NEWS.md

In multinma: Bayesian Network Meta-Analysis of Individual and Aggregate Data

multinma 0.5.1

• Fix: Now compatible with latest StanHeaders v2.26.25 (fixes #23)
• Fix: Dealt with various tidyverse deprecations
• Fix: Updated TSD URLs again (thanks to @ndunnewind)

multinma 0.5.0

• Feature: Treatment labels in network plots can now be nudged away from the nodes when weight_nodes = TRUE, using the new nudge argument to plot.nma_data() (#15).
• Feature: The data frame returned by calling as_tibble() or as.data.frame() on an nma_summary object (such as relative effects or predictions) now includes columns for the corresponding treatment (.trt) or contrast (.trta and .trtb), and a .category column may be included for multinomial models. Previously these details were only present as part of the parameter column
• Feature: Added log t prior distribution log_student_t(), which can be used for positive-valued parameters (e.g. heterogeneity variance).
• Improvement: set_agd_contrast() now produces an informative error message when the covariance matrix implied by the se column is not positive definite. Previously this was only checked by Stan after calling the nma() function.
• Improvement: Updated plaque psoriasis ML-NMR vignette to include new analyses, including assessing the assumptions of population adjustment and synthesising multinomial outcomes.
• Improvement: Improved behaviour of the .trtclass special in regression formulas, now main effects of .trtclass are always removed since these are collinear with .trt. This allows expansion of interactions with * to work properly, e.g. ~variable*.trtclass, whereas previously this resulted in an over-parametrised model.
• Fix: CRAN check note for manual HTML5 compatibility.
• Fix: Residual deviance and log likelihood parameters are now named correctly when only contrast-based aggregate data is present (PR #19).

multinma 0.4.2

• Fix: Error in get_nodesplits() when studies have multiple arms of the same treatment.
• Fix: print.nma_data() now prints the repeated arms when studies have multiple arms of the same treatment.
• Fix: CRAN warning regarding invalid img tag height attribute in documentation.

multinma 0.4.1

• Fix: tidyr v1.2.0 breaks ordered multinomial models when some studies do not report all categories (i.e. some multinomial category outcomes are NA in multi()) (PR #11)

multinma 0.4.0

• Feature: Node-splitting models for assessing inconsistency are now available with consistency = "nodesplit" in nma(). Comparisons to split can be chosen using the nodesplit argument, by default all possibly inconsistent comparisons are chosen using get_nodesplits(). Node-splitting results can be summarised with summary.nma_nodesplit() and plotted with plot.nodesplit_summary().
• Feature: The correlation matrix for generating integration points with add_integration() for ML-NMR models is now adjusted to the underlying Gaussian copula, so that the output correlations of the integration points better match the requested input correlations. A new argument cor_adjust controls this behaviour, with options "spearman", "pearson", or "none". Although these correlations typically have little impact on the results, for strict reproducibility the old behaviour from version 0.3.0 and below is available with cor_adjust = "legacy".
• Feature: For random effects models, the predictive distribution of relative/absolute effects in a new study can now be obtained in relative_effects() and predict.stan_nma() respectively, using the new argument predictive_distribution = TRUE.
• Feature: Added option to calculate SUCRA values when summarising the posterior treatment ranks with posterior_ranks() or posterior_rank_probs(), when argument sucra = TRUE.
• Improvement: Factor order is now respected when trt, study, or trt_class are factors, previously the order of levels was reset into natural sort order.
• Improvement: Update package website to Bootstrap 5 with release of pkgdown 2.0.0
• Fix: Model fitting is now robust to non-default settings of options("contrasts").
• Fix: plot.nma_data() no longer gives a ggplot deprecation warning (PR #6).
• Fix: Bug in predict.stan_nma() with a single covariate when newdata is a data.frame (PR #7).
• Fix: Attempting to call predict.stan_nma() on a regression model with only contrast data and no newdata or baseline specified now throws a descriptive error message.

