tests/testthat/test-summary.rpt.R

In rptR: Repeatability Estimation for Gaussian and Non-Gaussian Data

context("summary.rpt")

# Set a seed for reproducibility of the randomization 
suppressWarnings(RNGversion("3.5.0"))
set.seed(23)

# load data
data(BeetlesBody)
data(BeetlesMale)
data(BeetlesFemale)

# prepare proportion data
BeetlesMale$Dark <- BeetlesMale$Colour
BeetlesMale$Reddish <- (BeetlesMale$Colour-1)*-1
md <- aggregate(cbind(Dark, Reddish) ~ Population + Container, data=BeetlesMale, FUN=sum)


# summary without bootstraps or permutations
rpt_gaussian <- rpt(BodyL ~ (1|Population), grname="Population", data=BeetlesBody, 
        nboot=0, npermut=0, datatype = "Gaussian")
rpt_poisson <- rpt(Egg ~ Treatment + (1|Container), grname=c("Container"), data = BeetlesFemale,
        nboot=0, npermut=0, datatype = "Poisson")
rpt_binary <- rpt(Colour ~ (1|Population), grname=c("Population"), 
        data=BeetlesMale, nboot=0, npermut=0, datatype = "Binary")
rpt_proportion <- rpt(cbind(Dark, Reddish) ~ (1|Population), grname=c("Population"), data=md,
                nboot=0, npermut=0, datatype = "Proportion")



test_that("summary works for all distributions without perm or boot and defaults", {
        expect_error(test <- summary(rpt_gaussian), NA)
        expect_error(test <- summary(rpt_poisson), NA)
        expect_error(test <- summary(rpt_binary), NA)
        expect_error(test <- summary(rpt_proportion), NA)
})

# summary with bootstraps or permutations
rpt_gaussian <- rpt(BodyL ~ (1|Population), grname="Population", data=BeetlesBody, 
        nboot=2, npermut=2, datatype = "Gaussian")
rpt_poisson <- rpt(Egg ~ Treatment + (1|Container), grname=c("Container"), data = BeetlesFemale,
        nboot=2, npermut=2, datatype = "Poisson")
rpt_binary <- rpt(Colour ~ (1|Population), grname=c("Population"), 
        data=BeetlesMale, nboot=2, npermut=2, datatype = "Binary")
rpt_proportion <- rpt(cbind(Dark, Reddish) ~ (1|Population), grname=c("Population"), data=md,
        nboot=2, npermut=2, datatype = "Proportion")

test_that("summary works for all distributions with boot and permut", {
        expect_error(test <- summary(rpt_gaussian), NA)
        expect_error(test <- summary(rpt_poisson), NA)
        expect_error(test <- summary(rpt_binary), NA)
        expect_error(test <- summary(rpt_proportion), NA)
})


# summary with Residual, Overdispersion and Fixed
rpt_gaussian <- rpt(BodyL ~ (1|Population), grname=c("Population", "Residual", "Overdispersion", "Fixed"), data=BeetlesBody, 
        nboot=0, npermut=0, datatype = "Gaussian")
rpt_poisson <- rpt(Egg ~ Treatment + (1|Container), grname=c("Container", "Residual", "Overdispersion", "Fixed"), data = BeetlesFemale,
        nboot=0, npermut=0, datatype = "Poisson")
rpt_binary <- rpt(Colour ~ (1|Population), grname=c("Population", "Residual", "Fixed"), # no overdisp in binary
        data=BeetlesMale, nboot=0, npermut=0, datatype = "Binary")
rpt_proportion <- rpt(cbind(Dark, Reddish) ~ (1|Population), grname=c("Population", "Residual", "Overdispersion", "Fixed"), data=md,
        nboot=0, npermut=0, datatype = "Proportion")


test_that("wrapper function rpt works for all distributions with perm and boot and defaults", {
        expect_error(test <- summary(rpt_gaussian), NA)
        expect_error(test <- summary(rpt_poisson), NA)
        expect_error(test <- summary(rpt_binary), NA)
        expect_error(test <- summary(rpt_proportion), NA)
})