Revision history can be found here. version 0.99
changes and new features  Added the new function, occuFP, which fits occupancy models in which false positive detections are possible. See Royle and Link (Ecology, 2006) and Miller et al. (Ecology, 2011). The new methods getB and getFP can be used to extract relevant information from the fitted models.
 Added new function, gpcount, to fit the generalized Nmixture model discussed by Chandler et al. (Ecology 2011) to repeated count data collected using the robust design.
 Changed the way modelaveraged confidence intervals are computed using predict(fitList, ...). Rather than using the modelaveraged SEs, the confidence intervals from the individual models are averaged. Note: the "level" argument now works.
 nonparametric bootstrapping of fitted pcount() models now resamples sites only.
bug fixes  Fixed getP method for models fit using gdistsamp(..., keyfun="uniform")
 nonparboot now works with models fit using pcountOpen.
known bugs  Known bugs are same as for version 0.90 (see below), plus distsamp crashes on some Unix and Mac systems when engine="C". Use engine="R" if you encounter this problem. Hopefully all these issues will be fixed in version 1.00.
version 0.98
changes and new features  distsamp is now much faster because the likelihood is written in C++. The old slow version is still available by setting engine="R"
 Added 'level' argument to predict, defaults to 0.95 = 95% CI.
 Added new datasets: 'Switzerland', 'cruz', 'crossbill', and 'issj'. See their help pages for more information
 Updated the sppdist vignette. Now includes a distancesampling analysis of the scrubjay data
bug fixes  predict() method now returns the correct predictions of lambda when mixture="ZIP", but it currently does not return SE/CIs. This will be fixed eventually  in the meantime, the bootstrap can be used.
 ranef() method now works for pcountOpen(.., dynamics="trend")
version 0.97
changes new features  predict now works when newdata is an object of class RasterStack from the raster package
 formatDistData now works for data from replicated surveys, and returns a matrix suitable for use with gdistsamp
 added vignette on creating species distribution maps
bug fixes  fixed simulate and ranef method for models fit using gmultmix or gdistsamp with numPrimary=1.
 fixed getP method for gdistsamp
 pcountOpen would crash in an unusual situation involving many missing values. Fixed now.
version 0.95 changes and new features Added empirical Bayes methods to estimate posterior distributions of latent variables (abundance or occurrence). See help(ranef).
 Added vignette on fitting capturerecapture models
 pcountOpen is 25x faster now for "constant" and "notrend" dynamics
 Added bracket subset methods for unmarkedFrameGMM, GDS, and PCO, which make it possible to use nonparboot on models fit using gmultmix, gdistsamp, and pcountOpen.
bug fixes  The bracket subset method for unmarkedMultFrames was broken when yearlySiteCovs were present. This caused nonparboot to crash. Fixed now.
version 0.94 bug fixes The transition probability matrix was not being computed correctly in pcountOpen when "time gaps" were present, ie if there were missing data for an entire primary period at a particular site. Effect should have been minimal in most cases. Thanks to Jeff Hostetler for catching this.
 colext, gdistsamp, and pcountOpen were not handling certain types of missing values correctly. An error was being thrown when it shouldn't have been.
 contstant used to avoid log(0) was not small enough in pcountOpen. Now occu, pcount, and pcountOpen use DOUBLE_EXP in C code.
version 0.93changes and new features pcount and pcountOpen now allow for zeroinflated Poisson distribution (mixture="ZIP")
 pcountOpen is faster with likelihood written in C++
 pcountOpen has a new population dynamics model, dynamics="trend" (thanks to Jeff Hostetler for the suggestion)
 gmultmix now sets phi=1 if T=1
 additional arguments (eg control settings, lower, and upper bounds) can be passed to optim using the "..." argument of the fitting functions
bug fixes occuRN now returns AIC instead of AICclike criterion
 pcountOpen accepts offsets (previously they were ignored without a warning)
version 0.92changes and new features Added reference to new paper describing unmarked. This should be used to cite the package. Type citation("unmarked") for details.
 occu() and pcount() now have an argument "engine" allowing users to try a faster method of evaluating the likelihood. engine="C" should be 3050% faster than engine="R".
version 0.91changes and new features Added new function, gdistsamp, to fit the model of Chandler, Royle, and
King (2011) to distance sampling data. This allows g(0)<1 and
negative binomial distribution for N_{i}
 Added new vignette for colext. Thanks to Marc Kery for doing most of the work
bug fixes
 Fixed bug in predict method for gmultmix
 Fixed bug in simulate method for pcountOpen
 colext now returns AIC instead of AICc
 Known bugs are still the same as below (version 0.90)
version 0.90changes and new features Added the function pcountOpen() to fit the model of Dail and Madsen (Biometrics In press). See help(pcountOpen).
 unmarked now depends upon the Rcpp and RcppArmadillo packages.
 Added getP and simulate methods for colext fits so that parboot can be used.
 distsamp() reverts to an approximate integration when integrate() fails. This usually happens when the detection function is flat.
 Increased the default value of K used by pcount and gmultmix.
 Added help pages for each unmarkedFrame type describing how to format data.
 Added more quality control tests to R_home/inst/unitTests
bug fixes yearlySiteCovs were not being copied correctly to obsCovs during creation of design matrices used by colext().
known bugs
 colext fails when there are missing yearlySiteCovs
 formatMult converts numeric vectors to character vectors if factors are present in df.in
 predict fails when newdata contains factors that do not have exactly the same levels as the original covariate used in the analysis. There is a simple workaround described in this thread.
 predict does not properly handle scale in model formula.
version 0.89
changes and new features Added more tests to inst/unitTests
 Added example to ?unmarked
 logLik method is now available to the user. It returns a simple scalar in contrast to method in stats package.
bug fixes
 Model order is no longer important in LRT
 Corrected modelaveraged SE calculation in predict method for unmarkedFitList (thanks to Marc Mazerolle)
 Fixed multinomial cell probability calculation in distsamp for survey="point".
version 0.88changes and new features now depends on >= R2.12.0
 summary method for unmarkedMultFrames includes yearlySiteCovs
 predict methods for colext and fitList return CIs
 formatDistData returns matrix instead of data.frame
 added new unit tests in R_HOME/inst/unitTests
 added rel.tol argument to distsamp to provide some control of integrate function
 added coef and SE methods for fitList objects
 removed n from modSel show method
bug fixes fixed lambda offset of gmultmix
 fixed simulate method for gmultmix
 fixed cn() so that modSel won't break with singular hessians
 fixed NA handling for gmultmix
 fixed doublePiFun
 fixed bracket subsetting methods for unmarkedMultFrames
