diff --git a/.gitignore b/.gitignore index 9a49cbc..47b8285 100644 --- a/.gitignore +++ b/.gitignore @@ -80,5 +80,3 @@ _gsdata_/ # PolarMorphism/eur_w_ld_chr* # PolarMorphism/proxySearch_CAC_CAD* - - diff --git a/README.md b/README.md index 106e5ef..f54e2d0 100644 --- a/README.md +++ b/README.md @@ -23,14 +23,6 @@ You can load this project in RStudio by opening the file called 'AE_OLINK_LPL_an #### Project structure -File | Description | Usage ---------------------------- | -------------------------- | -------------- -README.md | Description of project | Human editable -AE_OLINK_LPL_and_MACE.Rproj | Project file | Loads project -LICENSE | User permissions | Read only -.worcs | WORCS metadata YAML | Read only -prepare_data.R | Script to process raw data | Human editable -renv.lock | Reproducible R environment | Read only File | Description | Usage --------------------------- | --------------------------- | -------------- README.md | Description of project | Human editable diff --git a/renv.lock b/renv.lock index 52c7b7f..aec9843 100644 --- a/renv.lock +++ b/renv.lock @@ -8,7 +8,26 @@ } ] }, + "Bioconductor": { + "Version": "3.15" + }, "Packages": { + "BiocManager": { + "Package": "BiocManager", + "Version": "1.30.18", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "b1a93bed5debda5775636086fdca017b", + "Requirements": [] + }, + "MASS": { + "Package": "MASS", + "Version": "7.3-58", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "4bf2c61e656bbc238634c798c208d386", + "Requirements": [] + }, "Matrix": { "Package": "Matrix", "Version": "1.4-1", @@ -19,6 +38,16 @@ "lattice" ] }, + "MatrixModels": { + "Package": "MatrixModels", + "Version": "0.5-0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "366a8838782928e398b8762c932a42a3", + "Requirements": [ + "Matrix" + ] + }, "R6": { "Package": "R6", "Version": "2.5.1", @@ -27,6 +56,14 @@ "Hash": "470851b6d5d0ac559e9d01bb352b4021", "Requirements": [] }, + "RColorBrewer": { + "Package": "RColorBrewer", + "Version": "1.1-3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "45f0398006e83a5b10b72a90663d8d8c", + "Requirements": [] + }, "Rcpp": { "Package": "Rcpp", "Version": "1.0.9", @@ -46,6 +83,22 @@ "Rcpp" ] }, + "SparseM": { + "Package": "SparseM", + "Version": "1.81", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "2042cd9759cc89a453c4aefef0ce9aae", + "Requirements": [] + }, + "abind": { + "Package": "abind", + "Version": "1.4-5", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "4f57884290cc75ab22f4af9e9d4ca862", + "Requirements": [] + }, "askpass": { "Package": "askpass", "Version": "1.1", @@ -56,6 +109,14 @@ "sys" ] }, + "backports": { + "Package": "backports", + "Version": "1.4.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "c39fbec8a30d23e721980b8afb31984c", + "Requirements": [] + }, "base64enc": { "Package": "base64enc", "Version": "0.1-3", @@ -64,6 +125,50 @@ "Hash": "543776ae6848fde2f48ff3816d0628bc", "Requirements": [] }, + "boot": { + "Package": "boot", + "Version": "1.3-28", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "0baa960e3b49c6176a4f42addcbacc59", + "Requirements": [] + }, + "brew": { + "Package": "brew", + "Version": "1.0-7", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "38875ea52350ff4b4c03849fc69736c8", + "Requirements": [] + }, + "brio": { + "Package": "brio", + "Version": "1.1.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "976cf154dfb043c012d87cddd8bca363", + "Requirements": [] + }, + "broom": { + "Package": "broom", + "Version": "1.0.