diff --git a/index.Rmd b/index.Rmd index 9b5e87d..7a797dd 100644 --- a/index.Rmd +++ b/index.Rmd @@ -7,10 +7,10 @@ date: "updated: `r format(Sys.time(), '%B %d, %Y')`" documentclass: book site: bookdown::bookdown_site bibliography: [book.bib, packages.bib] -biblio-style: apalike +csl: jrss.csl +link-citations: yes fontsize: '12pt, krantz2' monofontoptions: "Scale=0.7" -link-citations: yes colorlinks: yes lot: yes lof: yes diff --git a/jrss.csl b/jrss.csl new file mode 100644 index 0000000..c8d5098 --- /dev/null +++ b/jrss.csl @@ -0,0 +1,305 @@ + + diff --git a/latex_extras/preamble.tex b/latex_extras/preamble.tex index 8fd61f2..8f5c3ae 100644 --- a/latex_extras/preamble.tex +++ b/latex_extras/preamble.tex @@ -2,7 +2,6 @@ \usepackage[inline]{enumitem} \usepackage{float} \usepackage{graphicx} -%\usepackage[round]{natbib} \usepackage{geometry} \usepackage{tikz} \usepackage[english]{babel} @@ -97,4 +96,4 @@ \usepackage{framed} \setlength{\fboxsep}{.8em} -\usepackage{tcolorbox} \ No newline at end of file +\usepackage{tcolorbox} diff --git a/renv.lock b/renv.lock index 79d9b54..6b61be6 100644 --- a/renv.lock +++ b/renv.lock @@ -447,15 +447,16 @@ }, "bookdown": { "Package": "bookdown", - "Version": "0.26.3", + "Version": "0.34.2", "Source": "GitHub", "RemoteType": "github", "RemoteHost": "api.github.com", "RemoteUsername": "rstudio", "RemoteRepo": "bookdown", "RemoteRef": "main", - "RemoteSha": "169c43b6bb95213f2af63a95acd4e977a58a3e1f", + "RemoteSha": "e3cae95282f497c55864057e9e8255e2aed75120", "Requirements": [ + "R", "htmltools", "jquerylib", "knitr", @@ -464,7 +465,7 @@ "xfun", "yaml" ], - "Hash": "c7da7b837c058ef8eba7f64070954eeb" + "Hash": "cd70ae66241b6493b5f323aea8bac6b0" }, "boot": { "Package": "boot", @@ -515,26 +516,28 @@ }, "bslib": { "Package": "bslib", - "Version": "0.3.1.9000", + "Version": "0.5.0.9000", "Source": "GitHub", "RemoteType": "github", "RemoteHost": "api.github.com", - "RemoteUsername": "rstudio", "RemoteRepo": "bslib", + "RemoteUsername": "rstudio", "RemoteRef": "main", - "RemoteSha": "a4946a49499438e71dce29c810a41e2d05170376", + "RemoteSha": "64de13aa5634146e996e8874a87b91f48503f8bc", "Requirements": [ "R", + "base64enc", "cachem", "grDevices", "htmltools", "jquerylib", "jsonlite", "memoise", + "mime", "rlang", "sass" ], - "Hash": "e7bf4535fe6ec4cab479f1d54a432964" + "Hash": "cd8d7b51dda01b69ebbf048a016b16f9" }, "caTools": { "Package": "caTools", @@ -549,26 +552,27 @@ }, "cachem": { "Package": "cachem", - "Version": "1.0.6", + "Version": "1.0.8", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "fastmap", "rlang" ], - "Hash": "648c5b3d71e6a37e3043617489a0a0e9" + "Hash": "c35768291560ce302c0a6589f92e837d" }, "callr": { "Package": "callr", - "Version": "3.7.0", + "Version": "3.7.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ + "R", "R6", "processx", "utils" ], - "Hash": "461aa75a11ce2400245190ef5d3995df" + "Hash": "9b2191ede20fa29828139b9900922e51" }, "caret": { "Package": "caret", @@ -693,7 +697,7 @@ }, "colorspace": { "Package": "colorspace", - "Version": "2.0-3", + "Version": "2.1-0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -703,7 +707,7 @@ "methods", "stats" ], - "Hash": "bb4341986bc8b914f0f0acf2e4a3f2f7" + "Hash": "f20c47fd52fae58b4e377c37bb8c335b" }, "commonmark": { "Package": "commonmark", @@ -758,13 +762,13 @@ }, "curl": { "Package": "curl", - "Version": "4.3.2", + "Version": "5.0.