`netmeta`

added to list of suggested packages

- Reference SDs can now be used when modelling using SMDs to avoid using study-specific SDs, which can be problematic.
- Network Meta-Regression: Effect modifiers can now be incorporated using
`regress.vars`

argument in`mbnma.run()`

. Various sharing assumptions for effects can be specified in`regress.effect`

. - Predictions can be estimated for class effect models
- Fractional polynomial powers in
`dfpoly()`

can only take numeric values from set defined in Jansen 2015. - Added
`calc.edx()`

to allow easy estimation of different ED values (e.g. ED90 = the dose at which 90% of the maximum response (Emax) is reached) `get.relative()`

now allows simultaneous comparison of two models in a single league table - can be used to compare MBNMA models with different dose-response functions, or MBNMA and NMA models, or NMA models that assume consistency versus those that use Unrelated Mean Effects.- Plots of predictions look prettier
- Dose-response parameters that were previously modelled on an exponential scale (
`ed50`

,`hill`

,`onset`

) are now on the natural scale and are assigned truncated normal default priors - Separate prior distributions can be specified for different indices of a parameter - allows for agent-specific prior distributions on dose-response parameters.

- Fixed issue with duplication of studyIDs in
`getjagsdata()`

- Fixed bug with studyID labels in
`fitplot()`

and`devplot()`

- Fixed issue and documentation with splines to highlight that knot limits should not be specified

- Added
`get.relative()`

to allow estimation of relative effects between any doses of different agents. - Adding ranking for
`"relative.array"`

objects generated by`get.relative()`

. - Agent-specific dose-response functions run more smoothly. Can now incorporate splines with different knots
- Number of responders should now be included in dataset as
`n`

rather than`N`

so that datasets can be consistent with those used in`MBNMAtime`

- Simplified names of datasets included in the package
- Prediction intervals can be calculated in addition to credible intervals (the default) for
`predict.mbnma()`

and`get.relative()`

- Added
`devdev()`

for comparing deviance contributions between models

- Fixed issue with agent-specific dose-response functions that had different spline knot locations
- Fixed bug that cut out the wrong sections of JAGS output based on incorrect indexing of agent-specific dose-response functions

- Dose-response functions provided to
`mbnma.run()`

are now given as`class("dosefun")`

and dose-response parameters are specified within these functions. NOTE: Previous syntax of specifying a function name as a character (e.g.`fun="linear"`

) along with beta parameters (e.g.`mbnma.run(beta.1="rel")`

) will be removed in subsequent versions, along with wrapper functions. - Added log linear dose-response function (
`dloglin()`

) - Added spline function (
`dspline()`

) (piecewise linear splines, B-splines, restricted cubic splines, natural splines) - Added fractional polynomial function (
`dfpoly()`

) - Agent-specific dose-response functions work with all other functions (e.g. ranking, nodesplit, prediction)
- Added
`link="smd"`

to allow for analysis using Standardised Mean Differences - Uses
`calcom()`

to guess outcome measure scale for more careful specification of default priors for SD - Study IDs added to
`"mbnma.network"`

object

- Error with running random effects models in
`mbnma.nodesplit()`

fixed

- Spline functions also return doses as well as spline basis matrices in jagsdata
- Added informative error for if
`params`

in`plot.mbnma.rank()`

is not a subset of`x`

- Updated and simplified package structure plot in README file
`overlay.split()`

uses full distribution of`E0`

rather than summary statistics`mbnma.predict`

object now contains values assigned/estimated for`E0`

to be used in`overlay.split()`

- In
`plot.nodesplit()`

,`plot.type="forest"`

plots a single forest plot with results for each node-split comparison, rather than presenting results in panels.