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "c948329889c7b24a4201df3aef5058c2", + "Requirements": [ + "backports", + "dplyr", + "ellipsis", + "generics", + "ggplot2", + "glue", + "purrr", + "rlang", + "stringr", + "tibble", + "tidyr" + ] + }, "bslib": { "Package": "bslib", "Version": "0.4.0", @@ -91,6 +196,44 @@ "rlang" ] }, + "callr": { + "Package": "callr", + "Version": "3.7.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "2fda237f24bc56508f31394beaa56877", + "Requirements": [ + "R6", + "processx" + ] + }, + "car": { + "Package": "car", + "Version": "3.1-0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "afd3f5c7d144f00d05db8e7701af7829", + "Requirements": [ + "MASS", + "abind", + "carData", + "lme4", + "maptools", + "mgcv", + "nlme", + "nnet", + "pbkrtest", + "quantreg" + ] + }, + "carData": { + "Package": "carData", + "Version": "3.0-5", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "ac6cdb8552c61bd36b0e54d07cf2aab7", + "Requirements": [] + }, "cli": { "Package": "cli", "Version": "3.3.0", @@ -109,6 +252,51 @@ "Hash": "3f038e5ac7f41d4ac41ce658c85e3042", "Requirements": [] }, + "colorspace": { + "Package": "colorspace", + "Version": "2.0-3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "bb4341986bc8b914f0f0acf2e4a3f2f7", + "Requirements": [] + }, + "commonmark": { + "Package": "commonmark", + "Version": "1.8.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "2ba81b120c1655ab696c935ef33ea716", + "Requirements": [] + }, + "corrplot": { + "Package": "corrplot", + "Version": "0.92", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "fcf11a91936fd5047b2ee9bc00595e36", + "Requirements": [] + }, + "cowplot": { + "Package": "cowplot", + "Version": "1.1.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "b418e8423699d11c7f2087c2bfd07da2", + "Requirements": [ + "ggplot2", + "gtable", + "rlang", + "scales" + ] + }, + "cpp11": { + "Package": "cpp11", + "Version": "0.4.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "fa53ce256cd280f468c080a58ea5ba8c", + "Requirements": [] + }, "crayon": { "Package": "crayon", "Version": "1.5.1", @@ -139,6 +327,14 @@ "Hash": "022c42d49c28e95d69ca60446dbabf88", "Requirements": [] }, + "data.table": { + "Package": "data.table", + "Version": "1.14.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "36b67b5adf57b292923f5659f5f0c853", + "Requirements": [] + }, "desc": { "Package": "desc", "Version": "1.4.1", @@ -151,6 +347,46 @@ "rprojroot" ] }, + "devtools": { + "Package": "devtools", + "Version": "2.4.4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "d6ad91ae6533b84d227bb0b5262c111f", + "Requirements": [ + "cli", + "desc", + "ellipsis", + "fs", + "lifecycle", + "memoise", + "miniUI", + "pkgbuild", + "pkgdown", + "pkgload", + "profvis", + "rcmdcheck", + "remotes", + "rlang", + "roxygen2", + "rversions", + "sessioninfo", + "testthat", + "urlchecker", + "usethis", + "withr" + ] + }, + "diffobj": { + "Package": "diffobj", + "Version": "0.3.5", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "bcaa8b95f8d7d01a5dedfd959ce88ab8", + "Requirements": [ + "crayon" + ] + }, "digest": { "Package": "digest", "Version": "0.6.29", @@ -159,6 +395,54 @@ "Hash": "cf6b206a045a684728c3267ef7596190", "Requirements": [] }, + "downlit": { + "Package": "downlit", + "Version": "0.4.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "79bf3f66590752ffbba20f8d2da94c7c", + "Requirements": [ + "brio", + "desc", + "digest", + "evaluate", + "fansi", + "memoise", + "rlang", + "vctrs", + "withr", + "yaml" + ] + }, + "dplyr": { + "Package": "dplyr", + "Version": "1.0.9", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "f0bda1627a7f5d3f9a0b5add931596ac", + "Requirements": [ + "R6", + "generics", + "glue", + "lifecycle", + "magrittr", + "pillar", + "rlang", + "tibble", + "tidyselect", + "vctrs" + ] + }, + "ellipsis": { + "Package": "ellipsis", + "Version": "0.3.