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "022c42d49c28e95d69ca60446dbabf88" + "Hash": "2118af9cb164c8d2dddc7b89eaf732d9" }, "cvAUC": { "Package": "cvAUC", @@ -1050,14 +1054,14 @@ }, "evaluate": { "Package": "evaluate", - "Version": "0.15", + "Version": "0.21", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "699a7a93d08c962d9f8950b2d7a227f1" + "Hash": "d59f3b464e8da1aef82dc04b588b8dfb" }, "fansi": { "Package": "fansi", @@ -1080,10 +1084,22 @@ }, "fastmap": { "Package": "fastmap", - "Version": "1.1.0", + "Version": "1.1.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "f7736a18de97dea803bde0a2daaafb27" + }, + "fontawesome": { + "Package": "fontawesome", + "Version": "0.5.1", "Source": "Repository", "Repository": "CRAN", - "Hash": "77bd60a6157420d4ffa93b27cf6a58b8" + "Requirements": [ + "R", + "htmltools", + "rlang" + ], + "Hash": "1e22b8cabbad1eae951a75e9f8b52378" }, "forcats": { "Package": "forcats", @@ -1149,14 +1165,14 @@ }, "fs": { "Package": "fs", - "Version": "1.5.2", + "Version": "1.6.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "7c89603d81793f0d5486d91ab1fc6f1d" + "Hash": "94af08e0aa9675a16fadbb3aaaa90d2a" }, "future": { "Package": "future", @@ -1673,14 +1689,14 @@ }, "highr": { "Package": "highr", - "Version": "0.9", + "Version": "0.10", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "xfun" ], - "Hash": "8eb36c8125038e648e5d111c0d7b2ed4" + "Hash": "06230136b2d2b9ba5805e1963fa6e890" }, "hms": { "Package": "hms", @@ -1699,7 +1715,7 @@ }, "htmltools": { "Package": "htmltools", - "Version": "0.5.4", + "Version": "0.5.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1712,7 +1728,7 @@ "rlang", "utils" ], - "Hash": "9d27e99cc90bd701c0a7a63e5923f9b7" + "Hash": "ba0240784ad50a62165058a27459304a" }, "htmlwidgets": { "Package": "htmlwidgets", @@ -1729,7 +1745,7 @@ }, "httr": { "Package": "httr", - "Version": "1.4.3", + "Version": "1.4.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1740,7 +1756,7 @@ "mime", "openssl" ], - "Hash": "88d1b310583777edf01ccd1216fb0b2b" + "Hash": "7e5e3cbd2a7bc07880c94e22348fb661" }, "ids": { "Package": "ids", @@ -1839,19 +1855,24 @@ }, "jsonlite": { "Package": "jsonlite", - "Version": "1.8.4", + "Version": "1.8.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "methods" ], - "Hash": "a4269a09a9b865579b2635c77e572374" + "Hash": "266a20443ca13c65688b2116d5220f76" }, "kableExtra": { "Package": "kableExtra", - "Version": "1.3.4", - "Source": "Repository", - "Repository": "CRAN", + "Version": "1.3.4.9000", + "Source": "GitHub", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteRepo": "kableExtra", + "RemoteUsername": "kupietz", + "RemoteRef": "HEAD", + "RemoteSha": "3bf9b21a769c9e6c21c955689bf5f8175dc83350", "Requirements": [ "R", "digest", @@ -1873,11 +1894,11 @@ "webshot", "xml2" ], - "Hash": "49b625e6aabe4c5f091f5850aba8ff78" + "Hash": "64a6ab8b8aaf1dd6a6b96494ff2b1fe7" }, "knitr": { "Package": "knitr", - "Version": "1.39", + "Version": "1.43", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1885,12 +1906,11 @@ "evaluate", "highr", "methods", - "stringr", "tools", "xfun", "yaml" ], - "Hash": "029ab7c4badd3cf8af69016b2ba27493" + "Hash": "9775eb076713f627c07ce41d8199d8f6" }, "labeling": { "Package": "labeling", @@ -2199,13 +2219,13 @@ }, "openssl": { "Package": "openssl", - "Version": "2.0.2", + "Version": "2.0.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "askpass" ], - "Hash": "6d3bef2e305f55c705c674653c7d7d3d" + "Hash": "0f7cd2962e3044bb940cca4f4b5cecbe" }, "origami": { "Package": "origami", @@ -2408,7 +2428,7 @@ }, "processx": { "Package": "processx", - "Version": "3.5.3", + "Version": "3.8.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2417,7 +2437,7 @@ "ps", "utils" ], - "Hash": "8bbae1a548d0d3fdf6647bdd9d35bf6d" + "Hash": "3efbd8ac1be0296a46c55387aeace0f3" }, "prodlim": { "Package": "prodlim", @@ -2475,14 +2495,14 @@ }, "ps": { "Package": "ps", - "Version": "1.7.0", + "Version": "1.7.