tests/testthat/test-export.R
In Greensway/BIRDS: Biodiversity Information Review and Decision Support
context("Export BIRDS")
library(BIRDS)
data("SB", package = "BIRDS")
sampleGridCell<-sample(which(unlist(lapply(SB$overlaid, nrow))!=0),1)
sampleDate<-lubridate::date(SB$temporal[sample(1:nrow(SB$temporal),1),])
visitUID<-"visitUID"
scientificName<-"scientificName"
dimVar<-c("spatial", "temporal")
timeResVar<-c("NULL", "Yearly","Monthly", "Daily", "Month")
varVar<-c("nObs", "nVis", "nSpp", "avgSll", "nYears", "nDays")
methVar<-c("sum","median", "mean")
exportShouldWork<-array(TRUE, dim=c(length(dimVar),
length(timeResVar),
length(varVar),
length(methVar)),
dimnames = list(dimVar, timeResVar, varVar, methVar))
#nYears for spatial FALSE
exportShouldWork["spatial",c("Yearly","Monthly"),"nYears",]<-FALSE
#Daily for spatial FALSE
exportShouldWork["spatial","Daily",,]<-FALSE
#NULL for temporal FALSE
exportShouldWork["temporal", "NULL",,]<-FALSE
#nYears for temporal FALSE
exportShouldWork["temporal", c("NULL", "Yearly", "Monthly", "Daily"), "nYears",]<-FALSE
#nDays FALSE
# exportShouldWork["temporal", "Daily", "nDays",]<-FALSE
#Only sum for most
exportShouldWork[,c("NULL", "Yearly","Monthly", "Daily"), c("nObs", "nVis", "nSpp", "nYears", "nDays"), c("median", "mean")]<-FALSE
#Only median for SLL
exportShouldWork[,,"avgSll", c("sum")]<-FALSE
exportShouldWork[,c("NULL", "Yearly","Monthly", "Daily"),"avgSll", c("mean")]<-FALSE
#Only sum for Month and nYears
exportShouldWork[,"Month", "nYears", c("median", "mean")]<-FALSE
test_that("Test valid export variables", {
skip_on_os("solaris")
for(s in 1:length(dimVar)){
for(t in 1:length(timeResVar)){
for(v in 1:length(varVar)){
for(m in 1:length(methVar)){
if(exportShouldWork[s,t,v,m]){
if(timeResVar[t]=="NULL"){
expect_error(exportBirds(SB, !!dimVar[s], NULL, !!varVar[v], !!methVar[m]), NA)
}else{
expect_error(exportBirds(SB, !!dimVar[s], !!timeResVar[t], !!varVar[v], !!methVar[m]), NA)
}
}else{
if(timeResVar[t]=="NULL"){
expect_error(exportBirds(SB, !!dimVar[s], NULL, !!varVar[v], !!methVar[m]))
}else{
expect_error(exportBirds(SB, !!dimVar[s], !!timeResVar[t], !!varVar[v], !!methVar[m]))
}
}
}
}
}
}
})
test_that("Test correct export object classes", {
skip_on_cran()
skip_on_os("solaris")
for(s in 1:length(dimVar)){
for(t in 1:length(timeResVar)){
for(v in 1:length(varVar)){
for(m in 1:length(methVar)){
if(exportShouldWork[s,t,v,m]){
if(s==1){
if(timeResVar[t]=="NULL"){
expect_is(exportBirds(SB,!!dimVar[s],NULL,!!varVar[v],!!methVar[m]),"sf")
}else{
expect_is(exportBirds(SB,!!dimVar[s],!!timeResVar[t],!!varVar[v],!!methVar[m]),"sf")
}
}else if (s==1){
if(timeResVar[t]=="NULL"){
expect_is(exportBirds(SB,!!dimVar[s],NULL,!!varVar[v],!!methVar[m]),"numeric")
}else{
expect_is(exportBirds(SB,!!dimVar[s],!!timeResVar[t],!!varVar[v],!!methVar[m]),"numeric")
}
}
}
}
}
}
}
})
# test_that("Test correct export results",{
#
# expect_equal(exportBirds(SB, "spatial", NULL, "nObs", "sum")$nObs[!!sampleGridCell], SB$spatial$nObs[!!sampleGridCell])
# expect_equal(exportBirds(SB, "spatial", NULL, "nVis", "sum")$nVis[!!sampleGridCell], SB$spatial$nVis[!!sampleGridCell])
# expect_equal(exportBirds(SB, "spatial", NULL, "nSpp", "sum")$nSpp[!!sampleGridCell], SB$spatial$nSpp[!!sampleGridCell])
# expect_equal(exportBirds(SB, "spatial", NULL, "avgSll", "median")$avgSll[!!sampleGridCell], SB$spatial$avgSll[!!sampleGridCell])
# expect_equal(exportBirds(SB, "spatial", NULL, "nYears", "sum")$nYears[!!sampleGridCell], SB$spatial$nYears[!!sampleGridCell])
# expect_equal(exportBirds(SB, "spatial", NULL, "nDays", "sum")$nDays[!!sampleGridCell],
# length(unique(apply(SB$overlaid[[!!sampleGridCell]], 1, function(x) paste0(x[2],"-",x[3],"-",x[4])))))
#
# expect_equal(exportBirds(SB, "spatial", "Yearly", "nObs", "sum")@data[!!sampleGridCell, as.character(lubridate::year(!!sampleDate))],
# SB$spatioTemporal[!!sampleGridCell, as.character(lubridate::year(!!sampleDate)),13, "nObs"])
# expect_equal(exportBirds(SB, "spatial", "Yearly", "nVis", "sum")@data[!!sampleGridCell, as.character(lubridate::year(!!sampleDate))],
# SB$spatioTemporal[!!sampleGridCell, as.character(lubridate::year(!!sampleDate)),13, "nVis"])
