R: Creates a series of diagnostic graphs for a P matrix.

diagnosticsPmatrix

R Documentation

Creates a series of diagnostic graphs for a P matrix.

Description

Displays the effects of increasing number of bins and continuous (size) stage range on a number of predictions from the P matrix to verify that sufficient resolution and continuous stage range are being used.

the growth object used to construct the IPMmatrix object.

survObj

the survival object used to construct the IPMmatrix object.

dff

the dataframe from which the survival and growth objects were constructed; if not supplied, defaults to NULL, which will simply result in the size distribution not being plotted.

integrateType

integration type, defaults to midpoint (which uses probability density function); other option is cumul (which uses the cumulative density function).

correction

correction type, defaults to none. The first option is constant which will multiply every column of the IPM by a constant sufficient to adjust values to those predicted for survival at that size. The second option is discretizeExtremes which will place all transitions to sizes smaller than minSize into the smallest bin, and transitions to sizes larger than maxSize into the largest bin.

cov

a data-frame with one row containing all covariates; defaults to 1, and will be ignored if covariates do not exist in growth and survival objects

sizesToPlot

a vector containing desired sizes to plot growth resolution for (second panel); if not supplied, the function will use the quantiles

extendSizeRange

a vector containing desired size range for the matrix to be compared with a larger size range; if this vector has length 0 the defaults will be 0.5xminSize (unless minSize<0 in which case, 2*minSize is used) and 1.5*maxSize

Details

This function provides a series of plots indicative of whether bin choice and size range is adequate. On the first plot, the left panel shows the range of the data as a histogram (if a data-frame is provided) and the range of the state variable fitted in the current Pmatrix; as well as the range of the state variable in two Pmatrices used for comparison, one with the same number of bins but an extended size range (red), and one with the same size range but an increased number of bins (blue) (increased by about 50 percent). If the range in the data and the range in the Pmatrix are mis-matched, the limits of the data used in building the Pmatrix can be adjusted with the minSize and maxSize arguments in makeIPMPmatrix.

The discretization of a continuous function can result in under- or over-estimation of the true density. Where this occurs, the sum of the columns of the discretized Pmatrix will not match predictions from the fitted survival model. The middle panel plots these against each other for the three matrices in the first panel (current, extended range and increased bin number) using the same colours as in the first panel. Lines should fall along the (0,1) line shown in grey; if they do not, the argument correction="constant" may be of use. This ensures that the columns sum to the fitted survival by multiplying every column in the Integral Projection Model by the value that allows this. The third panel checks whether extending the size range included in the matrix and increasing the number of bins (by increasing nBigMatrix and thereby having narrower bins) does not alter basic predictions from the IPM.

The six panels on the next plot show the discretized IPM (histograms) for the current IPM (top) and one with an increased number of bins (bottom) and the theoretical density function (red line) . These are plotted either for three chosen sizes (sizesToPlot) or the 0.25, 0.5 and 0.75 quantiles of either the observed data or the range of meshpoints; this size is printed in the top right hand of every plot. If the theoretical density function curve is very distant from the histograms, increasing the nBigMatrix argument may correct this discrepancy.

Note that it is important that the comparison be "fair" - i.e., whatever the correction argument used in your current IPM, the same argument must be used in diagnosticsPmatrix.

Note also that if survival is constant across size, the patterns apparent in the life expectancy plot will reflect numerical slippage (since all sizes will have exactly the same life expectancy) and disagreement between the different lines should be ignored.

Finally, note that if the correction used is discretizeExtremes then the column sums of the Pmatrix and survival will not match towards the extremes.

Author(s)

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

References

Easterling, Ellner & Dixon. 2000. Size-specific sensitivity: a new structured population model. Ecology 81, p694-708.

Ellner & Rees. 2006. Integral projection models for species with complex demography. The American Naturalist 167, p410-428.

For effects of mesh size on IPM output: Zuidema, Jongejans, Chien, During & Schieving. Integral projection models for trees: a new parameterization method and a validation of model output. Journal of Ecology 98, p345-355.

