28/03/2021 Initial implementation. This package *REPLACES* the package "hse". Effectively this is a name-change only. A referee of a paper that I wrote, based around this package, objected to the name "hse" ("hope springs eternal") saying that readers might find this name too frivilous. Changelogs for the "hse" predecessors of this package may be found in the CRAN archives. Version 0.0-1. 29/03/2021 Added the data set "hrsRcePred" and documented it. Added the function mleBb() and documented it. Incremented the version number. Version 0.0-2 30/03/2021 Added the data set "visRecog" and documented it. Changed the name of the success probability parameter in mleBB() from "p" to "m" to be consistent with the notation used in rmutil. Added names to the vector returned by mleBB(). Incremented the version number. Version 0.0-3 04/04/2021 Got rid of mleBb(); going with just using the db distribution. Changed the default value of maxit in mleDb() from 100 to 1000. Added a maxit argument to simulate.mleDb(). Added maxit arguments to gof(). Modified ddb() to take a "log" argument (defaulting to FALSE). 06/04/2021 Added a "maxit" argument to mcCovMat(). Added the possibility that a warning may be issued (rather than an error being thrown) in mleDb() or mleBb(). Which of the two happens is controlled by options()[["maxitErrorOrWarn"]] which is set to "error" at startup. Added the function set.eow() to allow the user to switch between the two options. Added the function get.eow() to query this option. 07/04/2021 Added functions gradDb() and hessDb() and revised the grad() and hess() functions from gradHess.R to make use of them. Made some adjustments to mleDb() (eliminated an unnecessary complication) in respect of the way the hessian-cum-covariance matrix is calculated. 10/04/2021 Fixed a glitche in mleDb() in respect of the names of the gpar argument used by gfun. This was mucking everying up to an incredible extent! 11/04/2021 Added arguments "covmat" and "useGinv" to mleDb(). Amended mcCovMat to call mleDb() with covmat set equal to FALSE. Corrected sign errors in aHess() and nHess(). Added dimnames attribute to the value returned by nHess(). Added dimnames attribute to the value returned by hessDb(). 12/04/2021 Made various other (fairly minor) corrections to the code and to the help files, fixing errors that were noticed in the course of fiddling about with them. 13/04/2021 Added a simulate.Vpars() method for simulate. Added a function makeVpars() to create "Vpars" objects. Added an example using makeVpars() simulate.Vars() to the help for ndata. Incremented the version number. Version 0.0-4. 23/04/2021 Fixed a stupid glitch w.r.t. setting of seeds in simulate.Dbdpars() and simulate.mleDb(). Incremented the version number. Version 0.0-5. 26/04/2021 Amended mcCovMat() so that it works with objects of class "Dbdpars". Amended finfo() so that its arguments are the same as (in the same order as) those of makeDbdpars() Incremented the version number. Version 0.0-6. 29/04/2021 Uploaded to CRAN. 30/04/2021 Made changes/corrections at the behest of CRAN (explicitly Gregor Seyer). * wrapped all examples which use data from hmm.discnp in if(requireNamespace("hmm.discnp")) { ... } * changed instances of "if(require(...))" to "if(requireNamespace("..."))". * adjusted the value returned by logLik.mleDb() to have class "logLik" and an attribute "df" (equal to 2). Made a corresponding adjustment to the help file for logLik.mldDb(). Incremented the version number. Version 0.0-7. Made a correction (re-set par() values if these are changed in examples!) which I had neglected to make. Incremented the version number. Version 0.0-8. Uploaded to CRAN 01/05/2021 Fixed a typo "namep-change" (!!!) in this ChangeLog. Removed spurious links to meDb() (which is undocumented!) from some help files. 25/05/2021 Removed another spurious link to meDb() (from the help for mleDb()). Incremented the version number. Version 0.0-9. 11/07/2021 At the suggestion of a referee of the accompanying paper, added a function exactMeBb(), and documented it. Incremented the version number. Version 0.0-10. 12/07/2021 Made the zeta argument of exactMeDb() default to FALSE (matching up with mleDb()). Incremented the version number. Version 0.0-11. 