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testfrescalo.r
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context("Test frescalo")
### Frescalo testing is currently skipped if not on a ###
### windows machine, or if libcurl is not supported. ###
# Create data
n <- 1500 #size of dataset
nyr <- 20 # number of years in data
nSamples <- 100 # set number of dates
nSites <- 50 # set number of sites
set.seed(125)
# Create somes dates
first <- as.Date(strptime("1980/01/01", "%Y/%m/%d"))
last <- as.Date(strptime(paste(1980+(nyr-1),"/12/31", sep=''), "%Y/%m/%d"))
dt <- last-first
rDates <- first + (runif(nSamples)*dt)
# taxa are set as random letters
taxa <- sample(letters, size = n, TRUE)
# three sites are visited randomly
site <- sample(paste('a', 11:(nSites + 10), sep=''), size = n, TRUE)
# the date of visit is selected at random from those created earlier
time_period <- sample(rDates, size = n, TRUE)
df1 <- data.frame(taxa = taxa,
site = site,
year = as.numeric(format(time_period, '%Y')),
startdate = time_period,
enddate = time_period + 500)
allsites <- sort(unique(site))
weights <- merge(allsites, allsites)
weights$W <- runif(n = nrow(weights), min = 0, max = 1)
frespath <- file.path(tempdir(), 'fres.exe')
toms_PC <- Sys.info()['nodename'] == "WLL-3RHYM53"
if(toms_PC) frespath <- 'C:/Frescalo_3a_windows.exe'
test_that("Test errors", {
skip_on_appveyor()
skip_on_travis()
if (!capabilities('libcurl')) skip('skipping as libcurl not supported')
if(grepl("mac", .Platform$pkgType)) skip('Frescalo exe does not run on Mac OS')
if (.Platform$OS.type == "windows" & !toms_PC) skip('Carbon black blocks Frescalo')
if(!toms_PC){
if(.Platform$OS.type == "windows"){
download.file(url = 'https://github.com/BiologicalRecordsCentre/frescalo/raw/master/Frescalo_3a_windows.exe',
destfile = frespath,
method = "libcurl",
mode = 'wb', quiet = TRUE)
} else if(.Platform$OS.type == "unix"){
download.file(url = 'https://github.com/BiologicalRecordsCentre/frescalo/raw/master/Frescalo_3a_linux.exe',
destfile = frespath,
method = "libcurl",
quiet = TRUE)
system(command = paste('chmod', '+x', normalizePath(frespath)))
} else{
stop(paste('frescalo is not supported on', .Platform$OS.type))
}
}
temp <- tempfile(pattern = 'dir')
dir.create(temp)
expect_error(frescalo(Data = df1,
frespath = frespath,
time_periods = data.frame(start=c(1980,1990),end=c(1989,1999)),
site_col = 'site',
sp_col = 'FOO',
year = 'year',
sinkdir = temp),
'FOO is not the name of a column in data')
expect_error(frescalo(Data = df1,
frespath = frespath,
time_periods = c(1980,1990,1989,1999),
site_col = 'site',
sp_col = 'taxa',
year = 'year',
sinkdir = temp),
'time_periods should be a data.frame')
expect_error(frescalo(Data = df1,
frespath = frespath,
time_periods = data.frame(start=c(1980,1850),end=c(1989,1999)),
site_col = 'site',
sp_col = 'taxa',
year = 'year',
sinkdir = temp),
'In time_periods year ranges should not overlap')
expect_error(frescalo(Data = df1,
frespath = frespath,
time_periods = data.frame(start=c(1980,1990),end=c(1989,1999)),
site_col = 'site',
sp_col = 'taxa',
year = 'year',
sinkdir = temp),
'the sites in your data do not match those in your weights file')
})
test_that("Runs without error", {
skip_on_appveyor()
skip_on_travis()
if (!capabilities('libcurl')) skip('skipping as libcurl not supported')
if(grepl("mac", .Platform$pkgType)) skip('Frescalo exe does not run on Mac OS')
if (.Platform$OS.type == "windows" & !toms_PC) skip('Carbon black blocks Frescalo')
# This first run is done using years
temp <- tempfile(pattern = 'dir')
dir.create(temp)
sink(file.path(temp, 'null'))
fres_try <- try(frescalo(Data = df1,
Fres_weights = weights,
frespath = frespath,
time_periods = data.frame(start=c(1980,1990),end=c(1989,1999)),
site_col = 'site',
sp_col = 'taxa',
year = 'year',
sinkdir = temp),
silent=TRUE
)
sink()
unlink(temp, recursive = TRUE)
expect_equal(class(fres_try), "frescalo")
expect_true("paths" %in% names(fres_try) &
"trend" %in% names(fres_try) &
"stat" %in% names(fres_try) &
"freq" %in% names(fres_try) &
"log" %in% names(fres_try) &
"lm_stats" %in% names(fres_try))
dir.create(temp)
sink(file.path(temp, 'null'))
fres_try <- try(frescalo(Data = df1,
Fres_weights = weights,
start_col = 'startdate',
end_col = 'enddate',
frespath = frespath,
time_periods = data.frame(start=c(1980,1990),end=c(1989,1999)),
site_col = 'site',
sp_col = 'taxa',
year = 'year',
sinkdir = temp),
silent=TRUE
)
sink()
unlink(temp, recursive = TRUE)
expect_equal(class(fres_try), "frescalo")
expect_true("paths" %in% names(fres_try) &
