context("utilities")
test_that("utilities loads and returns correct result", {
# Ensure that trivial tests work correctly
expect_that(length("a"), equals(1))
library(codyn)
# Load our example data set
data(knz_001d)
expect_that(names(knz_001d)[4], equals("abundance"))
#take a subset
dat1 <- subset(knz_001d, knz_001d$subplot=="A_1")
# Does transpose_community correctly transform a long dataframe into a matrix?
com_wide_df <- transpose_community(df = dat1, "year", "species", "abundance")
expect_true(is.data.frame(com_wide_df))
df2 = subset(knz_001d, subplot == "A_1")
names(df2)=c("spp", "yr", "subplot", "abund")
com_wide_df <- transpose_community(df = df2, "yr", "spp", "abund")
expect_true(is.data.frame(com_wide_df))
# rownames should be timevar
expect_true(all(as.numeric(rownames(com_wide_df)) %in% dat1[["year"]]))
# colnames should be species
expect_true(all(colnames(com_wide_df) %in% dat1[["species"]]))
})
test_that("Name checking works", {
data(knz_001d)
#knz_001d <- read.csv(system.file("extdata", "knz_001d.csv", package="codyn"),
# sep=",", header=TRUE)
expect_error(check_names(given = c("AAA", "year", "subplot", "abundance"),
data = knz_001d),
"data does not have .*name.*")
expect_error(check_names(given = c("species", "BBB", "subplot", "abundance"),
data = knz_001d),
"data does not have .*name.*")
expect_error(check_names(given = c("species", "year", "CCC", "abundance"),
data = knz_001d),
"data does not have .*name.*")
expect_error(check_names(given = c("species", "year", "subplot", "DDD"),
data = knz_001d),
"data does not have .*name.*")
})
test_that("Single-record checks for species work", {
data(knz_001d)
expect_null(check_single(knz_001d, time.var = "year", species.var = "species", replicate.var = "subplot"))
knz_001d2<-knz_001d
names(knz_001d2)=c("spp", "yr", "subp", "abund")
expect_null(check_single(knz_001d2, time.var = "yr", species.var = "spp", replicate.var = "subp"))
dftog = rbind(knz_001d, knz_001d[nrow(knz_001d),])
expect_error(check_single(dftog, time.var = "year", species.var = "species", replicate.var = "subplot"))
dftog2 = rbind(knz_001d2, knz_001d2[nrow(knz_001d2),])
expect_error(check_single(dftog2, time.var = "yr", species.var = "spp", replicate.var = "subp"))
dfa = subset(knz_001d, subplot == "A_1")
expect_null(check_single_onerep(dfa, time.var = "year", species.var = "species"))
dfab = subset(knz_001d, subplot == "A_1" | subplot == "A_2")
expect_error(check_single_onerep(dfab, time.var = "year", species.var = "species"))
df2 = subset(knz_001d, subplot == "A_1")
names(df2)=c("spp", "yr", "subplot", "abund")
expect_null(check_single_onerep(df2, time.var = "yr", species.var = "spp"))
#check check_sppvar
comdf <- as.data.frame(matrix(1, 5, 5))
expect_error(check_sppvar(comdf))
comdf2 <-as.data.frame(matrix(c(1, 2, 3, 4, 5), 5, 5))
check_sppvar(comdf2)
})
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