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(IPMpack)
Loading required package: Matrix
Loading required package: MASS
Loading required package: nlme
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/IPMpack/diagnosticsPmatrix.Rd_%03d_medium.png", width=480, height=480)
> ### Name: diagnosticsPmatrix
> ### Title: Creates a series of diagnostic graphs for a P matrix.
> ### Aliases: diagnosticsPmatrix
>
> ### ** Examples
>
> # Example where mesh size does not have a major effect on model output:
> dff <- generateData()
> Pmatrix <- makeIPMPmatrix(minSize = min(dff$size, na.rm = TRUE),
+ maxSize = max(dff$size, na.rm = TRUE), growObj = makeGrowthObj(dff),
+ survObj = makeSurvObj(dff))
> diagnosticsPmatrix(Pmatrix, growObj = makeGrowthObj(dff),
+ survObj = makeSurvObj(dff), dff = dff)
[1] "Range of Pmatrix is "
[1] 1.078405e-30 7.236176e-02
[1] "Please hit any key for the next plot"
1:
> # Compare with the following example where mesh size has an important
> # effect on output:
> Pmatrix <- makeIPMPmatrix(nBigMatrix = 8,
+ minSize = min(dff$size, na.rm = TRUE),
+ maxSize = 0.5*max(dff$size, na.rm = TRUE),
+ growObj = makeGrowthObj(dff),
+ survObj = makeSurvObj(dff))
> diagnosticsPmatrix(Pmatrix, growObj = makeGrowthObj(dff),
+ survObj = makeSurvObj(dff), dff = dff)
[1] "Range of Pmatrix is "
[1] 2.161623e-08 1.787109e-01
[1] "Please hit any key for the next plot"
1:
> #with cumul
> Pmatrix <- makeIPMPmatrix(nBigMatrix = 10,
+ minSize = min(dff$size, na.rm = TRUE),
+ maxSize = max(dff$size, na.rm = TRUE), growObj = makeGrowthObj(dff),
+ survObj = makeSurvObj(dff),
+ integrateType = "cumul")
> diagnosticsPmatrix(Pmatrix, growObj = makeGrowthObj(dff),
+ survObj = makeSurvObj(dff), dff = dff, integrateType = "cumul")
[1] "Range of Pmatrix is "
[1] 0.0000000 0.3024477
[1] "Please hit any key for the next plot"
1:
>
> #with log increment
> Pmatrix <- makeIPMPmatrix(nBigMatrix = 50,
+ minSize = min(dff$size, na.rm = TRUE),
+ maxSize = max(dff$size, na.rm = TRUE),
+ growObj = makeGrowthObj(dff,Formula = logincr~size),
+ survObj = makeSurvObj(dff))
[1] "building incr as sizeNext - size"
[1] "building logincr as log(sizeNext - size) - pre-build if this is not appropriate"
Warning message:
In log(dataf$sizeNext - dataf$size) : NaNs produced
> diagnosticsPmatrix(Pmatrix,
+ growObj = makeGrowthObj(dff,Formula = logincr~size),
+ survObj = makeSurvObj(dff), dff = dff)
[1] "Range of Pmatrix is "
[1] 0.0000000 0.2812306
[1] "building incr as sizeNext - size"
[1] "building logincr as log(sizeNext - size) - pre-build if this is not appropriate"
[1] "Please hit any key for the next plot"
1:
Warning message:
In log(dataf$sizeNext - dataf$size) : NaNs produced
> #example with correction="discretizeExtremes"
> Pmatrix <- makeIPMPmatrix(minSize = min(dff$size, na.rm = TRUE),
+ maxSize = max(dff$size, na.rm = TRUE), growObj = makeGrowthObj(dff),
+ survObj = makeSurvObj(dff), correction="discretizeExtremes")
> diagnosticsPmatrix(Pmatrix, growObj = makeGrowthObj(dff),
+ survObj = makeSurvObj(dff), dff = dff, correction="discretizeExtremes")
[1] "Range of Pmatrix is "
[1] 1.078405e-30 7.236176e-02
[1] "Please hit any key for the next plot"
1:
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>
>
>
> dev.off()
null device
1
>