addPdfGrowthPic: Adds probability density functions of density function of...

In wpetry/IPMpack2: Builds and analyses Integral Projection Models (IPMs).

Adds probability density functions of density function of size or increment given current size and growth to plots.

Description

Function generates pdfs (probability density functions) corresponding to chosen sizes and adds them to a figure using growth methods.

Usage

addPdfGrowthPic(respType = "sizeNext", sizesPlotAt = c(20, 50, 60),
                            sizeRange = c(20, 400), incrRange = c(-10, 50), 
                            scalar = 100, growthObjList,
                            cols = 1:5,
                            cov = data.frame(covariate=1),
                            minShow = 1e-2,
                            jitt = 2,  
                            ...)
		

Arguments

respType	character string identifying the response variable for the growthModelComp. wither "sizeNext", "logincr" or "incr". Defaults to sizeNext.
sizesPlotAt	vector, list of sizes at which pdfs should be plotted.
sizeRange	sizeRange for which pdf should be estimated
incrRange	increment range for which pdf should be estimated
scalar	value by which pdf may be multiplied to improve visibility
growthObjList	list of growth objects for which pdfs are desired to be plotted
cols	colours corresponding to the list of growth objects for plotting
cov	a data-frame with one row containing all covariates other than size related covariates; defaults to 1; will be ignored if no covariates are fitted
minShow	minimum value below which pdf lines will not be shown (to avoid ugly vertical lines)
jitt	amount by which sequential pdfs should be separated on the x axis, for visibility
...	extra arguments to pass to the plot function.

Value

none

Author(s)

C. Jessica E. Metcalf, Sean M. McMahon, Roberto Salguero-Gomez, Eelke Jongejans & Cory Merow.

See Also

makeGrowthObj,makeSurvObj,plotGrowthModelComp, plotSurvModelComp

Examples

# Data with size and sizeNext
dff <- generateData()

a1 <- growthModelComp(dff, makePlot = TRUE)
addPdfGrowthPic(respType = "sizeNext", 
	sizesPlotAt = c(2, 6, 10), scalar = 1, jitt = 0.1, 
		sizeRange = c(-5, 25), 
			growthObjList = a1$growthObjects, cols = 2:5)

wpetry/IPMpack2 documentation built on Sept. 29, 2022, 9:41 a.m.