- M1mac fix

- Added
`Matdist`

to simplify the process of creating a vector distribution for`WeightedDiscrete`

distributions.`Matdist`

acts as a univariate distribution whilst technically being multivariate - it contains a matrix of probabilities and provides methods for acting on those. - Added methods:
`plot.Matdist`

to wrap`matplot`

around`Matdist`

,`c.Matdist`

to combine multiple matrix distributions into one,`[.Matdist`

for extracting`WeightedDiscrete`

or`Matdist`

distributions from`Matdist`

, and`as.Distribution`

. - Added
`mixMatrix`

as a specialised mixing method for`Matdist`

that creates a new`Matdist`

instead of a`MixtureDistribution`

- Possibly breaking change - Changed default of
`as.Distribution.matrix`

to now coerce to a`Matdist`

, a vector of`WeightedDisrete`

is still possible. - Slight speed improvements to EmpiricalMV
- Fixed r-devel linux warnings

- Fix for Apple M1

- WeightedDiscrete now correctly handles improper distributions by returning Inf and NA where appropriate
- Added constraint on WeightedDiscrete so
`cdf`

parameter must be increasing - Add distribution method
`confidence`

to calculate confidence intervals - Fix testing of suggested distributions

- Fixes error in c.VectorDistribution caused by R6 referencing

- Off-by-one error fixed in WeightedDiscrete distribution cdf function
- Speed-ups in pdf, cdf, rand functions in WeightedDiscrete

- Patch for testthat

- Bump param6 version to fix bug in HyperGeometric distribution

- Parameter set interface has been moved to param6. This should not cause breakages if parameters have only been accessed via distribution methods but may otherwise.
- R62S3 is no longer loaded by default, S3 methods must now be manually created with R62S3::R62Fun. This may cause breakages if scripts assume pre-loading but will work as before once R62Fun is called (see S3 and piping vignette)
- Kurtosis and skewness methods now vectorised
- Ids for vector distributions now forced to be alphanumeric
- Deprecated unused arguments from parameter methods
`print`

method now only shows active parameters- Many other internal improvements to code quality and efficiency

- Fix for M1mac

- Minor internal change

- Added
`as.Distribution.matrix`

for converting matrices to a`VectorDistribution`

of`WeightedDiscrete`

distributions - Added
`...`

to`dstrs`

to allow decorator argument to be passed through

- Internal changes only

- Fixed bug in extracting distributions from vector distributions

- Added
`ids`

active binding to more easily get ids of distributions in`VectorDistribution`

- Added
`length.VectorDistribution`

- Added
`ids`

parameter to`VectorDistribution`

to allow specifying names for wrapped distributions. Extended`extract.VectorDistribution`

so these ids can be used for extraction. - Added sugar function
`dstr`

to construct distributions more easily, e.g.`dstr("Binom", size = 4)`

instead of`Binomial$new(size = 4)`

. - Added sugar function
`dstrs`

to construct a`VectorDistribution`

of distributions. `ParameterSet`

method`setParameterValue`

now includes`resolveConflicts`

parameter for resolving conflicts between conflicting parameters (see below). This should primarily only be used internally and is useful for transforming composite distributions.

- The separator for composite (wrapped) distributions is now
`__`

(before`_`

). This may affect backwards compatibility in rare cases. - Construction and setting of parameters is now changed. Previously this relied on knowing a confusing hierarchy in parameters which would take priority over one another. Now if conflicting parameters are supplied in construction or on setting an error is returned, e.g.
`Binomial$new(prob = 0.1, qprob = 0.2)`

would cause an error. This may affect bacwards compatibility however should not do so if distributions are correctly constructed/updated without conflicts. `setParameterValue`

in`ParameterSet`

no longer errors if a non-settable parameter is updated, instead a`warning`

is given and the parameter is ignored.- Multivariate distributions no longer error if constructed with a single variate, though this is still advised against.
- Internal changes to how
`SDistribution`

parameter defaults are set. Previously these were set in the constructor with function defaults, now they are set in the`ParameterSet`

. This should not affect backwards compatibility. This should improve speed of distribution construction.

- Data parameter in
`WeightedDiscrete`

distribution has now been removed.