# expect_equal(exportBirds(SB, "spatial", "Yearly", "nSpp", "sum")@data[!!sampleGridCell, as.character(lubridate::year(!!sampleDate))],
# SB$spatioTemporal[!!sampleGridCell, as.character(lubridate::year(!!sampleDate)),13, "nSpp"])
# expect_equal(exportBirds(SB, "spatial", "Yearly", "avgSll", "median")@data[!!sampleGridCell, as.character(lubridate::year(!!sampleDate))],
# SB$spatioTemporal[!!sampleGridCell, as.character(lubridate::year(!!sampleDate)),13, "avgSll"])
# expect_equal(exportBirds(SB, "spatial", "Yearly", "nDays", "sum")@data[!!sampleGridCell, as.character(lubridate::year(!!sampleDate))],
# length(unique(apply(SB$overlaid[[!!sampleGridCell]][SB$overlaid[[!!sampleGridCell]][,"year"]==lubridate::year(!!sampleDate),], 1, function(x) paste0(x[2],"-",x[3],"-",x[4])))))
#
# expect_equal(exportBirds(SB, "spatial", "Monthly", "nObs", "sum")@data[!!sampleGridCell, paste0(as.character(lubridate::year(!!sampleDate)),"-",as.character(lubridate::month(!!sampleDate)))],
# SB$spatioTemporal[!!sampleGridCell, as.character(lubridate::year(!!sampleDate)),lubridate::month(!!sampleDate), "nObs"])
# expect_equal(exportBirds(SB, "spatial", "Monthly", "nVis", "sum")@data[!!sampleGridCell, paste0(as.character(lubridate::year(!!sampleDate)),"-",as.character(lubridate::month(!!sampleDate)))],
# SB$spatioTemporal[!!sampleGridCell, as.character(lubridate::year(!!sampleDate)),lubridate::month(!!sampleDate), "nVis"])
# expect_equal(exportBirds(SB, "spatial", "Monthly", "nSpp", "sum")@data[!!sampleGridCell, paste0(as.character(lubridate::year(!!sampleDate)),"-",as.character(lubridate::month(!!sampleDate)))],
# SB$spatioTemporal[!!sampleGridCell, as.character(lubridate::year(!!sampleDate)),lubridate::month(!!sampleDate), "nSpp"])
# expect_equal(exportBirds(SB, "spatial", "Monthly", "avgSll", "median")@data[!!sampleGridCell, paste0(as.character(lubridate::year(!!sampleDate)),"-",as.character(lubridate::month(!!sampleDate)))],
# SB$spatioTemporal[!!sampleGridCell, as.character(lubridate::year(!!sampleDate)),lubridate::month(!!sampleDate), "avgSll"])
# expect_equal(exportBirds(SB, "spatial", "Monthly", "nDays", "sum")@data[!!sampleGridCell, paste0(as.character(lubridate::year(!!sampleDate)),"-",as.character(lubridate::month(!!sampleDate)))],
# length(unique(apply(SB$overlaid[[!!sampleGridCell]][SB$overlaid[[!!sampleGridCell]][,"year"]==lubridate::year(!!sampleDate) & SB$overlaid[[!!sampleGridCell]][,"month"]==lubridate::month(!!sampleDate),], 1, function(x) paste0(x[2],"-",x[3],"-",x[4])))))
# expect_equal(exportBirds(SB, "spatial", "Month", "nObs", "sum")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# sum(SB$spatioTemporal[!!sampleGridCell,,lubridate::month(!!sampleDate),"nObs"]))
# expect_equal(exportBirds(SB, "spatial", "Month", "nObs", "median")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# median(SB$spatioTemporal[!!sampleGridCell,,lubridate::month(!!sampleDate),"nObs"]))
# expect_equal(exportBirds(SB, "spatial", "Month", "nObs", "mean")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# mean(SB$spatioTemporal[!!sampleGridCell,,lubridate::month(!!sampleDate),"nObs"]))
# expect_equal(exportBirds(SB, "spatial", "Month", "nVis", "sum")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# sum(SB$spatioTemporal[!!sampleGridCell,,lubridate::month(!!sampleDate),"nVis"]))
# expect_equal(exportBirds(SB, "spatial", "Month", "nVis", "median")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# median(SB$spatioTemporal[!!sampleGridCell,,lubridate::month(!!sampleDate),"nVis"]))
# expect_equal(exportBirds(SB, "spatial", "Month", "nVis", "mean")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# mean(SB$spatioTemporal[!!sampleGridCell,,lubridate::month(!!sampleDate),"nVis"]))
# expect_equal(exportBirds(SB, "spatial", "Month", "nSpp", "sum")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# sum(SB$spatioTemporal[!!sampleGridCell,,lubridate::month(!!sampleDate),"nSpp"]))
# expect_equal(exportBirds(SB, "spatial", "Month", "nSpp", "median")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# median(SB$spatioTemporal[!!sampleGridCell,,lubridate::month(!!sampleDate),"nSpp"]))
