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)
			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 = 1996,
					end_year = 2015,
					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)
			# overriding user schema to point to iav
			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 = "1996",
					end_year = 2015,
					silent = TRUE
			)
			r_mig_interannual <- connect(r_mig_interannual, silent = TRUE)
			invisible(capture.output(expect_error(summary(object = r_mig_interannual, silent = TRUE), NA)))
			ss <- summary(object = r_mig_interannual, year_choice=2012, silent = TRUE)
			expect_equal(ss$`6`$annee[1],"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)
			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 = "1996",
											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 ="iav")
			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 = 1997,
							end_year = 1998,
							silent = FALSE
					))
			
			rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
			
		})


test_that("Test supprime method",
		{
			skip_on_cran()
			stacomi(database_expected = TRUE, sch ="logrami")
			env_set_test_stacomi()			
			bmi_cha <- new("report_mig_interannual") #châtelrault
			bmi_cha <- 
					choice_c(
							bmi_cha,
							dc = c(21),
							taxa = c("Salmo salar"),
							stage = c("5"),
							start_year = "2004",
							end_year = "2006",
							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)
			# 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 = 1996,
					end_year = 1996,
					silent = TRUE
			)
			r_mig_interannual <- connect(r_mig_interannual, silent=TRUE)
			
			nb_r_mig_interannual <- sum(r_mig_interannual@data[r_mig_interannual@data$"bjo_labelquantite"=="Effectif_total","bjo_valeur" ])
			r_mig_mult <- new("report_mig_mult")
			r_mig_mult <- choice_c(
					r_mig_mult,
					dc = 6,
					taxa = c("Anguilla anguilla"),
					stage = c("AGJ"),
					datedebut = "1996-01-01",
					datefin = "1997-01-01",
					silent = TRUE
			)
			r_mig_mult <- charge(r_mig_mult, silent=TRUE)
			r_mig_mult <- connect(r_mig_mult, silent=TRUE)
			r_mig_mult <- calcule(r_mig_mult, silent=TRUE)
			nb_r_mig_mult = sum(r_mig_mult@calcdata$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)
			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 = 6,
					taxa = c("Anguilla anguilla"),
					stage = c("AGJ"),
					start_year = 1996,
					end_year = 2015,
					silent = TRUE
			)
			expect_output(plot(r_mig_interannual, plot.type = "step", silent = FALSE))
			r_mig_interannual <- connect(r_mig_interannual, silent = TRUE)
			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", 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 bmi for several dc", {
			skip_on_cran()
			stacomi(database_expected = TRUE)
			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 = 1996,
					end_year = 2015,
					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 that database is not written over and over", {
			skip_on_cran()
			stacomi(database_expected = TRUE)
			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(6),
					taxa = c("Anguilla anguilla"),
					stage = c("AGJ"),
					start_year = 2019,
					end_year = 2019,
					silent = TRUE
			)
			# writes Running report_mig to correct data for year 2019 => there was an error, fixed by commit 
			# 097e415df0af1d5e8534410d74f367ace27013ef
			expect_output(r_mig_interannual <- connect(r_mig_interannual, silent = TRUE),
					"No writing in the db."
			)
			rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
			
		})