rcompadre

R tools for obtaining and manupulating data from the COMPADRE and COMADRE Plant and Animal Matrix Databases

https://github.com/jonesor/rcompadre

Science Score: 49.0%

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 1 DOI reference(s) in README
○
Academic publication links
✓
Committers with academic emails
2 of 128 committers (1.6%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (18.7%) to scientific vocabulary

Last synced: 7 months ago · JSON representation

Repository

R tools for obtaining and manupulating data from the COMPADRE and COMADRE Plant and Animal Matrix Databases

Basic Info

Host: GitHub
Owner: jonesor
Language: R
Default Branch: main
Homepage: https://jonesor.github.io/Rcompadre/
Size: 5.8 MB

Statistics

Stars: 11
Watchers: 5
Forks: 11
Open Issues: 12
Releases: 8

Created over 8 years ago · Last pushed over 1 year ago

Metadata Files

Readme Changelog Codemeta

README.Rmd

---
output: github_document
---



```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = TRUE
)
```

# Rcompadre  






| Project | Main branch | Devel branch  |
|---------|:------------|:--------------|
| [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.html)  | [![R-CMD-check](https://github.com/jonesor/Rcompadre/actions/workflows/main_check.yaml/badge.svg)](https://github.com/jonesor/Rcompadre/actions/workflows/main_check.yaml) | [![R-CMD-check](https://github.com/jonesor/Rcompadre/actions/workflows/devel_build_check.yaml/badge.svg)](https://github.com/jonesor/Rcompadre/actions/workflows/devel_build_check.yaml) |
| [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) | [![codecov](https://codecov.io/gh/jonesor/Rcompadre/branch/main/graph/badge.svg?token=S9G2a5K9k9)](https://app.codecov.io/gh/jonesor/Rcompadre)     |     |
| ![Grand Total](http://cranlogs.r-pkg.org/badges/grand-total/Rcompadre) |[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/Rcompadre)](https://cran.r-project.org/package=Rcompadre)|
| ![CRAN](http://cranlogs.r-pkg.org/badges/Rcompadre)|  |     |




An R package to facilitate working with the [COM(P)ADRE](https://compadre-db.org/) Plant and Animal Matrix Population Databases.

## Installation

Install the stable release package from CRAN with:

```{r, eval=FALSE}
install.packages("Rcompadre")
```

Install the package from GitHub with:

```{r, eval=FALSE}
# install package 'remotes' if necessary
# will already be installed if 'devtools' is installed
install.packages("remotes")

# argument 'build_opts = NULL' only needed if you want to build vignettes
remotes::install_github("jonesor/Rcompadre", build_opts = NULL)
```

To install from the development branch use:

```{r, eval=FALSE}
remotes::install_github("jonesor/Rcompadre", ref = "devel")
```

## Usage

```{r, eval=FALSE}
library(Rcompadre)
```

#### Fetching a database

Fetch the most recent database version from [compadre-db.org](https://compadre-db.org/) with

```{r, eval=FALSE}
compadre <- cdb_fetch("compadre") # or use 'comadre' for the animal database
```

or load from a local `.RData` file with

```{r, eval=FALSE}
compadre <- cdb_fetch("path/to/file/COMPADRE_v.4.0.1.RData")
```

If you prefer using `load()` to load your local copy of a legacy database, use `as_cdb()` to convert it to the `CompadreDB` class

```{r, eval=FALSE}
load("COMPADRE_v.4.0.1.RData") # loads object 'compadre'
compadre <- as_cdb(compadre)
```

#### Subsetting

For the most part `CompadreDB` objects work like a data frame. They can be subset using `[`,  `subset()` or `filter()`

```{r, eval=FALSE, results="hide"}
# subset to the first 10 rows
compadre[1:10, ]

# subset to the species 'Echinacea angustifolia'
subset(compadre, SpeciesAccepted == "Echinacea angustifolia")

# subset to the species 'Echinacea angustifolia'
filter(compadre, SpeciesAccepted == "Echinacea angustifolia")
```

#### Example analysis: calculating population growth rates

First we'll use the function `cdb_flag()` to add columns to the database flagging potential issues with the projection matrices, such as missing values, or matrices that don't meet assumptions like ergodicity, irreducibility, or primitivity.

```{r,eval=FALSE}
compadre_flags <- cdb_flag(compadre)
```

We'll only be able to calculate population growth rates from matrices that don't contain missing values, and we only want to use matrices that meet the assumption of ergodicity, so we'll subset the database accordingly.

```{r, eval=FALSE}
compadre_sub <- subset(
  compadre_flags,
  check_NA_A == FALSE & check_ergodic == TRUE
)
```

Finally, we'll use the `eigs()` function from the [popdemo](https://CRAN.R-project.org/package=popdemo) package to calculate the population growth rate for every matrix in `compadre_sub`.

```{r, eval=FALSE}
compadre_sub$lambda <- sapply(matA(compadre_sub), popdemo::eigs, what = "lambda")
```

In the code above, the accessor function `matA()` is used to extract a list of projection matrices (the full matrix, `matA`) from every row of `compadre_sub`. There are also accessor functions for the matrix subcomponents (`matU()`, `matF()`, `matC()`), and for many other parts of the database too.