# expect_equal(exportBirds(SB, "spatial", "Month", "nSpp", "mean")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# mean(SB$spatioTemporal[!!sampleGridCell,,lubridate::month(!!sampleDate),"nSpp"]))
# expect_equal(exportBirds(SB, "spatial", "Month", "avgSll", "median")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# median(SB$spatioTemporal[!!sampleGridCell,,lubridate::month(!!sampleDate),"avgSll"]))
# expect_equal(exportBirds(SB, "spatial", "Month", "avgSll", "mean")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# mean(SB$spatioTemporal[!!sampleGridCell,,lubridate::month(!!sampleDate),"avgSll"]))
# #bug
# # expect_equal(exportBirds(SB, "spatial", "Month", "nYears", "sum")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# # length(unique(SB$overlaid[[!!sampleGridCell]][,"year"])))
# expect_equal(exportBirds(SB, "spatial", "Month", "nYears", "sum")@data[!!sampleGridCell, lubridate::month(sampleDate)],
# length(unique(SB$overlaid[[!!sampleGridCell]][SB$overlaid[[sampleGridCell]]$month==lubridate::month(sampleDate),"year"])))
#
# test<-SB$overlaid[[!!sampleGridCell]]
# test$ymd<-apply(test, 1, function(x) paste0(as.numeric(x[2]), "-", as.numeric(x[3]), "-", as.numeric(x[4])))
# test<-dplyr::group_by(test, year, month)
# test<-dplyr::summarise(test, res=n_distinct(ymd))
# test<-dplyr::summarise(dplyr::group_by(test, month), sum=sum(res), mean=mean(res), median=median(res))
#
# # expect_equal(exportBirds(SB, "spatial", "Month", "nDays", "sum")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# # test[test[,"month"]==lubridate::month(!!sampleDate),]$sum)
# # #bug in the test
# # expect_equal(exportBirds(SB, "spatial", "Month", "nDays", "sum")@data[!!sampleGridCell, lubridate::month(sampleDate)],
# # test[test[,"month"]==lubridate::month(sampleDate),]$sum)
# # #bug in the test
# # expect_equal(exportBirds(SB, "spatial", "Month", "nDays", "median")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# # test[test[,"month"]==lubridate::month(!!sampleDate),]$median)
# # #bug in the test
# # expect_equal(exportBirds(SB, "spatial", "Month", "nDays", "mean")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# # test[test[,"month"]==lubridate::month(!!sampleDate),]$mean)
#
# testO<-deconstructOverlay(SB$overlaid, attr(SB, "visitCol"))
# testM<-test[which(testO[,"month"]==lubridate::month(sampleDate)),]
# test<-test[which(testO[,"year"]==lubridate::year(sampleDate)),]
# avgSll<-median(dplyr::summarise(dplyr::group_by(test, !!visitUID),sll=n_distinct(!!scientificName))$sll)
#
#
# expect_equivalent(exportBirds(SB, "temporal", "Yearly", "nObs", "sum")[as.character(lubridate::year(!!sampleDate))],
# sum(SB$temporal[lubridate::year(SB$temporal)==lubridate::year(!!sampleDate),"nObs"]))
# expect_equivalent(exportBirds(SB, "temporal", "Yearly", "nVis", "sum")[as.character(lubridate::year(!!sampleDate))],
# sum(SB$temporal[lubridate::year(SB$temporal)==lubridate::year(!!sampleDate),"nVis"]))
# expect_equivalent(exportBirds(SB, "temporal", "Yearly", "nSpp", "sum")[as.character(lubridate::year(!!sampleDate))],
# sum(SB$temporal[lubridate::year(SB$temporal)==lubridate::year(!!sampleDate),"nSpp"]))
# expect_equivalent(exportBirds(SB, "temporal", "Yearly", "avgSll", "median")[as.character(lubridate::year(!!sampleDate))],
# avgSll)
# expect_equivalent(exportBirds(SB, "temporal", "Yearly", "nDays", "sum")[as.character(lubridate::year(!!sampleDate))],
# nrow(SB$temporal[lubridate::year(SB$temporal)==lubridate::year(!!sampleDate),]))
# # bugs in test
# # expect_equivalent(exportBirds(SB, "temporal", "Monthly", "nObs", "sum")[paste0(as.character(lubridate::year(!!sampleDate)),"-",as.character(lubridate::month(!!sampleDate)))],
# # nrow(test[test[,"month"]==lubridate::month(!!sampleDate),]))
# # bugs in test
# # expect_equivalent(exportBirds(SB, "temporal", "Monthly", "nVis", "sum")[paste0(as.character(lubridate::year(!!sampleDate)),"-",as.character(lubridate::month(!!sampleDate)))],
# # length(unique(test[test[,"month"]==lubridate::month(!!sampleDate),!!visitUID])))
# # expect_equivalent(exportBirds(SB, "temporal", "Monthly", "nSpp", "sum")[paste0(as.character(lubridate::year(!!sampleDate)),"-",as.character(lubridate::month(!!sampleDate)))],
# # length(unique(test[test[,"month"]==lubridate::month(!!sampleDate),!!scientificName])))
