https://github.com/efernandezpascual/seedr

seedr: Hydro and Thermal Time Seed Germination Models in R
https://github.com/efernandezpascual/seedr

agronomy botany ecology germination seeds

Last synced: 3 months ago
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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 (over 4 years ago)
• Default Branch: master
• Last Pushed: 2021-05-16T11:19:41.000Z (over 3 years ago)
• Last Synced: 2024-04-14T07:11:08.359Z (7 months ago)
• Topics: agronomy, botany, ecology, germination, seeds
• Language: R
• Homepage:
• Size: 30.1 MB
• Stars: 2
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.Rmd
  • License: LICENSE

Awesome Lists containing this project

• open-sustainable-technology - seedr - An R package that provides functions to fit hydro and thermal time germination models. (Consumption / Agriculture and Nutrition)

README

        
---

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.