12/07/2021 Adjusted the help file eow.Rd to make reference to exactMeBb() as well as mleDb(). Added "eow" to the aliases. Fixed a glitch (start of a sentence had been omitted). Added an example of set.eow() --- no effect when options()$eow is "error". Incremented the version number. Version 0.0-12. 26/07/2021 Added tools for dealing with the beta-binomial distribution. These were original created in the "Verdis" ("versatile discrete distributions") package, into which the dbd package morphed for a time. I decided to eschew use of the beta-binomial distribution, but have now decided to reinstate it, but to have it play a relatively minor with the db distribution holding prominence. * added function makeBbdpars() and method simulate.Bbdpars() * made mcCovMat() generic, with methods mcCovMat.mleDb() mcCovMat.mlebb() mcCovMat.Dbdpars() mcCovMat.Bbdpars() mcCovMat.default() The default method simply throws an error. * made a number of minor adjustments and corrections to the code and the help. * fixed a stupid glitch in the simulate methods, in respect of the "seed' argument, which could have resulted in all simulated data sets being identical. Incremented the version number. Version 0.0-13. 27/07/2021 Fixed a glitch pertaining to the extraction of "zeta" from the "object" argument of mcCovMat (the code had been trying to find zeta as an attibute of the object, whereas, when the object is of class "Dbdpars" or "Bbdpars", zeta is a *component* of the list consituting the object). Also adjusted some 'list$xxx' constructs to have the form 'list[["xxx"]' --- safer! Incremented the version number. Version 0.0-14. 29/07/2021 Replaced the functions finfoDb() and finfoB() by a single function finfo() the first argument of which is "distr" that specifies which distribution is to be considered. Incremented the version number. Version 0.0-15. 15/08/2021 Added the argument "verb" (defaulting to FALSE) to the gof methods. Setting it to TRUE causes "progress reports" to be issued during the course of the simulations that are conducted when MC is TRUE. Added the argument "seed" to the gof methods, for use when MC is TRUE. If MC is TRUE the value of the "seed" argument, or the random value chosen if "seed" is not supplied, is made an attribute of the returned value. Incremented the version number. Version 0.0-16. 16/08/2021 Adjusted the "Parsonnet scores" example in the help for gof(). Added references to the Wittenberg paper and to the spcadjust package. Incremented the version number. Version 0.0-17. 17/08/2021 Changed the plotting functions plotDb(), plotBb(), plot.mleDb() and plot.mleBb() to return values (invisibly). These values consist of the data that were plotted. Eliminated some redundant calculations in plot.mleDb() and plot.mleBb() (these calculations also being done by plotDb() and plotBb() respectively. Added an "incr" argument to plot.mleDb() and plot.mleBb(). This specifies the gap between the vertical lines representing the fitted probabilities and those representing the observed proportions. Previously the value of incr was hard-wired ... and then ignored (i.e. re-hard-wired in the call to lines()). Incremented the version number. Version 0.0-18. 17/08/2021 Added a "plot" (logical scalar) argument to the plotting functions plotDb(), plotBb(), plot.mleDb() and plot.mleBb(). Determines whether a plot is actually produced (rather than having the function simply return a value). Incremented the version number. Version 0.0-19. 17/08/2021 Changed the default value of "incr" to depend on "size" (plot.mleBb()) or "ntop" (plot.mleDb()). It now defaults to 0.1 for values of these quantities less than 20 and to 0.5 otherwise. Incremented the version number. Version 0.0-20. 17/08/2021 Wrapped some code in \dontrun{ } in makeBbdpars.Rd and hrsRcePred.Rd because it was taking too long for CRAN. Changed http to https in mleBb.Rd at the behest of CRAN. Incremented the version number. Version 0.0-21. 19/08/2021 Corrected a couple of major bugs in the gof() functions. (1) Setting of seed for the simulations was incorrectly handled. (2) Starting values used for fitting models to simulated data sets should have been set (to the parameters of the model being simulated) and had not been so set. Incremented the version number. Version 0.0-22.