-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
added codemeta and contributing files
- Loading branch information
1 parent
606b449
commit 5ac0780
Showing
3 changed files
with
295 additions
and
22 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,53 @@ | ||
| # Contributing to eDNAjoint | ||
|
|
||
| This file outlines how to propose a change to eDNAjoint. | ||
| It is based on the tidyverse contributing guidelines. | ||
|
|
||
| ## Planned development | ||
| This package is currently in a stable state of development. | ||
|
|
||
| ## Scope | ||
| The scope of eDNAjoint is limited to joint modeling of single-species environmental DNA (eDNA) data and traditional survey data. | ||
|
|
||
| ## Fixing typos | ||
|
|
||
| You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the *source* file. | ||
| This generally means you'll need to edit [roxygen2 comments](https://roxygen2.r-lib.org/articles/roxygen2.html) in an `.R`, not a `.Rd` file. | ||
| You can find the `.R` file that generates the `.Rd` by reading the comment in the first line. | ||
|
|
||
| ## Bigger changes | ||
|
|
||
| If you want to make a bigger change, it's a good idea to first file an issue and see if a maintainer agrees that it is necessary. | ||
| If you’ve found a bug, please file an issue that illustrates the bug with a minimal | ||
| [reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed). | ||
| You can check out the tidyverse guide on [how to create a great issue](https://code-review.tidyverse.org/issues/) for more advice. | ||
|
|
||
| ### Pull request process | ||
|
|
||
| * Fork the package and clone onto your computer. If you haven't done this before, you can use `usethis::create_from_github("abigailkeller/eDNAjoint", fork = TRUE)`. | ||
|
|
||
| * Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`. | ||
| If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. | ||
| * Create a Git branch for your pull request (PR). We recommend using `usethis::pr_init("brief-description-of-change")`. | ||
|
|
||
| * Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser. | ||
| The title of your PR should briefly describe the change. | ||
| The body of your PR should contain `Fixes #issue-number`. | ||
|
|
||
| * For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). Follow the style described in the tidyverse [style guide](https://style.tidyverse.org/news.html). | ||
|
|
||
| ### Code style | ||
|
|
||
| * New code should follow the tidyverse [style guide](https://style.tidyverse.org). | ||
| You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle existing code which is not altered as part of your PR. | ||
|
|
||
| * We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation. | ||
|
|
||
| * We use [testthat](https://cran.r-project.org/package=testthat) for unit tests. | ||
| Contributions with test cases included are easier to accept. | ||
|
|
||
| ## Code of Conduct | ||
|
|
||
| Please note that the gigs project is released with a | ||
| [Contributor Code of Conduct](https://ropensci.org/code-of-conduct/). | ||
| By contributing to this project you agree to abide by its terms. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,220 @@ | ||
| { | ||
| "@context": "https://doi.org/10.5063/schema/codemeta-2.0", | ||
| "@type": "SoftwareSourceCode", | ||
| "identifier": "eDNAjoint", | ||
| "description": "Models integrate environmental DNA (eDNA) detection data and traditional survey data to jointly estimate species catch rate. Models can be used with count data via traditional survey methods (i.e., trapping, electrofishing, visual) and replicated eDNA detection/nondetection data via polymerase chain reaction (i.e., PCR or qPCR) from multiple survey locations. Estimated parameters include probability of a false positive eDNA detection, a site-level covariates that scale the sensitivity of eDNA surveys relative to traditional surveys, and catchability coefficients for traditional gear types. Models are implemented with a Bayesian framework (Markov chain Monte Carlo) using the 'Stan' probabilistic programming language.", | ||
