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portalr

portalr: an R package for summarizing and using the Portal Project Data - Published in JOSS (2019)

https://github.com/weecology/portalr

Science Score: 95.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 13 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org, zenodo.org
  • ✓
    Committers with academic emails
    2 of 13 committers (15.4%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

community-ecology ecology small-mammal-trapping

Keywords from Contributors

portal shiny data-retrieval hacktobefest
Last synced: 6 months ago · JSON representation

Repository

A collection of functions to summarize the Portal Data

Basic Info
Statistics
  • Stars: 12
  • Watchers: 6
  • Forks: 12
  • Open Issues: 4
  • Releases: 17
Topics
community-ecology ecology small-mammal-trapping
Created about 9 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Zenodo

README.Rmd 

---
output: github_document
---



```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/"
)

library(portalr)
```

# portalr 


[![R-CMD-check](https://github.com/weecology/portalr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/weecology/portalr/actions/workflows/R-CMD-check.yaml)
[![License](https://img.shields.io/badge/license-MIT-blue.svg)](https://raw.githubusercontent.com/weecology/portalr/main/LICENSE)
[![Codecov test coverage](https://codecov.io/gh/weecology/portalr/graph/badge.svg)](https://app.codecov.io/gh/weecology/portalr)
[![CRAN downloads](https://cranlogs.r-pkg.org/badges/grand-total/portalr)](https://CRAN.R-project.org/package=portalr)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1429290.svg)](https://doi.org/10.5281/zenodo.1429290)
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01098/status.svg)](https://doi.org/10.21105/joss.01098)
[![NSF-1929730](https://img.shields.io/badge/NSF-1929730-blue.svg)](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1929730)


## Overview 

The **portalr** package provides collection of basic functions to summarize the Portal project data on rodents, plants, ants, and weather at our long-term field site in the Chihuahuan Desert. The data begin in 1977 and are continuously updated today. There are functions to summarize rodent abundance, biomass, or energy and by site, plot, or treatment type. There are functions to summarize the weather data collected from our automated weather stations and plant data that is collected each summer and fall.

## Installation

You can install portalr from CRAN with:

```{r CRAN-installation, eval = FALSE}
install.packages("portalr")
```

OR from github with:

```{r gh-installation, eval = FALSE}
# install.packages("remotes")
remotes::install_github("weecology/portalr")
```

## Examples

1. Load all data tables from the [PortalData GitHub repo](https://github.com/weecology/portalData):

```{r load data from repo, eval = FALSE}
data_tables <- load_rodent_data("repo")
```

2. Download and generate summaries of rodent abundance and biomass:

```{r download and summarize rodent data, eval = FALSE}
download_observations(".")

rodent_data <- abundance(".") # default grouping is by sampling period

rodent_biomass_by_plot <- biomass(".", level = "plot", type = "granivores", 
shape = "flat", time = "date")
```

3. Retrieve weather data:

```{r weather data, eval = FALSE}
weatherdata <- weather("Monthly", ".")
```

For more detailed info, checkout the vignettes associated with the package:
```{r browse vignettes, eval = FALSE}
browseVignettes("portalr")
```

## More Information

#### [Portal Data Repo](https://github.com/weecology/PortalData) 
The data repo contains useful details for issues with data collection, and background on why we handle them the way we do. Of course, it also contains the raw data, if you would like to create more complex data summaries than what is provided here.

#### [The Portal Project](https://portal.weecology.org/)
Find a list of previous publications using the Portal data at our website.

#### [The Portal Blog](https://portalproject.wordpress.com/)
Follow our blog to get the latest news on what is happening with our project and at the site.

## Citation

To cite `portalr`, please refer to either:

* [JOSS publication](https://doi.org/10.21105/joss.01098):

  Erica M. Christensen, Glenda M. Yenni, Hao Ye, Juniper L. Simonis, Ellen K. Bledsoe, Renata M. Diaz, Shawn D. Taylor, Ethan P. White, and S. K. Morgan Ernest. (2019). portalr: an R package for summarizing and using the Portal Project Data. Journal of Open Source Software, 4(33), 1098, https://doi.org/10.21105/joss.01098

* or use the most recent release on [Zenodo](https://doi.org/10.5281/zenodo.1429290).