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077", + "Requirements": [ + "rlang" + ] + }, "evaluate": { "Package": "evaluate", "Version": "0.15", @@ -167,6 +451,22 @@ "Hash": "699a7a93d08c962d9f8950b2d7a227f1", "Requirements": [] }, + "fansi": { + "Package": "fansi", + "Version": "1.0.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "83a8afdbe71839506baa9f90eebad7ec", + "Requirements": [] + }, + "farver": { + "Package": "farver", + "Version": "2.1.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "8106d78941f34855c440ddb946b8f7a5", + "Requirements": [] + }, "fastmap": { "Package": "fastmap", "Version": "1.1.0", @@ -175,6 +475,25 @@ "Hash": "77bd60a6157420d4ffa93b27cf6a58b8", "Requirements": [] }, + "fontawesome": { + "Package": "fontawesome", + "Version": "0.3.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "a36c4a3eade472039a3ec8cb824e6dc4", + "Requirements": [ + "htmltools", + "rlang" + ] + }, + "foreign": { + "Package": "foreign", + "Version": "0.8-82", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "32b25c97ce306a760c4d9f787991b5d9", + "Requirements": [] + }, "fs": { "Package": "fs", "Version": "1.5.2", @@ -183,6 +502,14 @@ "Hash": "7c89603d81793f0d5486d91ab1fc6f1d", "Requirements": [] }, + "generics": { + "Package": "generics", + "Version": "0.1.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "15e9634c0fcd294799e9b2e929ed1b86", + "Requirements": [] + }, "gert": { "Package": "gert", "Version": "1.6.0", @@ -198,6 +525,84 @@ "zip" ] }, + "ggplot2": { + "Package": "ggplot2", + "Version": "3.3.6", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "0fb26d0674c82705c6b701d1a61e02ea", + "Requirements": [ + "MASS", + "digest", + "glue", + "gtable", + "isoband", + "mgcv", + "rlang", + "scales", + "tibble", + "withr" + ] + }, + "ggpubr": { + "Package": "ggpubr", + "Version": "0.4.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "77089557d374c69db7cb77e65f0d6ab0", + "Requirements": [ + "cowplot", + "dplyr", + "ggplot2", + "ggrepel", + "ggsci", + "ggsignif", + "glue", + "gridExtra", + "magrittr", + "polynom", + "purrr", + "rlang", + "rstatix", + "scales", + "tibble", + "tidyr" + ] + }, + "ggrepel": { + "Package": "ggrepel", + "Version": "0.9.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "08ab869f37e6a7741a64ab9069bcb67d", + "Requirements": [ + "Rcpp", + "ggplot2", + "rlang", + "scales" + ] + }, + "ggsci": { + "Package": "ggsci", + "Version": "2.9", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "81ccb8213ed592598210afd10c3a5936", + "Requirements": [ + "ggplot2", + "scales" + ] + }, + "ggsignif": { + "Package": "ggsignif", + "Version": "0.6.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "2e82e829a1c4a6c5d41921c177051e85", + "Requirements": [ + "ggplot2" + ] + }, "gh": { "Package": "gh", "Version": "1.3.0", @@ -228,6 +633,24 @@ "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e", "Requirements": [] }, + "gridExtra": { + "Package": "gridExtra", + "Version": "2.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "7d7f283939f563670a697165b2cf5560", + "Requirements": [ + "gtable" + ] + }, + "gtable": { + "Package": "gtable", + "Version": "0.3.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "ac5c6baf7822ce8732b343f14c072c4d", + "Requirements": [] + }, "highr": { "Package": "highr", "Version": "0.9", @@ -251,6 +674,31 @@ "rlang" ] }, + "htmlwidgets": { + "Package": "htmlwidgets", + "Version": "1.5.4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "76147821cd3fcd8c4b04e1ef0498e7fb", + "Requirements": [ + "htmltools", + "jsonlite", + "yaml" + ] + }, + "httpuv": { + "Package": "httpuv", + "Version": "1.6.5", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "97fe71f0a4a1c9890e6c2128afa04bc0", + "Requirements": [ + "R6", + "Rcpp", + "later", + "promises" + ] + }, "httr": { "Package": "httr", "Version": "1.4.3", @@ -273,6 +721,14 @@ "Hash": "6154ec2223172bce8162d4153cda21f7", "Requirements": [] }, + "isoband": { + "Package": "isoband", + "Version": "0.2.5", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "7ab57a6de7f48a8dc84910d1eca42883", + "Requirements": [] + }, "jquerylib": { "Package": "jquerylib", "Version": "0.1.4", @@ -305,6 +761,25 @@ "yaml" ] }, + "labeling": { + "Package": "labeling", + "Version": "0.4.