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growthcurver

Growthcurver is an R package that fits growth curve data to a standard form of the logistic equation common in ecology and evolution whose parameters (the growth rate, the initial population size, and the carrying capacity) provide meaningful population-level information with straight-forward biological interpretation.

https://github.com/sprouffske/growthcurver

Science Score: 13.0%

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
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    .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
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    Academic publication links
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    Committers with academic emails
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    Scientific vocabulary similarity
    Low similarity (12.0%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Growthcurver is an R package that fits growth curve data to a standard form of the logistic equation common in ecology and evolution whose parameters (the growth rate, the initial population size, and the carrying capacity) provide meaningful population-level information with straight-forward biological interpretation.

Basic Info
  • Host: GitHub
  • Owner: sprouffske
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 171 KB
Statistics
  • Stars: 37
  • Watchers: 6
  • Forks: 14
  • Open Issues: 8
  • Releases: 0
Created almost 11 years ago · Last pushed over 4 years ago
Metadata Files
Readme

README.md

growthcurver

Travis-CI Build Status

Growthcurver is an R package that fits growth curve data to a standard form of the logistic equation common in ecology and evolution whose parameters (the growth rate, the initial population size, and the carrying capacity) provide meaningful population-level information with straight-forward biological interpretation.

You can install the latest released version from CRAN from within R with R install.packages("growthcurver") `

You can install the latest development version from github with ```R # install devtools first if you don't already have the package install.packages("devtools")

# then install growthcurver devtools::install_github("sprouffske/growthcurver") ```

The paper describing Growthcurver is available here.

Using growthcurver

The easiest way to get started with growthcurver is to work through the examples in the vignette. In the vignette, you can find information on

  • What your input data should look like
  • How to use growthcurver to get summary metrics on a single growth curve sample
  • How to use growthcurver to get summary metrics on an entire plate of growth curves
  • What those metrics mean and some best practices for quality control

You can find the vignette here.

A simple working example

This code loads the growthcurver package and some sample data. Then, it calls SummarizeGrowth to do the analysis. R library(growthcurver) # load the package d <- growthdata # load some sample, simulated data gc_fit <- SummarizeGrowth(d$time, d$A1) # do the analysis plot(gc_fit) # plot your data and the best fit gc_fit # view some returned metrics

GitHub Events

Total
  • Issues event: 1
  • Watch event: 5
Last Year
  • Issues event: 1
  • Watch event: 5

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 37
  • Total Committers: 5
  • Avg Commits per committer: 7.4
  • Development Distribution Score (DDS): 0.27
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
sprouffske s****e@g****m 27
Kathleen Sprouffske s****e@K****l 4
Frederiek - Maarten Kerckhof f****f@u****e 4
Kathleen Sprouffske s****e@k****l 1
Kieran Mace k****e@g****m 1
Committer Domains (Top 20 + Academic)
ugent.be: 1

Issues and Pull Requests

Last synced: over 2 years ago

All Time
  • Total issues: 13
  • Total pull requests: 3
  • Average time to close issues: 12 months
  • Average time to close pull requests: about 2 months
  • Total issue authors: 12
  • Total pull request authors: 3
  • Average comments per issue: 0.77
  • Average comments per pull request: 1.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Edison2021 (2)
  • mogusi8 (1)
  • kdzimm (1)
  • gauravdiwan89 (1)
  • emrowl1 (1)
  • GBSB12 (1)
  • thierryjanssens (1)
  • padpadpadpad (1)
  • gabrielle3333 (1)
  • EugeneAeolus (1)
  • GuilhemRoyer (1)
  • diegorojasa (1)
  • 2hr2sleep (1)
  • benjamin-elusers (1)
  • ehofmeister (1)
Pull Request Authors
  • FMKerckhof (1)
  • ttyskg (1)
  • kieran-mace (1)
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 630 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 5
  • Total maintainers: 1
cran.r-project.org: growthcurver

Simple Metrics to Summarize Growth Curves

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 630 Last month
Rankings
Forks count: 5.1%
Stargazers count: 8.3%
Average: 16.9%
Downloads: 18.3%
Dependent repos count: 24.0%
Dependent packages count: 28.8%
Maintainers (1)
sprouffske@gmail.com
Last synced: 12 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0 depends
  • grDevices >= 4.0 imports
  • graphics >= 4.0 imports
  • minpack.lm >= 1.2 imports
  • stats >= 4.0 imports
  • dplyr * suggests
  • ggplot2 * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests