Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.width=5,
fig.height=4
)
## -----------------------------------------------------------------------------
library(dominanceanalysis)
data("tropicbird")
## -----------------------------------------------------------------------------
str(tropicbird)
## ----test training,eval=FALSE-------------------------------------------------
# library(caTools)
# set.seed(101)
# sample <- caTools::sample.split(tropicbird$ID, SplitRatio = .70)
# train <- subset(tropicbird, sample == TRUE)
# test <- subset(tropicbird, sample == FALSE)
## ----echo=FALSE---------------------------------------------------------------
train<-readRDS(system.file("extdata", "da-lr-train.rds", package = "dominanceanalysis"))
test<-readRDS(system.file("extdata", "da-lr-train.rds", package = "dominanceanalysis"))
## -----------------------------------------------------------------------------
modpres <- glm(pres~rem+land+alt+slo+rain+coast, data=train, family=binomial(link='logit'))
## -----------------------------------------------------------------------------
summary(modpres)
## -----------------------------------------------------------------------------
anova(modpres, test="Chisq")
## -----------------------------------------------------------------------------
library(pscl)
pR2(modpres)
## -----------------------------------------------------------------------------
da.glm.fit()("names")
## -----------------------------------------------------------------------------
dapres<-dominanceAnalysis(modpres)
## -----------------------------------------------------------------------------
getFits(dapres,"r2.m")
## -----------------------------------------------------------------------------
dominanceMatrix(dapres, type="complete",fit.functions = "r2.m", ordered=TRUE)
## -----------------------------------------------------------------------------
contributionByLevel(dapres,fit.functions="r2.m")
## -----------------------------------------------------------------------------
plot(dapres, which.graph ="conditional",fit.function = "r2.m")
## -----------------------------------------------------------------------------
dominanceMatrix(dapres, type="conditional",fit.functions = "r2.m", ordered=TRUE)
## -----------------------------------------------------------------------------
averageContribution(dapres,fit.functions = "r2.m")
## -----------------------------------------------------------------------------
plot(dapres, which.graph ="general",fit.function = "r2.m")
## -----------------------------------------------------------------------------
dominanceMatrix(dapres, type="general",fit.functions = "r2.m", ordered=TRUE)
## ----eval=FALSE---------------------------------------------------------------
# bootmodpres100 <- bootDominanceAnalysis(modpres, R=100)
# summary(bootmodpres100,fit.functions="r2.m")
## ---- echo=FALSE--------------------------------------------------------------
readRDS(system.file("extdata", "bootmodpres100.rds", package = "dominanceanalysis"))
## ----eval=FALSE---------------------------------------------------------------
# bootavemodpres100<-bootAverageDominanceAnalysis(modpres,R=100)
# summary(bootavemodpres100,fit.functions=c("r2.m"))
## ---- echo=FALSE--------------------------------------------------------------
readRDS(system.file("extdata", "bootavemodpres100.rds", package = "dominanceanalysis"))
## ----echo=FALSE,eval=FALSE----------------------------------------------------
# # This code save the sample selection
# library(caTools)
# set.seed(101)
# sample <- caTools::sample.split(tropicbird$ID, SplitRatio = .70)
# train <- subset(tropicbird, sample == TRUE)
# test <- subset(tropicbird, sample == FALSE)
#
# saveRDS(train, "da-lr-train.rds")
# saveRDS(test, "da-lr-test.rds")
# bootmodpres100 <- bootDominanceAnalysis(modpres, R=100)
# bootavemodpres100<-bootAverageDominanceAnalysis(modpres,R=100)
#
# # This code allows to save the bootstrap analyses
# saveRDS(summary(bootmodpres100, fit.functions="r2.m"), "bootmodpres100.rds")
# saveRDS(summary(bootavemodpres100, fit.functions="r2.m"), "bootavemodpres100.rds")
#
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