- Minor bug fixes in some distribution properties.
`MixtureDistribution`

now uses`extraDistr::rmnom`

for speed improvements.- Slight improvement to error messages in
`ParameterSet`

but these will be improved further in a future update. - Minor internal changes to storage method of
`SDistribution`

`ParameterSet`

objects. - Fixed typos in parameter sets

- Documentation for
`SDistribution`

objects has been restructured for easier reading, the distribution default is now included. - Fixed typos

- Fixes for R devel

- Patch for set6
- Add
`rep.Distribution`

for replicating distributions into vectors, mixtures, or products - Kernels can now be used with vectors/mixtures/products

- Patch for solaris

- Added
`cdfSquared2Norm`

analytic methods to most kernels - Minor internal patches

- Added coercions from Vector/Mixture/ProductDistribution to Mixture/ProductDistribution via
`as.MixtureDistribution`

and`as.ProductDistribution`

- Bugfix in
`MixtureDistribution`

parameter set - Uneven vectors of
`WeightedDiscrete`

distributions are now truncated at the minimum length in the vector for`pdf, cdf, quantile`

`CoreStatistics`

methods now give the option to use`cubature::cubintegrate`

and all associated parameters.- Remove
`{pracma}`

requirement in`ExoticStatistics`

- Bugfix in
`WeightedDiscrete`

,`cdf`

was previously positive when below distribution support, now zero. - Added discrete p-norms in
`ExoticStatistics`

decorator - Removed
`suppressMoments`

argument in`Distribution`

and computation of movements in constructor, improving construction speeds. `kurtosis`

and`skewness`

type no longer included in properties. The kurtosis and skewness methods are still available as public methods, and the types are still in summary; to manually find these use`exkurtosisType`

and`skewType`

.- Empty
`ParameterSet`

now allowed

- Critical patch for patched Solaris: Updated precision in C++
`log`

- Critical patches for R devel:
`workingSupport`

is now a public method and not an active binding

- Multivariate functions in
`VectorDistribution`

now return arrays - Analytical
`median`

now available for`SDistribution`

s where closed form expressions are known - Kernels now implemented in
`Rcpp`

with analytical log-pdf expressions. Analytical lower.tail and log.p will come in future versions. - Adding plotting for bivariate distributions using
`{plotly}`

- Added
`EmpiricalMV`

for empirical multivariate distributions - All documentation now uses roxygen R6
- Distribution
`type`

is now required in construction custom`Distribution`

s as the previous method of ‘guessing’ was inefficient. - Added
`ParameterSetCollection`

for`Wrapper`

s. Same functionality as before but much more efficient. - Added
`$addDeps`

and`$deps`

to`ParameterSet`

s to replace`updateFunc`

. This allows faster and more precise control over parameter updates. - Added
`$addChecks`

and`$checks`

to`ParameterSet`

s to replace custom checks in distributions, and`$addTrafos`

and`$trafos`

to replace custom parameter transformations before setting. These allows clearner control over parameter setting. `categories`

parameter in`Categorical`

now called`nCategories`

- Constructor of
`Categorical`

now requires elements to be provided as a`list`

to`elements`

`settable`

in`ParameterSet`

now refers to the more intuitive flag that describes if a parameter can be set after construction- Added
`length`

active binding to`ParameterSet`

to return number of parameters in the set. - Renamed
`squared2Norm`

in`Kernel`

s to`pdfSquared2Norm`

and added`x`

to arguments to allow for shifted norms. - Added
`mixturiseVector`

for mixing vector distributions

- Individual property and trait accessors deprecated:
`$support, $symmetry, $kurtosisType, $skewnessType, $valueSupport, $variateForm, $type`

- Separated
`Loglogistic`

and`ShiftedLoglogistic`

so only the latter has a`location`

parameter. Additionally added an analytical`rand`

expression to`ShiftedLoglogistic`

, and`Loglogistic`

now implemented from package`actuar`

- Removed deprecated classes:
`ArrayDistribution`

- Removed deprecated functions:
`listSpecialSets`

`WeighedDiscrete`

distribution now stores samples and probabilities as parameters.- Removed
`verbose`

argument from distribution constructor - Public
`update`

method in`ParameterSet`

moved to`private`

- Removed
`squared2Norm`

from the`ExoticStatistics`

decorator - Deprecated
`updateFunc`

from`ParameterSet`

- Removed
`.getRefParams`

from`SDistribution`

s and added`deps`

- Bugfix in
`decorate`

function that was overwriting the`decorators`

private field instead of appending - Vastly improved speed of construction of
`SDistribution`

and`Kernel`

- Bugfix in
`$rand`

for`Geometric`

distribution with`trials == TRUE`

, previously was randomising between \([1, Inf)\) not \([0, Inf)\) - Changed default
`form`

parameter in`NegativeBinomial`

, now errors if supplied argument is not in one of the four choices (previously reverted to “fbs”) - Fixed bug in
`MultivariateNormal`

