Steps.md

In Javad-mun/activitycounts: Generating ActiLife Counts

library(devtools)

library(roxygen2)

library(usethis)

# #install.packages("data.table")

# #install.packages("data.table", repos="https://Rdatatable.gitlab.io/data.table")

library(data.table)

library(seewave)

library(signal)

============================================

Define all functions and then call them in the main file by source()

use use_r from use this package

use roxygen ==> go inside the function and then from menu --> code --> inser roxygen skeleton

use_r("trunc")

library(devtools)

devtools::install

if cant install, go to r studio settings and check R path

then add licence file like this use_cc0_license("Tomas Westlake")

?use_mit_license

use_mit_license(name = c("Rubin","Javad Khataei","Beap Lab"))

make document for whole package using this

usethis::use_package_doc()

Now try devtools::document() to see the changes made by roxygen

devtools::document()

add a logo

use_logo("Z:/Research/dfuller/Walkabilly/people/Seyed Javad/Pack/BEAP_Lab_logo.png")

add vignette by use_vignette("name_vignette")

if a function is using a package you need to do 2 things

1 #' @import seewave (, signal )each is a seperate line) in the function file

clean and build so it will be added to the namespace file

2 use use_package("name of the package") for each library

check description file, now it has the libraries

Note : if you want the external libraries got loaded when you packahe is loaded use Depend instead of import so

use_package("seewave",type = "Depends")

Note : after exporting each funtion use use_namespace to export the name of the functions so R can see your function to call

refresh the document by devtools::document()

===================

continuous integration

travis, check the package for different operation systems(linux and mac) and R versions

use github to log in

then add read me file

use_readme_rmd()

later edit the readme file

use_travis()

it will add something like this to readme.rmd file

Now we can edit travis file and for example add the R versions like this: r: - oldrel - release - devel Also to run for both osx and linux go with os: - linux - osx

Then Build and push. it will check all versions and os listed in yml file and even for warnings throews an error as warnings_are_errors: defualt value is true.

for Windows use use_appveyor() which is simillar to travis

There are other options like rhub package which I try here : https://r-hub.github.io/rhub/articles/rhub.html After installing rhub, validate your email by rhub::validate_email(email ="[e-mail]"), (if error retart rstudio) then run rhub::check() # now choose one os also check https://r-hub.github.io/rhub/articles/rhub.html

=========

to check the coverage instal covr and then use_coverage. it gives you some code to add to travis and it will add some info to read me

Now navigate to codecov.io and link the github repo to it.

===== Testing, install tester and testthat packages. then run use_testthat. usethis::use_testthat() it makes testthat.R and a folder and also adds a suggestion for testthat library to the description file. we have a message the, ● Call use_test() to initialize a basic test file and open it for editing.

Now we run use_test(name="name_of_the_test_fiel") and it will create a file inside the test/testthat folder and we can edit that and put the code there

We need to make a dataset and the expected output to check the code.

Import data into the package

with use_data(nameofthedata, compress= "xz") we can include the data in the package. It will create a folder, data, and the data will be compressed and stored there. the maximun for data size is 5 megabytes. "xz" can reduce a csv file size to 1/14. the "bzip2" compression method is stronger than "xz".the "gzip" is the weakest. Note when data is added to the package, there is a dependency on R versions jigher than 2.10, therefore add Depends: R (>= 2.10) in the description file before the licence.

When writing vignette file, using mark down . you can use CSS code to style the document like this: body{ text-align : justify; line-height: 2em; }

======== to add a help, documentation, file to the package itself, run usethis::use_package_doc(). it will create a dummy R file and after doing devtoos::document(), roxygen will create an .Rd file for the package. When writing the packge document, have a look at this link for more options: https://cran.r-project.org/web/packages/roxygen2/vignettes/rd.html

Javad-mun/activitycounts documentation built on June 6, 2019, 7:40 a.m.