AlleleShift (version 1.1-3)

shift.waffle.ggplot: Shifts of Allele Frequencies as Response to Climate Change

Description

The function shows changes in allele frequencies between the baseline and future/past climate.

Usage

shift.waffle.ggplot(future.waffle,
	manual.colour.values = c("black", "grey", "firebrick3", "chartreuse4"),
	manual.colour.codes = c("A baseline ", "B", "A decreasing", "A increasing"))
waffle.baker(freq.in, sort.index = "Pop.index",
	mean.change = FALSE, change.FUN = stats::median)

Value

The function generates a ggplot that depicts changes between baseline and future/past allele frequencies of the populations.

Arguments

future.waffle

Result from AlleleShift::waffle.baker.

manual.colour.values

Colours to be used in the plot.

manual.colour.codes

Sequence for the manual colour values.

freq.in

Result from AlleleShift::predFreq.

sort.index

Sequence of the populations in the plot.

mean.change

Aggregate changes among alleles.

change.FUN

Function used the aggregate changes.

Author

Roeland Kindt (World Agroforestry, CIFOR-ICRAF)

Details

Althought a package ggwaffle exists, I opted to bake my own waffles (possibly the Belgian in me.). As a separate row is created for each square/rectangle of the waffle, the resulting data is quite large. Hence trying to animate this is probably a bad idea (unless you want to make some real waffles while your computer is busy).

Examples

# The data can be obtained via the count.model and freq.model calibrations.
# These procedures are not repeated here.
data(Poptri.freq.baseline)
data(Poptri.freq.future)

Poptri.future.waffle <- waffle.baker(Poptri.freq.future,
                           sort.index="Latitude.index")

ggwaffle1 <- shift.waffle.ggplot(Poptri.future.waffle)
ggwaffle1