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.