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "3d5108641f47470611a32d0bdf357a72", + "Requirements": [] + }, + "later": { + "Package": "later", + "Version": "1.3.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "7e7b457d7766bc47f2a5f21cc2984f8e", + "Requirements": [ + "Rcpp", + "rlang" + ] + }, "lattice": { "Package": "lattice", "Version": "0.20-45", @@ -324,6 +799,24 @@ "rlang" ] }, + "lme4": { + "Package": "lme4", + "Version": "1.1-30", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "d9d5f45b57f68785c350504c0329d285", + "Requirements": [ + "MASS", + "Matrix", + "Rcpp", + "RcppEigen", + "boot", + "lattice", + "minqa", + "nlme", + "nloptr" + ] + }, "magrittr": { "Package": "magrittr", "Version": "2.0.3", @@ -332,6 +825,18 @@ "Hash": "7ce2733a9826b3aeb1775d56fd305472", "Requirements": [] }, + "maptools": { + "Package": "maptools", + "Version": "1.1-4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "e60a1728ad29c48a3491777e0c55a07d", + "Requirements": [ + "foreign", + "lattice", + "sp" + ] + }, "memoise": { "Package": "memoise", "Version": "2.0.1", @@ -343,14 +848,92 @@ "rlang" ] }, - "mime": { - "Package": "mime", - "Version": "0.12", + "mgcv": { + "Package": "mgcv", + "Version": "1.8-40", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "c6b2fdb18cf68ab613bd564363e1ba0d", + "Requirements": [ + "Matrix", + "nlme" + ] + }, + "mime": { + "Package": "mime", + "Version": "0.12", "Source": "Repository", "Repository": "CRAN", "Hash": "18e9c28c1d3ca1560ce30658b22ce104", "Requirements": [] }, + "miniUI": { + "Package": "miniUI", + "Version": "0.1.1.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "fec5f52652d60615fdb3957b3d74324a", + "Requirements": [ + "htmltools", + "shiny" + ] + }, + "minqa": { + "Package": "minqa", + "Version": "1.2.4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "eaee7d2a6f3ed4491df868611cb064cc", + "Requirements": [ + "Rcpp" + ] + }, + "munsell": { + "Package": "munsell", + "Version": "0.5.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "6dfe8bf774944bd5595785e3229d8771", + "Requirements": [ + "colorspace" + ] + }, + "nlme": { + "Package": "nlme", + "Version": "3.1-158", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "9469aeaeddf4f48a7ac70877d0b7ba36", + "Requirements": [ + "lattice" + ] + }, + "nloptr": { + "Package": "nloptr", + "Version": "2.0.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "277c67a08f358f42b6a77826e4492f79", + "Requirements": [ + "testthat" + ] + }, + "nnet": { + "Package": "nnet", + "Version": "7.3-17", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "cb1d8d9f300a7e536b89c8a88c53f610", + "Requirements": [] + }, + "numDeriv": { + "Package": "numDeriv", + "Version": "2016.8-1.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "df58958f293b166e4ab885ebcad90e02", + "Requirements": [] + }, "openssl": { "Package": "openssl", "Version": "2.0.2", @@ -361,6 +944,136 @@ "askpass" ] }, + "pbkrtest": { + "Package": "pbkrtest", + "Version": "0.5.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "b304ff5955f37b48bd30518faf582929", + "Requirements": [ + "MASS", + "Matrix", + "broom", + "dplyr", + "knitr", + "lme4", + "magrittr", + "numDeriv" + ] + }, + "pillar": { + "Package": "pillar", + "Version": "1.8.