Perform Deviance Partitioning of a Fitted GDM — gdm.partition.deviance • gdm

Partitions deviance explained from GDM into different user specified components - most typically environment versus space.

Usage

gdm.partition.deviance(sitePairTable, varSets=list(), partSpace=TRUE)

Arguments

sitePairTable: A correctly formatted site-pair table from formatsitepair.
varSets: A list in which each element is a vector of variable names across which deviance partitioning is to be performed, excluding geographic distance (which is set by the partSpace argument). Variable names must match those used to build the site-pair table. See example.
partSpace: Whether or not to perform the partitioning using geographic space. Default=TRUE.

Value

A dataframe summarizing deviance partitioning results.

Author

Matt Fitzpatrick and Karel Mokany

Examples

# set up site-pair table using the southwest data set
sppData <- southwest[, c(1,2,13,14)]
envTab <- southwest[, c(2:ncol(southwest))]
sitePairTab <- formatsitepair(sppData, 2, XColumn="Long", YColumn="Lat",
sppColumn="species", siteColumn="site", predData=envTab)
#> Warning: No abundance column was specified, so the biological data are assumed to be presences.
#> Aggregation function missing: defaulting to length

# EXAMPLE - Partition two groups of variables
# Make list of variable sets for partitioning
varSet <- vector("list", 2)

# now, name the variable groups for partitioning
# note you do not need to add "space" as this is only needed
# for environmental variables

# two groups (soils & climate)
names(varSet) <- c("soil", "climate")

# lastly, add variable names for
varSet$soil <- c("awcA", "phTotal", "sandA", "shcA", "solumDepth")
varSet$climate <- c("bio5", "bio6", "bio15", "bio18", "bio19")
varSet
#> $soil
#> [1] "awcA"       "phTotal"    "sandA"      "shcA"       "solumDepth"
#> 
#> $climate
#> [1] "bio5"  "bio6"  "bio15" "bio18" "bio19"
#> 

# run the function to partition soils, climate, and space (partSpace=TRUE)
scgPart <- gdm.partition.deviance(sitePairTab, varSet, partSpace=TRUE)

# EXAMPLE - Partition three groups of variables
# Make list of variable sets for partitioning
varSet <- vector("list", 3)
names(varSet) <- c("soil", "temp", "precip")
varSet$soil <- c("awcA", "phTotal", "sandA", "shcA", "solumDepth")
varSet$temp <- c("bio5", "bio6")
varSet$precip <- c("bio15", "bio18", "bio19")

# partition soils, temperature, and precip
# note we can't also partition space given the function's limit to a
# maximum of three variable sets, so we set partSpace=FALSE
scPart <- gdm.partition.deviance(sitePairTab, varSet, partSpace=FALSE)