- Ensured
`summary.mbnma.network()`

returns valid minimum doses per agent - Ensured models run in parallel when
`parallel=TRUE`

and added a warning when`pd`

is set to`"pd.kl"`

or`"popt"`

for these models. - Ensured results are printed properly for each parameter when using
`summary()`

for multiple dose-response function models

- Added restricted cubic spline dose-response function (
`fun="rcs"`

) in`mbnma.run()`

- Unrelated mean effects (UME) model now added to
`mbnma.run()`

to allow relaxing of the consistency assumption. This can be used to test its validity. `cumrank()`

added for cumulative ranking plots. Also calculates SUCRA values for each agent and dose-response parameter`autojags`

options added for`mbnma.run()`

to allow users to run models until they converge (convergence defined by`Rhat`

)`rank.mbnma()`

also calculates cumulative ranking probabilities and stores them in`cum.matrix`

- Data from
`getjagsdata()`

contains`studyID`

and has been added to`mbnma`

objects - Added studyID column to output from
`devplot()`

and`fitplot()`

`plot.nodesplit()`

scales y-axis if density is >50 times larger in panel with highest density than in panel with lowest density. This improves legibility of the graph.- All nodesplit models now return object of
`class("nodesplit")`

`mbnma.nodesplit()`

includes potential splits via dose-response curve and direct and indirect evidence contributions are calculated simultaneously in the same model.- Corrected calculation for Bayesian p-value in
`mbnma.nodesplit()`

and`nma.nodesplit()`

- Added legend options to
`plot.mbnma.network()`

- Added
`psoriasis`

and`ssri`

datasets to package - Used
`crayon`

package to neaten printed console outputs

- Ensured stringsAsFactors = FALSE does not affect package in preparation for R 4.0.0.
- Edited tests to ensure that any checks for matrix objects account for matrix objects now having matrix and array classes
- Allowed number of responders for binomial data to be greater than or equal to zero (rather than greater than zero)

- Ensured non-parametric functions are properly monotonic by setting default initial values. Each agent now includes an index dose level of 1, which corresponds to the reference treatment effect (placebo)

- Added Lujin Li to list of authors as a reviewer thanks to his considerable help in identifying issues in the previous version.
- Each agent can be assigned a different dose-response function (by assigning a vector of functions to
`fun`

in`mbnma.run()`

) so that multiple functions can be modelled simultaneously. Some downstream package functions still may not yet work with these models though. `mbnma.network`

objects returned from`plot.mbnma.network`

now have specific igraph attributes assigned to them, which can be easily changed by the user.`user.fun`

now takes a formula as an argument (for example`~ (beta.1 * dose) + (beta.2 * dose^2)`

) rather than a string.`plot.mbnma.network()`

now uses a`layout`

argument that takes an igraph layout function instead of`layout_in_circle`

(which was a logical argument). This allows any igraph layout to be plotted rather than just a circle (e.g.`igraph::as_star()`

)

- Changed
`if {class(x)=="matrix"}`

statements to`if {is.matrix(x)}`

to address R development changes

- Exponential function models were not working previously but the dose-response function has been rewritten so that it runs the model correctly.
- DIC reported correctly in output when using plugin (
`pd="plugin"`

), or Kullback-Leibler divergence (`pd="pd.kl"`

) - Using the argument
`parallel=TRUE`

in`mbnma.run()`

(or wrapper functions) now properly runs JAGS in parallel on multiple cores.

- Downstream mbnma-related objects now store
`mbnma.network`

in their output rather than just treatment and agent names.

- Update to README to ensure package workflow image works correctly on CRAN.
- Added JAGS as a System Requirement (JAGS >= 4.3.0) to the DESCRIPTION

- Fixed incorrect ordering of treatment codes in mbnma.network, which also led to problems in subsequent commands/plots

- Fixed minor with numeric vs character coding of treatments in arguments for ranking functions
- Fixed issue with
`nma.nodesplit()`

that prevented the model running if disconnected treatments were included in the analysis (`drop.discon=FALSE`

)

- Made corrections to some arguments specified in documentation
- Fixed incorrect vignette reference
- Allowed more examples in the vignette to run so that plots can be created which better illustrates how MBNMA.run() functions are used.

Welcome to MBNMAdose. Ready for release into the world. I hope it can be of service to you! For time-course MBNMA, also check out the sister package, MBNMAtime.