Climate variability indices for ecological and crop models in R

Climate variability indices for ecological and crop models in R: the climatrends package - Published in JOSS (2023)

https://github.com/agrdatasci/climatrends

Science Score: 95.0%

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

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 1 DOI reference(s) in JOSS metadata
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Academic publication links
Links to: joss.theoj.org, zenodo.org
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Committers with academic emails
1 of 3 committers (33.3%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
Published in Journal of Open Source Software

Keywords

climate-data climatology timeseries-analysis

Scientific Fields

Engineering Computer Science - 40% confidence

Last synced: 4 months ago · JSON representation

Repository

Climate Variability Indices for Ecological Modelling

Basic Info

Host: GitHub
Owner: AgrDataSci
License: mit
Language: R
Default Branch: master
Homepage:
Size: 18.3 MB

Statistics

Stars: 4
Watchers: 6
Forks: 6
Open Issues: 2
Releases: 3

Topics

climate-data climatology timeseries-analysis

Created almost 6 years ago · Last pushed 4 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Codemeta

climatrends

climatrends: Climate Variability Indices for Ecological Modelling

Overview

The climatrends package provides methods to compute precipitation and temperature indices for climate models in ecology. The indices produced here can be used as explanatory variables for ecological modelling, crop modelling, and to assess trends in climate change.

Statement of need

Reproducibility, the ability to repeat the analysis, and Replicability, the ability to repeat an experiment are key to perform collaborative scientific research. This is still a gap in most of the studies in agriculture and ecology. climatrends addresses this specific issue. The package originates from a set of scripts to compute climate indices in our previous studies. Building up on the interest in expanding the analysis to other regions and to enable reproducible and replicable studies we developed climatrends. Most of the package functions take into account the heterogeneity of testing sites (locations), dates and seasons, a common characteristic of decentralized agricultural trials. Further development was made to enable time series analysis with fixed periods of time and locations. The package climatrends computes temperature, precipitation, crop growing and crop stress indices that were validated by previous studies on climatology and crop science. Currently climatrends is part of the CRAN Task View in Agriculture (https://cran.r-project.org/web/views/Agriculture.html).

Package website

https://agrdatasci.github.io/climatrends/

Installation

The package may be installed from CRAN via

r install.packages("climatrends")

The development version can be installed via

r library("remotes") install_github("agrdatasci/climatrends", build_vignettes = TRUE)

Example

The default method for the function temperature() has as the basic input one numeric vector with the maximum temperature and one numeric vector with the minimum temperature:

```r library("climatrends")

data("innlandet", package = "climatrends")

temperature(innlandet$tmax, innlandet$tmin)

maxDT minDT maxNT minNT DTR SU TR CFD WSDI CSDI T10p T90p 1: 15.13 -14.86 6.77 -19.25 6 0 0 115 4 5 -15.81 9.09