# # expect_equivalent(exportBirds(SB, "temporal", "Monthly", "avgSll", "median")[paste0(as.character(lubridate::year(!!sampleDate)),"-",as.character(lubridate::month(!!sampleDate)))],
# # median(dplyr::summarise(dplyr::group_by(test[test[,"month"]==lubridate::month(!!sampleDate),],!!visitUID), sll=n_distinct(!!scientificName))$sll))
# # expect_equivalent(exportBirds(SB, "temporal", "Monthly", "nDays", "sum")[paste0(as.character(lubridate::year(!!sampleDate)),"-",as.character(lubridate::month(!!sampleDate)))],
# # length(unique(test[test[,"month"]==lubridate::month(!!sampleDate),"day"])))
#
# ## bug in test
# # test<-test[test[,"month"]==lubridate::month(sampleDate) & test[,"day"]==lubridate::day(sampleDate),]
# #
# # expect_equivalent(exportBirds(SB, "temporal", "Daily", "nObs", "sum")[as.character(!!sampleDate)],
# # SB$temporal[!!sampleDate, "nObs"])
# # expect_equivalent(exportBirds(SB, "temporal", "Daily", "nVis", "sum")[as.character(!!sampleDate)],
# # SB$temporal[!!sampleDate, "nVis"])
# # expect_equivalent(exportBirds(SB, "temporal", "Daily", "nSpp", "sum")[as.character(!!sampleDate)],
# # SB$temporal[!!sampleDate, "nSpp"])
# # expect_equivalent(exportBirds(SB, "temporal", "Daily", "avgSll", "median")[as.character(!!sampleDate)],
# # median(dplyr::summarise(dplyr::group_by(test, visitUID), sll=n_distinct(scientificName))$sll))
#
# # testM<-dplyr::group_by(testM, year)
# #
# # nyears<-max(testO[,"year"])-min(testO[,"year"])+1
# #
# # yearlynObs<-dplyr::summarise(testM, res=n())
# # nObs<-c(yearlynObs$res, rep(0, nyears-length(yearlynObs$res)))
# #
# # yearlynVis<-dplyr::summarise(testM, res=n_distinct(visitUID))
# # nVis<-c(yearlynObs$res, rep(0, nyears-length(yearlynVis$res)))
# #
# # yearlynSpp<-dplyr::summarise(testM, res=n_distinct(scientificName))
# # nSpp<-c(yearlynObs$res, rep(0, nyears-length(yearlynSpp$res)))
# #
# # sll<-dplyr::summarise(dplyr::group_by(testO, year, month, visitUID), sll=n_distinct(scientificName))
# #
# # avgSll<-dplyr::summarise(dplyr::group_by(sll, year, month), avgSll=median(sll))
# #
# # avgSll<-avgSll[avgSll[,"month"]==lubridate::month(!!sampleDate),]$avgSll
# #
# # avgSll<-c(avgSll, rep(0, nyears-length(avgSll$res)))
# #
# # yearlynDay<-dplyr::summarise(testM, res=n_distinct(year, month, day))
# #
# # nDay<-c(yearlynDay$res, rep(0, nyears-length(yearlynDay$res)))
# #
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nObs", "sum")[lubridate::month(!!sampleDate)],
# # nrow(testM[,]))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nObs", "median")[lubridate::month(!!sampleDate)],
# # median(nObs))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nObs", "mean"),
# # mean(nObs))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nVis", "sum"),
# # sum(nVis))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nVis", "median"),
# # median(nVis))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nVis", "mean"),
# # mean(nVis))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nSpp", "sum"),
# # sum(nSpp))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nSpp", "median"),
# # median(nSpp))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nSpp", "mean"),
# # mean(nSpp))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "avgSll", "median"),
# # median(avgSll))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "avgSll", "mean"),
# # mean(avgSll))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nYears", "sum")[as.character(lubridate::year(!!sampleDate))],
# # length(unique(lubridate::year(SB$temporal[lubridate::month(sb$temporal)==lubridate::month(!!sampleDate),]))))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nDays", "sum")[as.character(lubridate::year(!!sampleDate))],
# # length(unique(lubridate::date(SB$temporal[lubridate::month(sb$temporal)==lubridate::month(!!sampleDate),]))))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nDays", "median")[as.character(lubridate::year(!!sampleDate))],
# # median(nDay))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nDays", "mean")[as.character(lubridate::year(!!sampleDate))],
# # mean(nDay))
#
# })
Greensway/BIRDS documentation built on Oct. 19, 2023, 2:35 a.m.
