Download SettingUpBrailleR.Rmd
This set of instructions is quite comprehensive. It assumes you have
instaled R, and now you want to set up the tools you will need to get
the most out of the BrailleR package.
There are a range of tools we need and some that are just useful. Each section below states whether it is essential or optional. If it is optional, then the reason it is useful is indicated.
You should be able to copy and paste each line of code into the R session to get the desired outcome.
We need to get packages from two main sources. The main one is called the Comprehensive R Archive Network, or CRAN for short.
To get R to point towards one of the CRAN servers we need to tell R where to look. Use:
This package helps us install other packages in the instructions that follow later.
The tidyverse is a suite of packages that work well together for manipulating and graphing data. It isn’t actually much more than a wrapper for the suite of packages really, so this next command is almost certainly going to save you time installing all the other other packages.
This next command gets the latest version from the development archive. It gets tested using the same standards as the version on CRAN, but it is updated more frequently.
The R tools are mostly used by developers, but having them around in the background won’t hurt and might just make things happen behind the scenes.
Getting an up to date version of Python is necessary if you intend to use the WriteR editor which is part of the BrailleR package.
By the way, you can run Python commands in your R markdown documents. The following lines are simple tests that show that R can interact with Python. They are processed using the Python installation:
hello world2Python is working on my machine.You might have a zip tool somewhere, but 7zip is free and works well in Windows.
It is good to update packages when you update your R installation. I use:
rlang (1.0.6 -> 1.1.0 ) [CRAN]
xfun (0.37 -> 0.38 ) [CRAN]
openssl (2.0.5 -> 2.0.6 ) [CRAN]
cli (3.6.0 -> 3.6.1 ) [CRAN]
zip (2.2.2 -> 2.3.0 ) [CRAN]
vctrs (0.5.2 -> 0.6.2 ) [CRAN]
ps (1.7.2 -> 1.7.5 ) [CRAN]
fastmap (1.1.0 -> 1.1.1 ) [CRAN]
cachem (1.0.6 -> 1.0.7 ) [CRAN]
tinytex (0.44 -> 0.45 ) [CRAN]
htmltools (0.5.4 -> 0.5.5 ) [CRAN]
fontawesome (0.5.0 -> 0.5.1 ) [CRAN]
processx (3.8.0 -> 3.8.1 ) [CRAN]
rmarkdown (2.20 -> 2.21 ) [CRAN]
pillar (1.8.1 -> 1.9.0 ) [CRAN]
dplyr (1.1.0 -> 1.1.1 ) [CRAN]
tibble (3.1.8 -> 3.2.1 ) [CRAN]
broom (1.0.3 -> 1.0.4 ) [CRAN]
httr (1.4.4 -> 1.4.5 ) [CRAN]
googledrive (2.0.0 -> 2.1.0 ) [CRAN]