### Dataset Citation

To cite the Portal dataset, use:

```{r}
get_dataset_citation()
```

Owner

  • Name: Weecology
  • Login: weecology
  • Kind: organization

JOSS Publication

portalr: an R package for summarizing and using the Portal Project Data
Published
January 24, 2019
DOI
Volume 4, Issue 33, Page 1098
Authors
Erica M. Christensen ORCID
University of Florida, Jornada Experimental Range, New Mexico State University
Glenda M. Yenni ORCID
University of Florida
Hao Ye ORCID
University of Florida
Juniper L. Simonis ORCID
University of Florida
Ellen K. Bledsoe ORCID
University of Florida
Renata Diaz ORCID
University of Florida
Shawn D. Taylor ORCID
University of Florida
Ethan P. White ORCID
University of Florida
S. K. Morgan Ernest ORCID
University of Florida
Editor
Karthik Ram ORCID
Tags
Portal Project
View PDF Review Thread Software Archive

GitHub Events

Total
  • Create event: 3
  • Release event: 1
  • Issues event: 8
  • Watch event: 1
  • Delete event: 3
  • Issue comment event: 4
  • Push event: 10
  • Pull request event: 6
Last Year
  • Create event: 3
  • Release event: 1
  • Issues event: 8
  • Watch event: 1
  • Delete event: 3
  • Issue comment event: 4
  • Push event: 10
  • Pull request event: 6

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 623
  • Total Committers: 13
  • Avg Commits per committer: 47.923
  • Development Distribution Score (DDS): 0.549
Past Year
  • Commits: 10
  • Committers: 4
  • Avg Commits per committer: 2.5
  • Development Distribution Score (DDS): 0.4
Top Committers
Name Email Commits
Hao Ye l****d@g****m 281
Glenda Yenni g****a@w****g 148
Erica Christensen e****n@w****g 57
Morgan Ernest m****n@w****g 43
juniperlsimonis d****s@g****m 28
Renata Diaz d****m@g****m 23
Ethan White e****n@w****g 16
Hao Ye h****e@u****u 10
Ellen Bledsoe e****e@u****u 7
Shawn s****r 5
henrykironde h****e@g****m 2
Francisco Rodriguez-Sanchez f****c@g****m 2
olivroy 5****y 1
Committer Domains (Top 20 + Academic)
weecology.org: 4 ufl.edu: 1 ucsd.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 55
  • Total pull requests: 71
  • Average time to close issues: 9 months
  • Average time to close pull requests: 20 days
  • Total issue authors: 11
  • Total pull request authors: 7
  • Average comments per issue: 1.69
  • Average comments per pull request: 0.35
  • Merged pull requests: 63
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 5
  • Pull requests: 9
  • Average time to close issues: 3 months
  • Average time to close pull requests: 5 days
  • Issue authors: 3
  • Pull request authors: 1
  • Average comments per issue: 1.2
  • Average comments per pull request: 0.0
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • gmyenni (16)
  • ha0ye (11)
  • ethanwhite (8)
  • juniperlsimonis (7)
  • skmorgane (4)
  • jennybc (3)
  • gavinsimpson (2)
  • dill (1)
  • patdumandan (1)
  • olivroy (1)
  • bleds22e (1)
Pull Request Authors
  • gmyenni (54)
  • ha0ye (9)
  • juniperlsimonis (6)
  • henrykironde (5)
  • ethanwhite (2)
  • diazrenata (2)
  • olivroy (2)
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 850 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 5
  • Total versions: 22
  • Total maintainers: 1
cran.r-project.org: portalr

Create Useful Summaries of the Portal Data

  • Versions: 22
  • Dependent Packages: 0
  • Dependent Repositories: 5
  • Downloads: 850 Last month
Rankings
Forks count: 5.8%
Dependent repos count: 13.3%
Downloads: 15.2%
Average: 15.8%
Stargazers count: 16.5%
Dependent packages count: 28.0%
Maintainers (1)
glenda@weecology.org
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.2.3 depends
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  • clisymbols * imports
  • crayon * imports
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  • tidyselect >= 1.0.0 imports
  • zoo * imports
  • covr * suggests
  • cowplot * suggests
  • ggplot2 * suggests
  • httptest * suggests
  • knitr * suggests
  • pkgdown * suggests
  • rmarkdown * suggests
  • testthat * suggests
.github/workflows/pkgdown.yaml actions
  • actions/cache v3 composite
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  • r-lib/actions/setup-pandoc v2 composite
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.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v4 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
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.github/workflows/test-coverage.yaml actions
  • actions/checkout v4 composite
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  • codecov/codecov-action v4 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite