CHANGES in 0.3.3 (2022-11-15)

  * Ngumbang as maintainer.

CHANGES in 0.3.1 (2022-06-19)

  * Added function `predictAvg` and data set `toves`.

  * Updated URLs in help pages.

  * Changed if(class(.) == ...) to if(inherits(...))

  * Added additional information to the help page for `BoccSS`.

  * Fixed bug in `Bnormal` and `Bnormal2`: object returned has number of chains as attribute.

  * Fixed bug in input data checks for `occ2sps`.

  * Fixed: in data set `railSims`, `logArea` is now a vector, not a 1-column matrix; values unchanged.

CHANGES in 0.3.0 (2020-06-10)

  * Added package `mcmcOutput` to Depends; all functions handling MCMC chains removed: `acfPlot`, `crosscorrPlot`, `densityFolded`, `densityPlot`, `diagPlot`, `postPriorOverlap`, `tracePlot`; functions producing MCMC chains return an `mcmcOutput` object.

  * Class `Bwiqid` deprecated; `as.Bwiqid` warns and returns an `mcmcOutput` object.

  * `Bsecr0` now returns MCMC chains for activity centres; function `plotACs` added to plot these.

  * Fixed: in data set `railSims`, `logArea` is now a vector, not a 1-column matrix; values unchanged.

  * Functions with built-in `.Time` variable get `.Time2` and `.Time3` variables; no need now for I(.Time^2).

  * Intercepts are now labeled "Intrcpt" instead of "(Intercept)", so no need for backticks.

  * Fixed: issues running examples and tests when Suggests packages are not available.

  * Spelling checked with en-GB dictionary.

CHANGES in 0.2.3 (2019-12-31)

  * Added `secrFit` wrapper for `secr::secr.fit` with `fastproximity = FALSE`

  * References to "sample" replaced with "draws" in all MCMC-related locations.

  * Fixed: bug in `dt2`; also error in argument names for `*t2` functions;
    new `*t3` functions added.

  * Fixed: bug in `occ2sps` when Hessian not invertible.

  * Converted all data files to .RData instead of R. Needed Depends: R (>= 2.10).

  * `diagPlot` revamped; accepts a range of classes, not just `Bwiqid`; additional arguments.

CHANGES in 0.2.2

  * Fixed incorrect handling of class `bugs` objects in `diagPlot` and `as.Bwiqid`.

  * `as.Bwiqid` revamped; makes more effort to retain original Rhat and n.eff; parameter
    names conversion changed: a1[1,2] now becomes a1.1.2. instead of a11.2; original
    names retained as attribute `BUGSnames`.

  * Changed `diagPlot` display for integers to dynamite plot instead of histogram;
    separate means for each chain in `diagPlot` density plots.

  * Added `crosscorrPlot` function for a range of classes.

CHANGES in 0.2.1

  * `diagPlot` no longer uses its own colour palette.

  * `window.Bwiqid` now adds new diagnostics for Rhat and n.eff.

  * Rhat calculated with `simpleRhat`, n.eff with `safeNeff` everywhere.

CHANGES in 0.2.0

  * Continuous covariates now standardised to mean=0, SD=1 (instead of SD=0.5).
    Default priors for `BoccSS` and `BsurvCJS` changed to match this.

  * Added `standardize` and `standardize2match` functions.

  * Added `simpleRhat` and `getMCerror` functions; used by `as.Bwiqid`.

  * `diagPlot` gains a `howMany` argument to plot less than the whole chain.

  * `as.Bwiqid.data.frame` gains arguments `n.chains`, `Rhat` and `n.eff` and is
    included in the help page.

  * If the variance-covariance matrix cannot be calculated, MLE functions
    now return the log(likelihood) but number of parameters, df = NA.

  * `AICc` gains a `df` argument which overrides the df value in the model
    object, so an AICc value can be got even if the covariance matrix cannot be
    calculated.

  * Added `*beta2` and `*gamma2`, wrappers for `*beta` and `*gamma` with mean and sd
    parameters, and `*beta3` with mode and concentration.

  * Added `getBetaPar` and `getGammaPar` to convert mean/sd parameters to shape/rate.

CHANGES in 0.1.5 (2018-04-20)

  * Fixed check for installation of package `shiny` in `showShinyApp`.

CHANGES in 0.1.4 (2018-04-20)

  * new function `densityFolded`, used in `plotPost` and `plot.Bwiqid` when `showCurve=TRUE`.

  * `summary.Bwiqid` method added, prints background and returns values invisibly.

  * `diagPlot` now displays `n.eff`

  * fix: in `as.Bwiqid.mcmc.list`, call to `gelman.diag` wrapped in `try`.

  * fix: histogram breaks in `plotPost` are equidistant (as always intended).

  * fix: the first argument to `BoccSS0` can be a matrix or data frame with a detection history.

  * fix: `occSSrn0` now accepts scalar `n`, as documented.

CHANGES in 0.1.3 (2017-11-18)

  * Calculation of SEs of fitted values now uses less memory, works for large data sets.

  * Functions more robust to underflow/overflow: `closedCap*`, `occ2sps`, `occSS*`

  * Changed parameterization in `secr0` from lam0 to g0; better default priors.

  * Bug fix in `BoccSS0`: burnin iterations are now discarded.

CHANGES in 0.1.2 (2017-09-10)

  * Added `diagPlot` function and improved other diagnostic plots.

  * Added function `Bpoisson`; `Bbinom` renamed `Bbinomial`

CHANGES in 0.1.1 (2017-06-09)

  * Added `coef`, `vcov` and `predict` methods for `wiqid` objects.

  * `survCJS` gains an `interval` argument to deal with time intervals of unequal length.

  * dots argument added to MLE functions to pass parameters to `nlm`.

  * Improved coding of several functions to prevent under/overflow issues.