| "name": "eDNAjoint: Joint Modeling of Traditional and Environmental DNA Survey Data", | ||
| "codeRepository": "https://github.com/abigailkeller/eDNAjoint", | ||
| "issueTracker": "https://github.com/abigailkeller/eDNAjoint/issues", | ||
| "license": "https://spdx.org/licenses/GPL-3.0", | ||
| "version": "0.1", | ||
| "programmingLanguage": { | ||
| "@type": "ComputerLanguage", | ||
| "name": "R", | ||
| "url": "https://r-project.org" | ||
| }, | ||
| "runtimePlatform": "R version 4.2.2 (2022-10-31 ucrt)", | ||
| "author": [ | ||
| { | ||
| "@type": "Person", | ||
| "givenName": "Abigail G.", | ||
| "familyName": "Keller", | ||
| "email": "[email protected]" | ||
| } | ||
| ], | ||
| "contributor": [ | ||
| { | ||
| "@type": "Person", | ||
| "givenName": "Ryan P.", | ||
| "familyName": "Kelly", | ||
| "email": "[email protected]" | ||
| } | ||
| ], | ||
| "maintainer": [ | ||
| { | ||
| "@type": "Person", | ||
| "givenName": "Abigail G.", | ||
| "familyName": "Keller", | ||
| "email": "[email protected]" | ||
| } | ||
| ], | ||
| "softwareSuggestions": [ | ||
| { | ||
| "@type": "SoftwareApplication", | ||
| "identifier": "knitr", | ||
| "name": "knitr", | ||
| "provider": { | ||
| "@id": "https://cran.r-project.org", | ||
| "@type": "Organization", | ||
| "name": "Comprehensive R Archive Network (CRAN)", | ||
| "url": "https://cran.r-project.org" | ||
| }, | ||
| "sameAs": "https://CRAN.R-project.org/package=knitr" | ||
| }, | ||
| { | ||
| "@type": "SoftwareApplication", | ||
| "identifier": "rmarkdown", | ||
| "name": "rmarkdown", | ||
| "provider": { | ||
| "@id": "https://cran.r-project.org", | ||
| "@type": "Organization", | ||
| "name": "Comprehensive R Archive Network (CRAN)", | ||
| "url": "https://cran.r-project.org" | ||
| }, | ||
| "sameAs": "https://CRAN.R-project.org/package=rmarkdown" | ||
| }, | ||
| { | ||
| "@type": "SoftwareApplication", | ||
| "identifier": "testthat", | ||
| "name": "testthat", | ||
| "version": ">= 3.0.0", | ||
| "provider": { | ||
| "@id": "https://cran.r-project.org", | ||
| "@type": "Organization", | ||
| "name": "Comprehensive R Archive Network (CRAN)", | ||
| "url": "https://cran.r-project.org" | ||
| }, | ||
| "sameAs": "https://CRAN.R-project.org/package=testthat" | ||
| } | ||
| ], | ||
| "softwareRequirements": { | ||
| "1": { | ||
| "@type": "SoftwareApplication", | ||
| "identifier": "R", | ||
| "name": "R", | ||
| "version": ">= 3.4.0" | ||
| }, | ||
| "2": { | ||
| "@type": "SoftwareApplication", | ||
| "identifier": "bayestestR", | ||
| "name": "bayestestR", | ||
| "provider": { | ||
| "@id": "https://cran.r-project.org", | ||
| "@type": "Organization", | ||
| "name": "Comprehensive R Archive Network (CRAN)", | ||
| "url": "https://cran.r-project.org" | ||
| }, | ||
| "sameAs": "https://CRAN.R-project.org/package=bayestestR" | ||
| }, | ||
| "3": { | ||
| "@type": "SoftwareApplication", | ||
| "identifier": "dplyr", | ||
| "name": "dplyr", | ||
| "provider": { | ||
| "@id": "https://cran.r-project.org", | ||
| "@type": "Organization", | ||
| "name": "Comprehensive R Archive Network (CRAN)", | ||
| "url": "https://cran.r-project.org" | ||
| }, | ||
| "sameAs": "https://CRAN.R-project.org/package=dplyr" | ||
| }, | ||
| "4": { | ||
| "@type": "SoftwareApplication", | ||
| "identifier": "ggplot2", | ||
| "name": "ggplot2", | ||
| "provider": { | ||
| "@id": "https://cran.r-project.org", | ||
| "@type": "Organization", | ||
| "name": "Comprehensive R Archive Network (CRAN)", | ||
| "url": "https://cran.r-project.org" | ||
| }, | ||
| "sameAs": "https://CRAN.R-project.org/package=ggplot2" | ||
| }, | ||
| "5": { | ||
| "@type": "SoftwareApplication", | ||
| "identifier": "loo", | ||
| "name": "loo", | ||
| "provider": { | ||
| "@id": "https://cran.r-project.org", | ||
| "@type": "Organization", | ||
| "name": "Comprehensive R Archive Network (CRAN)", | ||
| "url": "https://cran.r-project.org" | ||
