# 目前使用的R套件列表與批次安裝指令

重灌系統、裝好 R 之後，總是只能憑記憶安裝套件，而且常常會在需要的時候才發現少裝了某套件，就要停下手邊的工作來安裝，多少會打亂工作節奏。因此，想把平常使用的套件記錄下來，之後如果又重新裝了 R 或者整個系統，就可以一次裝好。

在開始裝之前，我會先預設 CRAN mirror，在 R 資料夾的 `etc` 目錄底下，修改 `Profile.site` 檔案：
*[CRAN]:Comprehensive R Archive Network

# set a CRAN mirror
#Automatic redirection to servers worldwide, currently sponsored by Rstudio
local({r = getOption("repos")
r["CRAN"] = "https://cran.csie.ntu.edu.tw/"
options(repos=r)})

以下微微修改自網路上找到的指令：

batchinstall <- function(pkg){
    new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])]
    if (length(new.pkg)) 
        install.packages(new.pkg, dependencies = TRUE)
    sapply(pkg, require, character.only = TRUE)
}
batchinstall(pkgs)

只要把其中的 `pkgs` 填入自己要安裝的套件即可。安裝好之後，會列出安裝的各套件是否成功。
以下是自己常用的套件：

pkgs <- c("ade4", "adegenet", "ape", "Cairo", "dplyr", "data.table", "devtools", "e1071", "factoextra", "FactoMineR", "forecast", "ggplot2", "ggpubr", "ggrepel", "ggsci", "ggsignif", "ggthemes", "ggpmisc", "ggvenn", "gridExtra", "gtable", "Hmisc","indicspecies", "iNEXT", "insect", "lme4", "lmtest", "lubridate", "magrittr", "mgcv", "mlr3verse", "nlme", "openxlsx", "patchwork", "plotly", "plyr", "profvis", "psych", "purrr", "readxl", "reshape2", "rpart", "rstatix", "scales", "scatterplot3d", "showtext", "SpadeR", "SparseM", "stringi", "stringr", "tidyr", "vegan", "xgboost")

裝好 `devtools` 之後，就可以安裝位於 github 或者由 [Bioconductor](https://www.bioconductor.org/) 收錄的套件：

devtools::install_github("vqv/ggbiplot")
devtools::install_github("NightingaleHealth/ggforestplot")
devtools::install_github("sinhrks/ggfortify")
devtools::install_github("gavinsimpson/ggvegan")
devtools::install_bioc(c("Biostrings", "dada2", "phyloseq", "DESeq2", "ShortRead"))

清單會隨時更新，以備未來的不時之需。
<span style="font-size:30px">🐕‍🦺</span>