Nothing
tests/testthat/test-06-report_mig_interannual.R
In stacomiR: Fish Migration Monitoring
context("report_mig_interannual")
test_that("Test an instance of report_mig_interannual loaded with choice_c",
{
skip_on_cran()
env_set_test_stacomi()
stacomi(database_expected = TRUE, sch ="test")
r_mig_interannual <- new("report_mig_interannual")
# the following will load data for size,
# parameters 1786 (total size) C001 (size at video control)
# dc 5 and 6 are fishways located on the Arzal dam
# two stages are selected
suppressWarnings(r_mig_interannual <- choice_c(
r_mig_interannual,
dc = 6,
taxa = c("Anguilla anguilla"),
stage = c("AGJ"),
start_year = 2010,
end_year = 2013,
silent = TRUE
))
r_mig_interannual <- connect(r_mig_interannual, silent = TRUE)
# three warning produced, none shown due to silent=TRUE
options(warn = 0)
expect_s4_class(r_mig_interannual, "report_mig_interannual")
rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
})
#test_that("Test bug when writing data with Alice and Sebastien",
# {
# skip_on_cran()
# # env_set_test_stacomi()
# options(
# stacomiR.dbname = "bd_contmig_nat",
# stacomiR.host ="********************",
# stacomiR.port = "5432",
# stacomiR.user = "********************",
# stacomiR.password = "****************"
# )
# stacomi(database_expected = TRUE, sch ="seinormigr")
# r_mig_interannual <- new("report_mig_interannual")
# # the following will load data for size,
# # parameters 1786 (total size) C001 (size at video control)
# # dc 5 and 6 are fishways located on the Arzal dam
# # two stages are selected
# suppressWarnings(r_mig_interannual <- choice_c(
# r_mig_interannual,
# dc = 102,
# taxa = c("Anguilla anguilla"),
# stage = c("4"),
# start_year = 2014,
# end_year = 2023,
# silent = TRUE
# ))
# r_mig_interannual <- connect(r_mig_interannual, silent = TRUE)
# # three warning produced, none shown due to silent=TRUE
# options(warn = 0)
# expect_s4_class(r_mig_interannual, "report_mig_interannual")
# rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
#
# })
test_that("Test method summary in report_mig_interannual", {
skip_on_cran()
env_set_test_stacomi()
stacomi(database_expected = TRUE, sch ="test")
# overriding user schema to point to test
r_mig_interannual <- new("report_mig_interannual")
# the following will load data for size,
# parameters 1786 (total size) C001 (size at video control)
# dc 5 and 6 are fishways located on the Arzal dam
# two stages are selected
r_mig_interannual <- choice_c(
r_mig_interannual,
dc = 6,
taxa = c("Anguilla anguilla"),
stage = c("AGJ"),
start_year = 2010,
end_year = 2012,
silent = TRUE
)
r_mig_interannual <- connect(r_mig_interannual, silent = TRUE)
invisible(capture.output(ss <- summary(object = r_mig_interannual, year_choice=2012, silent = TRUE)))
# this one is failing in covr but not in test. I don't understand why
if ("year" %in% colnames(ss$`6`)) expect_equal(ss$`6`[1, "year"],"2012") else
expect_equal(ss$`6`[1, "année"],"2012")
# two warning produced
rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
})