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context("Export BIRDS")
library(BIRDS)
data("SB", package = "BIRDS")
sampleGridCell<-sample(which(unlist(lapply(SB$overlaid, nrow))!=0),1)
sampleDate<-lubridate::date(SB$temporal[sample(1:nrow(SB$temporal),1),])
visitUID<-"visitUID"
scientificName<-"scientificName"
dimVar<-c("spatial", "temporal")
timeResVar<-c("NULL", "Yearly","Monthly", "Daily", "Month")
varVar<-c("nObs", "nVis", "nSpp", "avgSll", "nYears", "nDays")
methVar<-c("sum","median", "mean")
exportShouldWork<-array(TRUE, dim=c(length(dimVar),
length(timeResVar),
length(varVar),
length(methVar)),
dimnames = list(dimVar, timeResVar, varVar, methVar))
#nYears for spatial FALSE
exportShouldWork["spatial",c("Yearly","Monthly"),"nYears",]<-FALSE
#Daily for spatial FALSE
exportShouldWork["spatial","Daily",,]<-FALSE
#NULL for temporal FALSE
exportShouldWork["temporal", "NULL",,]<-FALSE
#nYears for temporal FALSE
exportShouldWork["temporal", c("NULL", "Yearly", "Monthly", "Daily"), "nYears",]<-FALSE
#nDays FALSE
# exportShouldWork["temporal", "Daily", "nDays",]<-FALSE
#Only sum for most
exportShouldWork[,c("NULL", "Yearly","Monthly", "Daily"), c("nObs", "nVis", "nSpp", "nYears", "nDays"), c("median", "mean")]<-FALSE
#Only median for SLL
exportShouldWork[,,"avgSll", c("sum")]<-FALSE
exportShouldWork[,c("NULL", "Yearly","Monthly", "Daily"),"avgSll", c("mean")]<-FALSE
#Only sum for Month and nYears
exportShouldWork[,"Month", "nYears", c("median", "mean")]<-FALSE
test_that("Test valid export variables", {
skip_on_os("solaris")
for(s in 1:length(dimVar)){
for(t in 1:length(timeResVar)){
for(v in 1:length(varVar)){
for(m in 1:length(methVar)){
if(exportShouldWork[s,t,v,m]){
if(timeResVar[t]=="NULL"){
expect_error(exportBirds(SB, !!dimVar[s], NULL, !!varVar[v], !!methVar[m]), NA)
}else{
expect_error(exportBirds(SB, !!dimVar[s], !!timeResVar[t], !!varVar[v], !!methVar[m]), NA)
}
}else{
if(timeResVar[t]=="NULL"){
expect_error(exportBirds(SB, !!dimVar[s], NULL, !!varVar[v], !!methVar[m]))
}else{
expect_error(exportBirds(SB, !!dimVar[s], !!timeResVar[t], !!varVar[v], !!methVar[m]))
}
}
}
}
}
}
})
test_that("Test correct export object classes", {
skip_on_cran()
skip_on_os("solaris")
for(s in 1:length(dimVar)){
for(t in 1:length(timeResVar)){
for(v in 1:length(varVar)){
for(m in 1:length(methVar)){
if(exportShouldWork[s,t,v,m]){
if(s==1){
if(timeResVar[t]=="NULL"){
expect_is(exportBirds(SB,!!dimVar[s],NULL,!!varVar[v],!!methVar[m]),"sf")
}else{
expect_is(exportBirds(SB,!!dimVar[s],!!timeResVar[t],!!varVar[v],!!methVar[m]),"sf")
}
}else if (s==1){
if(timeResVar[t]=="NULL"){
expect_is(exportBirds(SB,!!dimVar[s],NULL,!!varVar[v],!!methVar[m]),"numeric")
}else{
expect_is(exportBirds(SB,!!dimVar[s],!!timeResVar[t],!!varVar[v],!!methVar[m]),"numeric")
}
}
}
}
}
}
}
})
# test_that("Test correct export results",{
#
# expect_equal(exportBirds(SB, "spatial", NULL, "nObs", "sum")$nObs[!!sampleGridCell], SB$spatial$nObs[!!sampleGridCell])
# expect_equal(exportBirds(SB, "spatial", NULL, "nVis", "sum")$nVis[!!sampleGridCell], SB$spatial$nVis[!!sampleGridCell])
# expect_equal(exportBirds(SB, "spatial", NULL, "nSpp", "sum")$nSpp[!!sampleGridCell], SB$spatial$nSpp[!!sampleGridCell])
# expect_equal(exportBirds(SB, "spatial", NULL, "avgSll", "median")$avgSll[!!sampleGridCell], SB$spatial$avgSll[!!sampleGridCell])
# expect_equal(exportBirds(SB, "spatial", NULL, "nYears", "sum")$nYears[!!sampleGridCell], SB$spatial$nYears[!!sampleGridCell])
# expect_equal(exportBirds(SB, "spatial", NULL, "nDays", "sum")$nDays[!!sampleGridCell],
# length(unique(apply(SB$overlaid[[!!sampleGridCell]], 1, function(x) paste0(x[2],"-",x[3],"-",x[4])))))
#
# expect_equal(exportBirds(SB, "spatial", "Yearly", "nObs", "sum")@data[!!sampleGridCell, as.character(lubridate::year(!!sampleDate))],
# SB$spatioTemporal[!!sampleGridCell, as.character(lubridate::year(!!sampleDate)),13, "nObs"])
# expect_equal(exportBirds(SB, "spatial", "Yearly", "nVis", "sum")@data[!!sampleGridCell, as.character(lubridate::year(!!sampleDate))],
# SB$spatioTemporal[!!sampleGridCell, as.character(lubridate::year(!!sampleDate)),13, "nVis"])
