efernandezpascual / seedr

seedr: Hydro and Thermal Time Seed Germination Models in R

README.md

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

# 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

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

## A list of physiological time germination models 
##  calculated for the following 2 groups: 
##  
## species: Anisantha rubens 
## Bradford's hydrotime model 
##  Water potential levels in experiment: -1.6 -1 -0.8 -0.6 -0.4 -0.2 0 
##  Theta - Hydrotime constant: 50.54 
##  Psib50 - Base water potential (median): -1.59 
##  Sigma of the base water potential: 0.4 
##  R2: 0.94 
##  
## species: Bromus hordeaceus 
## Bradford's hydrotime model 
##  Water potential levels in experiment: -1.6 -1 -0.8 -0.6 -0.4 -0.2 0 
##  Theta - Hydrotime constant: 59.81 
##  Psib50 - Base water potential (median): -1.75 
##  Sigma of the base water potential: 0.38 
##  R2: 0.86 
## 

# 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.