#
#test_that("Test example report_mig_interannual-example",
# {
# # check if built with examples (Rtools install --example)
# # the file is generate it examples but later loaded to examples from the class using @example
# # be sure you have built Roxygen documentation before running
# example_path <-
# file.path(.libPaths(),
# "stacomiR",
# "R-ex",
# "report_mig_interannual-class.R")
# test <- file.access(example_path, 0)
# if (test[1] != 0)
# warnings("Package example dir not created ?")
# else
# suppressWarnings(source(example_path))
# rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
# })
test_that("Test that loading two taxa will fail",
{
skip_on_cran()
stacomi(database_expected = TRUE, sch ="test")
env_set_test_stacomi()
r_mig_interannual <- new("report_mig_interannual")
# the following will load data for size,
# parameters 1786 (total size) C001 (size at video control)
# dc 5 and 6 are fishways located on the Arzal dam
# two stages are selected
invisible(capture.output(expect_error(
choice_c(
r_mig_interannual,
dc = 5,
taxa = c("Anguilla anguilla", "Petromyzon marinus"),
stage = c("AGJ"),
start_year = "2010",
end_year = 2015,
silent = TRUE
)
)))
rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
})
test_that("Test that report_mig_interannual displays message when silent = FALSE",
{
skip_on_cran()
stacomi(database_expected = TRUE, sch ="test")
env_set_test_stacomi()
r_mig_interannual <- new("report_mig_interannual")
expect_output(
r_mig_interannual <- choice_c(
r_mig_interannual,
dc = 6,
taxa = c("Anguilla anguilla"),
stage = c("AGJ"),
start_year = 2011,
end_year = 2012,
silent = FALSE
))
rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
})
test_that("Test supprime method",
{
skip_on_cran()
stacomi(database_expected = TRUE, sch ="test")
env_set_test_stacomi()
bmi_cha <- new("report_mig_interannual") #châtelrault
bmi_cha <-
choice_c(
bmi_cha,
dc = c(19),
taxa = c("Salmo salar"),
stage = c("5"),
start_year = "2010",
end_year = "2012",
silent = TRUE
)
bmi_cha <- charge(bmi_cha, silent = TRUE)
# deleting all data to ensure everything is loaded
supprime(bmi_cha)
expect_output(bmi_cha <- connect(bmi_cha, silent = TRUE))
rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
})
test_that("Test that different sums are the same, for report_mig_interannual, report_mig_mult",
{
skip_on_cran()
stacomi(database_expected = TRUE, sch ="test")
# overriding user schema
env_set_test_stacomi()
# this chunk is not launched from examples but loads the r_mig dataset if connection works
r_mig_interannual <- new("report_mig_interannual")
r_mig_interannual <- choice_c(
r_mig_interannual,
dc = 6,
taxa = c("Anguilla anguilla"),
stage = c("AGJ"),
start_year = 2010,
end_year = 2010,
silent = TRUE
)
r_mig_interannual <- connect(r_mig_interannual, silent=TRUE)
nb_r_mig_interannual <- sum(r_mig_interannual@data[r_mig_interannual@data$"bjo_labelquantite"=="Effectif_total","bjo_valeur" ])
r_mig_mult <- new("report_mig_mult")
r_mig_mult <- choice_c(
r_mig_mult,
dc = 6,
taxa = c("Anguilla anguilla"),
stage = c("AGJ"),
datedebut = "2010-01-01",
datefin = "2010-12-31",
silent = TRUE
)
r_mig_mult <- charge(r_mig_mult, silent=TRUE)
r_mig_mult <- connect(r_mig_mult, silent=TRUE)
r_mig_mult <- calcule(r_mig_mult, silent=TRUE)
nb_r_mig_mult = sum(r_mig_mult@calcdata$dc_6$data$Effectif_total)
expect_equal(round(nb_r_mig_interannual),round(nb_r_mig_mult))
rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
})
test_that("Test bmi plots", {
skip_on_cran()
stacomi(database_expected = TRUE, sch ="test")
env_set_test_stacomi()
report_mig_interannual <- new("report_mig_interannual")
# the following will load data for size,
# parameters 1786 (total size) C001 (size at video control)
# dc 5 and 6 are fishways located on the Arzal dam
# two stages are selected
report_mig_interannual <- choice_c(
report_mig_interannual,
dc = 6,
taxa = c("Anguilla anguilla"),
