View source: R/ppmlasso_functions.R
plotFit | R Documentation |
ppmlasso
modelThis function produces a levelplot of the predicted intensity from a fitted ppmlasso
model.
plotFit(fit, pred.data = data.frame(X = fit$x[fit$pres == 0], Y = fit$y[fit$pres == 0], 1, scale(fit$data[fit$pres == 0, -1], center = -fit$s.means/fit$s.sds, scale = 1/fit$s.sds)), coord = c("X", "Y"), asp = "iso", ylab = "", xlab = "", col.regions = heat.colors(1024)[900:1], cuts = length(col.regions), cex = 1.4, main.text = paste(toupper(fit$criterion), "fit"), cex.color = 1.4)
fit |
A fitted |
pred.data |
A data frame which defines the coordinates and the environmental variables for which the predicted intensity will be calculated. By default, this uses the coordinates and environmental variables from the object supplied to the |
coord |
A vector containing the names of the longitude and latitude coordinates,
as in |
asp |
Aspect of the plot, with "iso" as default. See the documentation for the |
ylab |
Label for the y-axis. Blank by default. |
xlab |
Label for the x-axis. Blank by default |
col.regions |
A vector of colours to define the intensity gradient. See the documentation for the |
cuts |
The number of levels the color gradient for the intensity surface is divided into. See the documentation for the |
cex |
Character size for axis labels. |
main.text |
Title of the plot. |
cex.color |
Character size for the colorkey labels. |
This function will compute the predicted intensity of a fitted ppmlasso
object using the model within the regularisation path which optimises the criterion specified in the call to ppmlasso
.
Ian W. Renner
data(BlueMountains) sub.env = BlueMountains$env[BlueMountains$env$Y > 6270 & BlueMountains$env$X > 300,] sub.euc = BlueMountains$eucalypt[BlueMountains$eucalypt$Y > 6270 & BlueMountains$eucalypt$X > 300,] ppm.form = ~poly(FC, TMP_MIN, TMP_MAX, RAIN_ANN, degree = 2) + poly(D_MAIN_RDS, D_URBAN, degree = 2) ppm.fit = ppmlasso(ppm.form, sp.xy = sub.euc, env.grid = sub.env, sp.scale = 1, n.fits = 20, writefile = FALSE) plotFit(ppm.fit)
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