Description Usage Arguments Value References See Also Examples

View source: R/GDM_Table_Funcs.R

plot is used to plot the I-splines and fit of a generalized dissimilarity model created using the `gdm`

function.

1 2 3 4 |

`x` |
A gdm model object returned from |

`plot.layout` |
This argument specifies the row and column layout for the plots, including: (1) a single page plot of observed response data against the raw linear predictor (ecological distance) from the model, and (2) a single page plot of the observed response against the predicted response from the model, i.e. after applying the link function, 1.0 - exp(-y), to the linear predictor, and (3) the I-splines fitted to the individual predictors. Default is 2 rows by 2 columns. To produce one predictor plot per page set plot.layout to c(1,1). The first two model plots are always produced on a single page each and therefore the layout parameter affects only the layout of the I-spline plots for those predictors that featured in the model fitting process (i.e., predictors with all-zero I-spline coefficients are not plotted). |

`plot.color` |
Color of the data points that are plotted for the overall plots. |

`plot.linewidth` |
The line width for the regression line over-plotted in the two overall plots to optimize the display of the line over the data points. |

`include.rug` |
Whether or not to include a rug plot of the predictor values used to fit the gdm in the I-spline plots. When set to TRUE, a site-pair table must be supplied for the rug.sitepair argument. Default is FALSE. |

`rug.sitepair` |
A site-pair table used to add a rug plot of the predictor values used to fit the gdm in the I-spline plots. This should be the same site-pair table used to fit the gdm model being plotted. The function does not check whether the supplied site-pair table matches that used in model fitting. |

`...` |
Ignored. |

plot returns NULL. Use `summary.gdm`

to obtain a synopsis of the model object.

Ferrier S, Manion G, Elith J, Richardson, K (2007) Using generalized dissimilarity modelling to analyse and predict patterns of beta diversity in regional biodiversity assessment. *Diversity & Distributions* 13, 252-264.

1 2 3 4 5 6 7 8 9 10 11 12 | ```
##sets up site-pair table
load(system.file("./data/gdm.RData", package="gdm"))
sppData <- gdmExpData[c(1,2,13,14)]
envTab <- gdmExpData[c(2:ncol(gdmExpData))]
sitePairTab <- formatsitepair(sppData, 2, XColumn="Long", YColumn="Lat", sppColumn="species",
siteColumn="site", predData=envTab)
##create GDM
gdmMod <- gdm(sitePairTab, geo=TRUE)
##plot GDM
plot(gdmMod, plot.layout=c(3,3))
``` |

gdm documentation built on Sept. 16, 2017, 1:02 a.m.

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