`NEWS.md`

- Added double-dot (dynamic) functionality to defSurv. Users can now specify double-dot variables in scale, shape, and formula parameters.
- It is possible to generate variable cluster sizes using the
*clusterSize*distribution in`defData`

and`defDataAdd`

. - Can set x-axis limits in plot generated by
`survParamPlot`

- Added function
`blockExchangekMat`

and`blockDecayMat`

. Users can now generate correlation matrices that can accommodate clustered observations over time where the within-cluster correlation in the same time period can be different from the within-cluster correlation across time periods. - Updated function
`genCorMat`

to allow generation of cluster-specific correlation matrices in case one wants to induce variability in correlation across clusters.

- Updated
`genFormula`

to allow for ‘double dot’ functionality. - Added new functions
`genSynthetic`

and`addSynthetic`

. Allows users to sample records with replacement from an existing data table. - Added argument ‘startProb’ to
`genMarkov`

. Allows user to set probability distribution of start state. - Added utility functions
`survGetParams`

and`survParamPlot`

to aid users in identifying parameters that can be used to generate desired distributions of time to event data. - Major updates to functions
`defSurv`

and`genSurv`

. It is now possible to generate survival outcomes with hazard functions that change over time. In addition, competing risk outcomes can be explicitly generated.

- You can now use non-scalar variables with double-dot notation. See the
*Dynamic Data Definition*Vignette. - The ‘categorical’ distribution now supports the variance parameter to introduce categories other than 1…n.
- You can now use [trtAssign()] as a distribution with [defData()].

- Added CITATION
- genData now warns that a set ‘id’ parameter will override previously defined ‘id’ names from the data definition.
- genData now handles NULL as ‘id’ value in data definitions (e.g. when definitions are not created via defData etc.) by defaulting to ‘id’.
- Fix an error in genOrdCat when only a single adjustment variable is given but more than one new category will be created.
- Fix a bug where ..variables did not work within a function using the
`dist="beta"`

.

- Add ‘backports’ for compatibility with R < 4.0
- Fix a bug on R < 4.0 in genOrdCat
- Current version is now only compatible with R version >= 3.3.0

- Moved genCorOrdCat’s functionality into genOrdCat. genCorOrdCat is now deprecated.
- Renamed catProbs to genCatFormula for naming consistency. catProbs is now deprecated.

- Introduced a new system for formula definitions and completely reworked the underlying code. See vignette “Dynamic Data Definition”.
- The new function genMixFormula generates mixture formulas from different inputs.
- Some simstudy functions now produce custom errors and warnings. Eventually all conditions will be replaced by the new system to make error handling easier for the user.
- Added new vignettes.
- Created documentation pages for:
- the release version https://kgoldfeld.github.io/simstudy/
- and development version https://kgoldfeld.github.io/simstudy/dev

- genCatFormula now warns if an additional category is created or probabilities are normalized.
- Fixed bug in trtAssign related new ratio argument.
- Fixed bug in trtAssign when strata had count of one.
- defData now also checks the first row in the definition table for validity.

- Added “mixture” distribution that takes a value from an existing column with a specified probability.
- Modified function trtAssign to improve speed performance of stratified sampling with very large numbers of strata.
- Add argument “ratio” to function trtAssign to allow users to specify more than 1:1 randomization.

- Added function trimData (that uses new rcpp function clipVec) to clip or truncate a longitudinal data set after a certain event has occurred.
- Fixed bug in addMarkov, added trimvalue argument to use trimData function
- Added trimvalue argument in genMarkov

- Added functions genMarkov and addMarkov to create data.table with (or add to existing data.table) individual chains of Markov processes.
- Added function genNthEvent to create data.table with binary event outcome in a longitudinal setting.
- Updated function genCluster so that cluster size can be specified as an integer, and will be constant across all clusters.
- Updated function addPeriods that period name can be specified.
- Updated function trtStepWedge so that a transition period can be included.
- Fixed bug in function delColumns related to multiple keys.

- Added negative binomial distribution as an option to function iccRE
- Fixed function genCorOrdCat so that it can accept user-specified correlation matrix
- Added function trtStepWedge to generate treatment assignment for a stepped-wedge design cluster randomized trial.

- Fixed genCorFlex and addMultiFac to accommodate bug fixes with package data.table

- Added negative binomial option to genCorGen, addCorGen, genCorFlex, and addCorFlex
- Fixed bug in function genFactor
- Added LAG() functionality to missing data generation - updated functions genMiss and added two new internal functions .checkLags and .addLags
- Function catProbs now accepts a vector of probabilities or weights as an argument
- Fixed bugs in function addCondition

- Added function genCorMat - generate an n x n correlation matrix
- Added function genCorOrdCat - generate correlated ordinal categorical data
- Added beta distribution option to function defData (and associated functions)
- Added function betaGetShapes
- Implemented Emrich and Piedmonte algorithm for correlated binary data for function genCorGen and addCorGen
- Modified function genOrdCat - allows adjVar = NULL
- Fixed bug in function addCorFlex

- Added function catProbs - to be used to generate categorical data
- Added binomial distribution
- Added ability to specify formula in variance
- Added function genMultiFac - generates multi-factorial design data
- Added function addMultiFac - adds multi-factorial design data
- Added function iccRE - generates required random effect variance for specified intra-class coefficients (ICCs)
- Fixed bug in function genCorFlex
- Fixed bug in numerous functions related to error checking and scoping
- Fixed bug in function addCondition

- Fixed function updateDef
- Fixed bug in internal function genbinom
- Added function genCorFlex - generate correlated data from variables that have different marginal distributions
- Added function genCorFlex - generate correlated data from variables that have different marginal distributions, can be dependent on previously defined data

- Added function genOrdCat - creates ordinal categorical data
- Added function genFormula - creates a linear formula in the form of a string
- Added function updateDef - modify existing data definition table (to be used in genData())
- Added function updateDefData - modify existing data def table (to be used in addColumns())

- Added uniform integer distribution (uniformInt)
- Added negative binomial distribution (negBinomial)
- Added exponential distribution (exponential)
- Added function delColumns - deletes one or more columns from data.table

- Added error check to verify that specified distributions are valid
- Added function genFactor - converts an existing (non-double) field in a data.table to a factor
- Added function genDummy - creates dummy variables from an integer or factor field in a data.table
- Added function defCondition - define distribution conditional on existing fields
- Added function defReadCond - read in conditional definitions from external csv file
- Added function addCondition - generate data based on conditional definition

- Modified “nonrandom” data generation to allow “log”” and “logit”” link options.
- Added function genCorGen - generate a new data.table with correlated data from various distributions.
- Added function addCorData - add correlated data from various distributions to existing data.tables.

- Fixed index variable issue related to generating categorical data
- Fixed index variable issue related to generating longitudinal data
- Fixed issue that arose when creating categorical variable in first field
- Increased speed required to generate categorical data with large sample sizes
- Categorical data can now accommodate probabilities condition on covariates
- Fix: package data.table 1.10.0 broke genMissDataMat. genMissDataMat has been updated.

Developed by Keith Goldfeld, Jacob Wujciak-Jens.

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