NEWS.md

In AIMS/bayesnec: A Bayesian No-Effect- Concentration (NEC) Algorithm

bayesnec 2.1.3.0

• Added citation for JSS manuscript describing bayesnec.

bayesnec 2.1.2.0

• Added step function to toolkit to allow for brms non-linear formula evaluation (89edef72).

bayesnec 2.1.1.0

• Fixed issues with summary and print methods (bf058f36).

• Plotting methods now display the proper no-effect toxicity legend label (2be55d51).

• Implemented native brms::beta_binomial() instead of custom family beta_binomial2 (c6c78fb7).

• compare_* functions now have N(S)EC as default behaviour (c4c84ba1).

• Changed argument name precision to resolution in many functions to maintain syntax compatibility with brms (727d6700).

• Standardised plot style between sample_priors and check_priors (6c59af07).

bayesnec 2.1.0.3

• Improved speed in test runs for CRAN (d5d097fb).

• Aligned generic method consistency for rhat (afb10577).

• Fixed a bug relating to 01 bounded x data in define_prior (3ab93e0).

• Fixed messages returned for set_distirbution (f483160).

• Reduced n_trials and deleted unnecessary set.seed in while call for make_good_inits (3c5f084).

bayesnec 2.1.0.2

• Fixed bug introduced when implementing recycling the seed passed to bnec (01394a17).

• Included additional criteria in the initial values algorithm to ensure initial values can be fit in stan (fe89484a).

bayesnec 2.1.0.1

• Cleaned parameter title names in sample_priors (6973bae1).

• Small tweak to initialisation search, such that the seed used for a bnec call (via ... arguments to brms::brm) gets recycled and therefore it generates the same initialisation values across platforms (c74a3c46).

bayesnec 2.1.0.0

• Many improvements to package following suggestions from JSS editors. These include many things like dependency on R 4.1 to support native pipeOp, revamp of predict method for classes, major overhaul on package documentation, and much more. All issues were dealt with collectively via a milestone.

bayesnec 2.0.2.5

• Fixed issue with new "inits"-->"init" argument name in brm (30eb8e6).

bayesnec 2.0.2.4

• Fixed issue with new prior structures in brms (c5c16be).

bayesnec 2.0.2.3

• Fixed issue with expand_manec (1ced4d4).

• Fixed issue with check_formula (87fab44).

bayesnec 2.0.2.2

• Fixed issue with gsub substitution of x in original brms non-linear formulas, and added various tests (fa588fb).

bayesnec 2.0.2.1

• Fixed vignette formula bugs (162fec9).

bayesnec 2.0.2

• Fixed CRAN bugs related to testthat (cfe9f20).

• Changed decline detection behaviour in function check_data (c2744e3).

bayesnec 2.0.1

• Addition of herbicide data (2b13ef5).

• streamlined check_* functions for negative predictors vectors -- no error anymore (via check_data), now drop models with informative message (via check_models) (f134311).

bayesnec 2.0

• bnec now works exclusively with formulas (4bccc07, d3531b4, bccb0da, 340269e).

• Added +, c and update methods via a common class bnecfit (d5e81ab, 3adf3fa).

• Fixes to ecx, nec and nsec following new formula-based implementation (6ec1372, 0a9d307 and 19a37b9).

• Fixes to predict methods following formula-based implementation (8843a1c, 08484a7).

• Dispersion now takes a bayesnecfit as input (200bc11).

bayesnec 1.1.0

• Added brms::bernoulli to the list of allowed model distributions (7606461).

• Made identity the default link (6640867).

• Added more controls and tweaks to checking model relative to input data (85a3819), 065a445).

• Added formula and model.frame methods to main classes (9df4a64).

• Upgraded ggbnec to autoplot as bayesnec standard ggplot2 plotting method (65fe15f).

• Enhanced handling of argument loo_controls in bnec to allow argument for both brms::add_criterion and loo::loo_model_weights (9712fcc).

• Added Bayesian R^2^ to summary (9a71a3c).

• Expanded bnec's capacity to accept input x and y vectors, data frames (f256b39) and formulas (32e74ac).

• Corrected error for logit link cases for the beta_binomial2 where data contain 0 and 1 to ensure appropriate prior values on top and bot (4158237).

• Series of internal fixes to standardise function class outputs (81369bb, 1c70efe, 5bce2b5, 455ca70, 5e6b41e).

bayesnec 1.0.1

• If link functions are not specified in bnec, then the default link function is used; previous versions of bayesnec used the identity link.

• An additional family has been added betabinomial2 for over dispersered binomial data.

• The package supports using link functions for generalized modelling, which appears to be more stable and is also in line with more typical generalised modelling approaches.

• There are multiple options for model weights calculation from the loo package. The default is "pseudobma BB".

• There is now a compare_posterior function that also includes a bootstrapping procedure. This can be used to compare model fits across different datasets, or even different model sets for the same dataset (ie nec v ecx models). Please see the vignette for examples of usage.

• There is a vignette detailing the models available in bayesnec. Note that not all models are suitable for all families, and also depending if link functions are used.

• A new check_chains function has been added to allow chain plotting in base R and that works more smoothly with plotting chains for multiple fits for bayesmanec objects.

AIMS/bayesnec documentation built on Aug. 20, 2024, 12:33 p.m.