A Appendix

A.1 Git

Setting up Git: git config with --global option to configure user name, email, editor, etc.
Creating a repository: git init to initialize a repo. Git stores all of its repo data in the .git directory.
Tracking changes:
- git status shows the status of the repo
  - File are stored in the project’s working directory (which users see)
  - The staging area (where the next commit is being built)
  - local repo is where commits are permanently recorded
- git add put files in the staging area
- git commit saves the staged content as a new commit in the local repo.
  - git commit -m "your own message" to give a messages for the purpose of your commit.
History
- git diff shows differences between commits
- git checkout recovers old version of fields
  - git checkout HEAD to go to the last commit
  - git checkout <unique ID of your commit> to go to such commit
Ignoring
- .gitignore file tells Git what files to ignore
- cat . gitignore *.dat results/ ignore files ending with “dat” and folder “results”.
Remotes in GitHub
- A local git repo can be connected to one or more remote repos.
- Use the HTTPS protocol to connect to remote repos
- git push copies changes from a local repo to a remote repo
- git pull copies changes from a remote repo to a local repo
Collaborating
- git clone copies remote repo to create a local repo with a remote called origin automatically set up
Branching
- git check - b <new-branch-name
- git checkout master to switch to master branch.
Conflicts
- occur when 2 or more people change the same lines of the same file
- the version control system does not allow to overwrite each other’s changes blindly, but highlights conflicts so that they can be resolved.
Licensing
- People who incorporate General Public License (GPL’d) software into their won software must make their software also open under the GPL license; most other open licenses do not require this.
- The Creative Commons family of licenses allow people to mix and match requirements and restrictions on attribution, creation of derivative works, further sharing and commercialization.
Citation:
- Add a CITATION file to a repo to explain how you want others to cite your work.
Hosting
- Rules regarding intellectual property and storage of sensitive info apply no matter where code and data are hosted.

A.2 Short-cut

These are shortcuts that you probably you remember when working with R. Even though it might take a bit of time to learn and use them as your second nature, but they will save you a lot of time.
Just like learning another language, the more you speak and practice it, the more comfortable you are speaking it.

function	short-cut
navigate folders in console	`" " + tab`
pull up short-cut cheat sheet	`ctrl + shift + k`
go to file/function (everything in your project)	`ctrl + .`
search everything	`cmd + shift + f`
navigate between tabs	`Crtl + shift + .`
type function faster	`snip + shift + tab`
type faster	`use tab for fuzzy match`
`cmd + up`
`ctrl + .`

Sometimes you can’t stage a folder because it’s too large. In such case, use Terminal pane in Rstudio then type git add -A to stage all changes then commit and push like usual.

A.3 Function short-cut

apply one function to your data to create a new variable: mutate(mod=map(data,function))
instead of using i in 1:length(object): for (i in seq_along(object))
apply multiple function: map_dbl
apply multiple function to multiple variables:map2
autoplot(data) plot times series data
mod_tidy = linear(reg) %>% set_engine('lm') %>% fit(price ~ ., data=data) fit lm model. It could also fit other models (stan, spark, glmnet, keras)

Sometimes, data-masking will not be able to recognize whether you’re calling from environment or data variables. To bypass this, we use .data$variable or .env$variable. For example data %>% mutate(x=.env$variable/.data$variable
Problems with data-masking:
- Unexpected masking by data-var: Use .data and .env to disambiguate
- Data-var cant get through:
- Tunnel data-var with {{}} + Subset .data with [[]]
Passing Data-variables through arguments

library("dplyr")
mean_by <- function(data,by,var){
    data %>%
        group_by({{{by}}}) %>%
        summarise("{{var}}":=mean({{var}})) # new name for each var will be created by tunnel data-var inside strings
}

mean_by <- function(data,by,var){
    data %>%
        group_by({{{by}}}) %>%
        summarise("{var}":=mean({{var}})) # use single {} to glue the string, but hard to reuse code in functions
}

Trouble with selection:

library("purrr")
name <- c("mass","height")
starwars %>% select(name) # Data-var. Here you are referring to variable named "name"

starwars %>% select(all_of((name))) # use all_of() to disambiguate when 

averages <- function(data,vars){ # take character vectors with all_of()
    data %>%
        select(all_of(vars)) %>%
        map_dbl(mean,na.rm=TRUE)
} 

x = c("Sepal.Length","Petal.Length")
iris %>% averages(x)


# Another way
averages <- function(data,vars){ # Tunnel selectiosn with {{}}
    data %>%
        select({{vars}}) %>%
        map_dbl(mean,na.rm=TRUE)
} 

x = c("Sepal.Length","Petal.Length")
iris %>% averages(x)

A.4 Citation

include a citation by [@Farjam_2015]

cite packages used in this session

package=ls(sessionInfo()$loadedOnly) for (i in package){print(toBibtex(citation(i)))}

package=ls(sessionInfo()$loadedOnly) 
for (i in package){
    print(toBibtex(citation(i)))
    }

