tests/testthat/test_fmrimodel.R

In bbuchsbaum/fmrireg: R package for the anlysis of fmri data

options(mc.cores=2)
facedes <- read.table(system.file("extdata", "face_design.txt", package = "fmrireg"), header=TRUE)


test_that("can construct and run an fmri_model", {

  facedes$repnum <- factor(facedes$rep_num)
  scans <- paste0("rscan0", 1:6, ".nii")
  dset <- fmri_dataset(scans=scans,
                       mask="mask.nii",
                       TR=1.5,
                       run_length=rep(436,6),
                       event_table=facedes)

 
  espec <- event_model(onset ~ hrf(repnum), data=facedes, block=~run, sampling_frame=dset$sampling_frame)
  bspec <- baseline_model(basis="bs", degree=5, sframe=dset$sampling_frame)
  fmod <- fmri_model(espec, bspec)
  expect_true(!is.null(fmod))
  expect_equal(length(terms(fmod)), 3)
  expect_equal(ncol(design_matrix(fmod)), length(conditions(fmod)))
  expect_equal(2, length(baseline_terms(fmod)))
  expect_null(contrast_weights(fmod)$repnum)
  #p<-print(fmod)
  expect_true(TRUE)
  
})



# test_that("a one-run, one-contrast linear model analysis", {
#   df1 <- subset(imagedes,run==1)
#   df1 <- subset(df1, !is.na(onsetTime))
#   
#   df1$sdur <- scale(df1$duration)[,1]
#   
#   dmat <- matrix(rnorm(400*100), 400, 100)
#   md <- matrix_dataset(dmat, TR=1.5, run_length=400, event_table=df1)
#   con <- contrast_set(contrast( ~ Thorns - Massage, name="Thorns_Massage"))
#   mod <- fmri_lm(onsetTime ~ hrf(imageName, subset = !is.na(onsetTime), contrasts=con), ~ run, dataset=md, durations=sdur)
#  
# })


# test_that("a two-run, one contrast linear model analysis", {
#   df1 <- subset(imagedes,run %in% c(1,2))
#   df1 <- subset(df1, !is.na(onsetTime))
#   
#   df1$sdur <- scale(df1$duration)[,1]
#   
#   dmat <- matrix(rnorm(800*100), 800, 100)
#   md <- matrix_dataset(dmat, TR=1.5, run_length=c(400,400), event_table=df1)
#   con <- contrast_set(contrast( ~ Thorns - Massage, name="Thorns_Massage"))
#   mod <- fmri_lm(onsetTime ~ hrf(imageName, contrasts=con), ~ run, dataset=md, durations=sdur)
#   
#   
# })

# test_that("can load and run a simple config file", {
#   config <- read_fmri_config("test_data/images_study/config.R")
#   dset <- fmri_dataset(config$scans, config$mask, config$TR, 
#                            config$run_length,
#                            config$event_table,
#                            config$aux_table, 
#                            base_path=config$base_path)
#   
#   frame <- sampling_frame(dset$run_length, config$TR)
#   mod <- fmri_model(config$event_model, config$baseline_model, config$design, dset$aux_table,
#                     basis=HRF_SPMG1, dset$runids, dset$run_length, config$TR, drop_empty=TRUE)
#                     
#   
#   mod <- fmri_glm(config$event_model, 
#                   dataset=dset, durations=0)
# })