tests/testthat/tests_addwmfs.R

In reumandc/wsyn: Wavelet Approaches to Studies of Synchrony in Ecology and Other Fields

context("addwmfs")

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<-addwmfs(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 wmf part for correct format
  expect_equal(class(res$wmfs),"list")
  expect_equal(length(res$wmfs),length(res$clusters))
  expect_equal(class(res$wmfs[[1]]),"list")
  expect_equal(class(res$wmfs[[2]]),"list")
  expect_equal(length(res$wmfs[[1]]),1)
  expect_equal(length(res$wmfs[[2]]),2)
  expect_equal(class(res$wmfs[[1]][[1]]),c("wmf","tts","list"))
  expect_equal(class(res$wmfs[[2]][[1]]),c("wmf","tts","list"))
  expect_equal(class(res$wmfs[[2]][[2]]),c("wmf","tts","list"))

  #these should be identical
  #plotmag(res$wmfs[[1]][[1]])
  #plotmag(wmf(dat,times))
  
  #these should look identical
  #plotmag(res$wmfs[[2]][[2]])
  #plotmag(wmf(dat[1:5,],times))
  
  #these should look identical
  #plotmag(res$wmfs[[2]][[1]])
  #plotmag(wmf(dat[6:10,],times))
  
  #the above pairs of plots were visually identical, so I commented and test for 
  #consistency through time 
  h<-res$wmfs
  h[[1]][[1]]<-Mod(h[[1]][[1]]$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/addwmfs_testval_01",update=FALSE)
})