Developed by Naeem Khoshnevis, Boyu Ren, Danielle Braun.
CONTRIBUTING.md
Contributions are appreciated and can take various forms, such as:
Please review the following documents before making changes to the codebase.
To contribute to the project, it’s recommended to have your own local copy of GPCERF on your Github account. As a result, please fork the project. Then open your terminal (or Gitbash for Windows, Anaconda prompt, …) and run the following command (brackets are not included):
git clone git@github.com:[your user name]/GPCERF.git
Now, you can modify the codebase and track your changes. Consider creating a new branch to work on the codebase. Refer to the following instructions for git branching.
While you can choose any branch name for your personal repository, maintaining consistency and understanding who’s working on what is crucial. In this project, we follow the convention that is proposed by Vincent Driessen in his A successful Git branching model post.
Here is the summary of the branches:
Submit all pull requests to base repository: NSAPH-Software/GPCERF and base: develop branch.
base repository: NSAPH-Software/GPCERF
base: develop
devtools::document()
devtools::load_all()
devtools::check()
Please report potential bugs by creating a new issue or sending us an email. Please include the following information in your bug report:
In this project, we follow the tidyverse style guide.
+#Acceptable: +z <- x + y + +#Not recommended: +z<-x+y # (no space) +z<- x+y +z<-x +y
#Acceptable: +z <- x + y + +#Not recommended: +z<-x+y # (no space) +z<- x+y +z<-x +y
+#Acceptable: +a <- matrix(c(1:100), nrow = 5) + +#Not recommended: +a <- matrix(c(1:100),nrow = 5) # (no space after comma) +a <- matrix( c(1:100), nrow = 5 ) # (extra space after and before parentheses) +a<-matrix(c(1:100), nrow = 5) # (no space around unary operator <- )
#Acceptable: +a <- matrix(c(1:100), nrow = 5) + +#Not recommended: +a <- matrix(c(1:100),nrow = 5) # (no space after comma) +a <- matrix( c(1:100), nrow = 5 ) # (extra space after and before parentheses) +a<-matrix(c(1:100), nrow = 5) # (no space around unary operator <- )
+#Acceptable: +# This is a comment + +#Not recommended: +#This is a comment +# This is a comment (more than one space after #) +## This is a comment (multiple #) +### This is a comment (multiple # and more than one space)
#Acceptable: +# This is a comment + +#Not recommended: +#This is a comment +# This is a comment (more than one space after #) +## This is a comment (multiple #) +### This is a comment (multiple # and more than one space)
+#Acceptable: +x <- (z + y) + +#Not recommended: +x <- ( z + y ) # (unnecessary space) +x <- (z + y ) +x <- ( z + y)
#Acceptable: +x <- (z + y) + +#Not recommended: +x <- ( z + y ) # (unnecessary space) +x <- (z + y ) +x <- ( z + y)
()
if
for
while
+ +#Acceptible +if (x > 2) { + print(x) +} + +# Not recommended +if(x > 2){ + print(x) +}
+#Acceptible +if (x > 2) { + print(x) +} + +# Not recommended +if(x > 2){ + print(x) +}
In this package we create a customized wrapper for the SuperLearner internal libraries. Please read Notes on SL Wrappers for more details.
Use the logger to examine the internal process. By default, the level is set to “INFO”, writing messages to the “GPCERF.log” file. To change the log file location and level, use the update_logger function.
If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the “copyright” line and a pointer to where the full notice is found.
<one line to give the program's name and a brief idea of what it does.> -Copyright (C) <year> <name of author> - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see <http://www.gnu.org/licenses/>.
<one line to give the program's name and a brief idea of what it does.> +Copyright (C) <year> <name of author> + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see <http://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode:
<program> Copyright (C) <year> <name of author> -This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. -This is free software, and you are welcome to redistribute it -under certain conditions; type 'show c' for details.
<program> Copyright (C) <year> <name of author> +This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. +This is free software, and you are welcome to redistribute it +under certain conditions; type 'show c' for details.
The hypothetical commands show w and show c should show the appropriate parts of the General Public License. Of course, your program’s commands might be different; for a GUI interface, you would use an “about box”.
show w
show c
You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer” for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see <http://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read <http://www.gnu.org/philosophy/why-not-lgpl.html>.
Naeem Khoshnevis. Author, maintainer. +
Naeem Khoshnevis. Author. HUIT
Boyu Ren. Author. +
Boyu Ren. Author, maintainer. McLean Hospital
CRAN release: 2024-04-15
CRAN release: 2024-03-02
R/compute_w_corr.R
compute_w_corr.Rd
estimate_cerf_nngp()
compute_rl_deriv_gp()
set_logger()