The "Pfalciparum_sero_sign" repository contains code and data for identification of serological markers of recent malaria exposure as described in Yman et al. Nature Communications 2021.
To clone contents of this repo:
- copy the repo url (green button “Code”).
- when using RStudio, click on (File/New Project..) in the menu bar.
- create project from "VersionControl" and "Git".
- paste the copied URL and give the respository a name.
The contents of this repository are publicly available under an MIT License (see LICENSE for details)
The file 'renv.lock' contains the information necessary to restore project-local R libraries prior to executing analysis (see 'src/README.md' for details)
code is located within repo folder 'src'
data is located within repo folder 'data'
results generated by executing analysis will be stored within repo folder 'results'
The code has been tested using the following platform, OS, software, and dependencies:
R version 4.1.1 (2021-08-10) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Monterey 12.0.1
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib
locale: [1] sv_SE.UTF-8/sv_SE.UTF-8/sv_SE.UTF-8/C/sv_SE.UTF-8/sv_SE.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] betareg_3.1-4 doParallel_1.0.16 iterators_1.0.13 randomForest_4.6-14 MASS_7.3-54
[6] MESS_0.5.7 Boruta_7.0.0 ROCR_1.0-11 pROC_1.18.0 contrast_0.22
[11] nlme_3.1-152 RColorBrewer_1.1-2 viridis_0.6.2 viridisLite_0.4.0 cowplot_1.1.1
[16] foreach_1.5.1 ggrepel_0.9.1 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7
[21] purrr_0.3.4 readr_2.0.2 tidyr_1.1.4 tibble_3.1.5 ggplot2_3.3.5
[26] tidyverse_1.3.1
loaded via a namespace (and not attached):
[1] readxl_1.3.1 backports_1.2.1 Hmisc_4.6-0 plyr_1.8.6
[5] splines_4.1.1 listenv_0.8.0 TH.data_1.1-0 digest_0.6.28
[9] htmltools_0.5.2 fansi_0.5.0 magrittr_2.0.1 checkmate_2.0.0
[13] cluster_2.1.2 tzdb_0.1.2 mosaicCore_0.9.0 recipes_0.1.17
[17] globals_0.14.0 modelr_0.1.8 gower_0.2.2 matrixStats_0.61.0
[21] sandwich_3.0-1 jpeg_0.1-9 colorspace_2.0-2 rvest_1.0.2
[25] haven_2.4.3 xfun_0.27 crayon_1.4.1 jsonlite_1.7.2
[29] survival_3.2-11 zoo_1.8-9 glue_1.4.2 geepack_1.3-2
[33] polyclip_1.10-0 gtable_0.3.0 ipred_0.9-12 MatrixModels_0.5-0
[37] ggformula_0.10.1 future.apply_1.8.1 rms_6.2-0 SparseM_1.81
[41] scales_1.1.1 mvtnorm_1.1-3 DBI_1.1.1 geeM_0.10.1
[45] Rcpp_1.0.7 htmlTable_2.3.0 ggstance_0.3.5 foreign_0.8-81
[49] Formula_1.2-4 stats4_4.1.1 lava_1.6.10 prodlim_2019.11.13
[53] htmlwidgets_1.5.4 httr_1.4.2 modeltools_0.2-23 ellipsis_0.3.2
[57] flexmix_2.3-17 pkgconfig_2.0.3 farver_2.1.0 nnet_7.3-16
[61] dbplyr_2.1.1 utf8_1.2.2 caret_6.0-90 tidyselect_1.1.1
[65] rlang_0.4.12 reshape2_1.4.4 munsell_0.5.0 cellranger_1.1.0
[69] tools_4.1.1 cli_3.0.1 generics_0.1.1 broom_0.7.9
[73] ggridges_0.5.3 fastmap_1.1.0 ModelMetrics_1.2.2.2 knitr_1.36
[77] fs_1.5.0 future_1.23.0 quantreg_5.86 xml2_1.3.2
[81] compiler_4.1.1 rstudioapi_0.13 png_0.1-7 reprex_2.0.1
[85] tweenr_1.0.2 stringi_1.7.5 lattice_0.20-44 Matrix_1.3-4
[89] vctrs_0.3.8 pillar_1.6.4 lifecycle_1.0.1 lmtest_0.9-39
[93] data.table_1.14.2 conquer_1.2.1 R6_2.5.1 latticeExtra_0.6-29
[97] gridExtra_2.3 parallelly_1.28.1 codetools_0.2-18 polspline_1.1.19
[101] assertthat_0.2.1 withr_2.4.2 multcomp_1.4-17 hms_1.1.1
[105] grid_4.1.1 rpart_4.1-15 labelled_2.9.0 timeDate_3043.102
[109] class_7.3-19 ggforce_0.3.3 lubridate_1.8.0 base64enc_0.1-3