lpjmlkit

lpjmlkit: A toolkit for operating LPJmL and model-specific data processing - Published in JOSS (2024)

https://github.com/pik-lpjml/lpjmlkit

Science Score: 98.0%

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Published in Journal of Open Source Software

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cran r r-package

Last synced: 6 months ago · JSON representation ·

Repository

A collection of basic functions to facilitate the work with the DGVM LPJmL hosted at the Potsdam Institute for Climate Impact Research. It provides functions for running LPJmL, as well as reading, processing and writing model-related data such as inputs and outputs or configuration files.

Basic Info

Host: GitHub
Owner: PIK-LPJmL
License: agpl-3.0
Language: R
Default Branch: master
Homepage:
Size: 5.63 MB

Statistics

Stars: 10
Watchers: 1
Forks: 5
Open Issues: 0
Releases: 3

Topics

cran r r-package

Created about 4 years ago · Last pushed 11 months ago

Metadata Files

Readme Contributing License Citation

README.md

Toolkit for Basic LPJmL Handling

R package lpjmlkit, version 1.7.9

Purpose and Functionality

A collection of basic functions to facilitate the work with the Dynamic Global Vegetation Model (DGVM) Lund-Potsdam-Jena managed Land (LPJmL) hosted at the Potsdam Institute for Climate Impact Research (PIK). It provides functions for performing LPJmL simulations, as well as reading, processing and writing model-related data such as inputs and outputs or configuration files.

Overview

LPJmL Runner 🏃 to perform LPJmL simulations

LPJmL Runner only supports Unix-based operating systems that have an LPJmL version >= 4 installed. - ✍ write_config() write config.json files using a data frame with parameters to be changed and a base configuration file - 🔍 check_config() check if generated config.json files are valid for LPJmL simulations - ▶ run_lpjml() run LPJmL directly (e.g. single cell simulations) or 🚀 submit_lpjml() to SLURM (e.g. global simulations)

LPJmL Data 💾 for reading and processing LPJmL data

read_io() read LPJmL input and output as a LPJmLData object, containing the data array and LPJmLMetaData
- 📈 plot() the data or get insights via summary() and other base stats
- 🔁 transform() it to other time and space formats
- ✂ subset() the underlying data
- 📦 as_array(), as_tibble() and as_raster() / as_terra() to export into common R data formats
read_meta() read meta or header files as LPJmLMetaData object

miscellaneous

calc_cellarea() to calculate the area of LPJmLData objects underlying grid or for other objects latitudes
functions to handle LPJmL file headers, read_header() read the header of LPJmL files, get_headersize() get the size of a file header or create_header() to create a header object for writing input files
get_datatype() get information on the data type used in different LPJmL files
asub() functionality of the subset method to be used on a base array, also to replace data
... more functions via library(help = "lpjmlkit")

Installation

For installation of the most recent package version an additional repository has to be added in R:

r options(repos = c(CRAN = "@CRAN@", pik = "https://rse.pik-potsdam.de/r/packages")) The additional repository can be made available permanently by adding the line above to a file called .Rprofile stored in the home folder of your system (Sys.glob("~") in R returns the home directory).

After that the most recent version of the package can be installed using install.packages:

r install.packages("lpjmlkit")

Package updates can be installed using update.packages (make sure that the additional repository has been added before running that command):

r update.packages()

Tutorial

The package comes with vignettes describing the basic functionality of the package and how to use it. You can load them with the following command (the package needs to be installed):

r vignette("lpjml-data") # LPJmL Data vignette("lpjml-runner") # LPJmL Runner

Questions / Problems

In case of questions / problems please contact Jannes Breier jannesbr@pik-potsdam.de.

Citation

To cite package lpjmlkit in publications use:

Breier J, Ostberg S, Wirth S, Minoli S, Stenzel F, Hötten D, Müller C (2025). "lpjmlkit: Toolkit for Basic LPJmL Handling." doi:10.5281/zenodo.7773134 https://doi.org/10.5281/zenodo.7773134, Version: 1.7.9, https://github.com/PIK-LPJmL/lpjmlkit.

A BibTeX entry for LaTeX users is

latex @Misc{, title = {lpjmlkit: Toolkit for Basic LPJmL Handling}, author = {Jannes Breier and Sebastian Ostberg and Stephen Björn Wirth and Sara Minoli and Fabian Stenzel and David Hötten and Christoph Müller}, doi = {10.5281/zenodo.7773134}, date = {2025-04-02}, year = {2025}, url = {https://github.com/PIK-LPJmL/lpjmlkit}, note = {Version: 1.7.9}, }

Owner

Name: LPJmL group @ PIK
Login: PIK-LPJmL
Kind: organization

Repositories: 3
Profile: https://github.com/PIK-LPJmL

JOSS Publication

lpjmlkit: A toolkit for operating LPJmL and model-specific data processing

Published

November 22, 2024

DOI

10.21105/joss.05447

Volume 9, Issue 103, Page 5447

Authors

Jannes Breier

Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, P.O. Box 60 12 03, 14412 Potsdam, Germany, Geography Department, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany

Sebastian Ostberg

Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, P.O. Box 60 12 03, 14412 Potsdam, Germany

Stephen Björn Wirth

Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, P.O. Box 60 12 03, 14412 Potsdam, Germany, Institute of Crop Science and Plant Breeding, Grass and Forage Science/Organic Agriculture, Kiel University, Hermann-Rodewald-Str. 9, 24118, Kiel, Germany

David Hötten
Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, P.O. Box 60 12 03, 14412 Potsdam, Germany

Sara Minoli

Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, P.O. Box 60 12 03, 14412 Potsdam, Germany, Climate Focus, Germany

Fabian Stenzel

Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, P.O. Box 60 12 03, 14412 Potsdam, Germany

Christoph Müller

Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, P.O. Box 60 12 03, 14412 Potsdam, Germany

Editor

Marcos Vital

Citation (CITATION.cff)

cff-version: 1.2.0
message: If you use this software, please cite it using the metadata from this file.
type: software
title: 'lpjmlkit: Toolkit for Basic LPJmL Handling'
version: 1.7.9
date-released: '2025-04-02'
abstract: A collection of basic functions to facilitate the work with the Dynamic
  Global Vegetation Model (DGVM) Lund-Potsdam-Jena managed Land (LPJmL) hosted at
  the Potsdam Institute for Climate Impact Research (PIK). It provides functions for
  performing LPJmL simulations, as well as reading, processing and writing model-related
  data such as inputs and outputs or configuration files.
authors:
- family-names: Breier
  given-names: Jannes
  email: jannesbr@pik-potsdam.de
  orcid: https://orcid.org/0000-0002-9055-6904
- family-names: Ostberg
  given-names: Sebastian
  email: ostberg@pik-potsdam.de
  orcid: https://orcid.org/0000-0002-2368-7015
- family-names: Wirth
  given-names: Stephen Björn
  email: wirth@pik-potsdam.de
  orcid: https://orcid.org/0000-0003-3090-3318
- family-names: Minoli
  given-names: Sara
  email: minoli@pik-potsdam.de
  orcid: https://orcid.org/0000-0001-7920-3107
- family-names: Stenzel
  given-names: Fabian
  email: stenzel@pik-potsdam.de
  orcid: https://orcid.org/0000-0002-5109-0048
- family-names: Hötten
  given-names: David
  email: davidho@pik-potsdam.de
- family-names: Müller
  given-names: Christoph
  email: cmueller@pik-potsdam.de
  orcid: https://orcid.org/0000-0002-9491-3550
license: AGPL-3.0
repository-code: https://github.com/PIK-LPJmL/lpjmlkit
doi: 10.5281/zenodo.7773134

GitHub Events

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Last Year

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Last synced: 7 months ago

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Total Commits: 157
Total Committers: 6
Avg Commits per committer: 26.167
Development Distribution Score (DDS): 0.408

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Commits: 17
Committers: 4
Avg Commits per committer: 4.25
Development Distribution Score (DDS): 0.529

Top Committers

Name	Email	Commits
Jannes	j**r@p**e	93
Sebastian Ostberg	o**g@p**e	28
Stephen Wirth	w**h@p**e	22
deepyama	d**a@p**e	8
davidho	d**o@p**e	5
cmueller	c**r@p**e	1

Committer Domains (Top 20 + Academic)

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Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 5
Total pull requests: 1
Average time to close issues: 2 months
Average time to close pull requests: 27 days
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Average comments per issue: 1.4
Average comments per pull request: 0.0
Merged pull requests: 1
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Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: 27 days
Issue authors: 0
Pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 0.0
Merged pull requests: 1
Bot issues: 0
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Total packages: 1
Total downloads:
- cran 35 last-month

Total dependent packages: 1
Total dependent repositories: 0
Total versions: 1
Total maintainers: 1

cran.r-project.org: lpjmlkit

Toolkit for Basic LPJmL Handling

Homepage: https://github.com/PIK-LPJmL/lpjmlkit
Documentation: http://cran.r-project.org/web/packages/lpjmlkit/lpjmlkit.pdf
License: AGPL-3
Status: removed
Latest release: 1.0.11
published almost 3 years ago

Versions: 1
Dependent Packages: 1
Dependent Repositories: 0
Downloads: 35 Last month

Rankings

Forks count: 21.9%

Stargazers count: 26.2%

Dependent packages count: 29.8%

Dependent repos count: 35.5%

Average: 40.6%

Downloads: 89.6%

Maintainers (1)

jannesbr@pik-potsdam.de

Last synced: 6 months ago

lpjmlkit

Science Score: 98.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Toolkit for Basic LPJmL Handling

Purpose and Functionality

Overview

LPJmL Runner 🏃 to perform LPJmL simulations

LPJmL Data 💾 for reading and processing LPJmL data

miscellaneous

Installation

Tutorial

Questions / Problems

Citation

Owner

JOSS Publication

lpjmlkit: A toolkit for operating LPJmL and model-specific data processing

Authors

Editor

Tags

Citation (CITATION.cff)

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: lpjmlkit

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Maintainers (1)