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "f95cf85794546c4ac2b9a6ca42e671ff", + "Requirements": [ + "cli", + "fansi", + "glue", + "lifecycle", + "rlang", + "utf8", + "vctrs" + ] + }, + "pkgbuild": { + "Package": "pkgbuild", + "Version": "1.3.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "66d2adfed274daf81ccfe77d974c3b9b", + "Requirements": [ + "R6", + "callr", + "cli", + "crayon", + "desc", + "prettyunits", + "rprojroot", + "withr" + ] + }, + "pkgconfig": { + "Package": "pkgconfig", + "Version": "2.0.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "01f28d4278f15c76cddbea05899c5d6f", + "Requirements": [] + }, + "pkgdown": { + "Package": "pkgdown", + "Version": "2.0.6", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "f958d0b2a5dabc5ffd414f062b1ffbe7", + "Requirements": [ + "bslib", + "callr", + "cli", + "desc", + "digest", + "downlit", + "fs", + "httr", + "jsonlite", + "magrittr", + "memoise", + "purrr", + "ragg", + "rlang", + "rmarkdown", + "tibble", + "whisker", + "withr", + "xml2", + "yaml" + ] + }, + "pkgload": { + "Package": "pkgload", + "Version": "1.3.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "4b20f937a363c78a5730265c1925f54a", + "Requirements": [ + "cli", + "crayon", + "desc", + "fs", + "glue", + "rlang", + "rprojroot", + "withr" + ] + }, + "plyr": { + "Package": "plyr", + "Version": "1.8.7", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "9c17c6ee41639ebdc1d7266546d3b627", + "Requirements": [ + "Rcpp" + ] + }, + "polynom": { + "Package": "polynom", + "Version": "1.4-1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "ceb5c2a59ba33d42d051285a3e8a5118", + "Requirements": [] + }, + "praise": { + "Package": "praise", + "Version": "1.0.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "a555924add98c99d2f411e37e7d25e9f", + "Requirements": [] + }, "prereg": { "Package": "prereg", "Version": "0.6.0", @@ -371,6 +1084,58 @@ "rmarkdown" ] }, + "prettyunits": { + "Package": "prettyunits", + "Version": "1.1.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "95ef9167b75dde9d2ccc3c7528393e7e", + "Requirements": [] + }, + "processx": { + "Package": "processx", + "Version": "3.7.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "f91df0f5f31ffdf88bc0b624f5ebab0f", + "Requirements": [ + "R6", + "ps" + ] + }, + "profvis": { + "Package": "profvis", + "Version": "0.3.7", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "e9d21e79848e02e524bea6f5bd53e7e4", + "Requirements": [ + "htmlwidgets", + "stringr" + ] + }, + "promises": { + "Package": "promises", + "Version": "1.2.0.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "4ab2c43adb4d4699cf3690acd378d75d", + "Requirements": [ + "R6", + "Rcpp", + "later", + "magrittr", + "rlang" + ] + }, + "ps": { + "Package": "ps", + "Version": "1.7.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "8b93531308c01ad0e56d9eadcc0c4fcd", + "Requirements": [] + }, "purrr": { "Package": "purrr", "Version": "0.3.4", @@ -382,6 +1147,31 @@ "rlang" ] }, + "quantreg": { + "Package": "quantreg", + "Version": "5.94", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "b8b2b861526c344a7e16e5991fa5a4ab", + "Requirements": [ + "MASS", + "Matrix", + "MatrixModels", + "SparseM", + "survival" + ] + }, + "ragg": { + "Package": "ragg", + "Version": "1.2.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "14932bb6f2739c771ca4ceaba6b4248e", + "Requirements": [ + "systemfonts", + "textshaping" + ] + }, "ranger": { "Package": "ranger", "Version": "0.14.1", @@ -402,6 +1192,45 @@ "Hash": "5e3c5dc0b071b21fa128676560dbe94d", "Requirements": [] }, + "rcmdcheck": { + "Package": "rcmdcheck", + "Version": "1.4.