physiotime {seedr}

Fits physiological time seed germination models

Description

physiotime fits physiological time models (thermal time, hydrotime) to seed germination data. It is a wrapper function that transforms data to class "physiodata" and allows to specify the physiological time model to be fitted (i.e. Bradford's hydrotime model or Garcia-Huidobro's thermal time model).

Usage

physiotime(d, t = "times", g = "germinated", pg = "germinable", x =
  "treatment", groups = NULL, method = "bradford", min.ptos = 3, tops =
  c("Max R2","Max value"), fractions = (1:9)/10)

Arguments

d

a data.frame containing the results of a germination experiment. The data frame should include columns with scoring times, germination counts (not cumulative), number of potentially germinable seeds, and the environmental variable of interest. (e.g. temperature or water potential) (see grasses example dataset for appropriate structure).

t

the name of a column in d containing a vector of numeric scoring times.

g

the name of a column in d containing a vector of integer germination counts (non cumulative).

pg

the name of a column in d containing a vector of integer numbers of potentially germinable seeds.

x

the name of a column in d containing a vector of numeric values for the environmental variable of interest (e.g. temperature, water potential).

groups

optional, the names of columns in d containing grouping variables for the experiment that have to be analysed separately (e.g. different species or populations, different temperatures in a water potential experiment, different treatments to break seed dormancy).

method

the method to be used to fit the models, can be "bradford" to fit a hydrotime model or "huidobro" to fit a thermal time model.

min.ptos

minimal number of data points (i.e. different temperature treatments) needed to fit the suboptimal and supraoptimal germination models if fitting a thermal time model. 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 if fitting a thermal time model. "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 if fitting a thermal time model. The default is the 9 deciles (i.e. t10, t20.. t90) as used by Garcia-Huidobro.

Value

physiotime returns a S3 object of class "physiotime". The object is a list containing, for each group (seedlot, species, etc.) the results of fitting the physiological time models. The generic functions summary and plot are used to obtain and visualize the model results.

Examples

m <- physiotime(centaury, x = "temperature",
                method = "huidobro", groups = c("species", "population"))
m
summary(m)
plot(m)