physiodata {seedr}

Transforms dataset to physiodata format

Description

physiodata takes the user's dataset and transforms it to an object of class "physiodata". This object will be used by the model-fitting functions, and it can also be used to explore the data.

Usage

physiodata(d, t = "times", g = "germinated", pg = "germinable", x =
  "treatment", groups = NULL)

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).

Value

physiodata returns a S3 object of class "physiodata". The object is a list containing, for each group, treatment and scoring time: the cumulative germination count; the cumulative germination proportion; and the lower and upper bounds of the 95 calculated with the Wilson method as implemented in the package binom. The object can be used to explore the data using the generic functions summary, barplot and plot.

Examples

cent <- physiodata(centaury, x = "temperature")
cent
summary(cent) # average final germination proportions and germination rates per treatment
barplot(cent) # bar plots for the final germination proportions and germination rates
plot(cent) # cumulative germination curves
physiodata(grasses, x = "psi", groups = "species") # grouping dataset by species