seedr

An R package that provides functions to fit hydro and thermal time germination models.
https://github.com/efernandezpascual/seedr

Category: Consumption
Sub Category: Agriculture and Nutrition

Keywords

agronomy botany ecology germination seeds

Last synced: about 9 hours ago
JSON representation

Repository metadata

seedr: Hydro and Thermal Time Seed Germination Models in R

• Host: GitHub
• URL: https://github.com/efernandezpascual/seedr
• Owner: efernandezpascual
• License: gpl-3.0
• Created: 2020-03-04T19:11:23.000Z (about 5 years ago)
• Default Branch: master
• Last Pushed: 2021-05-16T11:19:41.000Z (almost 4 years ago)
• Last Synced: 2024-10-29T20:59:55.500Z (6 months ago)
• Topics: agronomy, botany, ecology, germination, seeds
• Language: R
• Homepage:
• Size: 30.1 MB
• Stars: 2
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Releases: 0
• Metadata Files:
  • Readme: README.Rmd
  • License: LICENSE

README.Rmd

          ---
title: "README.md"
output: github_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

# seedr

![](seeds.png)


[![Travis build status](https://travis-ci.org/efernandezpascual/seedr.svg?branch=master)](https://travis-ci.com/efernandezpascual/seedr)



## Overview

`seedr` is an R package that provides functions to fit hydro and thermal time germination models. These models characterize seed lots by two sets of parameters: (i) the physiological thresholds (water, temperature) between which the seed lot can germinate, and (ii) the physiological-time units that the seed lot needs to accumulate before it can germinate. `seedr` fits the hydro time model of Bradford (Gummerson 1986, Bradford 1990, Bewley et al. 2013) and the thermal time model of Garcia-Huidobro (Garcia-Huidobro et al. 1982, Gummerson 1986, Bewley et al. 2013). It allows to fit models to grouped datasets, i.e. datasets containing multiple species, seedlots or experiments.

## Installation

```{r eval=FALSE}
# Install stable version from CRAN
install.packages("seedr")

# Install last development version from GitHub
install.packages("devtools") # Install devtools if you don't have it
devtools::install_github("efernandezpascual/seedr") # Get seedr from GitHub
```

## Usage

```{r }
library(seedr)
# seedr relies on physiotime(), a wrapper function that formats your data and fits a hydro/thermal time model
physiotime(grasses, # germination dataset
           x = "psi", # experimental treatment
           method = "bradford", # hydrotime model
           groups = c("species")) # group dataset by species
```


```{r eval=FALSE}
# for more information read the seedr vignette
vignette("seedr")
```

## References

* Bewley, J. D., Bradford, K. J., Hilhorst, H. W., & Nonogaki, H. (2013). Environmental Control of Germination. In *Seeds: Physiology of Development, Germination and Dormancy, 3rd Edition* (pp. 302-317). Springer, New York, NY.
* Bradford, K. J. (1990). A water relations analysis of seed germination rates. *Plant Physiology*, 94(2), 840-849.
* Garcia-Huidobro, J., Monteith, J. L., & Squire, G. R. (1982). Time, temperature and germination of pearl millet (*Pennisetum typhoides* S. & H.) I. Constant temperature. *Journal of Experimental Botany*, 33(2), 288-296.
* Gummerson, R. J. (1986). The effect of constant temperatures and osmotic potentials on the germination of sugar beet. *Journal of Experimental Botany*, 37(6), 729-741.

        

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Owner metadata

• Name: Eduardo Fernández-Pascual
• Login: efernandezpascual
• Email:
• Kind: user
• Description: 🌱 Seeds 🌿 Plants 🌏 Biodiversity
• Website: https://efernandezpascual.github.io/home/
• Location: Asturies, Spain
• Twitter:
• Company: University of Oviedo
• Icon url: https://avatars.githubusercontent.com/u/61799380?u=0e2ccaf43eabec94e531c30892d7260c3a538ab6&v=4
• Repositories: 3
• Last ynced at: 2023-02-28T13:07:36.226Z
• Profile URL: https://github.com/efernandezpascual

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GitHub Events

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Committers metadata

Last synced: 7 days ago

Name	Email	Commits
efernandezpascual	6****l	25

Committer domains:

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Issue and Pull Request metadata

Last synced: 1 day ago

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/efernandezpascual/seedr

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Package metadata

• Total packages: 1
• Total downloads:
  • cran: 243 last-month
• Total dependent packages: 0
• Total dependent repositories: 0
• Total versions: 1
• Total maintainers: 1

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Dependencies

Score: 6.1903154058531475