# expect_equal(exportBirds(SB, "spatial", "Yearly", "nSpp", "sum")@data[!!sampleGridCell, as.character(lubridate::year(!!sampleDate))],
# SB$spatioTemporal[!!sampleGridCell, as.character(lubridate::year(!!sampleDate)),13, "nSpp"])
# expect_equal(exportBirds(SB, "spatial", "Yearly", "avgSll", "median")@data[!!sampleGridCell, as.character(lubridate::year(!!sampleDate))],
# SB$spatioTemporal[!!sampleGridCell, as.character(lubridate::year(!!sampleDate)),13, "avgSll"])
# expect_equal(exportBirds(SB, "spatial", "Yearly", "nDays", "sum")@data[!!sampleGridCell, as.character(lubridate::year(!!sampleDate))],
# length(unique(apply(SB$overlaid[[!!sampleGridCell]][SB$overlaid[[!!sampleGridCell]][,"year"]==lubridate::year(!!sampleDate),], 1, function(x) paste0(x[2],"-",x[3],"-",x[4])))))
#
# expect_equal(exportBirds(SB, "spatial", "Monthly", "nObs", "sum")@data[!!sampleGridCell, paste0(as.character(lubridate::year(!!sampleDate)),"-",as.character(lubridate::month(!!sampleDate)))],
# SB$spatioTemporal[!!sampleGridCell, as.character(lubridate::year(!!sampleDate)),lubridate::month(!!sampleDate), "nObs"])
# expect_equal(exportBirds(SB, "spatial", "Monthly", "nVis", "sum")@data[!!sampleGridCell, paste0(as.character(lubridate::year(!!sampleDate)),"-",as.character(lubridate::month(!!sampleDate)))],
# SB$spatioTemporal[!!sampleGridCell, as.character(lubridate::year(!!sampleDate)),lubridate::month(!!sampleDate), "nVis"])
# expect_equal(exportBirds(SB, "spatial", "Monthly", "nSpp", "sum")@data[!!sampleGridCell, paste0(as.character(lubridate::year(!!sampleDate)),"-",as.character(lubridate::month(!!sampleDate)))],
# SB$spatioTemporal[!!sampleGridCell, as.character(lubridate::year(!!sampleDate)),lubridate::month(!!sampleDate), "nSpp"])
# expect_equal(exportBirds(SB, "spatial", "Monthly", "avgSll", "median")@data[!!sampleGridCell, paste0(as.character(lubridate::year(!!sampleDate)),"-",as.character(lubridate::month(!!sampleDate)))],
# SB$spatioTemporal[!!sampleGridCell, as.character(lubridate::year(!!sampleDate)),lubridate::month(!!sampleDate), "avgSll"])
# expect_equal(exportBirds(SB, "spatial", "Monthly", "nDays", "sum")@data[!!sampleGridCell, paste0(as.character(lubridate::year(!!sampleDate)),"-",as.character(lubridate::month(!!sampleDate)))],
# length(unique(apply(SB$overlaid[[!!sampleGridCell]][SB$overlaid[[!!sampleGridCell]][,"year"]==lubridate::year(!!sampleDate) & SB$overlaid[[!!sampleGridCell]][,"month"]==lubridate::month(!!sampleDate),], 1, function(x) paste0(x[2],"-",x[3],"-",x[4])))))
# expect_equal(exportBirds(SB, "spatial", "Month", "nObs", "sum")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# sum(SB$spatioTemporal[!!sampleGridCell,,lubridate::month(!!sampleDate),"nObs"]))
# expect_equal(exportBirds(SB, "spatial", "Month", "nObs", "median")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# median(SB$spatioTemporal[!!sampleGridCell,,lubridate::month(!!sampleDate),"nObs"]))
# expect_equal(exportBirds(SB, "spatial", "Month", "nObs", "mean")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# mean(SB$spatioTemporal[!!sampleGridCell,,lubridate::month(!!sampleDate),"nObs"]))
# expect_equal(exportBirds(SB, "spatial", "Month", "nVis", "sum")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# sum(SB$spatioTemporal[!!sampleGridCell,,lubridate::month(!!sampleDate),"nVis"]))
# expect_equal(exportBirds(SB, "spatial", "Month", "nVis", "median")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# median(SB$spatioTemporal[!!sampleGridCell,,lubridate::month(!!sampleDate),"nVis"]))
# expect_equal(exportBirds(SB, "spatial", "Month", "nVis", "mean")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# mean(SB$spatioTemporal[!!sampleGridCell,,lubridate::month(!!sampleDate),"nVis"]))
# expect_equal(exportBirds(SB, "spatial", "Month", "nSpp", "sum")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# sum(SB$spatioTemporal[!!sampleGridCell,,lubridate::month(!!sampleDate),"nSpp"]))
# expect_equal(exportBirds(SB, "spatial", "Month", "nSpp", "median")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# median(SB$spatioTemporal[!!sampleGridCell,,lubridate::month(!!sampleDate),"nSpp"]))
