modified vignette .Rnw files (AICcmodavg.Rnw, AICcmodavg-unmarked.Rnw) to remove usenames option when using xcolor LaTeX package following modifications of xcolor.sty
added a vignette for a full example using diagnostic tools and utility functions implemented in 'AICcmodavg' for models fit in 'unmarked' package
updated 'modavgEffect' with check to include case with a single predictor appearing in models
updated 'mb.gof.test' for 'unmarkedFitColExt' object to deal with seasons without any sampling
updated 'detHist' for 'unmarkedFitColExt' and 'unmarkedFitoccuMS' objects to deal with seasons without any sampling
updated 'detTime' for 'unmarkedFitoccuTTD' objects to deal with seasons without any sampling
updated 'countDist' for 'unmarkedFitPCO', 'unmarkedFitGMM', and 'unmarkedFitMMO' objects to deal with seasons without any sampling
updated 'countHist' for 'unmarkedFitDSO' objects to deal with seasons without any sampling
modified 'par' settings to return to original plot settings on exit for 'mb.gof.test', 'countDist', 'countHist', and 'detTime' (Suggestion by M. Meredith)
added a warning when using 'nls' with null model when 'fitted' produces scalar and 'nobs' = 1 (Thanks to D. Armstrong)
modified 'xtable' methods to include new argument 'auto' in 'xtable' package
corrected bug from change in 'mer' object structure when dealing with offsets
corrected bug in margin width when plotting results of 'mb.gof.test' with dynamic occupancy model models (thanks to M. Meredith)
added 'ncores' argument to 'mb.gof.test' and 'Nmix.gof.test' to control number of cores used parametric bootstrap (suggested by M. Meredith)
added arguments 'cex.axis', 'cex.lab', 'cex.main', and 'lwd' to add flexibility to various functions producing plots (i.e., 'mb.gof.test', 'Nmix.gof.test', 'detTime', 'countDist', 'countHist')
created an NEWS.Rd file
created a vignette for a tour of main functions of the package
added support for models of classes 'unmarkedFitOccuMS', 'unmarkedFitOccuTTD', 'unmarkedFitMMO, 'unmarkedFitDSO'
created new function 'detTime' to summarize time to detection data for models of class 'unmarkedFitOccuTTD'
addedd 'modavgPred' method for 'unmarkedFitOccuMulti' and 'unmarkedFitOccuMS' objects
modified default plotting parameters in functions 'countHist', 'countDist', 'detTime', 'mb.gof.test', and 'Nmix.gof.test'
modified 'mb.chisq' methods to allow for new default behavior of R to use stringsAsFactors = FALSE for characters in data frames
correction bug for GOF Royle-Nichols model (thanks to Ken Kellner)
added methods for 'lmerTest' objects
corrected bug when model names are NULL in 'modavgEffect' for certain model types
added 'DIC' and 'dictab' methods for objects of classes 'jagsUI'
added new functions 'ictab' and 'modavgIC' for generic information criteria, and added 'print' and 'xtable' methods for these classes
modified 'evidence' to include 'ictab' objects
modified sorting of models in 'aictab', 'bictab', 'dictab', 'aictabCustom', and 'bictabCustom' based on values of delta AIC instead of Akaike weights to avoid rounding error with low values
modified 'xtable' for nicer printing of K for 'aictab', 'bictab', and 'anovaOD'
modified value of 'out.type' argument to 'confint' in 'summaryOD'
added 'xtable' method for 'modavgCustom' class and modified 'xtable' method for 'modavg' when working with models of 'multinom' class
added examples in 'AICcmodavg-package' Rd file
added 'summaryOD' to compute confidence intervals around estimates or hypothesis tests adjusted for overdispersion (request by M. Kéry)
added methods for objects of 'glm.nb' class
added methods for glmmTMB models (request by Y. Paillet)
added 'parallel' argument in 'Nmix.gof.test' and 'mb.gof.test' for new 'parallel' argument in 'parboot'
included support of goodness-of-fit statistics of 'mb.chisq' and 'mb.gof.test' for Royle-Nichols models fit with 'occuRN' (thanks to Dan Linden)
included support for multispecies occupancy data and models of classes 'unmarkedFrameOccuMulti' and 'unmarkedFitOccuMulti'
added 'anovaOD' function to compute likelihood ratio tests corrected for overdispersion for models of various classes that use the Poisson or binomial distributions
modified 'covDiag' to handle missing values in data set
updated man page of 'modavgShrink' to include method for 'coxme' class
updated man page of 'importance' to correct typo (thanks to J. Carlisle)
corrected bug in modavg for parameter "b" in false-positive occupancy models
modified sort in 'aictab' and 'bictab' based on delta AIC instead of Akaike weight
