tests/testthat/test_formatInputs.R
In rbchan/unmarked: Models for Data from Unmarked Animals
context("input formatting functions")
test_that("formatDistData function works",{
dat <- data.frame(distance=1:100, site=gl(5, 20),
visit=factor(rep(1:4, each=5)))
cutpt <- seq(0, 100, by=25)
y <- formatDistData(dat, "distance", "site", cutpt)
expect_equivalent(y, matrix(c(20, 0, 0, 0,
5, 15, 0, 0,
0, 10, 10, 0,
0, 0, 15, 5,
0, 0, 0, 20), 5, 4, byrow=TRUE))
dat.bad <- dat
dat.bad$distance <- as.character(dat$distance)
expect_error(formatDistData(dat.bad, "distance", "site", cutpt))
dat.bad <- dat
dat.bad$site <- as.character(dat$site)
y2 <- expect_warning(formatDistData(dat.bad, "distance", "site", cutpt))
expect_equivalent(y2, matrix(c(20, 0, 0, 0,
5, 15, 0, 0,
0, 10, 10, 0,
0, 0, 15, 5,
0, 0, 0, 20), 5, 4, byrow=TRUE))
y3 <- formatDistData(dat, "distance", "site", cutpt, "visit")
expect_equivalent(y3, matrix(c(
5, 0, 0, 0, 5, 0, 0, 0, 5, 0, 0, 0, 5, 0, 0, 0,
5, 0, 0, 0, 0, 5, 0, 0, 0, 5, 0, 0, 0, 5, 0, 0,
0, 5, 0, 0, 0, 5, 0, 0, 0, 0, 5, 0, 0, 0, 5, 0,
0, 0, 5, 0, 0, 0, 5, 0, 0, 0, 5, 0, 0, 0, 0, 5,
0, 0, 0, 5, 0, 0, 0, 5, 0, 0, 0, 5, 0, 0, 0, 5), 5, 16, byrow=TRUE))
effortMatrix <- matrix(ncol=4, nrow=5,c(1,0))
y4 <- formatDistData(dat, "distance","site",cutpt, "visit",effortMatrix)
expect_equivalent(y4, matrix(c(
5, 0, 0, 0, NA,NA,NA,NA, 5, 0, 0, 0, NA,NA,NA,NA,
NA,NA,NA,NA, 0, 5, 0, 0, NA,NA,NA,NA, 0, 5, 0, 0,
0, 5, 0, 0, NA,NA,NA,NA, 0, 0, 5, 0, NA,NA,NA,NA,
NA,NA,NA,NA, 0, 0, 5, 0, NA,NA,NA,NA, 0, 0, 0, 5,
0, 0, 0, 5, NA,NA,NA,NA, 0, 0, 0, 5, NA,NA,NA,NA), 5, 16, byrow=TRUE))
effortMatrix <- matrix(ncol=4, nrow=5,"a")
expect_error(formatDistData(dat, "distance","site",cutpt, "visit",effortMatrix))
})
test_that("formatLong works correctly",{
df <- read.csv(system.file("csv","frog2001pcru.csv", package = "unmarked"),
stringsAsFactors=TRUE)
umf <- formatLong(df, type = "unmarkedFrameOccu")
## Add some assertions...
# Try simple with dates
test <- expand.grid(site = LETTERS[1:2], date = as.Date(c("2017-04-06", "2017-04-11")))
test <- test[with(test, order(site, date)), ]
set.seed(1231)
test <- within(test, {
# ocov = round(rnorm(nrow(test)), 2)
y = rbinom(nrow(test), 1, 0.6)
})
withdate <- formatLong(test, type = "unmarkedFrameOccu")
expect_equal(withdate,
new("unmarkedFrameOccu", y = structure(c(1L, 0L, 1L, 1L), .Dim = c(2L, 2L)),
obsCovs = structure(list(JulianDate = structure(c(17262, 17267, 17262, 17267),
class = "Date")),
class = "data.frame",
row.names = c(NA, -4L)),
siteCovs = NULL,
mapInfo = NULL,
obsToY = structure(c(1, 0, 0, 1), .Dim = c(2L, 2L))))
test <- expand.grid(site = LETTERS[1:4], julian = c(13, 20, 26))
test <- test[with(test, order(site, julian)), ]
set.seed(42)
test <- within(test, {
obsfac = factor(sample(LETTERS[1:2], nrow(test), replace = TRUE))
sitefac = factor(round(as.numeric(site)/5))
ocov = round(rnorm(nrow(test)), 2)
scov = 2 * as.numeric(test$site)
y = rbinom(nrow(test), 1, 0.6)
})
withfac <- formatLong(test, type = "unmarkedFrameOccu")
expect_equal(withfac,
new("unmarkedFrameOccu",
y = structure(c(1L, 0L, 1L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 1L, 0L), .Dim = 4:3),
obsCovs = structure(list(ocov = c(1.51, -0.09, 2.02, -0.06, 1.3, 2.29, -1.39, -0.28,
-0.13, 0.64, -0.28, -2.66),
obsfac = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 2L,
2L, 1L, 2L, 1L, 2L),
.Label = c("A", "B"), class = "factor"),
JulianDate = c(13, 20, 26, 13, 20, 26, 13, 20, 26, 13, 20, 26)),
class = "data.frame", row.names = c(NA, -12L)),
siteCovs = structure(list(scov = c(2, 4, 6, 8),
sitefac = structure(c(1L, 1L, 2L, 2L),
.Label = c("0", "1"), class = "factor")),
class = "data.frame", row.names = c(NA, -4L)),
mapInfo = NULL,
obsToY = structure(c(1, 0, 0, 0, 1, 0, 0, 0, 1), .Dim = c(3L, 3L))))
# Compare manual and automatic unmarkedPCount frames
# Manual creation from help
R <- 4 # number of sites
J <- 3 # number of visits
y <- matrix(c(1,2,0,0,0,0,1,1,1,2,2,1), nrow=R, ncol=J, byrow=TRUE)
site.covs <- data.frame(x1=1:4, x2=factor(c('A','B','A','B')))
obs.covs <- list(
x3 = matrix(c(
-1,0,1,
-2,0,0,
-3,1,0,
0,0,0), nrow=R, ncol=J, byrow=TRUE),
x4 = matrix(factor(c(
'a','b','c',
'd','b','a',
'a','a','c',
'a','b','a')), nrow=R, ncol=J, byrow=TRUE))
expect_warning(umf <- unmarkedFramePCount(y=y, siteCovs=site.covs,
obsCovs=obs.covs)) # organize data
# Corresponding long data.frame
pcdf <- data.frame(site = rep(seq(R), each = J),
occasion = rep(1:J, R),
y = as.vector(t(y)),
x1 = rep(1:4, each = J),
x2 = factor(rep(c('A','B', 'A', 'B'), each = J)),
x3 = as.vector(t(obs.covs$x3)),
x4 = as.vector(t(obs.covs$x4)))
expect_warning(umf1 <- formatLong(pcdf, type = "unmarkedFramePCount"))
# formatLong tacks on JulianDate to obsCovs, so ignore this difference
expect_equal(umf@y, umf1@y)
expect_equal(umf@siteCovs, umf1@siteCovs)
expect_equal(umf@obsCovs, umf1@obsCovs[, c("x3", "x4")])
expect_equal(umf@obsToY, umf1@obsToY)
# Compare manual and automatic open point count frame
y1 <- matrix(c(
0, 2, 3, 2, 0,
2, 2, 3, 1, 1,
1, 1, 0, 0, 3,
0, 0, 0, 0, 0), nrow=4, ncol=5, byrow=TRUE)
# Site-specific covariates
sc1 <- data.frame(x1 = 1:4, x2 = factor(c('A','A','B','B')))
# Observation-specific covariates
oc1 <- list(
x3 = matrix(1:5, nrow=4, ncol=5, byrow=TRUE),
x4 = matrix(letters[1:5], nrow=4, ncol=5, byrow=TRUE))
# Primary periods of surveys
primaryPeriod1 <- matrix(as.integer(c(
1, 2, 5, 7, 8,
1, 2, 3, 4, 5,
1, 2, 4, 5, 6,
1, 3, 5, 6, 7)), nrow=4, ncol=5, byrow=TRUE)
# Create the unmarkedFrame
expect_warning(umf1 <- unmarkedFramePCO(y=y1, siteCovs=sc1, obsCovs=oc1, numPrimary=5,
primaryPeriod=primaryPeriod1))
test <- data.frame(site = rep(1:4, each = 5),
obsnum = 1:5,
y = as.vector(t(y1)),
x1 = rep(1:4, each = 5),
x2 = factor(rep(c('A','A','B','B'), each = 5)),
x3 = 1:5,
x4 = letters[1:5])
expect_warning(umf2 <- formatLong(test, type = "unmarkedFramePCO", numPrimary = 5,
primaryPeriod = primaryPeriod1))
# formatLong tacks on JulianDate to obsCovs, so ignore this difference
expect_equal(umf1@y, umf2@y)
expect_equal(umf1@siteCovs, umf2@siteCovs)
expect_equal(umf1@obsCovs, umf2@obsCovs[, c("x3", "x4")])
expect_equal(umf1@obsToY, umf2@obsToY)
expect_equal(umf1@primaryPeriod, umf2@primaryPeriod)
# Compare manual and automatic unmarkedFrameDS object
# Manual creation from help
R <- 4 # number of sites
J <- 3 # number of distance classes
db <- c(0, 10, 20, 30) # distance break points
y <- matrix(c(
5,4,3, # 5 detections in 0-10 distance class at this transect
0,0,0,
2,1,1,
1,1,0), nrow=R, ncol=J, byrow=TRUE)
site.covs <- data.frame(x1=1:4, x2=factor(c('A','B','A','B')))
umf <- unmarkedFrameDS(y=y, siteCovs=site.covs, dist.breaks=db, survey="point",
unitsIn="m") # organize data
# Corresponding long data.frame
dsdf <- data.frame(site = rep(seq(R), each = J),
occasion = rep(1:J, R),
y = as.vector(t(y)),
x1 = rep(1:4, each = J),
x2 = factor(rep(c('A','B', 'A', 'B'), each = J)))
umf1 <- formatLong(dsdf, type = "unmarkedFrameDS", dist.breaks = db,
survey = "point", unitsIn = "m")
expect_equal(umf, umf1)
})
test_that("formatMult works correctly",{
test <- expand.grid(site = LETTERS[1:4], visit = 1:3, year = 2015:2016)
test <- test[with(test, order(site, year, visit)), ]
test <- test[, c("year", "site", "visit")]
set.seed(18939)
test <- within(test, {
ocov = round(rnorm(nrow(test)), 2)
scov = 2 * as.numeric(test$site)
yscov = 1.3 * as.numeric(interaction(test$site, test$year))
obsfac = factor(sample(LETTERS[1:2], nrow(test), replace = TRUE))
sitefac = factor(round(as.numeric(site)/5))
ysfac = factor(round(as.numeric(interaction(site, year))/10))
y = rpois(nrow(test), lambda = 2)
})
withfac <- formatMult(test)
expect_equal(withfac,
new("unmarkedMultFrame",
numPrimary = 2L,
yearlySiteCovs = structure(list(ysfac = structure(c(1L, 1L, 1L, 2L, 1L, 2L, 1L, 2L),
.Label = c("0", "1"), class = "factor"),
yscov = c(1.3, 6.5, 2.6, 7.8, 3.9, 9.1, 5.2, 10.4)),
class = "data.frame", row.names = c(NA, -8L)),
y = structure(c(0L, 1L, 3L, 3L, 2L, 2L, 2L, 1L, 1L, 0L, 3L, 3L, 1L, 1L, 0L, 0L, 3L, 1L, 2L,
2L, 2L, 1L, 3L, 3L), .Dim = c(4L, 6L)),
obsCovs = structure(list(visit = c(1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1,
2, 3, 1, 2, 3),
obsfac = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L,
2L, 1L, 2L, 1L, 1L, 2L, 1L,
2L, 2L, 2L, 1L, 2L, 1L, 2L), .Label = c("A", "B"), class = "factor"),
ocov = c(0.28, -1.41, -0.31, 0.05, -0.53, 0.84, -0.95, 1.63, 0.87,
1.03, 1.41, 1.25, -0.32, 0.11, -0.45, -0.83, 0.17, 0.28,
-0.13, -1.86, -1.82, 0.11, 1.29, -0.31)),
class = "data.frame", row.names = c(NA, -24L)),
siteCovs = structure(list(sitefac = structure(c(1L, 1L, 2L, 2L),
.Label = c("0", "1"), class = "factor"),
scov = c(2, 4, 6, 8)), class = "data.frame",
row.names = c(NA, -4L)),
mapInfo = NULL,
obsToY = structure(c(1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0,
0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0,
0, 0, 0, 0, 1), .Dim = c(6L, 6L))))
})
test_that("csvToUMF function works",{
expect_warning(umf <- csvToUMF(system.file("csv","csv_factor_test.csv",
package = "unmarked"), type="unmarkedFrameOccu"))
expect_warning(umf <- csvToUMF(system.file("csv","csv_factor_test.csv",
package = "unmarked"), type="unmarkedFrameOccu"))
expect_equal(sapply(siteCovs(umf), class), c(elev="numeric", forest="factor"))
expect_equal(sapply(obsCovs(umf), class), c(wind="numeric", rain="factor"))
df <- as(umf, "data.frame")
expect_equivalent(dim(df), c(20,11))
})
rbchan/unmarked documentation built on April 3, 2024, 10:11 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
context("input formatting functions")
test_that("formatDistData function works",{
dat <- data.frame(distance=1:100, site=gl(5, 20),
visit=factor(rep(1:4, each=5)))
cutpt <- seq(0, 100, by=25)
y <- formatDistData(dat, "distance", "site", cutpt)
expect_equivalent(y, matrix(c(20, 0, 0, 0,
5, 15, 0, 0,
0, 10, 10, 0,
0, 0, 15, 5,
0, 0, 0, 20), 5, 4, byrow=TRUE))
dat.bad <- dat
dat.bad$distance <- as.character(dat$distance)
expect_error(formatDistData(dat.bad, "distance", "site", cutpt))
dat.bad <- dat
dat.bad$site <- as.character(dat$site)
y2 <- expect_warning(formatDistData(dat.bad, "distance", "site", cutpt))
expect_equivalent(y2, matrix(c(20, 0, 0, 0,
5, 15, 0, 0,
0, 10, 10, 0,
0, 0, 15, 5,
0, 0, 0, 20), 5, 4, byrow=TRUE))
y3 <- formatDistData(dat, "distance", "site", cutpt, "visit")
expect_equivalent(y3, matrix(c(
5, 0, 0, 0, 5, 0, 0, 0, 5, 0, 0, 0, 5, 0, 0, 0,
5, 0, 0, 0, 0, 5, 0, 0, 0, 5, 0, 0, 0, 5, 0, 0,
0, 5, 0, 0, 0, 5, 0, 0, 0, 0, 5, 0, 0, 0, 5, 0,
0, 0, 5, 0, 0, 0, 5, 0, 0, 0, 5, 0, 0, 0, 0, 5,
0, 0, 0, 5, 0, 0, 0, 5, 0, 0, 0, 5, 0, 0, 0, 5), 5, 16, byrow=TRUE))
effortMatrix <- matrix(ncol=4, nrow=5,c(1,0))
y4 <- formatDistData(dat, "distance","site",cutpt, "visit",effortMatrix)
expect_equivalent(y4, matrix(c(
5, 0, 0, 0, NA,NA,NA,NA, 5, 0, 0, 0, NA,NA,NA,NA,
NA,NA,NA,NA, 0, 5, 0, 0, NA,NA,NA,NA, 0, 5, 0, 0,
0, 5, 0, 0, NA,NA,NA,NA, 0, 0, 5, 0, NA,NA,NA,NA,
NA,NA,NA,NA, 0, 0, 5, 0, NA,NA,NA,NA, 0, 0, 0, 5,
0, 0, 0, 5, NA,NA,NA,NA, 0, 0, 0, 5, NA,NA,NA,NA), 5, 16, byrow=TRUE))
effortMatrix <- matrix(ncol=4, nrow=5,"a")
expect_error(formatDistData(dat, "distance","site",cutpt, "visit",effortMatrix))
})
test_that("formatLong works correctly",{
df <- read.csv(system.file("csv","frog2001pcru.csv", package = "unmarked"),
stringsAsFactors=TRUE)
umf <- formatLong(df, type = "unmarkedFrameOccu")
## Add some assertions...
# Try simple with dates
test <- expand.grid(site = LETTERS[1:2], date = as.Date(c("2017-04-06", "2017-04-11")))
test <- test[with(test, order(site, date)), ]
set.seed(1231)
test <- within(test, {
# ocov = round(rnorm(nrow(test)), 2)
y = rbinom(nrow(test), 1, 0.6)
})
withdate <- formatLong(test, type = "unmarkedFrameOccu")
expect_equal(withdate,
new("unmarkedFrameOccu", y = structure(c(1L, 0L, 1L, 1L), .Dim = c(2L, 2L)),
obsCovs = structure(list(JulianDate = structure(c(17262, 17267, 17262, 17267),
class = "Date")),
class = "data.frame",
row.names = c(NA, -4L)),
siteCovs = NULL,
mapInfo = NULL,
obsToY = structure(c(1, 0, 0, 1), .Dim = c(2L, 2L))))
test <- expand.grid(site = LETTERS[1:4], julian = c(13, 20, 26))
test <- test[with(test, order(site, julian)), ]
set.seed(42)
test <- within(test, {
obsfac = factor(sample(LETTERS[1:2], nrow(test), replace = TRUE))
sitefac = factor(round(as.numeric(site)/5))
ocov = round(rnorm(nrow(test)), 2)
scov = 2 * as.numeric(test$site)
y = rbinom(nrow(test), 1, 0.6)
})
withfac <- formatLong(test, type = "unmarkedFrameOccu")
expect_equal(withfac,
new("unmarkedFrameOccu",
y = structure(c(1L, 0L, 1L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 1L, 0L), .Dim = 4:3),
obsCovs = structure(list(ocov = c(1.51, -0.09, 2.02, -0.06, 1.3, 2.29, -1.39, -0.28,
-0.13, 0.64, -0.28, -2.66),
obsfac = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 2L,
2L, 1L, 2L, 1L, 2L),
.Label = c("A", "B"), class = "factor"),
JulianDate = c(13, 20, 26, 13, 20, 26, 13, 20, 26, 13, 20, 26)),
class = "data.frame", row.names = c(NA, -12L)),
siteCovs = structure(list(scov = c(2, 4, 6, 8),
sitefac = structure(c(1L, 1L, 2L, 2L),
.Label = c("0", "1"), class = "factor")),
class = "data.frame", row.names = c(NA, -4L)),
mapInfo = NULL,
obsToY = structure(c(1, 0, 0, 0, 1, 0, 0, 0, 1), .Dim = c(3L, 3L))))
