1.3.0 purrr_1.0.1 magrittr_2.0.3
#> [41] backports_1.4.1 htmltools_0.5.5 ragg_1.2.5 utf8_1.2.3
#> [45] stringi_1.7.12 cachem_1.0.7 broom_1.0.4