modified printing of NA to "." to save space and improve alignment in 'detHist', 'countDist', 'xtable', and 'mb.chisq' methods
modified 'modavgPred' and 'modavgEffect' to use 'predict' for ZIP models fit with 'pcount'
created 'extractX' generic function to extract all predictors that appear in a given list of candidate models and provide info on these variables (added imports of getData from nlme and unmarked, and of formula for lme4)
corrected minor bug for unmarkedFitPCO model class with 'modavgShrink' to modify label of gamma depending on H0 (gamConst, gamAR, gamTrend)
cleaned up modavgEffect
added type = "certain" and "falsepos" as values for the 'parm.type' argument of 'modavgPred', 'modavgEffect', 'modavgShrink', and 'modavg' methods for objects of 'unmarkedFitOccuFP' class and added check for consistency of parameter occurrence in different models
added "iota" as a value for the 'parm.type' argument for 'modavgPred', 'modavgEffect', 'modavgShrink', and 'modavg' methods for objects of 'unmarkedFitPCO' class and added check for consistency of parameter occurrence in different models
added "detect" as a value for the 'parm.type' argument of 'modavgPred', 'modavgEffect', 'modavgShrink', and 'modavg' methods for objects of 'unmarkedFitDS' class
added "detect" as a value for the 'parm.type' argument of 'modavgPred', 'modavgEffect', 'modavgShrink', and 'modavg' methods for objects of 'unmarkedFitGDS' class
corrected minor bug in storing lower.CL in 'modavgPred' result
modified 'fam.link.mer' to account for negative binomial with 'glmer.nb'
corrected minor bug in rounding output of 'c_hat'
corrected bug in 'countDist' with GDS objects including NA's
modified ifelse( ) test when single site includes NA's in 'mb.chisq.unmarkedFitOccu' and 'mb.chisq.unmarkedFitColExt' (thanks to D. Linden)
added drop = FALSE to preserve matrix in 'mb.chisq.unmarkedFitOccu' and 'mb.chisq.unmarkedFitColExt'
added 'report' argument to print test statistic in terminal for functions 'mb.gof.test' and 'Nmix.gof.test'
added 'checkConv' function to check convergence status of algorithm at termination for different model classes
added 'checkParms' function to identify parameters with high SE's in different model classes
modified gls method for 'predictSE' to extract model formula following suggestion by C. R. Andersen
corrected bug in creating final plot of theoretical distribution of sums of chi-squares in mb.gof.test for dynamic occupancy models (thanks to M. Kéry)
corrected bug in 'covDiag'
added 'useBIC' and 'bictab' methods for different model objects based on Bayesian Information Criterion
added 'useBICCustom' function to compute BIC or QBIC from user-supplied inputs (log-likelihood, K, n, c.hat)
added 'bictabCustom' function to create model selection table using BIC or QBIC from user-supplied inputs
added methods for 'xtable' for objects of 'checkParms' and 'bictab' classes
added functionality of 'evidence' with dictab and bictab objects
added new 'useBIC' argument to 'modavgCustom' to conduct multimodel inference based on BIC from user-supplied inputs
removed functions that were moved to defunct during previous cycle of package
updated email address
modified 'mb.gof.test' to deal with dynamic occupancy data for entire visits without data, and seasons with only a single visit (Thanks to G. Sadoti for comments)
corrected bug for negative binomial models and dispersion argument in 'modavg', 'modavgShrink', 'modavgPred', 'modavgEffect', 'multComp'
corrected bug on parameter count when negative binomial formated to glm object with glm.convert( )
updated functionality for overdispersion correction of ZIP N-mixture models in unmarked with 'modavgPred'
added new estimators of overdispersion in 'c_hat' for GLM's (deviance, Farrington, and Fletcher) and print method
added comment on help page of 'mb.gof.test' to clarify that the table only shows the observed detection histories, but that unobserved detection histories are included in the computations, and that the chi-square test statistic should be compared against bootstrap distribution because low expected frequencies invalidate chi-square assumption
modified 'modavgEffect' to allow multiple variables to vary and print generic group names
modified 'modavgShrink' to allow cases where variables do not appear with the same frequency in models, but issues a warning
corrected bug in 'modavgShrink' to deal with 'unmarkedFitGDS' objects on lambda
added support for model selection of 'lavaan' class objects
added support for model selection of fitdistr class objects (package MASS)
added support for model selection of fitdist class objects (package fitdistrplus)
added functionality to request CI's (back-transformed when using type = "response") with 'modavgPred' and modified 'xtable.modavgPred'
added covariance diagnostic for lambda in N-mixture models based on Dennis et al. 2015 Biometrics 71: 237-246
added 'detHist' function to summarize information on detection histories
added 'countHist' function to summarize information on count data
added 'countDist' function to summarize information on count data collected by distance sampling
added 'xtable' methods for objects of 'detHist' and 'countHist' classes
added fat and body measurement data set
added GPA data set and test scores
moved deprecated functions to defunct
cleaned up print method of functions
modified CITATION file to use meta$Date and meta$Version as requested by CRAN
added the Red-spotted newt CMR data set (Gill 1985)
added support for c-hat argument for dynamic occupancy models fit with 'colext' and additional mixture models fit from 'distsamp', 'gdistsamp', 'gmultmix', 'gpcount', 'multinomPois', and 'occuRN'
made 'Nmix.chisq' and 'Nmix.gof.test' generic and added support for different N-mixture models and updated the Rd file
made 'mb.chisq' and 'mb.gof.test' generic for unmarkedFitOccu and unmarkedFitColExt models, modified structure of output, added new arguments 'print.seasons' for 'mb.gof.test.unmarkedFitColExt', and updated the Rd file
added new function to estimate c-hat in lme4 models and made 'c_hat' function generic and updated the Rd file
clarified examples in Rd file of 'modavg' to clearly illustrate how to exclude models when model-averaging the main effect of a variable also involved in an interaction
corrected bug in 'boot.wt' when sorting models in ascending order of Akaike weight
created a separate class for 'boot.wt' objects and print method to facilitate LaTeX formatting
created methods for 'xtable' to format objects from 'aictab', 'boot.wt', 'dictab', 'modavg', 'modavgShrink', 'modavgPred', 'modavgEffect', 'multComp', 'mb.chisq' to LaTeX
corrected bugs in 'modavg' and 'modavgShrink' for models of class 'unmarkedFitGMM' and 'unmarkedFitGPC'
corrected bugs in 'dictab' to return deviance of all models in model selection table
added logical test to identify cases with only a single cohort without missing values for 'mb.chisq'
added custom versions of 'AICc', 'aictabCustom', and 'modavgCustom' when user manually supplies log-Likelihood, K, estimates, and SE for model selection and multimodel inference when model type is not supported or SE's are not available from predict methods (convenient for importing output from other software such as PRESENCE)
added support for hurdle models for count data for model selection and model averaging parameter estimates
added support for model selection of models of the 'gnls' class
added support for model selection and multimodel inference of models of the 'betareg' class
added support for model selection and multimodel inference of models of the 'survreg' class
modified 'multComp' for computation of critical values with z value instead of t for certain model types
corrected minor bug of 'multComp' for some models with a factor consisting of two levels
added 'extractCN' function for models of 'unmarkedFit' classes
modified 'predictSE.lme' to handle the use of formulas specified externally from model call (suggested by Clark Andersen)
added support for named lists of candidate models and add generic model names when modnames vector is NULL in model selection and model averaging functions
replaced functions 'extract.LL', 'modavg.effect', 'modavgpred', 'modavg.shrink', 'mult.comp', with 'extractLL', 'modavgEffect', 'modavgPred', 'modavgShrink', and 'multComp' respectively, to avoid problems with generic functions
'extractLL', 'extractSE', 'AICc', 'aictab', 'modavg', 'modavgEffect', 'modavgShrink', 'modavgPred', 'multComp', and predictSE made generic
changed order of some arguments to present the most often used first
added a check in 'multComp' for missing values in data set, and added options to correct confidence intervals for multiple comparisons
added support for presence-only models of maxlikeFit class
added support for models of classes 'coxme' and 'lmekin'
added support for models of classes 'vglm' (package VGAM) and 'zeroinfl' (package pscl)
added support for models of 'unmarkedFitGMM', 'unmarkedFitMPois', and unmarkedFitGPC classes
added support for model averaging availability parameter (phi) for models of 'unmarkedFitGMM', 'unmarkedFitMPois', and unmarkedFitGPC classes
corrected minor bug in some cases of missing values in 'Nmix.chisq'
corrected minor bug in 'mb.gof.test' that produced warning( )
added 'aov' method for all generic functions of the package
simplified Rd files AICc.rd, aictab.Rd, boot.wt.Rd, DIC.Rd, dictab.Rd, importance.Rd, modavg.Rd, modavg.effect.Rd
added Bullfrog occupancy data set
added Spotted salamander capture-mark-recapture data
added Gopher Tortoise distance sampling data set
corrected minor bug in chi-square for N-mixture models in 'Nmix.chisq'
corrected minor bug in title display, now uses as.expression(substitute())
added functionality to compute model-averaged estimates (means) with 'mult.comp'
added functionality for clogit models
added one-way ANOVA turkey data set
added two-way ANOVA iron data set
modified 'predictSE.zip' to handle offsets and added c.hat argument
added functionality of overdispersion correction for N-mixture models in 'aictab', 'modavg', 'modavgpred', 'modavg.effect', 'modavg.shrink', 'predictSE.zip'
added functions 'Nmix.gof.test' and 'Nmix.chisq' to assess GOF of N-mixture models
added 'mult.comp' function to compute multiple comparisons on factors
added 'boot.wt' function to compute bootstrapped relative frequencies
corrected minor bug in 'mb.chisq' for certain patterns of missing values
added conditional test to avoid problems on CRAN with some packages unavailable on certain platforms
added the lizards habitat preference data set
corrected minor bug in 'modavg' when model-averaging with models of classes 'clm' and 'clmm' when the 'exclude' argument was used
corrected bug with certain types of missing values in 'mb.chisq'
added function to extract DIC and create model selection tables based on DIC (functions 'DIC' and 'dictab')
added functions to work with new 'merMod' classes of package lme4
modified example code of predictSE.zip( ) to avoid errors on some platforms during package building
added 'mb.chisq' to implement MacKenzie and Bailey (2004) goodness-of-fit test on single-season occupancy models and 'mb.gof.test' to compute P-values, c-hat, and histogram of bootstrapped test statistics
corrected bug for offsets in 'predictSE.mer'
added functionality for zip models to compute SE's of predictions on abundance of N-mixture models from unmarked
added functionality for 'occuFP' models (detections with false-positives)
implemented model-averaging estimates and predictions for 'gdistsamp' models
added support for nonlinear mixed models of class 'nlme'
added support for robust regression models of class 'rlm' - 'AICc', 'aictab', 'importance', 'modavg', 'modavg.effect', 'modavg.shrink', 'modavgpred'
added support for ordinal logistic regression models of classes 'clm' and 'clmm' - 'AICc', 'aictab', 'importance', 'modavg', 'modavg.effect', 'modavg.shrink'
modified modavg.unmarked( ) to enable treatment of gamma parameter in pcountOpen models with different formulations (Const, Trend, AR)
added reference of Luckacs et al. 2010 about model averaging with shrinkage in modavg.shrink.Rd file
added references Burnham et al. 2011 for using model selection as alternative to multiple comparisons in modavg.effect.Rd file
removed white space from formulas to reduce chance of reaching character limit in 'parse' in 'predictSE.mer', 'predictSE.lme', and 'predictSE.gls'
changed treatment of parm with modavg.unmarked to add object parm.strip (line 35) to enable functionality with 'regexpr'
added Cox proportional hazards model support
added modavg.effect functions to compute model-averaged effect sizes for true experiments as an information-theoretic analogue to multiple comparisons
corrected minor bug in 'AICc.nls' to determine number of observations automatically when "second.ord = TRUE"
corrected minor bug following revision 1.22 on 'predictSE.mer' to avoid problems with factors
modified example in 'modavg' help file
added error message for models without intercept with 'modavg'
added support for offset variable in 'predictSE.mer' for Poisson GLMM
added support for 'distsamp' and 'gdistsamp' models from unmarked package (Poisson or negative binomial abundance with log link)
added example in 'modavg' and 'modavgpred' for 'distsamp' models
added example for Poisson GLMM with log link and offset
corrected error in computing sample size for binomial model with events/trials syntax in 'AICc.glm' and 'AICc.mer'
added functionality of 'nobs' argument for objects created in unmarked package
created function 'predictSE.gls' to compute predicted values and SE's from 'gls' model fits and added functionality of 'modavgpred' with 'gls' model fit
added documentation with examples for 'gls'
modified functions 'extractSE.mer' and streamlined extraction of estimate labels of 'mer' objects in 'modavg.mer', 'modavg.shrink.mer', 'importance'
fixed minor bug for external calls to 'AICc' to assign 'unmarkedFit' classes
added functionality of 'AICc', 'aictab', 'evidence', 'importance', 'confset' with 'nls' fits
added model selection and multimodel inference functionality with unmarked package for objects of classes unmarkedFitOccu, unmarkedFitColExt, unmarkedFitPCount, unmarkedFitPCO, unmarkedFitOccuRN for models incorporating detectability
modifications of functions 'aictab', 'importance', 'confset', 'evidence', 'modavg', 'modavgpred', 'modavg.shrink', and extract.LL.unmarked utility function added
added new argument parm.type, to specify class of parameters for objects of unmarkedFit classes
added several examples for dealing with objects of 'unmarkedFit' classes
modified 'modavg', 'modavg.shrink', 'importance', and 'reverse.exclude' functions to strip white spaces within elements entered inadvertently by user in the parm and exclude arguments
in 'modavg' and related functions, added functionality of dealing with specification of interaction terms (e.g., A:B, B:A, A*B, B*A) by adding two new utility functions to recognize the terms when user is not consistent in his model syntax
created function 'modavg.shrink' for the shrinkage version of model-averaging estimates to reduce model selection bias when the same number of models include/exclude a variable
fixed minor bug in 'modavg.mer' regarding exclusion of interaction terms as 'formula' includes spaces within interaction terms
fixed minor bug in 'AICc.lme' on the computation of n in certain lme's with several levels
fixed minor bug in 'modavgpred.lme' that generated error message when second.ord = FALSE
fixed minor bug by dispatching 'mer' class objects to 'AICc.mer'
fixed minor bug with incorrect computation of n for 'mer' models with binomial distribution using cbind(incidence, size - incidence) or binary syntax
fixed minor bug in 'modavgpred.glm' that generated an error message for Poisson, binomial, and negative binomial distributions when 'c.hat' = 1
added additional example in 'predictSE.mer' with gaussian distribution but with log link
fixed minor bug in 'modavgpred.glm' for SE's of predictions from gaussian model
fixed minor bug in 'modavg.glm' for SE's of beta estimates from negative binomial glm
added function 'predictSE.mer' to compute predictions and SE's on predictions accounting only for fixed effects (mean population prediction) from objects of 'mer' class
added functionality to 'modavgpred' to include computation of model-averaged predictions from objects of class 'mer'
added a check for link function to ensure same link function was used for all models in 'modavg' when model averaging beta estimates
created a utility function to determine family and link function for objects of 'mer' class called by 'modavg', 'modavgpred', and 'predictSE.mer'
added a warning when some models have an identical (Q)AIC(c) and are possibly redundant in 'aictab'
corrected minor bug in number of observations in 'modavgpred'
added a check for binomial family with events/trials syntax to use sum of weights as number of observations in 'AICc.mer' when nobs = NULL
added Suggests "lme4" in DESCRIPTION file
modified modavg to include 'nobs' argument in call to 'modavg.lme' and 'modavg.gls'
added support for generalized linear mixed models of the mer class for 'AICc', 'aictab', 'modavg', 'evidence', 'importance', 'confset' functions
updated information on support for 'mer' class in help files
added examples in some of the help files with 'mer'
added a 'polr' class check to 'AICc' function
added function 'predictSE.lme' to make predictions based on fixed effects for objects of class 'lme' (mean population predictions) and compute associated SE's
added function 'modvagpred.lme' to compute model-averaged predictions and unconditional standard errors for 'lme' models
added statement in Rd files for 'aictab', 'confset', 'evidence', 'importance', 'modavgpred', 'modavg', and generics 'nobs = NULL' defaults to total number of observations in computations of information criteria
added NEWS file to document changes across versions of AICcmodavg package
