From a5d1bf1c9a00b0c961eaac0254f8ba7dbdb872cc Mon Sep 17 00:00:00 2001
From: Iain Dillingham <iain@dillingham.me.uk>
Date: Thu, 9 Feb 2023 11:38:04 +0000
Subject: [PATCH] Add forestploter

---
 packages.csv | 113 ++++++++++++++++++++++++++-------------------------
 packages.txt |   1 +
 2 files changed, 58 insertions(+), 56 deletions(-)

diff --git a/packages.csv b/packages.csv
index f261ac3..dd28e94 100644
--- a/packages.csv
+++ b/packages.csv
@@ -1,3 +1,52 @@
+"BH","1.72.0-3"
+"Brobdingnag","1.2-6"
+"DBI","1.1.0"
+"DT","0.15"
+"Epi","2.46"
+"FNN","1.1.3"
+"Formula","1.2-3"
+"GGally","2.0.0"
+"Gmisc","2.0.1"
+"HDInterval","0.2.2"
+"Hmisc","4.4-1"
+"KMsurv","0.1-5"
+"KernSmooth","2.23-17"
+"MASS","7.3-52"
+"MatchIt","4.2.0"
+"Matrix","1.2-18"
+"MatrixModels","0.4-1"
+"ModelMetrics","1.2.2.2"
+"NHPoisson","3.3"
+"Package","Version"
+"Publish","2020.12.23"
+"R.methodsS3","1.8.1"
+"R.oo","1.25.0"
+"R.utils","2.12.0"
+"R6","2.4.1"
+"RColorBrewer","1.1-2"
+"RConics","1.1.1"
+"RCurl","1.98-1.2"
+"ROI","1.0-0"
+"ROI.plugin.lpsolve","1.0-0"
+"RSpectra","0.16-1"
+"Rcpp","1.0.5"
+"RcppArmadillo","0.9.900.3.0"
+"RcppEigen","0.3.3.7.0"
+"RcppParallel","5.0.2"
+"RcppProgress","0.4.2"
+"RcppRoll","0.3.0"
+"RcppThread","2.1.3"
+"Rdpack","2.1.1"
+"SCCS","1.2"
+"SQUAREM","2020.5"
+"SparseM","1.78"
+"StanHeaders","2.21.0-6"
+"TH.data","1.1-0"
+"UpSetR","1.4.0"
+"V8","3.2.0"
+"VGAM","1.1-6"
+"WeightIt","0.13.1"
+"XML","3.99-0.6"
 "abind","1.4-5"
 "arrow","4.0.0.1"
 "ash","1.0-15"
@@ -11,7 +60,6 @@
 "bayesplot","1.7.2"
 "bayestestR","0.8.2"
 "bdsmatrix","1.3-4"
-"BH","1.72.0-3"
 "binom","1.1-1"
 "bit","4.0.4"
 "bit64","4.0.5"
@@ -21,14 +69,13 @@
 "brglm2","0.7.1"
 "bridgesampling","1.0-0"
 "brms","2.13.5"
-"Brobdingnag","1.2-6"
 "broom","0.7.5"
 "broom.helpers","1.2.1"
+"caTools","1.18.2"
 "callr","3.4.3"
 "car","3.0-9"
 "carData","3.0-4"
 "caret","6.0-86"
-"caTools","1.18.2"
 "cellranger","1.1.0"
 "checkmate","2.0.0"
 "class","7.3-17"
@@ -56,20 +103,18 @@
 "credentials","1.3.0"
 "crosstalk","1.1.0.1"
 "curl","4.3"
-"datasets","4.0.2"
 "data.table","1.13.0"
+"datasets","4.0.2"
 "date","1.2-39"
-"DBI","1.1.0"
 "dbplyr","1.4.4"
-"desc","1.2.0"
 "deSolve","1.28"
+"desc","1.2.0"
 "detectseparation","0.2"
 "dfidx","0.0-4"
 "digest","0.6.25"
 "distributional","0.2.0"
 "doParallel","1.0.15"
 "dplyr","1.0.2"
-"DT","0.15"
 "dtplyr","1.0.1"
