huidobro: Fits Garcia-Huidobro's thermal time model

In seedr: Hydro and Thermal Time Seed Germination Models in R

Description

huidobro fits a thermal time seed germination model using the method of Garcia-Huidobro (Garcia-Huidobro et al. 1982, Gummerson 1986, Bewley et al. 2013). This function can be used only with one-group dataset, i.e. one seed lot of one species. To fit models to grouped datasets (multi-seedlots, multi-species) use the function physiotime instead.

Usage

huidobro(d, min.ptos = 3, tops = c("Max R2","Max value"), fractions =
  (1:9)/10)

Arguments

d	a data.table within a "physiodata" object, containing the cumulative germination proportion at each scoring time and temperature treatment.
min.ptos	minimal number of data points (i.e. different temperature treatments) needed to fit the suboptimal and supraoptimal germination models. If the number of points available in the dataset is less than min.ptos, then the suboptimal or the supraoptimal models are not fitted.
tops	method used to divide the dataset in suboptimal and supraoptimal sections. "Max value" splits the data by the temperature that produces the highest seed germination rate. "Max R2" splits the data by the temperature that maximises the R2 of the suboptimal and supraoptimal linear regressions.
fractions	percentiles into which the seed population is split to fit the thermal time model. The default is the 9 deciles (i.e. t10, t20.. t90) as used by Garcia-Huidobro.

Value

huidobro returns a S3 object of class "huidobro" with the results of fitting the thermal time model. The generic functions summary and plot are used to obtain and visualize the model results.

References

Bewley, J. D., Bradford, K. J., Hilhorst, H. W., & Nonogaki, H. (2013). Thermal Time Models. In Seeds: Physiology of Development, Germination and Dormancy, 3rd Edition (pp. 312-317). 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.

Examples

# format dataset with physiodata
malva <- physiodata(subset(centaury, population == "La Malva"), x = "temperature")
# huidobro() uses the $proportions element within the physiodata object
h <- huidobro(malva$proportions)
h # prints the main thermal time variables
summary(h) # returns the main thermal time variables as a data.table
plot(h) # plots the fitted model

Example output

Garcia-Huidobro's thermal time model 
 Suboptimal temperature levels in experiment: 8.7 10.1 11.5 12.9 14.3 15.8 17.2 18.6 
 Supraoptimal temperature levels in experiment: 20 25 
 Tb - Base temperature: 5.2 
 To - Optimal temperature: 18.6 
 Tc - Ceiling temperature: 54.3 
 theta50 1 - Suboptimal thermal time (median): 33.52 
 Sigma of the suboptimal thermal time: 111.42 
 R2 of the suboptimal model: 0.39 
 theta50 2 - Supraoptimal thermal time (median): 449.8 
 Sigma of the supraoptimal thermal time: 460.87 
 R2 of the supraoptimal model: 0.23 
 
     method n.treatments.sub n.treatments.sup       Tb       To       Tc
1: huidobro                8                2 5.179545 18.60158 54.26304
   theta50.sub sigma.sub    R2.sub theta50.sup sigma.sup    R2.sup
1:    33.51573  111.4167 0.3923164    449.7998   460.867 0.2342135

seedr documentation built on Nov. 8, 2020, 4:29 p.m.