A.5 Install all necessary packages/libaries on your local machine

Get a list of packages you need to install from this book (or your local device)

installed <- as.data.frame(installed.packages())

head(installed)
#>             Package                            LibPath Version Priority
#> abind         abind C:/Program Files/R/R-4.4.3/library   1.4-8     <NA>
#> ade4           ade4 C:/Program Files/R/R-4.4.3/library  1.7-23     <NA>
#> ADGofTest ADGofTest C:/Program Files/R/R-4.4.3/library     0.3     <NA>
#> admisc       admisc C:/Program Files/R/R-4.4.3/library    0.37     <NA>
#> AER             AER C:/Program Files/R/R-4.4.3/library  1.2-14     <NA>
#> afex           afex C:/Program Files/R/R-4.4.3/library   1.4-1     <NA>
#>                                                                                          Depends
#> abind                                                                               R (>= 1.5.0)
#> ade4                                                                                R (>= 3.5.0)
#> ADGofTest                                                                                   <NA>
#> admisc                                                                              R (>= 3.5.0)
#> AER       R (>= 3.0.0), car (>= 2.0-19), lmtest, sandwich (>= 2.4-0),\nsurvival (>= 2.37-5), zoo
#> afex                                                               R (>= 3.5.0), lme4 (>= 1.1-8)
#>                                                                                   Imports
#> abind                                                                      methods, utils
#> ade4                  graphics, grDevices, methods, stats, utils, MASS, pixmap, sp,\nRcpp
#> ADGofTest                                                                            <NA>
#> admisc                                                                            methods
#> AER                                                             stats, Formula (>= 0.2-0)
#> afex      pbkrtest (>= 0.4-1), lmerTest (>= 3.0-0), car, reshape2,\nstats, methods, utils
#>                     LinkingTo
#> abind                    <NA>
#> ade4      Rcpp, RcppArmadillo
#> ADGofTest                <NA>
#> admisc                   <NA>
#> AER                      <NA>
#> afex                     <NA>
#>                                                                                                                                                                                                                                                                                                                                                                                                  Suggests
#> abind                                                                                                                                                                                                                                                                                                                                                                                                <NA>
#> ade4                                                                                                                                                                                                                      ade4TkGUI, adegraphics, adephylo, adespatial, ape, CircStats,\ndeldir, lattice, spdep, splancs, waveslim, progress, foreach,\nparallel, doParallel, iterators, knitr, rmarkdown
#> ADGofTest                                                                                                                                                                                                                                                                                                                                                                                            <NA>
#> admisc                                                                                                                                                                                                                                                                                                                                                                                       QCA (>= 3.7)
#> AER                                                                                                                                    boot, dynlm, effects, fGarch, forecast, foreign, ineq,\nKernSmooth, lattice, longmemo, MASS, mlogit, nlme, nnet, np,\nplm, pscl, quantreg, rgl, ROCR, rugarch, sampleSelection,\nscatterplot3d, strucchange, systemfit (>= 1.1-20), truncreg,\ntseries, urca, vars
#> afex      emmeans (>= 1.4), coin, xtable, parallel, plyr, optimx,\nnloptr, knitr, rmarkdown, R.rsp, lattice, latticeExtra,\nmultcomp, testthat, mlmRev, dplyr, tidyr, dfoptim, Matrix,\npsychTools, ggplot2, MEMSS, effects, carData, ggbeeswarm, nlme,\ncowplot, jtools, ggpubr, ggpol, MASS, glmmTMB, brms, rstanarm,\nstatmod, performance (>= 0.7.2), see (>= 0.6.4), ez,\nggResidpanel, grid, vdiffr
#>           Enhances            License License_is_FOSS License_restricts_use
#> abind         <NA> MIT + file LICENSE            <NA>                  <NA>
#> ade4          <NA>         GPL (>= 2)            <NA>                  <NA>
#> ADGofTest     <NA>                GPL            <NA>                  <NA>
#> admisc        <NA>         GPL (>= 3)            <NA>                  <NA>
#> AER           <NA>      GPL-2 | GPL-3            <NA>                  <NA>
#> afex          <NA>         GPL (>= 2)            <NA>                  <NA>
#>           OS_type MD5sum NeedsCompilation Built
#> abind        <NA>   <NA>               no 4.4.1
#> ade4         <NA>   <NA>              yes 4.4.3
#> ADGofTest    <NA>   <NA>             <NA> 4.2.0
#> admisc       <NA>   <NA>              yes 4.4.3
#> AER          <NA>   <NA>               no 4.4.3
#> afex         <NA>   <NA>               no 4.4.3

write.csv(installed, file.path(getwd(),'installed.csv'))

After having the installed.csv file on your new or local machine, you can just install the list of packages

# import the list of packages
installed <- read.csv('installed.csv')

# get the list of packages that you have on your device
baseR <- as.data.frame(installed.packages())

# install only those that you don't have
install.packages(setdiff(installed, baseR))

44 High-Performance Computing

B Bookdown cheat sheet