# expect_equal(exportBirds(SB, "spatial", "Month", "nSpp", "mean")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# mean(SB$spatioTemporal[!!sampleGridCell,,lubridate::month(!!sampleDate),"nSpp"]))
# expect_equal(exportBirds(SB, "spatial", "Month", "avgSll", "median")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# median(SB$spatioTemporal[!!sampleGridCell,,lubridate::month(!!sampleDate),"avgSll"]))
# expect_equal(exportBirds(SB, "spatial", "Month", "avgSll", "mean")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# mean(SB$spatioTemporal[!!sampleGridCell,,lubridate::month(!!sampleDate),"avgSll"]))
# #bug
# # expect_equal(exportBirds(SB, "spatial", "Month", "nYears", "sum")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# # length(unique(SB$overlaid[[!!sampleGridCell]][,"year"])))
# expect_equal(exportBirds(SB, "spatial", "Month", "nYears", "sum")@data[!!sampleGridCell, lubridate::month(sampleDate)],
# length(unique(SB$overlaid[[!!sampleGridCell]][SB$overlaid[[sampleGridCell]]$month==lubridate::month(sampleDate),"year"])))
#
# test<-SB$overlaid[[!!sampleGridCell]]
# test$ymd<-apply(test, 1, function(x) paste0(as.numeric(x[2]), "-", as.numeric(x[3]), "-", as.numeric(x[4])))
# test<-dplyr::group_by(test, year, month)
# test<-dplyr::summarise(test, res=n_distinct(ymd))
# test<-dplyr::summarise(dplyr::group_by(test, month), sum=sum(res), mean=mean(res), median=median(res))
#
# # expect_equal(exportBirds(SB, "spatial", "Month", "nDays", "sum")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# # test[test[,"month"]==lubridate::month(!!sampleDate),]$sum)
# # #bug in the test
# # expect_equal(exportBirds(SB, "spatial", "Month", "nDays", "sum")@data[!!sampleGridCell, lubridate::month(sampleDate)],
# # test[test[,"month"]==lubridate::month(sampleDate),]$sum)
# # #bug in the test
# # expect_equal(exportBirds(SB, "spatial", "Month", "nDays", "median")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# # test[test[,"month"]==lubridate::month(!!sampleDate),]$median)
# # #bug in the test
# # expect_equal(exportBirds(SB, "spatial", "Month", "nDays", "mean")@data[!!sampleGridCell, lubridate::month(!!sampleDate)],
# # test[test[,"month"]==lubridate::month(!!sampleDate),]$mean)
#
# testO<-deconstructOverlay(SB$overlaid, attr(SB, "visitCol"))
# testM<-test[which(testO[,"month"]==lubridate::month(sampleDate)),]
# test<-test[which(testO[,"year"]==lubridate::year(sampleDate)),]
# avgSll<-median(dplyr::summarise(dplyr::group_by(test, !!visitUID),sll=n_distinct(!!scientificName))$sll)
#
#
# expect_equivalent(exportBirds(SB, "temporal", "Yearly", "nObs", "sum")[as.character(lubridate::year(!!sampleDate))],
# sum(SB$temporal[lubridate::year(SB$temporal)==lubridate::year(!!sampleDate),"nObs"]))
# expect_equivalent(exportBirds(SB, "temporal", "Yearly", "nVis", "sum")[as.character(lubridate::year(!!sampleDate))],
# sum(SB$temporal[lubridate::year(SB$temporal)==lubridate::year(!!sampleDate),"nVis"]))
# expect_equivalent(exportBirds(SB, "temporal", "Yearly", "nSpp", "sum")[as.character(lubridate::year(!!sampleDate))],
# sum(SB$temporal[lubridate::year(SB$temporal)==lubridate::year(!!sampleDate),"nSpp"]))
# expect_equivalent(exportBirds(SB, "temporal", "Yearly", "avgSll", "median")[as.character(lubridate::year(!!sampleDate))],
# avgSll)
# expect_equivalent(exportBirds(SB, "temporal", "Yearly", "nDays", "sum")[as.character(lubridate::year(!!sampleDate))],
# nrow(SB$temporal[lubridate::year(SB$temporal)==lubridate::year(!!sampleDate),]))
# # bugs in test
# # expect_equivalent(exportBirds(SB, "temporal", "Monthly", "nObs", "sum")[paste0(as.character(lubridate::year(!!sampleDate)),"-",as.character(lubridate::month(!!sampleDate)))],
# # nrow(test[test[,"month"]==lubridate::month(!!sampleDate),]))
# # bugs in test
# # expect_equivalent(exportBirds(SB, "temporal", "Monthly", "nVis", "sum")[paste0(as.character(lubridate::year(!!sampleDate)),"-",as.character(lubridate::month(!!sampleDate)))],
# # length(unique(test[test[,"month"]==lubridate::month(!!sampleDate),!!visitUID])))
# # expect_equivalent(exportBirds(SB, "temporal", "Monthly", "nSpp", "sum")[paste0(as.character(lubridate::year(!!sampleDate)),"-",as.character(lubridate::month(!!sampleDate)))],
# # length(unique(test[test[,"month"]==lubridate::month(!!sampleDate),!!scientificName])))
