error with test_regional_analysis

[brynngithub]

Hi！ Recently I ran some examples in the test_mvpa_regional.R in testhat folder, but when I run the last line of the example "standard mvpa_regional and custom cross-validation runs without error/line 290" my RStudio throws me this error:

Error in purrr::map(): ℹ In index: 1. Caused by error in v@coords: ! no applicable method for @ applied to an object of class "integer"

Programming Language: R 4.3.1, Rstudio 2022.02.4 Operating System: Ununtu 16.04.7 Framework/Library Used: rMVPA 0.1.2, purr1.0.2, Matrix1.6-4

I really appreciate any help you can provide.

[bbuchsbaum]

Thanks for reporting this. This should now be fixed. Please don't hesitate to reach out to me if you want to use this package.

[brynngithub]

Thank you for your timely response. However, when I ran the following code, I faced the same error:

library(neuroim2) library(neurosurf) library(testthat) library(assertthat) library(rMVPA) test_that("standard mvpa_regional and custom cross-validation runs without error", { dataset <- gen_sample_dataset(c(5,5,5), 100, blocks=3) sample_set <- replicate(5, { list(train=sample(1:80), test=sample(1:100)) }, simplify=FALSE)

regionMask <- NeuroVol(sample(1:5, size=length(dataset$dataset$mask), replace=TRUE), space(dataset$dataset$mask)) cval <- custom_cross_validation(sample_set)

model <- load_model("sda_notune") mspec <- mvpa_model(model, dataset$dataset, design=dataset$design, model_type="classification", crossval=cval) res <- run_regional(mspec,regionMask) expect_true(!is.null(res)) })

[bbuchsbaum]

I don't think you successfully reinstalled the new version. I know this because the new code is as follows: (see the commented out line "#size <- sapply(vlist, function(v) nrow(v@coords))"

remotes::install_github("bbuchsbaum/rMVPA")

....

result <- purrr::map(1:length(batch_ids), function(i) { futile.logger::flog.info("mvpa_iterate: compute analysis for batch %s ...", i)

browser()

vlist <- vox_list[batch_ids[[i]]]
#size <- sapply(vlist, function(v) nrow(v@coords))
size <- sapply(vlist, function(v) length(v))

sf <- get_samples(dset, vox_list[batch_ids[[i]]]) %>% mutate(.id=batch_ids[[i]], rnum=rnums[[i]], size=size) %>% filter(size>=2)
if (nrow(sf) > 0) {
  sf <- sf %>% rowwise()  %>% mutate(roi=list(extract_roi(sample,dset))) %>% select(-sample) 
  fut_mvpa(mod_spec, sf, tot, do_fun, verbose, permute, compute_performance, return_fits, return_predictions)
}

}) %>% bind_rows()

[brynngithub]

Yes, as you mentioned, after successfully reinstalling the new version, the script runs smoothly now. Thank you very much for your help!