```

The indices can be splitted in intervals for series analysis. Here we get the temperature indices with intervals of 30 days.

```r

temperature(innlandet$tmax, innlandet$tmin, dates = innlandet$day, timeseries = TRUE, intervals = 30)

   id       date index  value
<int>     <date> <chr>  <dbl>

1: 1 2019-01-01 maxDT -0.15 2: 1 2019-01-01 minDT -14.86 3: 1 2019-01-01 maxNT -3.41 4: 1 2019-01-01 minNT -18.67

5: 1 2019-01-01 DTR 4.35

68: 1 2019-05-31 CFD 3.00 69: 1 2019-05-31 WSDI 2.00 70: 1 2019-05-31 CSDI 3.00 71: 1 2019-05-31 T10p 0.20 72: 1 2019-05-31 T90p 11.14 ```

Going further

The full functionality of climatrends is illustrated in the package vignette. The vignette can be found on the package website or from within R once the package has been installed, e.g. via

r vignette("Overview", package = "climatrends")

Meta

Package website
Please report any issues or bugs.
License: MIT
Get citation information for climatrends in R by typing citation(package = "climatrends").
You are welcome to contribute to the climatrends project. Please read our contribution guide lines.
Please note that the climatrends project is released with a Contributor Code of Conduct. By participating in the climatrends project you agree to abide by its terms.

Owner

Name: AgrDataSci
Login: AgrDataSci
Kind: organization
Email: k.desousa@cgiar.org
Location: France

Repositories: 8
Profile: https://github.com/AgrDataSci

We develop methods and tools to support sustainable food systems, rural development and digital inclusion

JOSS Publication

Climate variability indices for ecological and crop models in R: the climatrends package

Published

May 08, 2023

DOI

10.21105/joss.04405

Volume 8, Issue 85, Page 4405

Authors

Kauê de Sousa

Department of Agricultural Sciences, Inland Norway University of Applied Sciences, Hamar, Norway, Digital Inclusion, Bioversity International, Montpellier, France

Jacob van Etten

Digital Inclusion, Bioversity International, Montpellier, France

Magne Neby

Department of Agricultural Sciences, Inland Norway University of Applied Sciences, Hamar, Norway

Svein Ø. Solberg

Department of Agricultural Sciences, Inland Norway University of Applied Sciences, Hamar, Norway

Editor

Kristina Riemer

CodeMeta (codemeta.json)

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Papers & Mentions

Total mentions: 1

Data-driven decentralized breeding increases prediction accuracy in a challenging crop production environment

DOI: 10.1038/s42003-021-02463-w
OpenAlex ID: https://openalex.org/W3193973823
Published: August 2021

Last synced: 2 months ago

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Total Committers: 3
Avg Commits per committer: 36.0
Development Distribution Score (DDS): 0.019

Past Year

Commits: 5
Committers: 1
Avg Commits per committer: 5.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
kauedesousa	k**a@i**o	106
David LeBauer	d**r@a**u	1
istfer	f**m@g**m	1

Committer Domains (Top 20 + Academic)

arizona.edu: 1 inn.no: 1

Issues and Pull Requests

Last synced: 4 months ago

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Total issues: 15
Total pull requests: 3
Average time to close issues: 6 months
Average time to close pull requests: 2 months
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Total pull request authors: 2
Average comments per issue: 1.07
Average comments per pull request: 0.33
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 0

Past Year

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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

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Top Authors

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istfer (6)
kauedesousa (5)
dlebauer (4)

Pull Request Authors

dlebauer (2)
istfer (1)

Top Labels

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enhancement (3)

Pull Request Labels

Packages

Total packages: 3
Total downloads:
- cran 432 last-month
Total docker downloads: 21,613

Total dependent packages: 3
(may contain duplicates)
Total dependent repositories: 6
(may contain duplicates)
Total versions: 9
Total maintainers: 1

proxy.golang.org: github.com/agrdatasci/climatrends

Documentation: https://pkg.go.dev/github.com/agrdatasci/climatrends#section-documentation
License: mit
Latest release: v0.1.7
published over 5 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.4%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 4 months ago

proxy.golang.org: github.com/AgrDataSci/climatrends

Documentation: https://pkg.go.dev/github.com/AgrDataSci/climatrends#section-documentation
License: mit
Latest release: v0.1.7
published over 5 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.4%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 4 months ago

cran.r-project.org: climatrends

Climate Variability Indices for Ecological Modelling

Homepage: https://agrdatasci.github.io/climatrends/
Documentation: http://cran.r-project.org/web/packages/climatrends/climatrends.pdf
License: MIT + file LICENSE
Latest release: 0.1.13
published almost 4 years ago

Versions: 7
Dependent Packages: 3
Dependent Repositories: 6
Downloads: 432 Last month
Docker Downloads: 21,613

Rankings

Forks count: 9.7%

Dependent packages count: 10.6%

Dependent repos count: 12.1%

Average: 17.3%

Downloads: 26.0%

Stargazers count: 28.0%

Maintainers (1)

desousa.kaue@gmail.com

Last synced: 4 months ago

Dependencies

DESCRIPTION cran

R >= 3.5.0 depends
methods * depends
stats * imports
chirps * suggests
knitr * suggests
nasapower * suggests
rmarkdown * suggests
sf * suggests
testthat * suggests

Climate variability indices for ecological and crop models in R

Science Score: 95.0%

Keywords

Scientific Fields

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

climatrends

climatrends: Climate Variability Indices for Ecological Modelling

Overview

Statement of need

Package website

Installation

Example

5: 1 2019-01-01 DTR 4.35

Going further

Meta

Owner

JOSS Publication

Climate variability indices for ecological and crop models in R: the climatrends package

Authors

Editor

Tags

CodeMeta (codemeta.json)

Papers & Mentions

Data-driven decentralized breeding increases prediction accuracy in a challenging crop production environment

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

proxy.golang.org: github.com/agrdatasci/climatrends

Rankings

proxy.golang.org: github.com/AgrDataSci/climatrends

Rankings

cran.r-project.org: climatrends

Rankings

Maintainers (1)

Dependencies