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r-devel / r-project-sprint-2023

Material for the R project sprint
https://contributor.r-project.org/r-project-sprint-2023/
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Project: Addressing Bugs in nlme #42

Open hturner opened 1 year ago

hturner commented 1 year ago

Discussed in https://github.com/r-devel/r-project-sprint-2023/discussions/4

Originally posted by **giscus[bot]** June 26, 2023 # R Project Sprint 2023 - Addressing Bugs in nlme Addressing open bugs on the recommended package nlme for (non)linear mixed effect models. https://contributor.r-project.org/r-project-sprint-2023/projects/nlme-bugs/
MetaEntropy commented 1 year ago

I am interested to contribute to this project.

aitap commented 1 year ago

I'll be happy to help with bugs that involve compiled C/Fortran code.

aitap commented 10 months ago
Bug ID Topic Outcome
18505 behaviour changing with order of group variable
17884 new confint.lme method for fixed effects only
17988 what to return for corARMA with p = q = 0
18472 correct behaviour of gls
17712 conditions when algorithm should use decomposition
18285 how to handle rank deficiency
17961 appropriate df to use in tests
17866 Initializing corStruct outside gls call gives different results
16890 intervals.lmList does not work for with pool = FALSE
18192, 17227 crash in gnls when using spatial correlation structures Traced by Mikko Korpela and Benjamin Tyner to originate in nlme:::Dim.corStruct where val[["start"]] is calculated to contain offsets into c(loss_gradient, residuals) that result in corStruct_recalc → mult_mat overflowing a buffer on the heap.

It seems that the right values would have been c(0, cumsum(val[["len"]])[-val[["M"]]]), or maybe even the original value of val[['start'] = match(levels(groups), groups) - 1L), but the code has been there since the oldest version of nlme present on CRAN, so it's hard to argue in favour of changing it.
16864 lme fails to warn when data are near-redundant
16975 REML estimation incorrect with fixed sigma
17236 Correct df for intercept in lme
18433 infinite loop dependent on random seed
16806 method fails for individuals with single observations patch available as of 7th of October