multinma 0.3.0

• Feature: Added baseline_type and baseline_level arguments to predict.stan_nma(), which allow baseline distributions to be specified on the response or linear predictor scale, and at the individual or aggregate level.
• Feature: The baseline argument to predict.stan_nma() can now accept a (named) list of baseline distributions if newdata contains multiple studies.
• Improvement: Misspecified newdata arguments to functions like relative_effects() and predict.stan_nma() now give more informative error messages.
• Fix: Constructing models with contrast-based data previously gave errors in some scenarios (ML-NMR models, UME models, and in some cases AgD meta-regression models).
• Fix: Ensure CRAN additional checks with --run-donttest run correctly.

multinma 0.2.1

• Fix: Producing relative effect estimates for all contrasts using relative_effects() with all_contrasts = TRUE no longer gives an error for regression models.
• Fix: Specifying the covariate correlation matrix cor in add_integration() is not required when only one covariate is present.
• Improvement: Added more detailed documentation on the likelihoods and link functions available for each data type (likelihood and link arguments in nma()).

multinma 0.2.0

• Feature: The set_*() functions now accept dplyr::mutate() style semantics, allowing inline variable transformations.
• Feature: Added ordered multinomial models, with helper function multi() for specifying the outcomes. Accompanied by a new data set hta_psoriasis and vignette.
• Feature: Implicit flat priors can now be specified, on any parameter, using flat().
• Improvement: as.array.stan_nma() is now much more efficient, meaning that many post-estimation functions are also now much more efficient.
• Improvement: plot.nma_dic() is now more efficient, particularly with large numbers of data points.
• Improvement: The layering of points when producing "dev-dev" plots using plot.nma_dic() with multiple data types has been reversed for improved clarity (now AgD over the top of IPD).
• Improvement: Aggregate-level predictions with predict() from ML-NMR / IPD regression models are now calculated in a much more memory-efficient manner.
• Improvement: Added an overview of examples given in the vignettes.
• Improvement: Network plots with weight_edges = TRUE no longer produce legends with non-integer values for the number of studies.
• Fix: plot.nma_dic() no longer gives an error when attempting to specify .width argument when producing "dev-dev" plots.

multinma 0.1.3

• Format DESCRIPTION to CRAN requirements

multinma 0.1.2

• Wrapped long-running examples in \donttest{} instead of \dontrun{}

multinma 0.1.1

• Reduced size of vignettes
• Added methods paper reference to DESCRIPTION
• Added zenodo DOI

multinma 0.1.0

• Feature: Network plots, using a plot() method for nma_data objects.
• Feature: as.igraph(), as_tbl_graph() methods for nma_data objects.
• Feature: Produce relative effect estimates with relative_effects(), posterior ranks with posterior_ranks(), and posterior rank probabilities with posterior_rank_probs(). These will be study-specific when a regression model is given.
• Feature: Produce predictions of absolute effects with a predict() method for stan_nma objects.
• Feature: Plots of relative effects, ranks, predictions, and parameter estimates via plot.nma_summary().
• Feature: Optional sample_size argument for set_agd_*() that:
• Enables centering of predictors (center = TRUE) in nma() when a regression model is given, replacing the agd_sample_size argument of nma()
• Enables production of study-specific relative effects, rank probabilities, etc. for studies in the network when a regression model is given
• Allows nodes in network plots to be weighted by sample size
• Feature: Plots of residual deviance contributions for a model and "dev-dev" plots comparing residual deviance contributions between two models, using a plot() method for nma_dic objects produced by dic().
• Feature: Complementary log-log (cloglog) link function link = "cloglog" for binomial likelihoods.
• Feature: Option to specify priors for heterogeneity on the standard deviation, variance, or precision, with argument prior_het_type.
• Feature: Added log-Normal prior distribution.
• Feature: Plots of prior distributions vs. posterior distributions with plot_prior_posterior().
• Feature: Pairs plot method pairs().
• Feature: Added vignettes with example analyses from the NICE TSDs and more.
• Fix: Random effects models with even moderate numbers of studies could be very slow. These now run much more quickly, using a sparse representation of the RE correlation matrix which is automatically enabled for sparsity above 90% (roughly equivalent to 10 or more studies).

multinma 0.0.1

• Initial release.

multinma documentation built on May 31, 2023, 5:46 p.m.