# Compare manual and automatic unmarkedPCount frames
# Manual creation from help
R <- 4 # number of sites
J <- 3 # number of visits
y <- matrix(c(1,2,0,0,0,0,1,1,1,2,2,1), nrow=R, ncol=J, byrow=TRUE)
site.covs <- data.frame(x1=1:4, x2=factor(c('A','B','A','B')))
obs.covs <- list(
x3 = matrix(c(
-1,0,1,
-2,0,0,
-3,1,0,
0,0,0), nrow=R, ncol=J, byrow=TRUE),
x4 = matrix(factor(c(
'a','b','c',
'd','b','a',
'a','a','c',
'a','b','a')), nrow=R, ncol=J, byrow=TRUE))
expect_warning(umf <- unmarkedFramePCount(y=y, siteCovs=site.covs,
obsCovs=obs.covs)) # organize data
# Corresponding long data.frame
pcdf <- data.frame(site = rep(seq(R), each = J),
occasion = rep(1:J, R),
y = as.vector(t(y)),
x1 = rep(1:4, each = J),
x2 = factor(rep(c('A','B', 'A', 'B'), each = J)),
x3 = as.vector(t(obs.covs$x3)),
x4 = as.vector(t(obs.covs$x4)))
expect_warning(umf1 <- formatLong(pcdf, type = "unmarkedFramePCount"))
# formatLong tacks on JulianDate to obsCovs, so ignore this difference
expect_equal(umf@y, umf1@y)
expect_equal(umf@siteCovs, umf1@siteCovs)
expect_equal(umf@obsCovs, umf1@obsCovs[, c("x3", "x4")])
expect_equal(umf@obsToY, umf1@obsToY)
# Compare manual and automatic open point count frame
y1 <- matrix(c(
0, 2, 3, 2, 0,
2, 2, 3, 1, 1,
1, 1, 0, 0, 3,
0, 0, 0, 0, 0), nrow=4, ncol=5, byrow=TRUE)
# Site-specific covariates
sc1 <- data.frame(x1 = 1:4, x2 = factor(c('A','A','B','B')))
# Observation-specific covariates
oc1 <- list(
x3 = matrix(1:5, nrow=4, ncol=5, byrow=TRUE),
x4 = matrix(letters[1:5], nrow=4, ncol=5, byrow=TRUE))
# Primary periods of surveys
primaryPeriod1 <- matrix(as.integer(c(
1, 2, 5, 7, 8,
1, 2, 3, 4, 5,
1, 2, 4, 5, 6,
1, 3, 5, 6, 7)), nrow=4, ncol=5, byrow=TRUE)
# Create the unmarkedFrame
expect_warning(umf1 <- unmarkedFramePCO(y=y1, siteCovs=sc1, obsCovs=oc1, numPrimary=5,
primaryPeriod=primaryPeriod1))
test <- data.frame(site = rep(1:4, each = 5),
obsnum = 1:5,
y = as.vector(t(y1)),
x1 = rep(1:4, each = 5),
x2 = factor(rep(c('A','A','B','B'), each = 5)),
x3 = 1:5,
x4 = letters[1:5])
expect_warning(umf2 <- formatLong(test, type = "unmarkedFramePCO", numPrimary = 5,
primaryPeriod = primaryPeriod1))
# formatLong tacks on JulianDate to obsCovs, so ignore this difference
expect_equal(umf1@y, umf2@y)
expect_equal(umf1@siteCovs, umf2@siteCovs)
expect_equal(umf1@obsCovs, umf2@obsCovs[, c("x3", "x4")])
expect_equal(umf1@obsToY, umf2@obsToY)
expect_equal(umf1@primaryPeriod, umf2@primaryPeriod)
# Compare manual and automatic unmarkedFrameDS object
# Manual creation from help
R <- 4 # number of sites
J <- 3 # number of distance classes
db <- c(0, 10, 20, 30) # distance break points
y <- matrix(c(
5,4,3, # 5 detections in 0-10 distance class at this transect
0,0,0,
2,1,1,
1,1,0), nrow=R, ncol=J, byrow=TRUE)
site.covs <- data.frame(x1=1:4, x2=factor(c('A','B','A','B')))
umf <- unmarkedFrameDS(y=y, siteCovs=site.covs, dist.breaks=db, survey="point",
