Here I provide a summary of all R packages used and their versions.
library(dartR)
library(ggpubr)
library(gplots)
library(grid)
library(gridExtra)
library(janitor)
library(knitr)
library(LinkageMapView)
library(pander)
library(parallel)
library(pivottabler)
library(reshape2)
library(rrBLUP)
library(SNPassoc)
library(stringr)
library(tidyverse)## Warning: package 'tidyr' was built under R version 4.0.5library(xtable)sessionInfo()## R version 4.0.3 (2020-10-10)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS High Sierra 10.13.6
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
##
## attached base packages:
## [1] parallel grid stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] xtable_1.8-4 forcats_0.5.1 purrr_0.3.4
## [4] readr_1.4.0 tidyr_1.2.0 tibble_3.1.6
## [7] tidyverse_1.3.1 stringr_1.4.0 SNPassoc_2.0-17
## [10] rrBLUP_4.6.1 reshape2_1.4.4 pivottabler_1.5.4
## [13] pander_0.6.3 LinkageMapView_2.1.2 knitr_1.40
## [16] janitor_2.1.0 gridExtra_2.3 gplots_3.1.0
## [19] ggpubr_0.4.0 dartR_2.0.4 dplyr_1.0.7
## [22] ggplot2_3.3.5 adegenet_2.1.3 ade4_1.7-15
##
## loaded via a namespace (and not attached):
## [1] rappdirs_0.3.3
## [2] rtracklayer_1.48.0
## [3] SparseM_1.78
## [4] GGally_2.0.0
## [5] R.methodsS3_1.8.1
## [6] coda_0.19-4
## [7] bit64_4.0.5
## [8] multcomp_1.4-20
## [9] DelayedArray_0.14.1
## [10] R.utils_2.10.1
## [11] data.table_1.13.0
## [12] rpart_4.1-15
## [13] RCurl_1.98-1.2
## [14] doParallel_1.0.16
## [15] generics_0.0.2
## [16] BiocGenerics_0.34.0
## [17] GenomicFeatures_1.40.1
## [18] TH.data_1.1-1
## [19] RSQLite_2.2.12
## [20] polspline_1.1.19
## [21] combinat_0.0-8
## [22] bit_4.0.4
## [23] BiocStyle_2.16.1
## [24] xml2_1.3.2
## [25] lubridate_1.8.0
## [26] httpuv_1.5.4
## [27] SummarizedExperiment_1.18.2
## [28] assertthat_0.2.1
## [29] viridis_0.5.1
## [30] xfun_0.30
## [31] dismo_1.1-4
## [32] hms_1.1.1
## [33] jquerylib_0.1.4
## [34] evaluate_0.17
## [35] promises_1.1.1
## [36] fansi_0.4.1
## [37] progress_1.2.2
## [38] dbplyr_2.1.1
## [39] caTools_1.18.0
## [40] readxl_1.3.1
## [41] igraph_1.2.6
## [42] DBI_1.1.0
## [43] htmlwidgets_1.5.3
## [44] reshape_0.8.8
## [45] stats4_4.0.3
## [46] spdep_1.1-5
## [47] ellipsis_0.3.2
## [48] mmod_1.3.3
## [49] backports_1.1.10
## [50] permute_0.9-5
## [51] arsenal_3.6.3
## [52] calibrate_1.7.7
## [53] biomaRt_2.44.4
## [54] deldir_0.1-29
## [55] vctrs_0.3.8
## [56] Biobase_2.48.0
## [57] quantreg_5.74
## [58] genetics_1.3.8.1.2
## [59] abind_1.4-5
## [60] cachem_1.0.6
## [61] withr_2.3.0
## [62] BSgenome_1.56.0
## [63] checkmate_2.0.0
## [64] rgdal_1.5-28
## [65] GenomicAlignments_1.24.0
## [66] vegan_2.5-7
## [67] prettyunits_1.1.1
## [68] cluster_2.1.0
## [69] ape_5.4-1
## [70] dotCall64_1.0-1
## [71] crayon_1.4.2
## [72] pkgconfig_2.0.3
## [73] units_0.8-0
## [74] GenomeInfoDb_1.24.2
## [75] nlme_3.1-149
## [76] nnet_7.3-14
## [77] rlang_1.0.2
