- 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)

- 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).

- 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.

- 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)

- 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.

- 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.

- 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()`

).

- 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.

- Format DESCRIPTION to CRAN requirements

- Wrapped long-running examples in
`\donttest{}`

instead of`\dontrun{}`

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

- 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

- Enables centering of predictors (
- 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).

- Initial release.