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "8f25ebe2ec38b1f2aef3b0d2ef76f6c4", + "Requirements": [ + "R6", + "callr", + "cli", + "curl", + "desc", + "digest", + "pkgbuild", + "prettyunits", + "rprojroot", + "sessioninfo", + "withr", + "xopen" + ] + }, + "rematch2": { + "Package": "rematch2", + "Version": "2.1.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "76c9e04c712a05848ae7a23d2f170a40", + "Requirements": [ + "tibble" + ] + }, + "remotes": { + "Package": "remotes", + "Version": "2.4.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "227045be9aee47e6dda9bb38ac870d67", + "Requirements": [] + }, "renv": { "Package": "renv", "Version": "0.15.5", @@ -410,6 +1239,18 @@ "Hash": "6a38294e7d12f5d8e656b08c5bd8ae34", "Requirements": [] }, + "reshape2": { + "Package": "reshape2", + "Version": "1.4.4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "bb5996d0bd962d214a11140d77589917", + "Requirements": [ + "Rcpp", + "plyr", + "stringr" + ] + }, "rlang": { "Package": "rlang", "Version": "1.0.4", @@ -437,6 +1278,30 @@ "yaml" ] }, + "roxygen2": { + "Package": "roxygen2", + "Version": "7.2.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "da1f278262e563c835345872f2fef537", + "Requirements": [ + "R6", + "brew", + "cli", + "commonmark", + "cpp11", + "desc", + "digest", + "knitr", + "pkgload", + "purrr", + "rlang", + "stringi", + "stringr", + "withr", + "xml2" + ] + }, "rprojroot": { "Package": "rprojroot", "Version": "2.0.3", @@ -445,6 +1310,26 @@ "Hash": "1de7ab598047a87bba48434ba35d497d", "Requirements": [] }, + "rstatix": { + "Package": "rstatix", + "Version": "0.7.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "aa020f8efde649badd0b2b5456e942fe", + "Requirements": [ + "broom", + "car", + "corrplot", + "dplyr", + "generics", + "magrittr", + "purrr", + "rlang", + "tibble", + "tidyr", + "tidyselect" + ] + }, "rstudioapi": { "Package": "rstudioapi", "Version": "0.13", @@ -467,6 +1352,17 @@ "yaml" ] }, + "rversions": { + "Package": "rversions", + "Version": "2.1.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "f88fab00907b312f8b23ec13e2d437cb", + "Requirements": [ + "curl", + "xml2" + ] + }, "sass": { "Package": "sass", "Version": "0.4.2", @@ -481,6 +1377,80 @@ "rlang" ] }, + "scales": { + "Package": "scales", + "Version": "1.2.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "6e8750cdd13477aa440d453da93d5cac", + "Requirements": [ + "R6", + "RColorBrewer", + "farver", + "labeling", + "lifecycle", + "munsell", + "rlang", + "viridisLite" + ] + }, + "sessioninfo": { + "Package": "sessioninfo", + "Version": "1.2.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "3f9796a8d0a0e8c6eb49a4b029359d1f", + "Requirements": [ + "cli" + ] + }, + "shiny": { + "Package": "shiny", + "Version": "1.7.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "4f7970a3edb0a153ac6b376785a1944a", + "Requirements": [ + "R6", + "bslib", + "cachem", + "commonmark", + "crayon", + "ellipsis", + "fastmap", + "fontawesome", + "glue", + "htmltools", + "httpuv", + "jsonlite", + "later", + "lifecycle", + "mime", + "promises", + "rlang", + "sourcetools", + "withr", + "xtable" + ] + }, + "sourcetools": { + "Package": "sourcetools", + "Version": "0.1.7", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "947e4e02a79effa5d512473e10f41797", + "Requirements": [] + }, + "sp": { + "Package": "sp", + "Version": "1.5-0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "2a118bdd2db0a301711e0a9e3e3206d5", + "Requirements": [ + "lattice" + ] + }, "stringi": { "Package": "stringi", "Version": "1.7.8", @@ -501,6 +1471,16 @@ "stringi" ] }, + "survival": { + "Package": "survival", + "Version": "3.3-1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "f6189c70451d3d68e0d571235576e833", + "Requirements": [ + "Matrix" + ] + }, "sys": { "Package": "sys", "Version": "3.4", @@ -509,6 +1489,105 @@ "Hash": "b227d13e29222b4574486cfcbde077fa", "Requirements": [] }, + "systemfonts": { + "Package": "systemfonts", + "Version": "1.0.4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "90b28393209827327de889f49935140a", + "Requirements": [ + "cpp11" + ] + }, + "testthat": { + "Package": "testthat", + "Version": "3.1.4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "f76c2a02d0fdc24aa7a47ea34261a6e3", + "Requirements": [ + "R6", + "brio", + "callr", + "cli", + "crayon", + "desc", + "digest", + "ellipsis", + "evaluate", + "jsonlite", + "lifecycle", + "magrittr", + "pkgload", + "praise", + "processx", + "ps", + "rlang", + "waldo", + "withr" + ] + }, + "textshaping": { + "Package": "textshaping", + "Version": "0.3.6", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "1ab6223d3670fac7143202cb6a2d43d5", + "Requirements": [ + "cpp11", + "systemfonts" + ] + }, + "tibble": { + "Package": "tibble", + "Version": "3.1.8", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "56b6934ef0f8c68225949a8672fe1a8f", + "Requirements": [ + "fansi", + "lifecycle", + "magrittr", + "pillar", + "pkgconfig", + "rlang", + "vctrs" + ] + }, + "tidyr": { + "Package": "tidyr", + "Version": "1.2.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "d8b95b7fee945d7da6888cf7eb71a49c", + "Requirements": [ + "cpp11", + "dplyr", + "ellipsis", + "glue", + "lifecycle", + "magrittr", + "purrr", + "rlang", + "tibble", + "tidyselect", + "vctrs" + ] + }, + "tidyselect": { + "Package": "tidyselect", + "Version": "1.1.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "17f6da8cfd7002760a859915ce7eef8f", + "Requirements": [ + "ellipsis", + "glue", + "purrr", + "rlang", + "vctrs" + ] + }, "tinytex": { "Package": "tinytex", "Version": "0.40", @@ -519,6 +1598,18 @@ "xfun" ] }, + "urlchecker": { + "Package": "urlchecker", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "409328b8e1253c8d729a7836fe7f7a16", + "Requirements": [ + "cli", + "curl", + "xml2" + ] + }, "usethis": { "Package": "usethis", "Version": "2.1.6", @@ -547,6 +1638,50 @@ "yaml" ] }, + "utf8": { + "Package": "utf8", + "Version": "1.2.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "c9c462b759a5cc844ae25b5942654d13", + "Requirements": [] + }, + "vctrs": { + "Package": "vctrs", + "Version": "0.4.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "8b54f22e2a58c4f275479c92ce041a57", + "Requirements": [ + "cli", + "glue", + "rlang" + ] + }, + "viridisLite": { + "Package": "viridisLite", + "Version": "0.4.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "55e157e2aa88161bdb0754218470d204", + "Requirements": [] + }, + "waldo": { + "Package": "waldo", + "Version": "0.4.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "035fba89d0c86e2113120f93301b98ad", + "Requirements": [ + "cli", + "diffobj", + "fansi", + "glue", + "rematch2", + "rlang", + "tibble" + ] + }, "whisker": { "Package": "whisker", "Version": "0.4", @@ -592,6 +1727,32 @@ "Hash": "a318c6f752b8dcfe9fb74d897418ab2b", "Requirements": [] }, + "xml2": { + "Package": "xml2", + "Version": "1.3.3", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "40682ed6a969ea5abfd351eb67833adc", + "Requirements": [] + }, + "xopen": { + "Package": "xopen", + "Version": "1.0.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "6c85f015dee9cc7710ddd20f86881f58", + "Requirements": [ + "processx" + ] + }, + "xtable": { + "Package": "xtable", + "Version": "1.8-4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2", + "Requirements": [] + }, "yaml": { "Package": "yaml", "Version": "2.3.5",