# # expect_equivalent(exportBirds(SB, "temporal", "Monthly", "avgSll", "median")[paste0(as.character(lubridate::year(!!sampleDate)),"-",as.character(lubridate::month(!!sampleDate)))],
# # median(dplyr::summarise(dplyr::group_by(test[test[,"month"]==lubridate::month(!!sampleDate),],!!visitUID), sll=n_distinct(!!scientificName))$sll))
# # expect_equivalent(exportBirds(SB, "temporal", "Monthly", "nDays", "sum")[paste0(as.character(lubridate::year(!!sampleDate)),"-",as.character(lubridate::month(!!sampleDate)))],
# # length(unique(test[test[,"month"]==lubridate::month(!!sampleDate),"day"])))
#
# ## bug in test
# # test<-test[test[,"month"]==lubridate::month(sampleDate) & test[,"day"]==lubridate::day(sampleDate),]
# #
# # expect_equivalent(exportBirds(SB, "temporal", "Daily", "nObs", "sum")[as.character(!!sampleDate)],
# # SB$temporal[!!sampleDate, "nObs"])
# # expect_equivalent(exportBirds(SB, "temporal", "Daily", "nVis", "sum")[as.character(!!sampleDate)],
# # SB$temporal[!!sampleDate, "nVis"])
# # expect_equivalent(exportBirds(SB, "temporal", "Daily", "nSpp", "sum")[as.character(!!sampleDate)],
# # SB$temporal[!!sampleDate, "nSpp"])
# # expect_equivalent(exportBirds(SB, "temporal", "Daily", "avgSll", "median")[as.character(!!sampleDate)],
# # median(dplyr::summarise(dplyr::group_by(test, visitUID), sll=n_distinct(scientificName))$sll))
#
# # testM<-dplyr::group_by(testM, year)
# #
# # nyears<-max(testO[,"year"])-min(testO[,"year"])+1
# #
# # yearlynObs<-dplyr::summarise(testM, res=n())
# # nObs<-c(yearlynObs$res, rep(0, nyears-length(yearlynObs$res)))
# #
# # yearlynVis<-dplyr::summarise(testM, res=n_distinct(visitUID))
# # nVis<-c(yearlynObs$res, rep(0, nyears-length(yearlynVis$res)))
# #
# # yearlynSpp<-dplyr::summarise(testM, res=n_distinct(scientificName))
# # nSpp<-c(yearlynObs$res, rep(0, nyears-length(yearlynSpp$res)))
# #
# # sll<-dplyr::summarise(dplyr::group_by(testO, year, month, visitUID), sll=n_distinct(scientificName))
# #
# # avgSll<-dplyr::summarise(dplyr::group_by(sll, year, month), avgSll=median(sll))
# #
# # avgSll<-avgSll[avgSll[,"month"]==lubridate::month(!!sampleDate),]$avgSll
# #
# # avgSll<-c(avgSll, rep(0, nyears-length(avgSll$res)))
# #
# # yearlynDay<-dplyr::summarise(testM, res=n_distinct(year, month, day))
# #
# # nDay<-c(yearlynDay$res, rep(0, nyears-length(yearlynDay$res)))
# #
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nObs", "sum")[lubridate::month(!!sampleDate)],
# # nrow(testM[,]))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nObs", "median")[lubridate::month(!!sampleDate)],
# # median(nObs))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nObs", "mean"),
# # mean(nObs))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nVis", "sum"),
# # sum(nVis))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nVis", "median"),
# # median(nVis))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nVis", "mean"),
# # mean(nVis))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nSpp", "sum"),
# # sum(nSpp))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nSpp", "median"),
# # median(nSpp))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nSpp", "mean"),
# # mean(nSpp))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "avgSll", "median"),
# # median(avgSll))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "avgSll", "mean"),
# # mean(avgSll))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nYears", "sum")[as.character(lubridate::year(!!sampleDate))],
# # length(unique(lubridate::year(SB$temporal[lubridate::month(sb$temporal)==lubridate::month(!!sampleDate),]))))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nDays", "sum")[as.character(lubridate::year(!!sampleDate))],
# # length(unique(lubridate::date(SB$temporal[lubridate::month(sb$temporal)==lubridate::month(!!sampleDate),]))))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nDays", "median")[as.character(lubridate::year(!!sampleDate))],
# # median(nDay))
# # expect_equivalent(exportBirds(SB, "temporal", "Month", "nDays", "mean")[as.character(lubridate::year(!!sampleDate))],
# # mean(nDay))
#
# })
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