"trend" %in% names(fres_try) &
"stat" %in% names(fres_try) &
"freq" %in% names(fres_try) &
"log" %in% names(fres_try) &
"lm_stats" %in% names(fres_try))
# test a very low value of phi
temp <- tempfile(pattern = 'dir')
dir.create(temp)
sink(file.path(temp, 'null'))
fres_try <- try(suppressWarnings(frescalo(Data = df1,
phi = 0.51,
Fres_weights = weights,
frespath = frespath,
time_periods = data.frame(start=c(1980,1990),end=c(1989,1999)),
site_col = 'site',
sp_col = 'taxa',
year = 'year',
sinkdir = temp)),
silent=TRUE)
sink()
unlink(temp, recursive = TRUE)
expect_equal(class(fres_try), "frescalo")
expect_true("paths" %in% names(fres_try) &
"trend" %in% names(fres_try) &
"stat" %in% names(fres_try) &
"freq" %in% names(fres_try) &
"log" %in% names(fres_try) &
"lm_stats" %in% names(fres_try))
})
# Create data
n <- 1500 #size of dataset
nyr <- 20 # number of years in data
nSamples <- 100 # set number of dates
nSites <- 50 # set number of sites
set.seed(125)
# Create somes dates
first <- as.Date(strptime("1980/01/01", "%Y/%m/%d"))
last <- as.Date(strptime(paste(1980+(nyr-1),"/12/31", sep=''), "%Y/%m/%d"))
dt <- last-first
rDates <- first + (runif(nSamples)*dt)
# taxa are set as random letters
taxa <- sample(letters, size = n, TRUE)
# three sites are visited randomly
site <- sample(paste('SK', 11:(nSites + 10), sep=''), size = n, TRUE)
# the date of visit is selected at random from those created earlier
time_period <- sample(rDates, size = n, TRUE)
df1 <- data.frame(taxa = taxa,
site = site,
year = as.numeric(format(time_period, '%Y')),
startdate = time_period,
enddate = time_period + 500)
allsites <- sort(unique(site))
weights <- merge(allsites, allsites)
weights$W <- runif(n = nrow(weights), min = 0, max = 1)
test_that("Test plotting", {
skip_on_travis()
skip_on_appveyor()
if (!capabilities('libcurl')) skip('skipping as libcurl not supported')
if(grepl("mac", .Platform$pkgType)) skip('Frescalo exe does not run on Mac OS')
if (.Platform$OS.type == "windows" & !toms_PC) skip('Carbon black blocks Frescalo')
# test plotting
temp <- tempfile(pattern = 'dir')
dir.create(temp)
sink(file.path(temp, 'null'))
fres_try <- try(frescalo(Data = df1,
Fres_weights = weights,
frespath = frespath,
time_periods = data.frame(start=c(1980,1990),end=c(1989,1999)),
site_col = 'site',
sp_col = 'taxa',
year = 'year',
plot_fres = TRUE,
sinkdir = temp),
silent=TRUE
)
sink()
unlink(temp, recursive = TRUE)
expect_equal(class(fres_try), "frescalo")
expect_true("paths" %in% names(fres_try) &
"trend" %in% names(fres_try) &
"stat" %in% names(fres_try) &
"freq" %in% names(fres_try) &
"log" %in% names(fres_try) &
"lm_stats" %in% names(fres_try))
})
# Create data
n <- 15000 #size of dataset
nyr <- 20 # number of years in data
nSamples <- 100 # set number of dates
nSites <- 50 # set number of sites
set.seed(125)
# Create somes dates
first <- as.Date(strptime("1980/01/01", "%Y/%m/%d"))
last <- as.Date(strptime(paste(1980+(nyr-1),"/12/31", sep=''), "%Y/%m/%d"))
dt <- last-first
rDates <- first + (runif(nSamples)*dt)
# taxa are set as random letters
taxa <- sample(letters, size = n, TRUE)
# three sites are visited randomly
site <- sample(paste('A', 1:nSites, sep=''), size = n, TRUE)
# the date of visit is selected at random from those created earlier
time_period <- sample(rDates, size = n, TRUE)
df1 <- data.frame(taxa = taxa,
site = site,
year = as.numeric(format(time_period, '%Y')),
startdate = time_period,
enddate = time_period + 500)
allsites <- sort(unique(site))
weights <- merge(allsites, allsites)
weights$W <- runif(n = nrow(weights), min = 0, max = 1)
test_that("Runs high value of phi", {
skip_on_appveyor()
skip_on_travis()
if (!capabilities('libcurl')) skip('skipping as libcurl not supported')
if(grepl("mac", .Platform$pkgType)) skip('Frescalo exe does not run on Mac OS')
if (.Platform$OS.type == "windows" & !toms_PC) skip('Carbon black blocks Frescalo')
# test a very low value of phi
temp <- tempfile(pattern = 'dir')
dir.create(temp)
sink(file.path(temp, 'null'))
fres_try <- try(suppressWarnings(frescalo(Data = df1,
Fres_weights = weights,
phi = NULL,
frespath = frespath,
time_periods = data.frame(start=c(1980,1990),end=c(1989,1999)),
site_col = 'site',
sp_col = 'taxa',
year = 'year',
sinkdir = temp)),
silent=TRUE)
sink()
unlink(temp, recursive = TRUE)
expect_equal(class(fres_try), "frescalo")
expect_true("paths" %in% names(fres_try) &
"trend" %in% names(fres_try) &
"stat" %in% names(fres_try) &
"freq" %in% names(fres_try) &
"log" %in% names(fres_try) &
"lm_stats" %in% names(fres_try))
})