## Previous releases

Specific earlier releases of this package can be installed using the appropriate `@` tag. 

For example to install version 0.1.0:

```{r, eval=FALSE}
remotes::install_github("jonesor/Rcompadre@v0.1.0")
```

See the Changelog for more details.

## Citation

Jones, Owen R., Patrick Barks, Iain M. Stott, Tamora D. James, Sam C. Levin, William K. Petry, Pol Capdevila, et al. 2022. "Rcompadre and Rage -- Two R Packages to Facilitate the Use of the COMPADRE and COMADRE Databases and Calculation of Life History Traits from Matrix Population Models." _Methods in Ecology and Evolution_. doi: 10.1111/2041-210X.13792.

## Contributions

All contributions are welcome. Please note that this project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By participating in this project you agree to abide by its terms.

There are numerous ways of contributing. 

1. You can submit bug reports, suggestions etc. by [opening an issue](https://github.com/jonesor/Rcompadre/issues).

2. You can copy or fork the repository, make your own code edits and then send us a pull request. [Here's how to do that](https://jarv.is/notes/how-to-pull-request-fork-github/).

3. You can get to know us and join as a collaborator on the main repository.

4. You are also welcome to email us.

Owner

Name: Owen Jones
Login: jonesor
Kind: user
Location: Odense, Denmark
Company: University of Southern Denmark

Website: https://ecoevo.social/@jonesor
Twitter: jonesor
Repositories: 24
Profile: https://github.com/jonesor

I'm an Associate Professor working on life history evolution, senescence/aging and population dynamics at the University of Southern Denmark.

CodeMeta (codemeta.json)

