David Phillippo
dmphillippo.bsky.social
David Phillippo
@dmphillippo.bsky.social
44 followers 110 following 67 posts
Statistician at University of Bristol | Bayesian, meta-analysis and evidence synthesis, #rstats
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The marginal_effects() function wraps predict() to create differences or ratios of absolute predictions.
For example:
* risk differences/ratios from an analysis of log odds ratios
* marginal differences in RMST or time-varying marginal hazard ratios from a survival analysis
📣 multinma update v0.7.1 on CRAN * New marginal_effects() function for computing marginal relative effects
* Progress bars for long operations
* trt_ref argument to predict() has been renamed to baseline_ref for consistency
* Bug fixes Full details 👉https://t.co/abYabQCvKS
This is now resolved: Stan has been patched, and multinma is back on CRAN
https://x.com/dmphillippo/status/1765397920130510965?s=20
multinma is back on CRAN 🎉

Stan has been patched to fix the memory allocation bug

This release (v0.6.1) also includes a bugfix for piecewise exponential hazards models - changelog here 👉
https://t.co/abYabQCvKS

Binaries will be built by CRAN over the next few days https://t.co/4UHJPzfgig
PSA: multinma is temporarily unavailable from CRAN

A small memory allocation bug in Stan tripped some additional CRAN checks, which needs to be patched by rstan.

multinma is still fully functional and passes all tests. In the meantime:
If you need to install, you can use R-universe:
install.packages("multinma", repos = c("https://dmphillippo.r-universe.dev", getOption("repos")))
Automatic checking of integration error for ML-NMR:
- Checks sufficient number of integration points within a single model run
- Gives nice warnings if action is required
- Much lower default n_int=64 (previously 1000!) means much faster models!
Multilevel network meta-regression for general likelihoods: synthesis of individual and aggregate data with applications to survival analysis
Network meta-analysis combines aggregate data (AgD) from multiple randomised controlled trials, assuming that any effect modifiers are balanced across populations. Individual patient data (IPD) meta-regression is the "gold standard" method to relax this assumption, however IPD are frequently only available in a subset of studies. Multilevel network meta-regression (ML-NMR) extends IPD meta-regression to incorporate AgD studies whilst avoiding aggregation bias, but currently requires the aggregate-level likelihood to have a known closed form. Notably, this prevents application to time-to-event outcomes. We extend ML-NMR to individual-level likelihoods of any form, by integrating the individual-level likelihood function over the AgD covariate distributions to obtain the respective marginal likelihood contributions. We illustrate with two examples of time-to-event outcomes, showing the performance of ML-NMR in a simulated comparison with little loss of precision from a full IPD analysis, and demonstrating flexible modelling of baseline hazards using cubic M-splines with synthetic data on newly diagnosed multiple myeloma. ML-NMR is a general method for synthesising individual and aggregate level data in networks of all sizes. Extension to general likelihoods, including for survival outcomes, greatly increases the applicability of the method. R and Stan code is provided, and the methods are implemented in the multinma R package.
arxiv.org
More survival analysis:
- Left/right/interval censoring, delayed entry
- Predict and plot survival probabilities, hazards, cumulative hazards, mean survival times, restricted mean survival times, quantiles of the survival time distribution, and median survival times
📣multinma v0.6.0 update on CRAN

Major new features (details below):
- Survival analysis
- Automatic integration convergence checking (faster models!)

Plus other improvements and bugfixes

Full changelog 👉https://dmphillippo.github.io/multinma/news/
Changelog
dmphillippo.github.io
More nuggets in this paper:
- A new algorithm for automatic convergence checking for numerical integration 👉 fewer integration samples needed, nice warnings, MUCH faster ML-NMR models
- M-spline baseline hazard model with a novel random walk shrinkage prior 👀
Survival analysis with multilevel network meta-regression? Yes please! New preprint extending ML-NMR to likelihoods of any form, including for survival analysis. Accompanied by a new multinma release v0.6.0, which is on CRAN now. https://arxiv.org/abs/2401.12640
📣 multinma update 0.4.2 is on CRAN

Fixes a couple of bugs when trials have repeated arms of the same treatment 🐙
✅ get_nodesplits() for node-splitting no longer errors
✅ printing the network now shows the repeated arms

Details 👉 https://dmphillippo.github.io/multinma/news/index.html
Changelog
dmphillippo.github.io
📣 Bugfix update multinma 0.4.1 rolling out on CRAN

Fixes an issue introduced with tidyr 1.2.0 that broke ordered multinomial models

Details 👉 https://dmphillippo.github.io/multinma/news
Changelog
dmphillippo.github.io
📣 Update to multinma v0.4.0 on CRAN
- Node-splitting for checking inconsistency
- Predictive distributions for random effects models
- Improved handling of correlations for integration points (ML-NMR models)
- And more! Details 👉 https://dmphillippo.github.io/multinma/news
#rstats #metaanalysis
Booking now open for our network meta-analysis course 👇 https://x.com/sdias_stats/status/1486706844466827267
PhD opportunity in Glasgow - still time to apply!

Predictors of early trial termination using individual-level participant data and aggregate-level data from multiple trials

Co-supervised by myself, advisory team includes @sdias_stats and @WeltonNicky

https://t.co/h4USGbeADd
📣Update to multinma (v0.3.0) now on CRAN

- New features for flexibly specifying baseline distributions when producing absolute predictions
- Squashes bugs when specifying certain types of models with contrast data

Full details: https://dmphillippo.github.io/multinma/news/
#rstats #metaanalysis
Changelog
dmphillippo.github.io
Looking forward to speaking at @HERC_Oxford this Wednesday - details and registration at the link below https://x.com/HERC_Oxford/status/1373967203851251715
Catching up on @cantabile's excellent #ESMARConf2021 talk from earlier this morning, developing NMA reporting toolchains for stakeholders like Cochrane. Great to see {multinma} and {nmathresh} being used in the wild too! https://x.com/eshackathon/status/1352529752419164160
📣Update to multinma (v0.2.1) now on CRAN

- Squashed a couple of bugs
- Improved documentation of available likelihoods and link functions

Details: https://dmphillippo.github.io/multinma/news/
Changelog
dmphillippo.github.io