Douglas Bates

Creating DictEncoded in the presence of missing values

2

When, e.g. a `PooledArray` column, that contains missing values is converted to `DictEncoded` the dictionary is based on the result of `DataAPI.refpool`, which includes `missing`. As a result both the...

Test failures on Julia v1.11.0-alpha and v1.12.0-DEV

1

Testing under v1.11.0-alpha2 and v1.12.0-DEV.199 on aarch64 systems fails with ```julia Test Summary: | Pass Total Time oxide | 2 2 1.6s ERROR: LoadError: UndefVarError: `@with` not defined in `Suppressor`...

Consider RegressionTests.jl and Chairmarks.jl for benchmarking

4

- Initially this branch just provides a `bench/runbenchmarks.jl` that uses `Chairmarks.jl` - The method is to construct a table of dataset names, formulas and number of seconds to run the...

Use init_from_lmm as default in fit! method for GLMM

9

I have been much more successful when using `init_from_lmm` when fitting GLMMs with `PRIMA.bobyqa` but have only tried it with `Bernoulli` responses. Shall we make it the default?

Oxide example model fit may be an inappropriate model

1

One of the tests in `test/pls.jl` uses the `:oxide` models defined in `test/modelcache.jl` ```julia :oxide => [@formula(Thickness ~ 1 + (1|Lot/Wafer)), @formula(Thickness ~ 1 + Source + (1+Source|Lot) + (1+Source|Lot&Wafer))],...

Switch to PRIMA.bobyqa for optimization?

1

See the discussion in https://github.com/lme4/lme4/issues/744 regarding `PRIMA.bobyqa` in linear mixed models. It may be even more useful to switch to `PRIMA.bobyqa` for GLMM optimization because that version of `bobyqa` allows...

Need to adjust parametricbootstrap display for GLMMs w/o scale parameter

3

A Bernoulli/binomial/Poisson GLMM does not have a scale parameter and `parametricbootstrap` produces a result in which the σ values are a vector of `missing`. The display or storage should be...

Change raneftable return type again - i.e. undo #634 a bit

1

In #634 we changed the output type of `raneftables` to be a `NamedTuple` of `DictTable`s. That is proving to be awkward. I thought it would be common to want to...

Re-export a few generics and types from the TypedTables package

7

I am finding it quite convenient to work with the `Table` type from [TypedTables.jl](https://github.com/JuliaData/TypedTables.jl) and have added a dependency on that package in the `profile` branch. I plan to re-export...

warning: false seems to be ignored

6

I'm not sure if this is related to QuartoNotebookRunner.jl or occurs downstream. Please let me know if I should report this at https://github.com/quarto-dev/quarto-cli instead. Rendering the enclosed with Quarto v1.5.31...