 "dtw","1.23-1"
 "dtwclust","5.5.10"
@@ -79,7 +124,6 @@
 "egg","0.4.5"
 "ellipsis","0.3.1"
 "enrichwith","0.3.1"
-"Epi","2.46"
 "estimatr","0.30.2"
 "etm","1.1.1"
 "evaluate","0.14"
@@ -94,7 +138,6 @@
 "finalfit","1.0.4"
 "flexclust","1.4-1"
 "flexsurv","1.1.1"
-"FNN","1.1.3"
 "fontBitstreamVera","0.1.1"
 "fontLiberation","0.1.0"
 "fontquiver","0.2.1"
@@ -102,7 +145,7 @@
 "foreach","1.5.0"
 "foreign","0.8-80"
 "forestplot","1.10.1"
-"Formula","1.2-3"
+"forestploter","1.0.0"
 "fs","1.5.0"
 "furrr","0.1.0"
 "future","1.18.0"
@@ -113,7 +156,6 @@
 "getopt","1.20.3"
 "gets","0.29"
 "ggalluvial","0.12.3"
-"GGally","2.0.0"
 "ggdist","2.2.0"
 "ggfortify","0.4.15"
 "ggh4x","0.2.1"
@@ -129,11 +171,10 @@
 "glmnet","4.1-4"
 "globals","0.12.5"
 "glue","1.4.2"
-"Gmisc","2.0.1"
 "gnm","1.1-1"
 "gower","0.2.2"
-"graphics","4.0.2"
 "grDevices","4.0.2"
+"graphics","4.0.2"
 "grid","4.0.2"
 "gridExtra","2.3"
 "gt","0.2.2"
@@ -141,11 +182,9 @@
 "gtools","3.8.2"
 "gtsummary","1.3.7"
 "haven","2.3.1"
-"HDInterval","0.2.2"
 "hdrcde","3.3"
 "here","0.1"
 "highr","0.8"
-"Hmisc","4.4-1"
 "hms","0.5.3"
 "htmlTable","2.0.1"
 "htmltools","0.5.0"
@@ -167,9 +206,7 @@
 "jtools","2.1.2"
 "kableExtra","1.3.4"
 "kernlab","0.9-29"
-"KernSmooth","2.23-17"
 "km.ci","0.5-2"
-"KMsurv","0.1-5"
 "knitr","1.29"
 "ks","1.11.7"
 "labeling","0.3"
@@ -193,11 +230,7 @@
 "maptools","1.0-2"
 "markdown","1.1"
 "marqLevAlg","2.0.7"
-"MASS","7.3-52"
-"MatchIt","4.2.0"
 "mathjaxr","1.6-0"
-"Matrix","1.2-18"
-"MatrixModels","0.4-1"
 "matrixStats","0.56.0"
 "maxstat","0.7-25"
 "mclust","5.4.7"
@@ -213,7 +246,6 @@
 "mitools","2.4"
 "mlogit","1.1-1"
 "mnlogit","1.2.6"
-"ModelMetrics","1.2.2.2"
 "modelr","0.1.8"
 "modelsummary","0.6.6"
 "modeltools","0.2-23"
@@ -224,7 +256,6 @@
 "munsell","0.5.0"
 "mvtnorm","1.1-1"
 "naniar","0.6.0"
-"NHPoisson","3.3"
 "nleqslv","3.3.2"
 "nlme","3.1-149"
 "nloptr","1.2.2.2"
@@ -234,7 +265,7 @@
 "openssl","1.4.2"
 "openxlsx","4.1.5"
 "optparse","1.6.6"
-"Package","Version"
+"pROC","1.16.2"
 "packrat","0.5.0"
 "pacman","0.5.1"
 "pammtools","0.5.8"
@@ -261,7 +292,6 @@
 "praise","1.0.0"
 "predtools","0.0.2"
 "prettyunits","1.1.1"
-"pROC","1.16.2"
 "processx","3.4.4"
 "prodlim","2019.11.13"
 "progress","1.2.2"
@@ -269,12 +299,10 @@
 "proxy","0.4-27"
 "ps","1.3.4"
 "pseudo","1.4.3"
-"Publish","2020.12.23"
 "purrr","0.3.4"
 "quadprog","1.5-8"