unitsIn="m") # organize data
# Corresponding long data.frame
dsdf <- data.frame(site = rep(seq(R), each = J),
occasion = rep(1:J, R),
y = as.vector(t(y)),
x1 = rep(1:4, each = J),
x2 = factor(rep(c('A','B', 'A', 'B'), each = J)))
umf1 <- formatLong(dsdf, type = "unmarkedFrameDS", dist.breaks = db,
survey = "point", unitsIn = "m")
expect_equal(umf, umf1)
})
test_that("formatMult works correctly",{
test <- expand.grid(site = LETTERS[1:4], visit = 1:3, year = 2015:2016)
test <- test[with(test, order(site, year, visit)), ]
test <- test[, c("year", "site", "visit")]
set.seed(18939)
test <- within(test, {
ocov = round(rnorm(nrow(test)), 2)
scov = 2 * as.numeric(test$site)
yscov = 1.3 * as.numeric(interaction(test$site, test$year))
obsfac = factor(sample(LETTERS[1:2], nrow(test), replace = TRUE))
sitefac = factor(round(as.numeric(site)/5))
ysfac = factor(round(as.numeric(interaction(site, year))/10))
y = rpois(nrow(test), lambda = 2)
})
withfac <- formatMult(test)
expect_equal(withfac,
new("unmarkedMultFrame",
numPrimary = 2L,
yearlySiteCovs = structure(list(ysfac = structure(c(1L, 1L, 1L, 2L, 1L, 2L, 1L, 2L),
.Label = c("0", "1"), class = "factor"),
yscov = c(1.3, 6.5, 2.6, 7.8, 3.9, 9.1, 5.2, 10.4)),
class = "data.frame", row.names = c(NA, -8L)),
y = structure(c(0L, 1L, 3L, 3L, 2L, 2L, 2L, 1L, 1L, 0L, 3L, 3L, 1L, 1L, 0L, 0L, 3L, 1L, 2L,
2L, 2L, 1L, 3L, 3L), .Dim = c(4L, 6L)),
obsCovs = structure(list(visit = c(1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1,
2, 3, 1, 2, 3),
obsfac = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L,
2L, 1L, 2L, 1L, 1L, 2L, 1L,
2L, 2L, 2L, 1L, 2L, 1L, 2L), .Label = c("A", "B"), class = "factor"),
ocov = c(0.28, -1.41, -0.31, 0.05, -0.53, 0.84, -0.95, 1.63, 0.87,
1.03, 1.41, 1.25, -0.32, 0.11, -0.45, -0.83, 0.17, 0.28,
-0.13, -1.86, -1.82, 0.11, 1.29, -0.31)),
class = "data.frame", row.names = c(NA, -24L)),
siteCovs = structure(list(sitefac = structure(c(1L, 1L, 2L, 2L),
.Label = c("0", "1"), class = "factor"),
scov = c(2, 4, 6, 8)), class = "data.frame",
row.names = c(NA, -4L)),
mapInfo = NULL,
obsToY = structure(c(1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0,
0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0,
0, 0, 0, 0, 1), .Dim = c(6L, 6L))))
})
test_that("csvToUMF function works",{
expect_warning(umf <- csvToUMF(system.file("csv","csv_factor_test.csv",
package = "unmarked"), type="unmarkedFrameOccu"))
expect_warning(umf <- csvToUMF(system.file("csv","csv_factor_test.csv",
package = "unmarked"), type="unmarkedFrameOccu"))
expect_equal(sapply(siteCovs(umf), class), c(elev="numeric", forest="factor"))
expect_equal(sapply(obsCovs(umf), class), c(wind="numeric", rain="factor"))
df <- as(umf, "data.frame")
expect_equivalent(dim(df), c(20,11))
})
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.