stage = c("AGJ"),
start_year = 2010,
end_year = 2013,
silent = TRUE
)
# first test if there is nothing in data
expect_output(plot(report_mig_interannual, plot.type = "step", silent = FALSE))
report_mig_interannual <- connect(report_mig_interannual, silent = TRUE)
report_mig_interannual <- calcule(report_mig_interannual, silent = TRUE)
# test plots
expect_error(suppressWarnings(plot(report_mig_interannual, plot.type = "step", silent = TRUE)),NA)
expect_error(suppressWarnings(plot(report_mig_interannual, plot.type = "line", silent = TRUE)),NA)
expect_error(suppressWarnings(plot(report_mig_interannual, plot.type = "standard", silent = TRUE)),NA)
expect_error(plot(report_mig_interannual, plot.type = "barchart", silent = TRUE),NA)
expect_error(plot(report_mig_interannual, plot.type = "barchart", timesplit="2 weeks", silent = TRUE),NA)
expect_error(plot(report_mig_interannual, plot.type = "barchart", timesplit="week", silent = TRUE),NA)
expect_error(plot(report_mig_interannual, plot.type = "barchart", timesplit="day", silent = TRUE),NA)
expect_error(suppressMessages(plot(report_mig_interannual, plot.type = "pointrange", silent = TRUE)),NA)
expect_error(plot(report_mig_interannual, plot.type = "density", silent = TRUE),NA)
expect_error(plot(report_mig_interannual, plot.type = "seasonal", silent = TRUE),NA)
expect_error(suppressWarnings(plot(report_mig_interannual, plot.type = "seasonal", timesplit="semaine", silent = TRUE)),NA)
expect_error(suppressWarnings(plot(report_mig_interannual, plot.type = "seasonal", timesplit="day", silent = TRUE)),NA)
rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
})
test_that("Test bmi plots bug", {
skip_on_cran()
stacomi(database_expected = TRUE, sch ="test")
env_set_test_stacomi()
report_mig_interannual <- new("report_mig_interannual")
# the following will load data for size,
# parameters 1786 (total size) C001 (size at video control)
# dc 5 and 6 are fishways located on the Arzal dam
# two stages are selected
report_mig_interannual <- choice_c(
report_mig_interannual,
dc = 5,
taxa = c("Anguilla anguilla"),
stage = c("AGJ"),
start_year = 2010,
end_year = 2013,
silent = TRUE
)
report_mig_interannual <- connect(report_mig_interannual, silent = TRUE)
report_mig_interannual <- calcule(report_mig_interannual, silent = TRUE)
# test plots
expect_error(plot(report_mig_interannual, plot.type = "density", silent = TRUE),NA)
rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
})
test_that("Test bmi for several dc", {
skip_on_cran()
stacomi(database_expected = TRUE, sch ="test")
env_set_test_stacomi()
r_mig_interannual <- new("report_mig_interannual")
# the following will load data for size,
# parameters 1786 (total size) C001 (size at video control)
# dc 5 and 6 are fishways located on the Arzal dam
# two stages are selected
r_mig_interannual <- choice_c(
r_mig_interannual,
dc = c(5,6),
taxa = c("Anguilla anguilla"),
stage = c("AGJ"),
start_year = 2010,
end_year = 2013,
silent = TRUE
)
r_mig_interannual <- connect(r_mig_interannual, silent = TRUE)
# calcule is only needed for seasonal
r_mig_interannual <- calcule(r_mig_interannual, silent = TRUE)
expect_error(suppressWarnings(plot(r_mig_interannual, plot.type = "step", silent = TRUE)),NA)
expect_error(suppressWarnings(plot(r_mig_interannual, plot.type = "line", silent = TRUE)),NA)
expect_error(suppressWarnings(plot(r_mig_interannual, plot.type = "standard", silent = TRUE)),NA)
expect_error(plot(r_mig_interannual, plot.type = "barchart", timesplit="day",silent = TRUE),NA)
expect_error(suppressMessages(plot(r_mig_interannual, plot.type = "pointrange", silent = TRUE)),NA)
expect_error(plot(r_mig_interannual, plot.type = "density", silent = TRUE),NA)
expect_error(plot(r_mig_interannual, plot.type = "seasonal", silent = TRUE),NA)
expect_error(suppressWarnings(plot(r_mig_interannual, plot.type = "seasonal", timesplit="semaine", silent = TRUE)),NA)
rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
})
test_that("Test method summary when data are not every month", {
skip_on_cran()
env_set_test_stacomi()
stacomi(database_expected = TRUE, sch ="test")
# overriding user schema to point to test
# the following will load data for size,
# parameters 1786 (total size) C001 (size at video control)
# dc 5 and 6 are fishways located on the Arzal dam
# two stages are selected
rmi <- new("report_mig_interannual")
rmi <- choice_c(rmi,
dc=c(5),
taxa=c("Salmo trutta trutta"),
stage=c("IND"),
start_year="2010",
end_year="2013",
silent=TRUE)
invisible(capture.output(rmi <- connect(rmi, silent=TRUE)))
rmi <- charge(rmi, silent=TRUE)
rmi <- calcule(rmi)
invisible(capture.output(ss <- summary(object = rmi, year_choice=2013, silent = TRUE)))
expect_equal(nrow(ss$`5`),4) # only 4 month of data in 2013
# two warning produced
rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
})
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context("report_mig_interannual")
test_that("Test an instance of report_mig_interannual loaded with choice_c",
{
skip_on_cran()
env_set_test_stacomi()
stacomi(database_expected = TRUE, sch ="test")
r_mig_interannual <- new("report_mig_interannual")
# the following will load data for size,
# parameters 1786 (total size) C001 (size at video control)
# dc 5 and 6 are fishways located on the Arzal dam
# two stages are selected
suppressWarnings(r_mig_interannual <- choice_c(
r_mig_interannual,
dc = 6,
taxa = c("Anguilla anguilla"),
stage = c("AGJ"),
start_year = 2010,
end_year = 2013,
silent = TRUE
))
r_mig_interannual <- connect(r_mig_interannual, silent = TRUE)
# three warning produced, none shown due to silent=TRUE
options(warn = 0)
expect_s4_class(r_mig_interannual, "report_mig_interannual")
rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
})
#test_that("Test bug when writing data with Alice and Sebastien",
# {
# skip_on_cran()
# # env_set_test_stacomi()
# options(
# stacomiR.dbname = "bd_contmig_nat",
# stacomiR.host ="********************",
# stacomiR.port = "5432",
# stacomiR.user = "********************",
# stacomiR.password = "****************"
# )
# stacomi(database_expected = TRUE, sch ="seinormigr")
# r_mig_interannual <- new("report_mig_interannual")
# # the following will load data for size,
# # parameters 1786 (total size) C001 (size at video control)
# # dc 5 and 6 are fishways located on the Arzal dam
# # two stages are selected
# suppressWarnings(r_mig_interannual <- choice_c(
# r_mig_interannual,
# dc = 102,
# taxa = c("Anguilla anguilla"),
# stage = c("4"),
# start_year = 2014,
# end_year = 2023,
# silent = TRUE
# ))
# r_mig_interannual <- connect(r_mig_interannual, silent = TRUE)
# # three warning produced, none shown due to silent=TRUE
# options(warn = 0)
# expect_s4_class(r_mig_interannual, "report_mig_interannual")
# rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
#
# })
test_that("Test method summary in report_mig_interannual", {
skip_on_cran()
env_set_test_stacomi()
stacomi(database_expected = TRUE, sch ="test")
# overriding user schema to point to test
r_mig_interannual <- new("report_mig_interannual")
# the following will load data for size,
# parameters 1786 (total size) C001 (size at video control)
# dc 5 and 6 are fishways located on the Arzal dam
# two stages are selected
r_mig_interannual <- choice_c(
r_mig_interannual,
dc = 6,
taxa = c("Anguilla anguilla"),
stage = c("AGJ"),
start_year = 2010,
end_year = 2012,
silent = TRUE
)
r_mig_interannual <- connect(r_mig_interannual, silent = TRUE)
invisible(capture.output(ss <- summary(object = r_mig_interannual, year_choice=2012, silent = TRUE)))
# this one is failing in covr but not in test. I don't understand why
if ("year" %in% colnames(ss$`6`)) expect_equal(ss$`6`[1, "year"],"2012") else
expect_equal(ss$`6`[1, "année"],"2012")
# two warning produced
rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
})