gargle (1.3.0 -> 1.4.0 ) [CRAN]
data.table (1.14.6 -> 1.14.8 ) [CRAN]
gtable (0.3.1 -> 0.3.3 ) [CRAN]
distribut... (0.3.1 -> 0.3.2 ) [CRAN]
ggplot2 (3.4.1 -> 3.4.2 ) [CRAN]
testthat (3.1.6 -> 3.1.7 ) [CRAN]
lme4 (1.1-31 -> 1.1-32 ) [CRAN]
htmlwidgets (1.6.1 -> 1.6.2 ) [CRAN]
igraph (1.4.0 -> 1.4.2 ) [CRAN]
xts (0.12.2 -> 0.13.1 ) [CRAN]
zoo (1.8-11 -> 1.8-12 ) [CRAN]
wk (0.7.1 -> 0.7.2 ) [CRAN]
quantreg (5.94 -> 5.95 ) [CRAN]
scatterpl... (0.3-42 -> 0.3-43 ) [CRAN]
multcompView (0.1-8 -> 0.1-9 ) [CRAN]
emmeans (1.8.4-1 -> 1.8.5 ) [CRAN]
ellipse (0.4.3 -> 0.4.5 ) [CRAN]
car (3.1-1 -> 3.1-2 ) [CRAN]
RcppParallel (5.1.6 -> 5.1.7 ) [CRAN]
blob (1.2.3 -> 1.2.4 ) [CRAN]
RCurl (1.98-1.10 -> 1.98-1.12 ) [CRAN]
hms (1.1.2 -> 1.1.3 ) [CRAN]
qpdf (1.3.0 -> 1.3.2 ) [CRAN]
FNN (1.1.3.1 -> 1.1.3.2 ) [CRAN]
packrat (0.9.0 -> 0.9.1 ) [CRAN]
memisc (0.99.31.3 -> 0.99.31.6 ) [CRAN]
inum (1.0-4 -> 1.0-5 ) [CRAN]
Formula (1.2-4 -> 1.2-5 ) [CRAN]
partykit (1.2-16 -> 1.2-20 ) [CRAN]
scs (3.0-1 -> 3.2.4 ) [CRAN]
sets (1.0-22 -> 1.0-24 ) [CRAN]
datawizard (0.6.5 -> 0.7.1 ) [CRAN]
insight (0.19.0 -> 0.19.1 ) [CRAN]
terra (1.7-3 -> 1.7-23 ) [CRAN]
commonmark (1.8.1 -> 1.9.0 ) [CRAN]
haven (2.5.1 -> 2.5.2 ) [CRAN]
labelled (2.10.0 -> 2.11.0 ) [CRAN]
classInt (0.4-8 -> 0.4-9 ) [CRAN]
styler (1.9.0 -> 1.9.1 ) [CRAN]
quantmod (0.4.20 -> 0.4.22 ) [CRAN]
RcppArmad... (0.11.4.4.0 -> 0.12.2.0.0) [CRAN]
markdown (1.5 -> 1.6 ) [CRAN]
magick (2.7.3 -> 2.7.4 ) [CRAN]
reactR (NA -> 0.4.4 ) [CRAN]
V8 (4.2.2 -> 4.3.0 ) [CRAN]
reactable (NA -> 0.4.4 ) [CRAN]
triebeard (0.3.0 -> 0.4.1 ) [CRAN]
bayestestR (0.13.0 -> 0.13.1 ) [CRAN]
TH.data (1.1-1 -> 1.1-2 ) [CRAN]
DEoptimR (1.0-11 -> 1.0-12 ) [CRAN]
parallelly (1.34.0 -> 1.35.0 ) [CRAN]
loo (2.5.1 -> 2.6.0 ) [CRAN]
posterior (1.3.1 -> 1.4.1 ) [CRAN]
XML (3.99-0.13 -> 3.99-0.14 ) [CRAN]
gh (1.3.1 -> 1.4.0 ) [CRAN]
BiocManager (1.30.19 -> 1.30.20 ) [CRAN]
TMB (1.9.2 -> 1.9.4 ) [CRAN]
servr (0.25 -> 0.26 ) [CRAN]
git2r (0.31.0 -> 0.32.0 ) [CRAN]
sf (1.0-9 -> 1.0-12 ) [CRAN]
modelr (0.1.10 -> 0.1.11 ) [CRAN]
googleshe... (1.0.1 -> 1.1.0 ) [CRAN]
dtplyr (1.2.2 -> 1.3.1 ) [CRAN]
dbplyr (2.3.0 -> 2.3.2 ) [CRAN]
conflicted (NA -> 1.2.0 ) [CRAN]
ggfortify (0.4.15 -> 0.4.16 ) [CRAN]
spData (2.2.1 -> 2.2.2 ) [CRAN]
FactoMineR (2.7 -> 2.8 ) [CRAN]
RcppNumer... (0.4-0 -> 0.5-0 ) [CRAN]
raster (3.6-14 -> 3.6-20 ) [CRAN]
rstantools (2.2.0 -> 2.3.1 ) [CRAN]
truncnorm (1.0-8 -> 1.0-9 ) [CRAN]
duckdb (0.7.0 -> 0.7.1-1 ) [CRAN]
psych (2.2.9 -> 2.3.3 ) [CRAN]
randomForest (NA -> 4.7-1.1 ) [CRAN]
