tests_addwpmfs.R
In wsyn: Wavelet Approaches to Studies of Synchrony in Ecology and Other Fields

context("addwpmfs")

test_that("test it",{
  set.seed(101)
  sig<-matrix(.8,5,5)
  diag(sig)<-1
  lents<-50
  #dat1<-t(mvtnorm::rmvnorm(lents,mean=rep(0,5),sigma=sig))
  #dat2<-t(mvtnorm::rmvnorm(lents,mean=rep(0,5),sigma=sig))
  dat1<-t(copy_rmvnorm(lents,mean=rep(0,5),sigma=sig)) #This copy function is in helper-utils.R. I made this change to avoid having to condition the performance of these tests on the availability of mvtnorm on the platform, since mvtnorm is in (and should be in) Suggests.
  dat2<-t(copy_rmvnorm(lents,mean=rep(0,5),sigma=sig))
  dat<-rbind(dat1,dat2)
  times<-1:lents
  dat<-cleandat(dat,times,clev=1)$cdat
  coords<-data.frame(Y=rep(0,10),X=1:10)
  method<-"coh.sig.fast"
  clustobj<-clust(dat,times,coords,method,nsurrogs = 100)
  res<-addwpmfs(clustobj)
  
  #old tests, to make sure other parts have not changed
  expect_equal(class(res),c("clust","list"))
  expect_equal(res$dat,dat)
  expect_equal(res$times,times)
  expect_equal(res$coords,coords)
  expect_equal(names(res$methodspecs),c("method","tsrange","nsurrogs",
                                        "scale.min","scale.max.input","sigma","f0",
                                        "weighted","sigthresh"))
  expect_equal(diag(res$adj),rep(NA*numeric(1),10))
  expect_true(isSymmetric(res$adj))
  expect_equal(class(res$clusters),"list")
  h<-sapply(FUN=length,X=res$clusters)
  expect_equal(h,rep(10,length(h)))
  expect_equal(res$clusters[[1]],rep(1,10))
  expect_equal(class(res$modres),"list")
  expect_equal(length(res$modres),length(res$clusters))
  expect_equal(class(res$modres[[1]]),"list")
  expect_equal(names(res$modres[[1]]),c("totQ","modQ","nodeQ"))
  expect_equal(class(res$mns),"list")
  expect_equal(length(res$mns),length(res$clusters))
  expect_equal(dim(res$mns[[1]]),c(1,lents))
  expect_equal(dim(res$mns[[2]]),c(2,lents))
  expect_equal(as.vector(res$mns[[1]]),apply(FUN=mean,X=dat,MARGIN=2))
  
  #now look at wpmf part for correct format
  expect_equal(class(res$wpmfs),"list")
  expect_equal(length(res$wpmfs),length(res$clusters))
  expect_equal(class(res$wpmfs[[1]]),"list")
  expect_equal(class(res$wpmfs[[2]]),"list")
  expect_equal(length(res$wpmfs[[1]]),1)
  expect_equal(length(res$wpmfs[[2]]),2)
  expect_equal(class(res$wpmfs[[1]][[1]]),c("wpmf","tts","list"))
  expect_equal(class(res$wpmfs[[2]][[1]]),c("wpmf","tts","list"))
  expect_equal(class(res$wpmfs[[2]][[2]]),c("wpmf","tts","list"))
  
  #these should be identical, except for sampling-error-level differences in the contour
  #plotmag(res$wpmfs[[1]][[1]])
  #plotmag(wpmf(dat,times,sigmethod="quick",nrand=1000))
  
  #these should look identical, except for sampling-error-level differences in the contour
  #plotmag(res$wpmfs[[2]][[2]])
  #plotmag(wpmf(dat[1:5,],times,sigmethod="quick",nrand=1000))
  
  #these should look identical, except for sampling-error-level differences in the contour
  #plotmag(res$wpmfs[[2]][[1]])
  #plotmag(wpmf(dat[6:10,],times,sigmethod="quick",nrand=1000))
  
  #the above pairs of plots were close enough to identical, so I commented and test for 
  #consistency through time 
  h<-res$wpmfs
  h[[1]][[1]]<-Mod(h[[1]][[1]]$values[20:30,20:30])
  h[[2]][[2]]<-Mod(h[[2]][[2]]$values[20:30,20:30])
  h[[2]][[1]]<-Mod(h[[2]][[1]]$values[20:30,20:30]) #these changes are for file size reasons
  expect_known_value(h,file="../vals/addwpmfs_testval_01",update=FALSE)
})