Last updated: 2026-02-09
Checks: 6 1
Knit directory: ~/Documents/GitHub/PAINT/
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hyperlinks in the table below to view the files as they were in that
past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 441e6fe | Lily Heald | 2026-02-09 | echo false for clean workflowr |
| html | 441e6fe | Lily Heald | 2026-02-09 | echo false for clean workflowr |
| Rmd | 790813f | Lily Heald | 2026-02-09 | add distribution of simons genomes |
| html | 790813f | Lily Heald | 2026-02-09 | add distribution of simons genomes |
| Rmd | 4a52a41 | Lily Heald | 2026-02-04 | Add distribution bar chart |
| html | 4a52a41 | Lily Heald | 2026-02-04 | Add distribution bar chart |
| Rmd | 289d9ed | Lily Heald | 2026-01-30 | add den3 |
| html | 289d9ed | Lily Heald | 2026-01-30 | add den3 |
| Rmd | fe99e78 | Lily Heald | 2026-01-14 | add Denisova 25 |
| html | fe99e78 | Lily Heald | 2026-01-14 | add Denisova 25 |
| Rmd | 2cac6c9 | Lily Heald | 2026-01-14 | add vindija 87 |
| html | 2cac6c9 | Lily Heald | 2026-01-14 | add vindija 87 |
| Rmd | c6f38f2 | Lily Heald | 2026-01-14 | Add Chag8 |
| html | c6f38f2 | Lily Heald | 2026-01-14 | Add Chag8 |
| Rmd | 7bb18d4 | Lily Heald | 2025-11-20 | update sample names |
| Rmd | 9ac4aca | Lily Heald | 2025-11-20 | add mez2 |
| html | 9ac4aca | Lily Heald | 2025-11-20 | add mez2 |
| Rmd | 9209569 | Lily Heald | 2025-11-20 | add altai neanderthal |
| html | 9209569 | Lily Heald | 2025-11-20 | add altai neanderthal |
| Rmd | 1f311d9 | Lily Heald | 2025-11-18 | update figures |
| Rmd | 4a652c1 | Lily Heald | 2025-11-18 | fix paths |
| html | 4a652c1 | Lily Heald | 2025-11-18 | fix paths |
| Rmd | c8573bb | Lily Heald | 2025-11-18 | add les Cottes |
| html | c8573bb | Lily Heald | 2025-11-18 | add les Cottes |
| Rmd | 0236dab | Lily Heald | 2025-11-13 | log transformed depth |
| html | 08dda7e | Lily Heald | 2025-11-13 | update depth plot |
| Rmd | 1bfb83f | Lily Heald | 2025-11-13 | update map, axes |
| Rmd | a1afed5 | Lily Heald | 2025-11-07 | update visibility |
| html | a1afed5 | Lily Heald | 2025-11-07 | update visibility |
| html | 735357b | Lily Heald | 2025-11-07 | Build site. |
| Rmd | 50940c0 | Lily Heald | 2025-11-07 | Update introduction.Rmd |
| Rmd | f1b70cb | Lily Heald | 2025-11-07 | add Hstadel depth |
| Rmd | 7beeddd | Lily Heald | 2025-11-07 | add depth figure |
| Rmd | 967f438 | Lily Heald | 2025-11-07 | update callout |
| html | 967f438 | Lily Heald | 2025-11-07 | update callout |
| html | cc7d134 | Lily Heald | 2025-11-06 | updated figures |
| Rmd | b2f5585 | Lily Heald | 2025-11-06 | Update introduction.Rmd |
| html | 13755f1 | Lily Heald | 2025-11-06 | workflowr |
| Rmd | 46a0913 | Lily Heald | 2025-11-06 | start workflowr |
Genome availability
Modern reference genomes
Sequencing coverage
| Version | Author | Date |
|---|---|---|
| 790813f | Lily Heald | 2026-02-09 |
| 289d9ed | Lily Heald | 2026-01-30 |
| fe99e78 | Lily Heald | 2026-01-14 |
| 2cac6c9 | Lily Heald | 2026-01-14 |
| c6f38f2 | Lily Heald | 2026-01-14 |
| 9ac4aca | Lily Heald | 2025-11-20 |
| 9209569 | Lily Heald | 2025-11-20 |
| 4a652c1 | Lily Heald | 2025-11-18 |
| 08dda7e | Lily Heald | 2025-11-13 |
| 735357b | Lily Heald | 2025-11-07 |
sessionInfo()R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS 26.2
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Detroit
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] wesanderson_0.3.7 showtext_0.9-7 showtextdb_3.0
[4] sysfonts_0.8.9 reshape2_1.4.5 lubridate_1.9.4
[7] forcats_1.0.1 stringr_1.6.0 dplyr_1.2.0
[10] purrr_1.2.1 readr_2.1.6 tidyr_1.3.2
[13] tibble_3.3.1 tidyverse_2.0.0 ggrepel_0.9.6
[16] viridis_0.6.5 viridisLite_0.4.2 ggspatial_1.1.10
[19] raster_3.6-32 sp_2.2-0 sf_1.0-24
[22] rnaturalearthdata_1.0.0 rnaturalearth_1.2.0 ggplot2_4.0.2
[25] workflowr_1.7.2
loaded via a namespace (and not attached):
[1] tidyselect_1.2.1 farver_2.1.2 S7_0.2.1 fastmap_1.2.0
[5] promises_1.5.0 digest_0.6.39 timechange_0.4.0 lifecycle_1.0.5
[9] processx_3.8.6 terra_1.8-93 magrittr_2.0.4 compiler_4.4.2
[13] rlang_1.1.7 sass_0.4.10 tools_4.4.2 yaml_2.3.12
[17] knitr_1.51 labeling_0.4.3 classInt_0.4-11 curl_7.0.0
[21] plyr_1.8.9 RColorBrewer_1.1-3 KernSmooth_2.23-26 withr_3.0.2
[25] grid_4.4.2 git2r_0.36.2 e1071_1.7-17 scales_1.4.0
[29] cli_3.6.5 rmarkdown_2.30 generics_0.1.4 otel_0.2.0
[33] rstudioapi_0.18.0 httr_1.4.7 tzdb_0.5.0 DBI_1.2.3
[37] cachem_1.1.0 proxy_0.4-29 vctrs_0.7.1 jsonlite_2.0.0
[41] callr_3.7.6 hms_1.1.4 jquerylib_0.1.4 units_1.0-0
[45] glue_1.8.0 codetools_0.2-20 ps_1.9.1 stringi_1.8.7
[49] gtable_0.3.6 later_1.4.5 pillar_1.11.1 htmltools_0.5.9
[53] R6_2.6.1 rprojroot_2.1.1 evaluate_1.0.5 lattice_0.22-7
[57] httpuv_1.6.16 bslib_0.10.0 class_7.3-23 Rcpp_1.1.1
[61] gridExtra_2.3 whisker_0.4.1 xfun_0.56 fs_1.6.6
[65] getPass_0.2-4 pkgconfig_2.0.3