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], - "Hash": "eef74b13f32cae6bb0d495e53317c44c" + "Hash": "709d852d33178db54b17c722e5b1e594" }, "psych": { "Package": "psych", @@ -2781,13 +2801,14 @@ }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.14", + "Version": "2.23", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "bslib", "evaluate", + "fontawesome", "htmltools", "jquerylib", "jsonlite", @@ -2800,7 +2821,7 @@ "xfun", "yaml" ], - "Hash": "31b60a882fabfabf6785b8599ffeb8ba" + "Hash": "79f14e53725f28900d936f692bfdd69f" }, "roxygen2": { "Package": "roxygen2", @@ -2864,10 +2885,10 @@ }, "rstudioapi": { "Package": "rstudioapi", - "Version": "0.13", + "Version": "0.14", "Source": "Repository", "Repository": "CRAN", - "Hash": "06c85365a03fdaf699966cc1d3cf53ea" + "Hash": "690bd2acc42a9166ce34845884459320" }, "rversions": { "Package": "rversions", @@ -2883,24 +2904,27 @@ }, "rvest": { "Package": "rvest", - "Version": "1.0.2", + "Version": "1.0.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", + "cli", + "glue", "httr", "lifecycle", "magrittr", "rlang", "selectr", "tibble", + "withr", "xml2" ], - "Hash": "bb099886deffecd6f9b298b7d4492943" + "Hash": "a4a5ac819a467808c60e36e92ddf195e" }, "sass": { "Package": "sass", - "Version": "0.4.1", + "Version": "0.4.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2910,7 +2934,7 @@ "rappdirs", "rlang" ], - "Hash": "f37c0028d720bab3c513fd65d28c7234" + "Hash": "cc3ec7dd33982ef56570229b62d6388e" }, "scales": { "Package": "scales", @@ -3074,7 +3098,7 @@ }, "svglite": { "Package": "svglite", - "Version": "2.1.0", + "Version": "2.1.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3082,14 +3106,14 @@ "cpp11", "systemfonts" ], - "Hash": "68dfdf211af6aa4e5f050f064f64d401" + "Hash": "29442899581643411facb66f4add846a" }, "sys": { "Package": "sys", - "Version": "3.4", + "Version": "3.4.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "b227d13e29222b4574486cfcbde077fa" + "Hash": "3a1be13d68d47a8cd0bfd74739ca1555" }, "systemfonts": { "Package": "systemfonts", @@ -3278,13 +3302,13 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.39", + "Version": "0.45", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "xfun" ], - "Hash": "29f67ab15405b390b90e56ff22198ead" + "Hash": "e4e357f28c2edff493936b6cb30c3d65" }, "tmle3": { "Package": "tmle3", @@ -3537,13 +3561,13 @@ }, "viridisLite": { "Package": "viridisLite", - "Version": "0.4.1", + "Version": "0.4.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R" ], - "Hash": "62f4b5da3e08d8e5bcba6cac15603f70" + "Hash": "c826c7c4241b6fc89ff55aaea3fa7491" }, "visNetwork": { "Package": "visNetwork", @@ -3608,7 +3632,7 @@ }, "webshot": { "Package": "webshot", - "Version": "0.5.3", + "Version": "0.5.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -3617,7 +3641,7 @@ "jsonlite", "magrittr" ], - "Hash": "7261ab7f98e97c771217e6b87c085d6e" + "Hash": "16858ee1aba97f902d24049d4a44ef16" }, "wesanderson": { "Package": "wesanderson", @@ -3651,14 +3675,14 @@ }, "xfun": { "Package": "xfun", - "Version": "0.31", + "Version": "0.39", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "stats", "tools" ], - "Hash": "a318c6f752b8dcfe9fb74d897418ab2b" + "Hash": "8f56e9acb54fb525e66464d57ab58bcb" }, "xgboost": { "Package": "xgboost", @@ -3676,14 +3700,14 @@ }, "xml2": { "Package": "xml2", - "Version": "1.3.3", + "Version": "1.3.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "methods" ], - "Hash": "40682ed6a969ea5abfd351eb67833adc" + "Hash": "6c40e5cfcc6aefd88110666e18c31f40" }, "xopen": { "Package": "xopen",