Rejuvenation

[strengejacke]

Fixes #525

Fixing workflows, possibly unresolved issues from #618?

Related to:

• Use #' @examplesIf roxygen directive over if() in the docs easystats#318
• Cleaning lints across easystats packages easystats#334
• Suppress (or attend to) warnings and messages in examples easystats#343
• Suppress (or attend to) warnings and messages in vignettes easystats#348

[strengejacke]

@IndrajeetPatil Here are some issues with not available packages, do you know how to fix this?
https://github.com/easystats/bayestestR/actions/runs/6361179508/job/17275434553?pr=625

[IndrajeetPatil]

@IndrajeetPatil Here are some issues with not available packages, do you know how to fix this? https://github.com/easystats/bayestestR/actions/runs/6361179508/job/17275434553?pr=625

Should be fixed for runs from here on.

[strengejacke]

Hm, there were actually quite some bugs in package functions which were not captured by the CI tests? @mattansb Here's an example that seems to have worked in the past (at least, we had a test for it), but now no longer works:

library(bayestestR)
library(blavaan)
#> Loading required package: Rcpp
#> This is blavaan 0.5-1
#> On multicore systems, we suggest use of future::plan("multicore") or
#>   future::plan("multisession") for faster post-MCMC computations.

data("PoliticalDemocracy", package = "lavaan")

model <- "
  # latent variable definitions
  dem60 =~ y1 + a*y2
  dem65 =~ y5 + a*y6

  # regressions
  dem65 ~ dem60

  # residual correlations
  y1 ~~ y5
"

model2 <- "
  # latent variable definitions
  dem60 =~ y1 + a*y2
  dem65 =~ y5 + a*y6

  # regressions
  dem65 ~ 0*dem60

  # residual correlations
  y1 ~~ 0*y5
"
suppressWarnings(capture.output({
  bfit <- blavaan::bsem(model,
    data = PoliticalDemocracy,
    n.chains = 1, burnin = 50, sample = 100
  )
  bfit2 <- blavaan::bsem(model2,
    data = PoliticalDemocracy,
    n.chains = 1, burnin = 50, sample = 100
  )
}))

bayesfactor_models(bfit, bfit2)
#> Warning: Bayes factors might not be precise.
#>   For precise Bayes factors, sampling at least 40,000 posterior samples is
#>   recommended.
#> Error in apply(diffs, 2, sum): dim(X) must have a positive length

^{Created on 2023-10-02 with reprex v2.0.2}

[codecov]

Codecov Report

Merging #625 (bb91bfb) into main (5f81276) will increase coverage by 2.36%.
Report is 31 commits behind head on main.
The diff coverage is 69.48%.

❗ Current head bb91bfb differs from pull request most recent head 36f0a3e. Consider uploading reports for the commit 36f0a3e to get more accurate results

@@            Coverage Diff             @@
##             main     #625      +/-   ##
==========================================
+ Coverage   50.87%   53.24%   +2.36%     
==========================================
  Files          65       65              
  Lines        5185     5287     +102     
==========================================
+ Hits         2638     2815     +177     
+ Misses       2547     2472      -75     

Files	Coverage Δ
R/area_under_curve.R	77.77% <ø> (ø)
R/bayesfactor_inclusion.R	96.55% <ø> (ø)
R/bayesfactor_models.R	75.94% <ø> (ø)
R/bayesfactor_restricted.R	66.66% <ø> (ø)
R/check_prior.R	0.00% <ø> (ø)
R/contr.equalprior.R	82.60% <100.00%> (+0.79%)	⬆️
R/convert_bayesian_to_frequentist.R	46.25% <ø> (ø)
R/convert_pd_to_p.R	80.00% <100.00%> (+80.00%)	⬆️
R/describe_prior.R	70.83% <ø> (ø)
R/effective_sample.R	50.00% <ø> (ø)
... and 31 more

... and 3 files with indirect coverage changes

[IndrajeetPatil]

Thanks, @strengejacke!

[strengejacke]

We should schedule a new release-round... Something like

easystats -> see -> insight -> bayestestR -> ... (parameters? performance?)

[strengejacke]

what about report, @rempsyc?

datawizard, parameters and performance are quite recent, so probably no update needed shortly.

[DominiqueMakowski]

Shouldn't easystats be last to have new versions reqs?

[strengejacke]

Yes, makes sense.

[rempsyc]

It's been almost 28 weeks for report, I'm happy to resubmit to CRAN. Seems like the other easystats packages devel versions I was relying on (insight, effectsize) were already pushed to CRAN, so technically I could do it next weekend?

[strengejacke]

I suggest adding all GitHub version to the REMOTES field, so you can test report on the latest devel versions first - otherwise, we may find revdep issues when we submit packages after report was accepted on CRAN.

[rempsyc]

Oh good idea, thanks!