 "quantreg","5.61"
 "qvcalc","1.0.2"
-"R6","2.4.1"
 "rainbow","3.6"
 "randomForest","4.6-14"
 "randomForestExplainer","0.10.1"
@@ -282,17 +310,6 @@
 "ranger","0.13.1"
 "rappdirs","0.3.1"
 "rbibutils","2.0"
-"RColorBrewer","1.1-2"
-"RConics","1.1.1"
-"Rcpp","1.0.5"
-"RcppArmadillo","0.9.900.3.0"
-"RcppEigen","0.3.3.7.0"
-"RcppParallel","5.0.2"
-"RcppProgress","0.4.2"
-"RcppRoll","0.3.0"
-"RcppThread","2.1.3"
-"RCurl","1.98-1.2"
-"Rdpack","2.1.1"
 "readr","1.3.1"
 "readxl","1.3.1"
 "recipes","0.1.15"
@@ -311,26 +328,19 @@
 "riskRegression","2021.10.10"
 "rlang","0.4.10"
 "rmarkdown","2.3"
-"R.methodsS3","1.8.1"
 "rms","6.2-0"
 "rngWELL","0.10-7"
-"ROI","1.0-0"
-"ROI.plugin.lpsolve","1.0-0"
-"R.oo","1.25.0"
 "rpart","4.1-15"
 "rprojroot","1.3-2"
 "rsconnect","0.8.16"
-"RSpectra","0.16-1"
 "rstan","2.21.2"
 "rstantools","2.1.1"
 "rstatix","0.6.0"
 "rstudioapi","0.11"
-"R.utils","2.12.0"
 "rvest","0.3.6"
 "sandwich","2.5-1"
 "sass","0.3.0"
 "scales","1.1.1"
-"SCCS","1.2"
 "segmented","1.4-1"
 "selectr","0.4-2"
 "sf","0.9-5"
@@ -344,27 +354,23 @@
 "snakecase","0.11.0"
 "sourcetools","0.1.7"
 "sp","1.4-2"
-"SparseM","1.78"
-"splines2","0.4.1"
 "splines","4.0.2"
-"SQUAREM","2020.5"
-"StanHeaders","2.21.0-6"
+"splines2","0.4.1"
 "statmod","1.4.34"
 "stats","4.0.2"
 "stats4","4.0.2"
 "stringi","1.4.6"
 "stringr","1.4.0"
+"survMisc","0.5.5"
 "survey","4.1-1"
 "survival","3.2-3"
 "survminer","0.4.8"
-"survMisc","0.5.5"
 "svglite","1.2.3.2"
 "sys","3.4"
 "systemfonts","0.3.2"
 "tables","0.9.6"
 "tcltk","4.0.2"
 "testthat","2.3.2"
-"TH.data","1.1-0"
 "threejs","0.3.3"
 "tibble","3.0.3"
 "tictoc","1.0"
@@ -377,24 +383,19 @@
 "tools","4.0.2"
 "tsModel","0.6"
 "units","0.6-7"
-"UpSetR","1.4.0"
 "usethis","2.0.1"
 "utf8","1.1.4"
 "utils","4.0.2"
-"V8","3.2.0"
 "vcd","1.4-9"
 "vctrs","0.3.4"
-"VGAM","1.1-6"
 "viridis","0.5.1"
 "viridisLite","0.3.0"
 "visdat","0.5.3"
 "webshot","0.5.2"
-"WeightIt","0.13.1"
 "whisker","0.4"
 "withr","2.4.1"
 "xfun","0.16"
 "xml2","1.3.2"
-"XML","3.99-0.6"
 "xtable","1.8-4"
 "xts","0.12-0"
 "yaml","2.2.1"
diff --git a/packages.txt b/packages.txt
index 882d94d..7ba152d 100644
--- a/packages.txt
+++ b/packages.txt
@@ -107,3 +107,4 @@ dtwclust  # repo https://cran.microsoft.com/snapshot/2022-09-23/
 randomForest  # repo: https://cran.microsoft.com/snapshot/2022-02-03
 randomForestExplainer
 ggfortify
+forestploter