| }, | ||
| "sameAs": "https://CRAN.R-project.org/package=loo" | ||
| }, | ||
| "6": { | ||
| "@type": "SoftwareApplication", | ||
| "identifier": "magrittr", | ||
| "name": "magrittr", | ||
| "provider": { | ||
| "@id": "https://cran.r-project.org", | ||
| "@type": "Organization", | ||
| "name": "Comprehensive R Archive Network (CRAN)", | ||
| "url": "https://cran.r-project.org" | ||
| }, | ||
| "sameAs": "https://CRAN.R-project.org/package=magrittr" | ||
| }, | ||
| "7": { | ||
| "@type": "SoftwareApplication", | ||
| "identifier": "methods", | ||
| "name": "methods" | ||
| }, | ||
| "8": { | ||
| "@type": "SoftwareApplication", | ||
| "identifier": "Rcpp", | ||
| "name": "Rcpp", | ||
| "version": ">= 0.12.0", | ||
| "provider": { | ||
| "@id": "https://cran.r-project.org", | ||
| "@type": "Organization", | ||
| "name": "Comprehensive R Archive Network (CRAN)", | ||
| "url": "https://cran.r-project.org" | ||
| }, | ||
| "sameAs": "https://CRAN.R-project.org/package=Rcpp" | ||
| }, | ||
| "9": { | ||
| "@type": "SoftwareApplication", | ||
| "identifier": "RcppParallel", | ||
| "name": "RcppParallel", | ||
| "version": ">= 5.0.1", | ||
| "provider": { | ||
| "@id": "https://cran.r-project.org", | ||
| "@type": "Organization", | ||
| "name": "Comprehensive R Archive Network (CRAN)", | ||
| "url": "https://cran.r-project.org" | ||
| }, | ||
| "sameAs": "https://CRAN.R-project.org/package=RcppParallel" | ||
| }, | ||
| "10": { | ||
| "@type": "SoftwareApplication", | ||
| "identifier": "rstan", | ||
| "name": "rstan", | ||
| "version": ">= 2.26.23", | ||
| "provider": { | ||
| "@id": "https://cran.r-project.org", | ||
| "@type": "Organization", | ||
| "name": "Comprehensive R Archive Network (CRAN)", | ||
| "url": "https://cran.r-project.org" | ||
| }, | ||
| "sameAs": "https://CRAN.R-project.org/package=rstan" | ||
| }, | ||
| "11": { | ||
| "@type": "SoftwareApplication", | ||
| "identifier": "rstantools", | ||
| "name": "rstantools", | ||
| "version": ">= 2.3.1.1", | ||
| "provider": { | ||
| "@id": "https://cran.r-project.org", | ||
| "@type": "Organization", | ||
| "name": "Comprehensive R Archive Network (CRAN)", | ||
| "url": "https://cran.r-project.org" | ||
| }, | ||
| "sameAs": "https://CRAN.R-project.org/package=rstantools" | ||
| }, | ||
| "12": { | ||
| "@type": "SoftwareApplication", | ||
| "identifier": "tidyr", | ||
| "name": "tidyr", | ||
| "provider": { | ||
| "@id": "https://cran.r-project.org", | ||
| "@type": "Organization", | ||
| "name": "Comprehensive R Archive Network (CRAN)", | ||
| "url": "https://cran.r-project.org" | ||
| }, | ||
| "sameAs": "https://CRAN.R-project.org/package=tidyr" | ||
| }, | ||
| "SystemRequirements": "GNU make" | ||
| }, | ||
| "fileSize": "1277.027KB", | ||
| "readme": "https://github.com/abigailkeller/eDNAjoint/blob/master/README.md" | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,22 +1,22 @@ | ||
| Version: 1.0 | ||
|
|
||
| RestoreWorkspace: No | ||
| SaveWorkspace: No | ||
| AlwaysSaveHistory: Default | ||
|
|
||
| EnableCodeIndexing: Yes | ||
| UseSpacesForTab: Yes | ||
| NumSpacesForTab: 2 | ||
| Encoding: UTF-8 | ||
|
|
||
| RnwWeave: Sweave | ||
| LaTeX: pdfLaTeX | ||
|
|
||
| AutoAppendNewline: Yes | ||
| StripTrailingWhitespace: Yes | ||
| LineEndingConversion: Posix | ||
|
|
||
| BuildType: Package | ||
| PackageUseDevtools: Yes | ||
| PackageInstallArgs: --no-multiarch --with-keep.source | ||
| PackageRoxygenize: rd,collate,namespace | ||
| Version: 1.0 | ||
| RestoreWorkspace: No | ||
| SaveWorkspace: No | ||
| AlwaysSaveHistory: Default | ||
| EnableCodeIndexing: Yes | ||
| UseSpacesForTab: Yes | ||
| NumSpacesForTab: 2 | ||
| Encoding: UTF-8 | ||
| RnwWeave: Sweave | ||
| LaTeX: pdfLaTeX | ||
| AutoAppendNewline: Yes | ||
| StripTrailingWhitespace: Yes | ||
| LineEndingConversion: Posix | ||
| BuildType: Package | ||
| PackageUseDevtools: Yes | ||
| PackageInstallArgs: --no-multiarch --with-keep.source | ||
| PackageRoxygenize: rd,collate,namespace |