#
#test_that("Test example report_mig_interannual-example",
# {
# # check if built with examples (Rtools install --example)
# # the file is generate it examples but later loaded to examples from the class using @example
# # be sure you have built Roxygen documentation before running
# example_path <-
# file.path(.libPaths(),
# "stacomiR",
# "R-ex",
# "report_mig_interannual-class.R")
# test <- file.access(example_path, 0)
# if (test[1] != 0)
# warnings("Package example dir not created ?")
# else
# suppressWarnings(source(example_path))
# rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
# })
test_that("Test that loading two taxa will fail",
{
skip_on_cran()
stacomi(database_expected = TRUE, sch ="test")
env_set_test_stacomi()
r_mig_interannual <- new("report_mig_interannual")
# the following will load data for size,
# parameters 1786 (total size) C001 (size at video control)
# dc 5 and 6 are fishways located on the Arzal dam
# two stages are selected
invisible(capture.output(expect_error(
choice_c(
r_mig_interannual,
dc = 5,
taxa = c("Anguilla anguilla", "Petromyzon marinus"),
stage = c("AGJ"),
start_year = "2010",
end_year = 2015,
silent = TRUE
)
)))
rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
})
test_that("Test that report_mig_interannual displays message when silent = FALSE",
{
skip_on_cran()
stacomi(database_expected = TRUE, sch ="test")
env_set_test_stacomi()
r_mig_interannual <- new("report_mig_interannual")
expect_output(
r_mig_interannual <- choice_c(
r_mig_interannual,
dc = 6,
taxa = c("Anguilla anguilla"),
stage = c("AGJ"),
start_year = 2011,
end_year = 2012,
silent = FALSE
))
rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
})
test_that("Test supprime method",
{
skip_on_cran()
stacomi(database_expected = TRUE, sch ="test")
env_set_test_stacomi()
bmi_cha <- new("report_mig_interannual") #châtelrault
bmi_cha <-
choice_c(
bmi_cha,
dc = c(19),
taxa = c("Salmo salar"),
stage = c("5"),
start_year = "2010",
end_year = "2012",
silent = TRUE
)
bmi_cha <- charge(bmi_cha, silent = TRUE)
# deleting all data to ensure everything is loaded
supprime(bmi_cha)
expect_output(bmi_cha <- connect(bmi_cha, silent = TRUE))
rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
})
test_that("Test that different sums are the same, for report_mig_interannual, report_mig_mult",
{
skip_on_cran()
stacomi(database_expected = TRUE, sch ="test")
# overriding user schema
env_set_test_stacomi()
# this chunk is not launched from examples but loads the r_mig dataset if connection works
r_mig_interannual <- new("report_mig_interannual")
r_mig_interannual <- choice_c(
r_mig_interannual,
dc = 6,
taxa = c("Anguilla anguilla"),
stage = c("AGJ"),
start_year = 2010,
end_year = 2010,
silent = TRUE
)
r_mig_interannual <- connect(r_mig_interannual, silent=TRUE)
nb_r_mig_interannual <- sum(r_mig_interannual@data[r_mig_interannual@data$"bjo_labelquantite"=="Effectif_total","bjo_valeur" ])
r_mig_mult <- new("report_mig_mult")
r_mig_mult <- choice_c(
r_mig_mult,
dc = 6,
taxa = c("Anguilla anguilla"),
stage = c("AGJ"),
datedebut = "2010-01-01",
datefin = "2010-12-31",
silent = TRUE
)
r_mig_mult <- charge(r_mig_mult, silent=TRUE)
r_mig_mult <- connect(r_mig_mult, silent=TRUE)
r_mig_mult <- calcule(r_mig_mult, silent=TRUE)
nb_r_mig_mult = sum(r_mig_mult@calcdata$dc_6$data$Effectif_total)
expect_equal(round(nb_r_mig_interannual),round(nb_r_mig_mult))
rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
})
test_that("Test bmi plots", {
skip_on_cran()
stacomi(database_expected = TRUE, sch ="test")
env_set_test_stacomi()
report_mig_interannual <- new("report_mig_interannual")
# the following will load data for size,
# parameters 1786 (total size) C001 (size at video control)
# dc 5 and 6 are fishways located on the Arzal dam
# two stages are selected
report_mig_interannual <- choice_c(
report_mig_interannual,
dc = 6,
taxa = c("Anguilla anguilla"),
stage = c("AGJ"),
start_year = 2010,
end_year = 2013,
silent = TRUE
)
# first test if there is nothing in data
expect_output(plot(report_mig_interannual, plot.type = "step", silent = FALSE))
report_mig_interannual <- connect(report_mig_interannual, silent = TRUE)
report_mig_interannual <- calcule(report_mig_interannual, silent = TRUE)
# test plots
expect_error(suppressWarnings(plot(report_mig_interannual, plot.type = "step", silent = TRUE)),NA)
