litterfitter

Package for fitting and testing alternative models for single cohort litter decomposition data

https://github.com/traitecoevo/litterfitter

Science Score: 23.0%

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Found 2 DOI reference(s) in README
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3 of 6 committers (50.0%) from academic institutions
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Low similarity (14.9%) to scientific vocabulary

Keywords

carbon carboncycle decomposition ecology-modelling soil

Last synced: 6 months ago · JSON representation

Repository

Package for fitting and testing alternative models for single cohort litter decomposition data

Basic Info

Host: GitHub
Owner: traitecoevo
License: other
Language: R
Default Branch: master
Homepage: http://traitecoevo.github.io/litterfitter/
Size: 15.4 MB

Statistics

Stars: 5
Watchers: 9
Forks: 2
Open Issues: 5
Releases: 2

Topics

carbon carboncycle decomposition ecology-modelling soil

Created over 12 years ago · Last pushed 6 months ago

Metadata Files

Readme License

README.md

litterfitter

R package for fitting and testing alternative models for single cohort litter decomposition data

Installation

``` r #install.packages("remotes") remotes::install_github("cornwell-lab-unsw/litterfitter")

library(litterfitter) ```

Getting started

At the moment there is one key function which is fit_litter which can fit 6 different types of decomposition trajectories. Note that the fitted object is a litfit object

``` r fit <- fit_litter(time=c(0,1,2,3,4,5,6), mass.remaining =c(1,0.9,1.01,0.4,0.6,0.2,0.01), model="weibull", iters=500)

class(fit) ```

You can visually compare the fits of different non-linear equations with the plot_multiple_fits function:

r plot_multiple_fits(time=c(0,1,2,3,4,5,6), mass.remaining=c(1,0.9,1.01,0.4,0.6,0.2,0.01), model=c("neg.exp","weibull"), iters=500)

Calling plot on a litfit object will show you the data, the curve fit, and even the equation, with the estimated coefficients:

r plot(fit)

The summary of a litfit object will show you some of the summary statistics for the fit.

#> Summary of litFit object
#> Model type: weibull 
#> Number of observations:  7 
#> Parameter fits: 4.19 
#> Parameter fits: 2.47 
#> Time to 50% mass loss: 3.61 
#> Implied steady state litter mass: 3.71 in units of yearly input 
#> AIC:  -3.8883 
#> AICc:  -0.8883 
#> BIC:  -3.9965

From the litfit object you can then see the uncertainty in the parameter estimate by bootstrapping

Owner

Name: Trait Ecology and Evolution
Login: traitecoevo
Kind: organization
Location: Australia

Repositories: 64
Profile: https://github.com/traitecoevo

GitHub Events

Total

Release event: 1
Push event: 6
Fork event: 1

Last Year

Release event: 1
Push event: 6
Fork event: 1

Committers

Last synced: about 2 years ago

All Time

Total Commits: 169
Total Committers: 6
Avg Commits per committer: 28.167
Development Distribution Score (DDS): 0.633

Past Year

Commits: 16
Committers: 2
Avg Commits per committer: 8.0
Development Distribution Score (DDS): 0.188

Top Committers

Name	Email	Commits
wcornwell	w**l@g**m	62
James Weedon	j**n@g**m	42
Will Cornwell	w**l@u**u	31
Will Cornwell	w**l@v**l	18
Fonti Kar	f**r@u**u	14
liuguofang	l**4@1**m	2

Committer Domains (Top 20 + Academic)

unsw.edu.au: 2 126.com: 1 vu.nl: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 0
Total pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Total issue authors: 0
Total 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

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

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Packages

Total packages: 1
Total downloads:
- cran 202 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 3
Total maintainers: 1

cran.r-project.org: litterfitter

Fits a Collection of Curves to Single-Cohort Decomposition Data

Homepage: http://traitecoevo.github.io/litterfitter/
Documentation: http://cran.r-project.org/web/packages/litterfitter/litterfitter.pdf
License: MIT + file LICENSE
Latest release: 0.1.4
published 6 months ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 202 Last month

Rankings

Forks count: 21.9%

Stargazers count: 22.5%

Dependent packages count: 29.8%

Dependent repos count: 35.5%

Average: 37.6%

Downloads: 78.5%

Maintainers (1)

wcornwell@gmail.com

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

R >= 3.1.0 depends
grDevices * imports
graphics * imports
methods * imports
plyr * imports
stats * imports
devtools * suggests
knitr * suggests
roxygen2 * suggests
testthat * suggests

.github/workflows/R-CMD-check.yaml actions

actions/checkout v2 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/pkgdown.yaml actions

JamesIves/github-pages-deploy-action 4.1.4 composite
actions/checkout v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/test-coverage.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite