NEWS

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wiqid 0.3.2

• Ngumbang as maintainer.

wiqid 0.3.1 (2022-06-20)

• 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.

wiqid 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.

wiqid 0.2.3 (2020-01-08)

• 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.

wiqid 0.2.2 (2019-06-05)

• 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.

wiqid 0.2.1 (2019-01-02)

• '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.

wiqid 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.

wiqid 0.1.5 (2018-04-20)

• Fixed check for installation of package 'shiny' in 'showShinyApp'.

wiqid 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.

wiqid 0.1.3 (2017-11-19)

• 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.

wiqid 0.1.2 (2017-09-10)

• Added 'diagPlot' function and improved other diagnostic plots.
• Added function 'Bpoisson'; 'Bbinom' renamed 'Bbinomial'

wiqid 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.