cati (version 0.8)

ses.listofindex: Standardized effect size for a list of index.

Description

Standardized effect size and confidence interval for a list of index.

Usage

ses.listofindex(index.list = NULL, val.quant = c(0.025, 0.975))

Arguments

index.list

A list of index obtain using the function as.listofindex.

val.quant

Numeric vectors of length 2, giving the quantile to calcul confidence interval. By default val.quant=c(0.025,0.975) for a bilateral test with alpha = 5%.

Value

• A list which each component correspond to the result of the ses function for an index. Further, each component is a list of three components:
• $ses
  Observed value of standardized effect size.
• $ses.inf
  Lower limit of the confidence interval.
• $ses.sup
  Upper limit of the confidence interval.

See Also

as.listofindex; ses

Examples

data(finch.ind)
	res.finch<-Tstats(traits.finch, ind_plot=ind.plot.finch, sp=sp.finch, 
	nperm=9, print=FALSE)
	
	#Calcul of means by population (name_sp_site is a name of a population) 
	#like in the function com.index and determine the site 
	#for each population (sites_bypop)
	
	name_sp_sites=paste(sp.finch, ind.plot.finch,sep="_")
	traits.by.pop<-apply(traits.finch, 2 , function (x) 
	tapply(x, name_sp_sites, mean , na.rm=TRUE))
	
	require(e1071)
	
	sites_bypop<-lapply(strsplit(paste(rownames(traits.by.pop), sep="_")
	, split="_"), function(x) x[3])
	
	funct.withoutIV<-c("tapply(x, unlist(sites_bypop), 
	function(x) mean(x, na.rm=TRUE))",
	"tapply(x, unlist(sites_bypop), function(x) kurtosis(x, na.rm=TRUE))",
	"tapply(x, unlist(sites_bypop), function(x) 
	max(x, na.rm=TRUE) - min(x, na.rm=TRUE) )", 
	"tapply(x, unlist(sites_bypop), function(x) CVNND(x))"  )
	
	
	funct.withIV<-c("tapply(x, ind.plot.finch, 
	function(x) mean(x, na.rm=TRUE))",
	"tapply(x, ind.plot.finch, function(x) kurtosis(x, na.rm=TRUE))",
	"tapply(x, ind.plot.finch, function(x) 
	max(x, na.rm=TRUE) - min(x, na.rm=TRUE) )", 
	"tapply(x, ind.plot.finch, function(x) CVNND(x))"  )
	
	
	res.finch.withIV<-com.index(traits=traits.finch, index=funct.withIV,
	sp=sp.finch, nullmodels=c(2,2,2,2), ind.plot=ind.plot.finch, nperm=9
	, print=FALSE)
	
	res.finch.withoutIV<-com.index(traits=traits.finch, 
	index=funct.withoutIV, sp=sp.finch, nullmodels=c(3,3,3,3), 
	ind.plot=ind.plot.finch, nperm=9, print=FALSE)


	##Plot T-statistics and custom metrics thanks to 
	#the plot.listofindex function.
	
	list.ind<-list(res.finch.withIV, res.finch.withoutIV ,res.finch)
	index.list<-as.listofindex(list.ind, 
	namesindex=c("mean", "kurtosis", "range", "CVNND",
				 "mean.pop", "kurtosis.pop", "range.pop", "CVNND.pop",
                 "T_IP.IC", "T_IC.IR", "T_PC.PR"))
	
	class(index.list)
	
	par(mfrow=c(2,3))
	plot(index.list, plot.ask=FALSE)
	
	par(mfrow=c(2,2))
	plot(index.list, plot.ask=FALSE, bysite=FALSE)
	par(mfrow=c(1,1))
	
	ses.list<-ses.listofindex(index.list)
	
	#### An other way to see "ses values" 
	
	# Custom theme (from rasterVis package)
	require(rasterVis)
	
	my.theme <- BuRdTheme()
	# Customize the colorkey
	my.ckey <- list(col=my.theme$regions$col)
	
	levelplot(t(rbind(ses.list[[1]]$ses, ses.list[[2]]$ses, 
	ses.list[[3]]$ses,  ses.list[[4]]$ses)), colorkey=my.ckey, 
	par.settings=my.theme,border="black")
	
	levelplot(t(rbind(ses.list[[1]]$ses>ses.list[[1]]$ses.sup, 
	ses.list[[2]]$ses>ses.list[[2]]$ses.sup, 
	ses.list[[3]]$ses>ses.list[[3]]$ses.sup,
	ses.list[[4]]$ses>ses.list[[4]]$ses.sup)), 
	colorkey=my.ckey, par.settings=my.theme,border="black")
	

	#For all metrics of the list of index
	ses.list.levelplot<-c()
	for(i in 1: length(ses.list)){
		ses.list.levelplot<-rbind(ses.list.levelplot, ses.list[[i]]$ses)
	}
	
	levelplot(t(ses.list.levelplot), colorkey=my.ckey, 
	par.settings=my.theme,border="black")