{
  "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
  "@type": "SoftwareSourceCode",
  "identifier": "Rcompadre",
  "description": "Utility functions for interacting with the 'COMPADRE' and 'COMADRE' databases of matrix population models. Described in Jones et al. (2021) <doi:10.1101/2021.04.26.441330>.",
  "name": "Rcompadre: Utilities for using the 'COM(P)ADRE' Matrix Model Database",
  "codeRepository": "https://github.com/jonesor/Rcompadre",
  "issueTracker": "https://github.com/jonesor/Rcompadre/issues",
  "license": "https://spdx.org/licenses/GPL-3.0",
  "version": "1.4.0",
  "programmingLanguage": {
    "@type": "ComputerLanguage",
    "name": "R",
    "url": "https://r-project.org"
  },
  "runtimePlatform": "R version 4.4.1 (2024-06-14)",
  "provider": {
    "@id": "https://cran.r-project.org",
    "@type": "Organization",
    "name": "Comprehensive R Archive Network (CRAN)",
    "url": "https://cran.r-project.org"
  },
  "author": [
    {
      "@type": "Person",
      "givenName": "Patrick",
      "familyName": "Barks",
      "email": "barks@biology.sdu.dk",
      "@id": "https://orcid.org/0000-0002-5947-8151"
    },
    {
      "@type": "Person",
      "givenName": "Danny",
      "familyName": "Buss",
      "email": "dlb50@cam.ac.uk"
    },
    {
      "@type": "Person",
      "givenName": "Roberto",
      "familyName": "Salguero-Gomez",
      "email": "rob.salguero@zoo.ox.ac.uk",
      "@id": "https://orcid.org/0000-0002-6085-4433"
    },
    {
      "@type": "Person",
      "givenName": "Iain",
      "familyName": "Stott",
      "email": "stott@biology.sdu.dk",
      "@id": "https://orcid.org/0000-0003-2724-7436"
    },
    {
      "@type": "Person",
      "givenName": "William K.",
      "familyName": "Petry",
      "email": "wpetry@ncsu.edu",
      "@id": "https://orcid.org/0000-0002-5230-5987"
    },
    {
      "@type": "Person",
      "givenName": "Tamora",
      "familyName": "James",
      "email": "tamoradjames@protonmail.com",
      "@id": "https://orcid.org/0000-0003-1363-4742"
    },
    {
      "@type": "Person",
      "givenName": "Owen",
      "familyName": "Jones",
      "email": "jones@biology.sdu.dk",
      "@id": "https://orcid.org/0000-0001-5720-4686"
    },
    {
      "@type": "Person",
      "givenName": "Julia",
      "familyName": "Jones",
      "email": "juagjones@gmail.com",
      "@id": "https://orcid.org/0000-0001-9223-1778"
    },
    {
      "@type": "Person",
      "givenName": "Gesa",
      "familyName": "Römer",
      "email": "gesa@biology.sdu.dk",
      "@id": "https://orcid.org/0000-0002-4859-5870"
    },
    {
      "@type": "Person",
      "givenName": "Sam",
      "familyName": "Levin",
      "email": "levisc8@gmail.com",
      "@id": "https://orcid.org/0000-0002-3289-9925"
    }
  ],
  "maintainer": [
    {
      "@type": "Person",
      "givenName": "Owen",
      "familyName": "Jones",
      "email": "jones@biology.sdu.dk",
      "@id": "https://orcid.org/0000-0001-5720-4686"
    }
  ],
  "softwareSuggestions": [
    {
      "@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"
    },
    {
      "@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"
    },
    {
      "@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": "maps",
      "name": "maps",
      "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=maps"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "rcrossref",
      "name": "rcrossref",
      "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=rcrossref"
    },
    {
      "@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",
      "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": ">= 2.10"
    },
    "2": {
      "@type": "SoftwareApplication",
      "identifier": "methods",
      "name": "methods"
    },
    "3": {
      "@type": "SoftwareApplication",
      "identifier": "popdemo",
      "name": "popdemo",
      "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=popdemo"
    },
    "4": {
      "@type": "SoftwareApplication",
      "identifier": "stats",
      "name": "stats"
    },
    "5": {
      "@type": "SoftwareApplication",
      "identifier": "tibble",
      "name": "tibble",
      "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=tibble"
    },
    "6": {
      "@type": "SoftwareApplication",
      "identifier": "utils",
      "name": "utils"
    },
    "SystemRequirements": null
  },
  "fileSize": "553.715KB",
  "citation": [
    {
      "@type": "ScholarlyArticle",
      "datePublished": "2022",
      "author": [
        {
          "@type": "Person",
          "givenName": [
            "Owen",
            "R."
          ],
          "familyName": "Jones"
        },
        {
          "@type": "Person",
          "givenName": "Patrick",
          "familyName": "Barks"
        },
        {
          "@type": "Person",
          "givenName": [
            "Iain",
            "M."
          ],
          "familyName": "Stott"
        },
        {
          "@type": "Person",
          "givenName": [
            "Tamora",
            "D."
          ],
          "familyName": "James"
        },
        {
          "@type": "Person",
          "givenName": [
            "Sam",
            "C."
          ],
          "familyName": "Levin"
        },
        {
          "@type": "Person",
          "givenName": [
            "William",
            "K."
          ],
          "familyName": "Petry"
        },
        {
          "@type": "Person",
          "givenName": "Pol",
          "familyName": "Capdevila"
        },
        {
          "@type": "Person",
          "givenName": "Judy",
          "familyName": "Che-Castaldo"
        },
        {
          "@type": "Person",
          "givenName": "John",
          "familyName": "Jackson"
        },
        {
          "@type": "Person",
          "givenName": "Gesa",
          "familyName": "Römer"
        },
        {
          "@type": "Person",
          "givenName": "Caroline",
          "familyName": "Schuette"
        },
        {
          "@type": "Person",
          "givenName": [
            "Chelsea",
            "C"
          ],
          "familyName": "Thomas"
        },
        {
          "@type": "Person",
          "givenName": "Roberto",
          "familyName": "Salguero-Gómez"
        }
      ],
      "name": "Rcompadre and Rage - two {R} packages to facilitate the use of\n              the {COMPADRE} and {COMADRE} databases and calculation of life\n              history traits from matrix population models",
      "identifier": "10.1111/2041-210X.13792",
      "pagination": "770-781",
      "@id": "https://doi.org/10.1111/2041-210X.13792",
      "sameAs": "https://doi.org/10.1111/2041-210X.13792",
      "isPartOf": {
        "@type": "PublicationIssue",
        "datePublished": "2022",
        "isPartOf": {
          "@type": [
            "PublicationVolume",
            "Periodical"
          ],
          "volumeNumber": "13",
          "name": "Methods in Ecology and Evolution"
        }
      }
    }
  ],
  "releaseNotes": "https://github.com/jonesor/Rcompadre/blob/master/NEWS.md",
  "readme": "https://github.com/jonesor/Rcompadre/blob/main/README.md",
  "contIntegration": [
    "https://github.com/jonesor/Rcompadre/actions/workflows/main_check.yaml",
    "https://github.com/jonesor/Rcompadre/actions/workflows/devel_build_check.yaml",
    "https://app.codecov.io/gh/jonesor/Rcompadre"
  ],
  "developmentStatus": "https://www.repostatus.org/#active",
  "relatedLink": "https://CRAN.R-project.org/package=Rcompadre"
}

