These scripts will reproduce the analyses reported in Jutla A, Turner JB, Snyder LG, Chung WK, Veenstra-VanderWeele J. "Psychotic symptoms in 16p11.2 copy number variant carriers." Autism Research. 2020;13(2):187-198.
Extract the Simons_VIP__16p11.2_Dataset_v10.0 archive into data/clean and place CSV of M-SOPS data into data/raw. Run r/0_initialize.r in a clean R environment, and look in r/output for results.
Output of sessionInfo() for my environment:
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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] bindrcpp_0.2.2 fifer_1.1 arm_1.10-1 lme4_1.1-19 Matrix_1.2-14
[6] MASS_7.3-50 conflicted_1.0.1 imputeTS_2.7 geepack_1.2-1 broom_0.5.0
[11] forcats_0.3.0 stringr_1.3.1 dplyr_0.7.8 purrr_0.2.5 readr_1.1.1
[16] tidyr_0.8.2 tibble_1.4.2 ggplot2_3.1.0 tidyverse_1.2.1 checkpoint_0.4.5
loaded via a namespace (and not attached):
[1] TH.data_1.0-9 minqa_1.2.4 colorspace_1.3-2
[4] modeltools_0.2-22 estimability_1.3 htmlTable_1.12
[7] base64enc_0.1-3 rstudioapi_0.8 mice_3.3.0
[10] mvtnorm_1.0-8 lubridate_1.7.4 coin_1.2-2
[13] xml2_1.2.0 codetools_0.2-15 splines_3.5.1
[16] knitr_1.20 spam_2.2-0 Formula_1.2-3
[19] jsonlite_1.5 nloptr_1.2.1 cluster_2.0.7-1
[22] compiler_3.5.1 httr_1.3.1 randomForestSRC_2.7.0
[25] lsmeans_2.30-0 emmeans_1.3.0 backports_1.1.2
[28] assertthat_0.2.0 lazyeval_0.2.1 strucchange_1.5-1
[31] cli_1.0.1 acepack_1.4.1 htmltools_0.3.6
[34] tools_3.5.1 dotCall64_1.0-0 coda_0.19-2
[37] gtable_0.2.0 glue_1.3.0 maps_3.3.0
[40] Rcpp_1.0.0 cellranger_1.1.0 fracdiff_1.4-2
[43] urca_1.3-0 nlme_3.1-137 lmtest_0.9-36
[46] timeDate_3043.102 rvest_0.3.2 pan_1.6
[49] zoo_1.8-4 scales_1.0.0 hms_0.4.2
[52] parallel_3.5.1 sandwich_2.5-0 RColorBrewer_1.1-2
[55] fields_9.6 quantmod_0.4-13 curl_3.2
[58] memoise_1.1.0 gridExtra_2.3 uroot_2.0-9
[61] rpart_4.1-13 latticeExtra_0.6-28 stringi_1.2.4
[64] tseries_0.10-45 randomForest_4.6-14 plotrix_3.7-4
[67] checkmate_1.8.5 TTR_0.23-4 rlang_0.3.0.1
[70] pkgconfig_2.0.2 lattice_0.20-35 bindr_0.1.1
[73] stinepack_1.4 htmlwidgets_1.3 cowplot_0.9.3
[76] tidyselect_0.2.5 plyr_1.8.4 magrittr_1.5
[79] R6_2.3.0 Hmisc_4.1-1 mitml_0.3-6
[82] multcomp_1.4-8 pillar_1.3.0 haven_1.1.2
[85] foreign_0.8-70 withr_2.1.2 xts_0.11-2
[88] survival_2.42-3 abind_1.4-5 nnet_7.3-12
[91] modelr_0.1.2 crayon_1.3.4 jomo_2.6-5
[94] party_1.3-1 grid_3.5.1 readxl_1.1.0
[97] data.table_1.11.8 forecast_8.4 digest_0.6.18
[100] xtable_1.8-3 stats4_3.5.1 munsell_0.5.0
[103] quadprog_1.5-5
- 20201207: updated citation.
- 20190417: cleaned up a little.
- 20190416: uploaded code.
- 20190202: created repository.
Contact [email protected].