site.match: Match test sites with reference sites

In p-schaefer/BenthicAnalysis: Benthic Analysis with Test Site Anlysis

Match test sites with reference sites

Description

Methods for matching test sites with nearest neighbour reference sites based on ecological similarity. The Assessment by Nearest-Neighbour Analysis (ANNA) and Redundancy Analysis ANNA (RDA-ANNA) are implimented as in (http://www.bioone.org/doi/abs/10.1086/678702). Ecological distance are calculated as Euchlidean distance across significant ordination axis. Axis are standardized and weighted according the proportion of variance explained. Significance of axis is determined by the broken-stick method for ANNA and a permutation test for RDA-ANNA.

Usage

site.match(Test, Reference, k = NULL, adaptive = T, ad.factor = 2,
  ad.constant = 1, RDA.reference = NULL)

Arguments

Test	Vector of environmental variables at Test site
Reference	Data frame of environmental Variables at Reference sites
k	Numeric, the numer of nearest neighbour reference sites to find. Ignored if NULL
adaptive	Logical, whether to use adaptive breaks to select nearest neighbour reference sites.
ad.factor	Power factor used in the inverse-power function if adaptive==T
ad.constant	Constant factor used in the inverse-power function if adaptive==T
RDA.reference	Data frame containing indicator metric data at reference sites. Row names must match with Reference. If it is supplied the function will perform RDA-ANNA, otherwise ANNA.

Details

An option for adaptive selection of k of based on dynamic 1-dimensional k-means clustering implimented in Ckmeans.1d.dp is available, otherwise k must be supplied.

Value

$final.dist - Vector containing nearest neighbour reference sites to test site as well as the ecological distance of the test site to each reference site.

$method - Whether ANNA or RDA-ANNA was used

$k - The number of reference sites requested or "Adaptive"

$all.dist - The ecological distance of all reference sites to the test site

$ref.scores - Ordination axis scores of reference sites

$test.scores - Ordination axis scores of test site

Examples

#load datasets
data(YKEnvData,envir = environment()) #Biological dataset
data(YKBioData,envir = environment()) #Environmental dataset

#Calculate indicator metrics from raw biological data
bio.data.test<-benth.met(YKBioData,2,2)

#Extract just the summary metrics
bio.data<-bio.data.test$Summary.Metrics

#standardize row names between datasets
rownames(YKEnvData)<-bio.data.test$Site.List

#Match a test site (#201) to the nearest neighbour reference set
nn.sites<-site.match(YKEnvData[201,-c(1)],YKEnvData[1:118,-c(1)],k=NULL,adaptive=T)

#Evaluate nearest neighbour selections
plot(nn.sites)
sitematch.plot(nn.sites)

p-schaefer/BenthicAnalysis documentation built on May 3, 2023, 5:49 a.m.