`rand()`

which was not adding the`mean`

correctly - Massive bottleneck in
`VectorDistribution`

for same distribution type removed in d/p/q/r functions as well as non-generating function methods - Improved speed in
`VectorDistribution`

when only one row or column of data passed to d/p/q `Dirichlet, DiscreteUniform, Frechet Gumbel, Pareto, Rayleigh, Triangular, Wald`

now implemented from package`extraDistr`

- Bug fix in
`Frechet`

`$cdf`

- Analytical
`log`

and`lower.tail`

now available for all`SDistributions`

and imputation possible for customs with`CoreStatistics`

`NegativeBinomial`

now uses Rcpp for d/p/q/r- Distributions from
`stats`

are now vectorised across parameters in C `Degenerate`

,`ShiftedLoglogistic`

now Rcpp- Removed redundant
`K`

parameter from`MultivariateNormal`

- Bugfix in
`Wald`

, symmetry was incorrectly flagged as “symmetric” - Fixed bug in
`TruncatedDistribution`

support - previously support interval type was`"[]"`

instead of`"(]"`

. An important implication is that even if truncating at or outside of the distribution limits, the support will still be changed if the distribution was left-closed to become left-open. - Improved speed of assertions by using package
`{checkmate}`

- Bugfix in
`listDistributions`

which was overriding filtering with`simplify`

- Minor internal Updates
- Next release will be 1.4.0, due to nature of R6 this will break dependencies.

- Bugfix in
`decorate`

function that was overwriting the`decorators`

private field instead of appending - Added
`plot.VectorDistribution`

for more efficient plotting of mutiple distributions at the same time - Two bug fixes in
`MultivariateNormal$rand()`

. i) the distribution mean wasn’t being added to the transformation correctly; ii) the Choleskey decomposition wasn’t transposed causing incorrect simulations

- Added Erlang distribution
- Fixed mistake in documentation for
`Weibull`

, thanks to Paul Northrop (@paulnorthrop) for pointing this out. - Fixed bug in
`plot`

preventing only`quantile`

being plotted on its own - Converted descriptive public methods to active bindings. Unfortunately this will break reverse dependencies as there’s no way to soft deprecate these. Affected methods are:
`decorators, traits, valueSupport, variateForm, type, properties, support, symmetry, sup, inf, dmax, dmin, kurtosisType, skewnessType`

- Bug fix in
`VectorDistribution`

that was causing decorators not to be added properly - Bug fix in
`VectorDistribution`

that was causing an error when extracting decorated wrapped distributions - Moved package
`pracma`

to suggests. Removed`utils`

dependency. - Added checks to assert all packages are installed when required by distributions
- Deprecated
`package`

field in distributions, now called`packages`

`packages`

lists all packages required to be installed for a distribution, if`NULL`

only distr6 required- Abstracted SetInterval and related classes to the
`set6`

package - Deprecated
`listSpecialSets`

, use`set6::listSpecialSets`

instead - Removed secondary checks on
`update`

of`ParameterSet`

, any properly defined distributions will have this covered in primary parameter, thus increasing speed.

`as.data.table`

has been moved from a`ParameterSet`

method to an S3 dispatch. Fixes an important bug of overloading`as.data.table`

but may affect backwards compatibility.- Added
`distrSimulate`

for convenient simulation from any distribution - Updated
`plot`

to be able to handle distributions without`quantile`

or`rand`

. Optimised runtime by preventing automatic computation of`pdf`

and`cdf`

.

- Bug fix in
`VectorDistribution`

- missing`which`

argument - Bug fix in
`Bernoulli`

-`rand`

was incorrectly calling`dbinom`

not`rbinom`

- Bug fix in the
`mode`

of distributions - Added
`mode`

to documentation

- Added wrapper for VectorDistribution for quick concatenation of constructed distributions,
`c.Distribution`

`VectorDistribution`

`print`

method more in line with base R vectors

`plot`

function for plotting the`pdf, cdf, survival, quantile, hazard, cumhazard`

or`distr6`

objects`lines`

function for superimposing`distr6`

plots`qqplot`

function for comparing`distr6`

distributions to each other or to other theoretical distributions- Added
`Extract.VectorDistribution`

for extracted distributions from inside a`VectorDistribution`

, see the big update below.

`decorate`

now allows users to specify the Decorator as a character as well as supplying the object, this makes it simpler when using distr6 whilst unattached**Big changes**(and hopefully final) to the`VectorDistribution`

. Now the`VectorDistribution`

only constructs the internal wrapped distributions when they are extracted or when a function, such as d/p/q/r, are called. This massively reduces a bottleneck in constructing the distribution. Additionally added functions for extracting distributions from inside the`VectorDistribution`

. The only difference that should affect backwards compatibility is that the`distribution`

argument must now be a character and not an object. Custom (i.e. non-`SDistribution`

) distributions should be used in conjunction with the`distlist`

initializer.- Changed the lower bound of positive Sets to .Machine$double.xmin as the previous value of 1.1e-15 was too restrictive
- Added
`skewness`