GitHub Events

Total

Push event: 5

Last Year

Push event: 5

Committers

Last synced: over 2 years ago

All Time

Total Commits: 834
Total Committers: 128
Avg Commits per committer: 6.516
Development Distribution Score (DDS): 0.622

Past Year

Commits: 122
Committers: 3
Avg Commits per committer: 40.667
Development Distribution Score (DDS): 0.016

Top Committers

Name	Email	Commits
Owen Jones	j**s@b**k	315
Owen Jones	j**r@g**m	182
patrickbarks	p**s@g**m	149
levisc8	l**8@g**m	26
iainmstott	i**t@g**m	20
Tamora James	t**1@s**k	7
bartholdja	j**s@g**m	6
dannylbuss	d**4@e**k	4
wpetry	w****y	3
Julia Barthold	b**a@g**m	3
Julia Barthold	V**a@V**l	2
runner	r**r@M**l	1
runner	r**r@M**l	1
runner	r**r@M**l	1
runner	r**r@M**l	1
runner	r**r@M**l	1
runner	r**r@M**l	1
runner	r**r@M**l	1
runner	r**r@M**l	1
runner	r**r@M**l	1
runner	r**r@M**l	1
runner	r**r@M**l	1
runner	r**r@M**l	1
runner	r**r@M**l	1
runner	r**r@M**l	1
runner	r**r@M**l	1
runner	r**r@M**l	1
runner	r**r@M**l	1
runner	r**r@M**l	1
runner	r**r@M**l	1
and 98 more...

Committer Domains (Top 20 + Academic)

nat.c.sdu.dk: 1 exeter.ac.uk: 1 sheffield.ac.uk: 1 biology.sdu.dk: 1

Issues and Pull Requests

Last synced: 9 months ago

All Time

Total issues: 50
Total pull requests: 55
Average time to close issues: 6 months
Average time to close pull requests: 5 days
Total issue authors: 9
Total pull request authors: 6
Average comments per issue: 1.46
Average comments per pull request: 0.35
Merged pull requests: 50
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

jonesor (30)
patrickbarks (7)
wpetry (3)
levisc8 (3)
iainmstott (2)
bramdhondt (1)
GesaRoemer (1)
darrennorris (1)
DannyLBuss (1)

Pull Request Authors

jonesor (46)
patrickbarks (5)
wpetry (1)
levisc8 (1)
GesaRoemer (1)
darrennorris (1)

Top Labels

Issue Labels

help wanted (8) enhancement (7) devel-resolved (5) bug (3) good first issue (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 385 last-month

Total dependent packages: 3
Total dependent repositories: 2
Total versions: 6
Total maintainers: 1

cran.r-project.org: Rcompadre

Utilities for using the 'COM(P)ADRE' Matrix Model Database

Homepage: https://github.com/jonesor/Rcompadre
Documentation: http://cran.r-project.org/web/packages/Rcompadre/Rcompadre.pdf
License: GPL-3
Latest release: 1.4.0
published over 1 year ago

Versions: 6
Dependent Packages: 3
Dependent Repositories: 2
Downloads: 385 Last month

Rankings

Forks count: 5.8%

Dependent packages count: 10.9%

Average: 15.6%

Stargazers count: 15.8%

Dependent repos count: 19.2%

Downloads: 26.5%

Maintainers (1)

jones@biology.sdu.dk

Last synced: 8 months ago

Dependencies

DESCRIPTION cran

R >= 2.10 depends
methods * imports
popdemo * imports
tibble * imports
covr * suggests
dplyr * suggests
ggplot2 * suggests
knitr * suggests
maps * suggests
rcrossref * suggests
rmarkdown * suggests
spelling * suggests
testthat * suggests

.github/workflows/devel_build_check.yaml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/upload-artifact main composite
r-lib/actions/setup-pandoc v1 composite
r-lib/actions/setup-r v1 composite

.github/workflows/devel_pull_check.yaml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/upload-artifact main composite
r-lib/actions/setup-pandoc v1 composite
r-lib/actions/setup-r v1 composite

.github/workflows/main_check.yaml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/upload-artifact main composite
r-lib/actions/setup-pandoc v1 composite
r-lib/actions/setup-r v1 composite

.github/workflows/weekly-build-check.yml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/upload-artifact main composite
r-lib/actions/setup-pandoc v1 composite
r-lib/actions/setup-r v1 composite

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

rcompadre

Science Score: 49.0%

Repository

Basic Info

Statistics

Metadata Files

README.Rmd

Owner

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

cran.r-project.org: Rcompadre

Rankings

Maintainers (1)

Dependencies