ape (5.6-2 -> 5.7-1 ) [CRAN]
interp (1.1-3 -> 1.1-4 ) [CRAN]
forecast (8.20 -> 8.21 ) [CRAN]
hexbin (1.28.2 -> 1.28.3 ) [CRAN]
ggimage (0.3.1 -> 0.3.2 ) [CRAN]
gt (0.8.0 -> 0.9.0 ) [CRAN]
broom.hel... (1.12.0 -> 1.13.0 ) [CRAN]
ggsci (2.9 -> 3.0.0 ) [CRAN]
future (1.31.0 -> 1.32.0 ) [CRAN]
deSolve (1.34 -> 1.35 ) [CRAN]
GenSA (1.1.7 -> 1.1.8 ) [CRAN]
dae (3.2-14 -> 3.2.15 ) [CRAN]
parameters (0.20.2 -> 0.21.0 ) [CRAN]
multcomp (1.4-22 -> 1.4-23 ) [CRAN]
robustbase (0.95-0 -> 0.95-1 ) [CRAN]
gridSVG (1.7-4 -> 1.7-5 ) [CRAN]
flexmix (2.3-18 -> 2.3-19 ) [CRAN]
VGAM (1.1-7 -> 1.1-8 ) [CRAN]
klaR (1.7-1 -> 1.7-2 ) [CRAN]
tidyverse (1.3.2 -> 2.0.0 ) [CRAN]
tidybayes (3.0.3 -> 3.0.4 ) [CRAN]
svd (0.5.3 -> 0.5.4 ) [CRAN]
splines2 (0.4.7 -> 0.4.8 ) [CRAN]
spelling (2.2 -> 2.2.1 ) [CRAN]
spdep (1.2-7 -> 1.2-8 ) [CRAN]
SixSigma (0.10.3 -> 0.11.0 ) [CRAN]
simr (1.0.6 -> 1.0.7 ) [CRAN]
secr (4.5.8 -> 4.5.10 ) [CRAN]
santoku (0.9.0 -> 0.9.1 ) [CRAN]
s20x (3.1-34 -> 3.1-38 ) [CRAN]
rstanarm (2.21.3 -> 2.21.4 ) [CRAN]
rgl (1.0.1 -> 1.1.3 ) [CRAN]
rfishbase (4.1.0 -> 4.1.1 ) [CRAN]
readtext (0.81 -> 0.82 ) [CRAN]
Rcsdp (0.1.57.4 -> 0.1.57.5 ) [CRAN]
psychTools (2.2.9 -> 2.3.3 ) [CRAN]
projpred (2.4.0 -> 2.5.0 ) [CRAN]
MPV (1.59 -> 1.62 ) [CRAN]
leaflet (2.1.1 -> 2.1.2 ) [CRAN]
lavaan (0.6-14 -> 0.6-15 ) [CRAN]
HSAUR3 (1.0-13 -> 1.0-14 ) [CRAN]
Hmisc (4.8-0 -> 5.0-1 ) [CRAN]
GPArotation (2022.10-2 -> 2023.3-1 ) [CRAN]
ggmap (3.0.1 -> 3.0.2 ) [CRAN]
gdtools (0.3.0 -> 0.3.3 ) [CRAN]
gapminder (0.3.0 -> 1.0.0 ) [CRAN]
gam (1.22-1 -> 1.22-2 ) [CRAN]
emayili (0.7.13 -> 0.7.15 ) [CRAN]
edibble (0.1.2 -> 0.1.3 ) [CRAN]
drake (7.13.4 -> 7.13.5 ) [CRAN]
desplot (1.9 -> 1.10 ) [CRAN]
DescTools (0.99.47 -> 0.99.48 ) [CRAN]
daewr (1.2-7 -> 1.2-9 ) [CRAN]
covr (3.6.1 -> 3.6.2 ) [CRAN]
conquer (1.3.2 -> 1.3.3 ) [CRAN]
chron (2.3-59 -> 2.3-60 ) [CRAN]
brms (2.18.0 -> 2.19.0 ) [CRAN]
bookdown (0.32 -> 0.33 ) [CRAN]
asbio (1.8-4 -> 1.9-2 ) [CRAN]
AICcmodavg (2.3-1 -> 2.3-2 ) [CRAN]Skipping 10 packages not available: gdata, graph, translations, Rgraphviz, RDCOMClient, lightsout, htmltab, gameofthrones, ELMER, BiocGenericsSkipping 3 packages ahead of CRAN: StanHeaders, rstan, BrailleRInstalling 155 packages: rlang, xfun, openssl, cli, zip, vctrs, ps, fastmap, cachem, tinytex, htmltools, fontawesome, processx, rmarkdown, pillar, dplyr, tibble, broom, httr, googledrive, gargle, data.table, gtable, distributional, ggplot2, testthat, lme4, htmlwidgets, igraph, xts, zoo, wk, quantreg, scatterplot3d, multcompView, emmeans, ellipse, car, RcppParallel, blob, RCurl, hms, qpdf, FNN, packrat, memisc, inum, Formula, partykit, scs, sets, datawizard, insight, terra, commonmark, haven, labelled, classInt, styler, quantmod, RcppArmadillo, markdown, magick, reactR, V8, reactable, triebeard, bayestestR, TH.data, DEoptimR, parallelly, loo, posterior, XML, gh, BiocManager, TMB, servr, git2r, sf, modelr, googlesheets4, dtplyr, dbplyr, conflicted, ggfortify, spData, FactoMineR, RcppNumerical, raster, rstantools, truncnorm, duckdb, psych, randomForest, ape, interp, forecast, hexbin, ggimage, gt, broom.helpers, ggsci, future, deSolve, GenSA, dae, parameters, multcomp, robustbase, gridSVG, flexmix, VGAM, klaR, tidyverse, tidybayes, svd, splines2, spelling, spdep, SixSigma, simr, secr, santoku, s20x, rstanarm, rgl, rfishbase, readtext, Rcsdp, psychTools, projpred, MPV, leaflet, lavaan, HSAUR3, Hmisc, GPArotation, ggmap, gdtools, gapminder, gam, emayili, edibble, drake, desplot, DescTools, daewr, covr, conquer, chron, brms, bookdown, asbio, AICcmodavgWarning: packages 'dplyr', 'tibble', 'ggplot2', 'lme4', 'igraph', 'tidyverse'
are in use and will not be installedInstalling packages into 'C:/Users/ajgodfre/AppData/Local/R/win-library/4.2'
(as 'lib' is unspecified)
There is a binary version available (and will be installed) but the
source version is later:
binary source
xfun 0.38 0.39
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to C:\Users\ajgodfre\AppData\Local\R\win-library\4.2\rlang\libs\x64\rlang.dll:
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to C:\Users\ajgodfre\AppData\Local\R\win-library\4.2\xfun\libs\x64\xfun.dll:
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to C:\Users\ajgodfre\AppData\Local\R\win-library\4.2\cli\libs\x64\cli.dll:
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to C:\Users\ajgodfre\AppData\Local\R\win-library\4.2\vctrs\libs\x64\vctrs.dll:
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C:\Users\ajgodfre\AppData\Local\R\win-library\4.2\ps\libs\x64\ps.dll:
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to
C:\Users\ajgodfre\AppData\Local\R\win-library\4.2\fastmap\libs\x64\fastmap.dll:
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to
C:\Users\ajgodfre\AppData\Local\R\win-library\4.2\processx\libs\x64\processx.dll:
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package 'bookdown' successfully unpacked and MD5 sums checked
package 'asbio' successfully unpacked and MD5 sums checked
package 'AICcmodavg' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\ajgodfre\AppData\Local\Temp\RtmpmqZoD0\downloaded_packages