added check that same response variable is used throughout model set for 'aictab' and generics with lapply(X = cand.set, FUN = function(b) formula(b))
added functionality of 'AICc', 'aictab', 'confset', 'evidence', 'importance', 'modavg' with objects of 'gls' class
added additional flexibility to 'evidence' function when model selection table provided is not sorted ('evidence' now sorts table internally) and set default comparison to top-ranked model vs second-ranked model
added check/error message when no dispersion parameter (i.e., 'gamdisp') is specified for 'modavg' and 'modavgpred' and generics with gamma regression models
added additional check/error message when c.hat < 1 in 'AICc.glm'
modified number of digits to print with 'importance' to be consistent with revision 1.04
added parenthesis where one was missing in aictab.Rd under value at line for (Q)AIC(c)
corrected example in evidence.Rd for faulty name of model.low - should have been 'model.low = raw density'
deleted CumWt when 'sort = FALSE' in 'aictab' - by modifying argument in 'print.aictab'
for 'AICc.glm', 'AICc.mult', c.hat > 1 && c.hat <= 4 now gives warning
added a column for logLik, quasi-logLik, or restricted logLik in 'aictab'
added options in 'print.aictab' to select items to display
added a check for 'exclude =' in 'modavg' and generics to warn if exclude is not a list
documented 'aictab' with new LL, Quasi.LL, Res.LL elements
used 'vcov' and argument 'dispersion =' to scale SE's in a single step instead of adding more code to scale it on separate lines - works with Poisson, Binomial, Gamma
in 'modavg.polr' and 'modavg.mult', added a logical test to distinguish between 'coef' or zeta which are the intercepts
modified 'print.aictab' so that c_hat is printed only when c_hat appears in AICc table (i.e, when any(names(x)=="c_hat"))
modified 'print.modavg' so that c_hat is printed only when c_hat appears in AICc table (i.e, when any(names(oldtab)=="c_hat")) AND deleted Cum.Wt from x$Mod.avg.table
added a check for the order for aictab and modavg and generics so that LL and other measures are displayed properly in table and sorted at the very end (placed line of sort and cumsum at very end of code) with Results[rev(order(Results[,5])), ]
added Cum.Wt in last column of Results
changed order of elements with colnames so that prints nicely - this affects 'importance', 'confset', and 'evidence' - number of columns used might differ depending on what is requested
in 'modavg' and generics, changed 'regexpr' to determine whether parameter appears alone in the model and added 'fixed = TRUE', to find matches "as is" to avoid problems with 'mult' (e.g., "well|mild")
added the new equation for unconditional SE based on equation 6.12 of Burnham and Anderson (2002) in 'modavg' and 'modavgpred' and new argument 'uncond.se' with default value "revised" - 'uncond.se = old' uses equation 4.19
added a check to determine whether all link functions are identical for 'modavg' as averaging over beta estimates under different link functions is not appropriate and returns error)
added a check to determine whether all link functions are identical for 'modavgpred' when linear predictor is used
changed default to display only 2 digits after decimal point for all output 'print' generic functions
replaced 'regexpr' in 'modavg.glm', 'modavg.lme', 'modavg.mult' with 'match'
-added functionality for 'polr'
cleaned up code with indentations
added 'exclude' argument to manually exclude models with interaction terms/quadratic terms in 'modavg'
added 'warn' argument (to suppress warning that variables with similar names appear in a given model) to 'modavg' function. This is a fundamental difference with the previous versions of the function as now the user must specify the variables (as a list) to exclude models for the computation of model-averaged estimates (case when interaction/polynomial terms are present). This modication also solved the problem of variables with similar names
corrected small bug for computation of AICc (in 'AICc.glm') for binomial models with events/trials syntax to use the correct samplesize
added function to compute (Q)AIC(c) for multinomial models and updated 'aictab' function accordingly
added citation file
changed 'Depends' to 'Suggests' for packages MASS, nnet, nlme
modified 'importance' to include 'multinom' objects
removed dependencies with nlme to avoid potential problems with lme4
cleaned up documentation file, added a few more sentences and added space within formulas for the example to display properly in pdf