tests/testthat/tests_clust.R

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

context("clust")

test_that("test error checking",{
  dat<-matrix(rnorm(300),10,30)
  times<-1:30
  dat<-cleandat(dat,times,2)$cdat
  coords<-data.frame(X=1:10,Y=11:20)
  expect_error(clust(dat,times,coords,"coh",weighted=FALSE),
               "Error in clust: unweighted networks available only if method involves a significance test")
  expect_error(clust(dat,times,coords,"test"),"Error in clust: bad value of method")
  
  coords<-matrix(1:20,10,2)
  expect_error(clust(dat,times,coords,"coh"),"Error in clust: coords must be a data frame")  
  
  coords<-data.frame(X=1:9,Y=11:19)
  expect_error(clust(dat,times,coords,"coh"),"Error in clust: coords must have one row for each row of dat")
  
  coords<-data.frame(A=1:10,B=11:20)
  expect_error(clust(dat,times,coords,"coh"),"Error in clust: coords must have columns X and Y, or lon and lat, or longitude and latitude")
})

test_that("test for correct format",{
  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"
  res<-clust(dat,times,coords,method,nsurrogs = 100)
  
  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))
  expect_true(is.na(res$wmfs))
  expect_true(is.na(res$wpmfs))
})