## [78] pegas_0.14
## [79] lifecycle_1.0.1
## [80] haplo.stats_1.8.7
## [81] poisbinom_1.0.1
## [82] MatrixModels_0.4-1
## [83] sandwich_3.0-2
## [84] seqinr_4.2-4
## [85] BiocFileCache_1.12.1
## [86] modelr_0.1.8
## [87] cellranger_1.1.0
## [88] matrixStats_0.57.0
## [89] Matrix_1.2-18
## [90] raster_3.3-13
## [91] carData_3.0-4
## [92] boot_1.3-25
## [93] zoo_1.8-8
## [94] reprex_2.0.1
## [95] base64enc_0.1-3
## [96] StAMPP_1.6.1
## [97] png_0.1-7
## [98] viridisLite_0.3.0
## [99] bitops_1.0-6
## [100] R.oo_1.24.0
## [101] gdistance_1.3-6
## [102] KernSmooth_2.23-17
## [103] spam_2.8-0
## [104] Biostrings_2.56.0
## [105] blob_1.2.1
## [106] classInt_0.4-3
## [107] jpeg_0.1-8.1
## [108] rstatix_0.6.0
## [109] S4Vectors_0.26.1
## [110] ggsignif_0.6.0
## [111] scales_1.1.1
## [112] memoise_1.1.0
## [113] magrittr_2.0.2
## [114] plyr_1.8.6
## [115] gdata_2.18.0
## [116] zlibbioc_1.34.0
## [117] compiler_4.0.3
## [118] RColorBrewer_1.1-2
## [119] gdsfmt_1.24.1
## [120] Rsamtools_2.4.0
## [121] snakecase_0.11.0
## [122] cli_3.1.1
## [123] XVector_0.28.0
## [124] LearnBayes_2.15.1
## [125] patchwork_1.1.0
## [126] htmlTable_2.1.0
## [127] Formula_1.2-4
## [128] MASS_7.3-53
## [129] mgcv_1.8-33
## [130] tidyselect_1.1.0
## [131] stringi_1.5.3
## [132] yaml_2.2.1
## [133] askpass_1.1
## [134] latticeExtra_0.6-29
## [135] sass_0.4.1
## [136] VariantAnnotation_1.34.0
## [137] SNPRelate_1.22.0
## [138] tools_4.0.3
## [139] rio_0.5.16
## [140] RgoogleMaps_1.4.5.3
## [141] rstudioapi_0.13
## [142] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
## [143] foreach_1.5.1
## [144] foreign_0.8-80
## [145] PopGenReport_3.0.4
## [146] digest_0.6.26
## [147] BiocManager_1.30.10
## [148] shiny_1.5.0
## [149] Rcpp_1.0.8
## [150] GenomicRanges_1.40.0
## [151] car_3.0-10
## [152] broom_0.7.12
## [153] later_1.1.0.1
## [154] org.Hs.eg.db_3.11.4
## [155] httr_1.4.2
## [156] AnnotationDbi_1.50.3
## [157] sf_1.0-6
## [158] colorspace_1.4-1
## [159] rvest_1.0.2
## [160] fs_1.5.0
## [161] XML_3.99-0.9
## [162] IRanges_2.22.2
## [163] splines_4.0.3
## [164] fields_13.3
## [165] expm_0.999-5
## [166] conquer_1.0.2
## [167] sp_1.4-4
## [168] spData_0.3.8
## [169] jsonlite_1.7.3
## [170] gap_1.2.2
## [171] R6_2.4.1
## [172] gmodels_2.18.1
## [173] Hmisc_4.6-0
## [174] pillar_1.7.0
## [175] htmltools_0.5.2
## [176] mime_0.9
## [177] glue_1.4.2
## [178] fastmap_1.1.0
## [179] BiocParallel_1.22.0
## [180] class_7.3-17
## [181] codetools_0.2-16
## [182] maps_3.4.0
## [183] mvtnorm_1.1-1
## [184] utf8_1.1.4
## [185] lattice_0.20-41
## [186] bslib_0.4.0
## [187] curl_4.3
## [188] gtools_3.8.2
## [189] openssl_1.4.3
## [190] zip_2.1.1
## [191] openxlsx_4.2.2
## [192] survival_3.2-7
## [193] rmarkdown_2.17
## [194] munsell_0.5.0
## [195] e1071_1.7-4
## [196] GenomeInfoDbData_1.2.3
## [197] iterators_1.0.13
## [198] haven_2.3.1
## [199] gtable_0.3.0
## [200] rms_6.2-0