Last updated: 2021-03-04
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Knit directory: PSYMETAB/
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Unstaged changes:
Modified: analysis/genetic_quality_control.Rmd
Modified: cache_log.csv
Modified: post_impute.log
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These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | dab6add | Jenny Sjaarda | 2021-03-04 | Building plans Rmd |
| html | b4487b7 | Jenny Sjaarda | 2021-03-03 | Build site. |
| Rmd | 0304998 | Jenny Sjaarda | 2021-03-03 | testing genetics_qc |
| Rmd | 13aa9db | jennysjaarda | 2021-03-03 | misc updates to website Rmd pages |
| Rmd | 941b66d | Jenny Sjaarda | 2021-03-02 | add new Rmd files and respective html files |
| html | 941b66d | Jenny Sjaarda | 2021-03-02 | add new Rmd files and respective html files |
drake was used to manage all workflow.
outdated(qc_prep)character(0)deps_profile(fam_munge, qc_prep)# A tibble: 5 x 4
name changed old new
<chr> <lgl> <chr> <chr>
1 command FALSE "10272f045cceef79" "10272f045cceef79"
2 depend FALSE "6f42c78ff74035a6" "6f42c78ff74035a6"
3 file_in FALSE "" ""
4 file_out FALSE "" ""
5 seed FALSE "722845642" "722845642" deps_code(munge_fam)# A tibble: 4 x 2
name type
<chr> <chr>
1 return globals
2 merge globals
3 c globals
4 colnames<- globalsdeps_target(fam_munge, qc_prep)# A tibble: 3 x 3
name type hash
<chr> <chr> <chr>
1 munge_fam globals 45d8a46ac51139fe
2 fam_raw globals b43e1377f18cf415
3 id_code globals a243fab17081d08fvis_drake_graph(qc_prep, main="QC Preparation Plan")vis_drake_graph(pre_impute_qc, main="Pre-Imputation Plan")vis_drake_graph(download_impute, main="Download Imputation Plan")vis_drake_graph(post_impute, main="Post-Imputation Plan")#vis_drake_graph(analysis)
#vis_drake_graph(download_impute, make_imports = FALSE)
#vis_drake_graph(post_impute, make_imports = FALSE)
options(scipen=999)
sessionInfo()R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /data/sgg2/jenny/bin/R-3.5.3/lib64/R/lib/libRblas.so
LAPACK: /data/sgg2/jenny/bin/R-3.5.3/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] tidyselect_0.2.5 rbgen_0.1 ukbtools_0.11.3
[4] hrbrthemes_0.8.0 OpenImageR_1.1.6 fuzzyjoin_0.1.5
[7] kableExtra_1.1.0 R.utils_2.9.2 R.oo_1.23.0
[10] R.methodsS3_1.7.1 TwoSampleMR_0.4.25 reader_1.0.6
[13] NCmisc_1.1.6 optparse_1.6.4 readxl_1.3.1
[16] ggthemes_4.2.0 tryCatchLog_1.1.6 futile.logger_1.4.3
[19] DataExplorer_0.8.0 taRifx_1.0.6.1 qqman_0.1.4
[22] MASS_7.3-51.5 bit64_0.9-7 bit_1.1-14
[25] rslurm_0.5.0 rmeta_3.0 devtools_2.2.1
[28] usethis_1.5.1 data.table_1.12.8 clustermq_0.8.8.1
[31] future.batchtools_0.8.1 future_1.15.1 rlang_0.4.5
[34] knitr_1.26 drake_7.12.0.9000 forcats_0.4.0
[37] stringr_1.4.0 dplyr_0.8.3 purrr_0.3.3
[40] readr_1.3.1 tidyr_1.0.3 tibble_2.1.3
[43] ggplot2_3.3.2 tidyverse_1.3.0 pacman_0.5.1
[46] processx_3.4.1 workflowr_1.6.0
loaded via a namespace (and not attached):
[1] backports_1.1.6 systemfonts_0.2.3 plyr_1.8.5
[4] igraph_1.2.5 storr_1.2.1 listenv_0.8.0
[7] digest_0.6.25 foreach_1.4.7 htmltools_0.4.0
[10] tiff_0.1-5 fansi_0.4.1 magrittr_1.5
[13] checkmate_1.9.4 memoise_1.1.0 base64url_1.4
[16] doParallel_1.0.15 remotes_2.1.0 globals_0.12.5
[19] extrafont_0.17 modelr_0.1.5 extrafontdb_1.0
[22] prettyunits_1.1.0 jpeg_0.1-8.1 colorspace_1.4-1
[25] rvest_0.3.5 rappdirs_0.3.1 haven_2.2.0
[28] xfun_0.11 callr_3.4.0 crayon_1.3.4
[31] jsonlite_1.6 iterators_1.0.12 brew_1.0-6
[34] glue_1.4.0 gtable_0.3.0 webshot_0.5.2
[37] pkgbuild_1.0.6 Rttf2pt1_1.3.8 scales_1.1.0
[40] futile.options_1.0.1 DBI_1.1.0 Rcpp_1.0.3
[43] xtable_1.8-4 viridisLite_0.3.0 progress_1.2.2
[46] txtq_0.2.0 htmlwidgets_1.5.1 httr_1.4.1
[49] getopt_1.20.3 calibrate_1.7.5 ellipsis_0.3.0
[52] XML_3.98-1.20 pkgconfig_2.0.3 dbplyr_1.4.2
[55] utf8_1.1.4 reshape2_1.4.3 later_1.0.0
[58] visNetwork_2.0.9 munsell_0.5.0 cellranger_1.1.0
[61] tools_3.5.3 cli_2.0.1 generics_0.0.2
[64] broom_0.5.3 fastmap_1.0.1 evaluate_0.14
[67] yaml_2.2.0 fs_1.3.1 packrat_0.5.0
[70] nlme_3.1-143 mime_0.8 whisker_0.4
[73] formatR_1.7 proftools_0.99-2 xml2_1.2.2
[76] compiler_3.5.3 rstudioapi_0.10 png_0.1-7
[79] filelock_1.0.2 testthat_2.3.1 reprex_0.3.0
[82] stringi_1.4.5 ps_1.3.0 desc_1.2.0
[85] gdtools_0.2.2 lattice_0.20-38 vctrs_0.2.4
[88] pillar_1.4.3 lifecycle_0.1.0 networkD3_0.4
[91] httpuv_1.5.2 R6_2.4.1 promises_1.1.0
[94] gridExtra_2.3 sessioninfo_1.1.1 codetools_0.2-16
[97] lambda.r_1.2.4 assertthat_0.2.1 pkgload_1.0.2
[100] rprojroot_1.3-2 withr_2.1.2 batchtools_0.9.12
[103] parallel_3.5.3 hms_0.5.3 grid_3.5.3
[106] rmarkdown_1.18 git2r_0.26.1 shiny_1.4.0
[109] lubridate_1.7.4