-
```
n_repeat upper | c(rep(FALSE, 65), TRUE)][1]
p_adaptive = mean(res_rerandom$z[1:L_m] > res_rerandom$res_z[1:L_m])
x
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Some overhead function that calls `tmbstan::tmbstan(Assessment)` or `tmbstan(RCModel)` and calculates posteriors of derived parameters. Also needs to interface with `rshinystan`
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When calculating TMB for all public studies, we found `cscc_hgsc_bcm_2014` with unexpected high TMB scores (see this PR: https://github.com/cBioPortal/datahub/pull/1428). Altho in MAF all mutations ar…
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Show MSI-H and TMB-H under alteration column
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The existing model debugging vignette is a bit low-level. Mention using things like g3a_trace_nan and g3_to_desc (to make sure the model has everything you expect).
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When trying to predict with standard errors from a fitted model (mixed effects beta regression), like so:
```
predict(m, newdata=df, se.fit=TRUE)
```
I often get the following error message:
```
…
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Getting this on A LOT of files.... I ran the following:
slack-cleaner --token xxxxxxxxxxxxxxx --file --types snippets,images
```
Failed to delete ->
{ 'channels': ['CAEABN55M'],
'commen…
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Mikael Jagan has pointed in [this thread](https://github.com/lme4/lme4/issues/768#issuecomment-1941857396) that checking on built vs. current versions of upstream packages (TMB, Matrix) can be done mo…
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### Description
This issue will be a collect all for small tasks that need to be completed for quality control after features are implemented in milestone 2. For example, @rklasky mentioned there a…
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Support the use of TMB::oneStepPredict() in gadget3-generated models. This
will require the addition of an “indicator variable”, with the same dimensions as the
observations array, used to turn indi…