Nothing
## ----, warning=FALSE, message=FALSE--------------------------------------
library(EcoSimR) # load EcoSimR library
set.seed(56) # for reproducible results
## ----, echo=FALSE, results='asis'----------------------------------------
knitr::kable(dataWiFinches[,1:6], caption='Occurrence matrix of West Indies finches. Data from Gotelli & Abele (1982)')
## ----, echo=FALSE, results='asis'----------------------------------------
Algorithm <- (paste("sim",1:10,sep=""))
E <- "Equiprobable"
P <- "Proportional"
f <- "Fixed"
RowSums <- c(E,f,E,f,P,E,P,P,f,"External Weights")
ColSums <- c(E,E,f,P,f,P,E,P,f, "External Weights")
Notes <- rep("not recommended",9)
Notes[2] <- "recommended"
Notes[9] <- "recommended (DEFAULT)"
Notes[10] <- "recommended"
AlgoTable <- as.data.frame(cbind(Algorithm,
RowSums, ColSums, Notes))
knitr::kable(AlgoTable, caption='Randomization algorithms for co-occurrence (Gotelli 2000).')
## ----, echo=FALSE,fig.height=4,fig.width=4,fig.align='center'------------
myModel <- cooc_null_model(dataWiFinches,suppressProg=TRUE)
plot(myModel,type="hist")
## ----, echo=FALSE,message=FALSE,warning=FALSE,fig.height=4,fig.width=6,fig.align='center'----
myModel <- cooc_null_model(dataWiFinches,suppressProg=TRUE)
plot(myModel,type="cooc")
## ----, echo=FALSE,message=FALSE,warning=FALSE,fig.height=4,fig.width=4,fig.align='center'----
plot(myModel,type='burn_in')
## ----, eval=FALSE--------------------------------------------------------
#
# speciesData # user must supply a data frame; speciesData=dataWiFinches for default run
# algo = "sim9" # randomize occurrences but preserve observed row and columns sums
# metric = "c_score" # Stone and Roberts (1990) C-score
# nReps = 1000 # number of null assemblage created
# rowNames=TRUE # reads speciesData as a data frame wtih row labels in the first column
# saveSeed=FALSE # if TRUE, saves random number seed
# burn_in=500 # number of burn-in iterations for sim9
# algoOpts=list() # list of other specific options for the algorithm (used for sim10)
# metricOpts=list() # list of other specific options for the metric
# suppressProg= FALSE # suppress printing of progress bar (for creating markdown files)
## ----,fig.height=4,fig.width=4,fig.align='center'------------------------
# run default settings and show all output
myModel <- cooc_null_model(speciesData=dataWiFinches,suppressProg=TRUE)
summary(myModel)
plot(myModel,type = "hist")
## ----,fig.height=4,fig.width=6,fig.align='center'------------------------
plot(myModel,type = "cooc")
## ----,fig.height=4,fig.width=4,fig.align='center'------------------------
plot(myModel,type = "burn_in")
# create a model with sim10 and user-supplied species and site weights
myModel <- cooc_null_model(speciesData=dataWiFinches,algo="sim10",
suppressProg=TRUE,algoOpts=list(rowWeights
=(1:17),colWeights=(1:19)))
summary(myModel)
plot(myModel,type="hist")
## ----,fig.height=4,fig.width=6,fig.align='center'------------------------
plot(myModel,type="cooc")
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