,`kurtosis`

,`entropy`

,`mgf`

,`cf`

, and`pgf`

to`WeightedDiscrete`

and`Empirical`

- Added support for custom distributions in
`VectorDistribution`

and for`CoreStatistics`

functions as well as support for only one arguments passed to d/p/q/r for fast comparisons between wrapped distributions

- Bug fix in
`WeightedDiscrete`

distribution`variance`

calculation - Fixed bug in
`Empirical`

that was stopping the cdf of the first point in the distribution being evaluated - Fixed bug that allowed invalid parameter values to be set for non-reference parameters
- Updated parameter error messages to be more informative
- Improved speed and efficiency in
`Distribution`

constructor for wrappers

- Added non-central F, T, Chi-Squared, and Beta distributions
- Added WeightedDiscrete distribution. This allows users to supply a data.frame of samples and pdf/cdfs for more efficient usage with empirical discrete estimators (e.g. Kaplan-Meier)

- Added the common survival parameterisation of Weibull distribution
- Updated the listX functions to make them quicker and functional when distr6 is not attached
- Added
`suppressMoments`

argument to`Distribution`

constructor to allow for faster construction

- Added
`errormsg`

argument to assertions so a custom error message can be provided - Fixed error in quantile function in
`Empirical`

that was causing results to be dropped - Fixed bug in
`TruncatedDistribution`

that prevented multivariate distributions being truncated - Fixed error in variance of
`Empirical`

that was calculating sample not population - Moved rare imports to suggests

`Empirical`

distribution for distributions arising from observed samples (e.g. from MC sampling methods)`simulateEmpiricalDistribution`

: function for sampling*without*replacement from an`Empirical`

distribution

`ArrayDistribution`

- This wrapper is now merged with`ProductDistribution`

by adding two new parameters to`ProductDistribution`

that allow for construction either by a distribution list of by naming a distribution and providing a parameter list or data.table

- Added quantile to Categorical distribution and updated its cdf efficiency
`cdf`

of discrete distributions evaluated between integers are now evaluated after rounding down and do not return 0, e.g.`Binomial$new()$cdf(1.8) == Binomial$new()$cdf(1)`

- Added two additional parameters to
`ProductDistribution`

:`params`

and`distribution`

, so that it can either function as before or as the`ArrayDistribution`

wrapper which is now deprecated. - Added two additional parameters to
`VectorDistribution`

:`params`

and`distribution`

, so that it can either function as before or as a generalisation to the`ArrayDistribution`

wrapper which is now deprecated. - Removed automated rounding of numerics when
`ParameterSet`

expected integer in`setParameterValue`

- Added parameter
`n`

to`strprint`

and`print`

to clean the print method for distributions (especially wrappers) with multiple parameters - Added optional
`vectordist`

argument to`MixtureDistribution`

for better compatibility with`VectorDistribution`

- Changed
`short_name`

of Uniform, Logistic, Normal, and Triangular kernels to remove`Kern`

. The`ClassName`

s (and thus constructors) remain the same `listKernels`

and`listSpecialSet`

now return data.tables with`stringsAsFactors = FALSE`

`Degenerate`

distribution re-classified as discrete

- Bug fix in quantile function of huberization wrapper
- Fixed the
`rand`

return of a Vector Distribution (transposed data.table and added column names) - Fixed spelling mistakes in extension guidelines and removed calls to redundant parameters
- Removed redundant
`crayon`

dependency - Fixed bug in
`MixtureDistribution`

that was causing`rand`

to erroneously return integers - Removed error in
`Categorical`

documentation - Fixed bug in multi-modal
`Categorical`

distribution `summary`

and`print`

now return`self`

invisibly for better piping

- Updated vignettes to remove redundant distr6 installation via GitHub that was causing a warning on Debian
- Redundant
`stopwarn`

argument removed from`parameters()`

method in`Distribution`

and`ParameterSet`

classes - Updated Kernel$new() error message to point user to Distribution class
- Fixed broken if/else statement in liesInSetInterval method of SetInterval class

- v1 API is ready to be shipped to CRAN!
- Again see here for the updated API lifecycle
- Tutorials, extension guidelines and other documentation (in appendices) are now on the website
- distr6 is a complete, unified, object-oriented interface to probability distributions in R. Complete with 36 probability distributions and another 11 kernels, distr6 also allows functionality for numerical imputation of methods and statistical functions.

- Now public!
- distr6 API as whole is still very much experimental but analytic features are fairly stable, see here for details on feature lifecycles
- Development continues to be internal, through UCL and The Alan Turing Institute, but we welcome external users to test the API and report bugs, see our contributing guidelines for details including our code of conduct