v4.4.1

[Neves-P]

DAISIE 4.4.1

• Fix bug in the calculation of shift loglikelihoods.
• Fix bug where parameters being optimized could incorrectly be Inf Relaxed-rate model cannot take Inf K as initial parameter #159 Error when relaxed parameter mean or sd is infinite #160 (@joshwlambert).
• DAISIE_SR_loglik_CS_M1() is now DAISIE_loglik_CS_shift().
• New pkgdown website.
• Several improvements to the relaxed rate code.

[Neves-P]

@joshwlambert @rsetienne , could you please take a quick look at the NEWS.md and see if I'm forgetting anything? The text is the same as the first comment of this PR.

[joshwlambert]

It would be useful to link the pkgdown website in the About section on the DAISIE github repo.

[joshwlambert]

I've reviewed the changes and everything looks good to me.

There is nothing missing from the NEWS file that I could see other than extremely minor changes, e.g. explicit namespacing of tests.

I would suggest submitting to CRAN in order to easily use the new changes when running models locally and on the cluster.

[joshwlambert]

As far as I can see the test that has the numerical discrepancy issue has now been skipped. Would it be possible to log an issue stating which test (file name and line number) is causing the issue? This can then be tackled in a follow-up PR.

[joshwlambert]

@rsetienne @Neves-P It would be great to get these changes merged and a new version of DAISIE sent to CRAN to easily install the package across different platforms.

[Neves-P]

This looks good to me, I just added a tolerance again and unskipped the test after having checked with Hanno and @rsetienne that these numerical differences are to be expected. @rsetienne , as soon as GHA are done, could you please merge or should I go ahead (there is already one review, so I can merge it).

[codecov-commenter]

Codecov Report

Merging #162 (35cad4c) into master (ebf13e6) will decrease coverage by 1.43%.
Report is 1 commits behind head on master.
The diff coverage is 73.80%.

❗ Current head 35cad4c differs from pull request most recent head b0d29f2. Consider uploading reports for the commit b0d29f2 to get more accurate results

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@@            Coverage Diff             @@
##           master     #162      +/-   ##
==========================================
- Coverage   68.54%   67.11%   -1.43%     
==========================================
  Files          78       79       +1     
  Lines        7964     8123     +159     
==========================================
- Hits         5459     5452       -7     
- Misses       2505     2671     +166     

Files	Coverage Δ
R/DAISIE_ML1.R	82.50% <100.00%> (-0.77%)	⬇️
R/DAISIE_ML_CS.R	41.26% <ø> (ø)
R/DAISIE_SR_loglik_CS.R	29.55% <100.00%> (-55.37%)	⬇️
R/DAISIE_loglik_CS.R	81.27% <100.00%> (-0.86%)	⬇️
R/DAISIE_utils.R	55.31% <ø> (ø)
R/create_pars.R	71.15% <ø> (ø)
R/DAISIE_loglik_integrate.R	88.41% <75.00%> (-0.48%)	⬇️
R/DAISIE_loglik_CS_shift.R	71.71% <71.71%> (ø)

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