expect_error(suppressWarnings(plot(report_mig_interannual, plot.type = "line", silent = TRUE)),NA)
expect_error(suppressWarnings(plot(report_mig_interannual, plot.type = "standard", silent = TRUE)),NA)
expect_error(plot(report_mig_interannual, plot.type = "barchart", silent = TRUE),NA)
expect_error(plot(report_mig_interannual, plot.type = "barchart", timesplit="2 weeks", silent = TRUE),NA)
expect_error(plot(report_mig_interannual, plot.type = "barchart", timesplit="week", silent = TRUE),NA)
expect_error(plot(report_mig_interannual, plot.type = "barchart", timesplit="day", silent = TRUE),NA)
expect_error(suppressMessages(plot(report_mig_interannual, plot.type = "pointrange", silent = TRUE)),NA)
expect_error(plot(report_mig_interannual, plot.type = "density", silent = TRUE),NA)
expect_error(plot(report_mig_interannual, plot.type = "seasonal", silent = TRUE),NA)
expect_error(suppressWarnings(plot(report_mig_interannual, plot.type = "seasonal", timesplit="semaine", silent = TRUE)),NA)
expect_error(suppressWarnings(plot(report_mig_interannual, plot.type = "seasonal", timesplit="day", silent = TRUE)),NA)
rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
})
test_that("Test bmi plots bug", {
skip_on_cran()
stacomi(database_expected = TRUE, sch ="test")
env_set_test_stacomi()
report_mig_interannual <- new("report_mig_interannual")
# the following will load data for size,
# parameters 1786 (total size) C001 (size at video control)
# dc 5 and 6 are fishways located on the Arzal dam
# two stages are selected
report_mig_interannual <- choice_c(
report_mig_interannual,
dc = 5,
taxa = c("Anguilla anguilla"),
stage = c("AGJ"),
start_year = 2010,
end_year = 2013,
silent = TRUE
)
report_mig_interannual <- connect(report_mig_interannual, silent = TRUE)
report_mig_interannual <- calcule(report_mig_interannual, silent = TRUE)
# test plots
expect_error(plot(report_mig_interannual, plot.type = "density", silent = TRUE),NA)
rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
})
test_that("Test bmi for several dc", {
skip_on_cran()
stacomi(database_expected = TRUE, sch ="test")
env_set_test_stacomi()
r_mig_interannual <- new("report_mig_interannual")
# the following will load data for size,
# parameters 1786 (total size) C001 (size at video control)
# dc 5 and 6 are fishways located on the Arzal dam
# two stages are selected
r_mig_interannual <- choice_c(
r_mig_interannual,
dc = c(5,6),
taxa = c("Anguilla anguilla"),
stage = c("AGJ"),
start_year = 2010,
end_year = 2013,
silent = TRUE
)
r_mig_interannual <- connect(r_mig_interannual, silent = TRUE)
# calcule is only needed for seasonal
r_mig_interannual <- calcule(r_mig_interannual, silent = TRUE)
expect_error(suppressWarnings(plot(r_mig_interannual, plot.type = "step", silent = TRUE)),NA)
expect_error(suppressWarnings(plot(r_mig_interannual, plot.type = "line", silent = TRUE)),NA)
expect_error(suppressWarnings(plot(r_mig_interannual, plot.type = "standard", silent = TRUE)),NA)
expect_error(plot(r_mig_interannual, plot.type = "barchart", timesplit="day",silent = TRUE),NA)
expect_error(suppressMessages(plot(r_mig_interannual, plot.type = "pointrange", silent = TRUE)),NA)
expect_error(plot(r_mig_interannual, plot.type = "density", silent = TRUE),NA)
expect_error(plot(r_mig_interannual, plot.type = "seasonal", silent = TRUE),NA)
expect_error(suppressWarnings(plot(r_mig_interannual, plot.type = "seasonal", timesplit="semaine", silent = TRUE)),NA)
rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
})
test_that("Test method summary when data are not every month", {
skip_on_cran()
env_set_test_stacomi()
stacomi(database_expected = TRUE, sch ="test")
# overriding user schema to point to test
# the following will load data for size,
# parameters 1786 (total size) C001 (size at video control)
# dc 5 and 6 are fishways located on the Arzal dam
# two stages are selected
rmi <- new("report_mig_interannual")
rmi <- choice_c(rmi,
dc=c(5),
taxa=c("Salmo trutta trutta"),
stage=c("IND"),
start_year="2010",
end_year="2013",
silent=TRUE)
invisible(capture.output(rmi <- connect(rmi, silent=TRUE)))
rmi <- charge(rmi, silent=TRUE)
rmi <- calcule(rmi)
invisible(capture.output(ss <- summary(object = rmi, year_choice=2013, silent = TRUE)))
expect_equal(nrow(ss$`5`),4) # only 4 month of data in 2013
# two warning produced
rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
})
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