changes in version 1.1.9 (2008-07-08) * fixed error in vitalsens example noted by Jay Rotella. Previously, Sf3 is set to 1 in last loop and then not reset to .8943 when calculating vitalsens(goose.el, goose.vr). * changed x@gradient[i] to attr(x, "gradient")[i] in vitalsens to avoid error in R-devel 2.8: trying to get slot "gradient" from an objet of a basic class ("numeric") with no slots * added ChangeLog and Citation. Now citation("popbio") will return JSS article. * saved hudcorrs as *.rda file type with two just elements, corrin and corrout (ie, removed vector of vital rate labels). * set varF=NULL as default in multiresultm * fixed test.census and projection.matrix examples to match names used in JSS paper (eg, trans01 was previously named test.trans and trans) changes in version 1.1.8 (2008-03-13) * added grizzly bear population counts for count-based PVAs * added extCDF function for extinction time cdfs. This function is called by countCDFxt and was previously hidden in that function. * added plot option to countCDFxt and set default value for tq option, which is usually equal to number of tranistions (nt) for regularly censused populations. changes in version 1.1.7 (2008-02-21) * added Calathea to LTRE example with plot, year, and interaction effects * added s3 method for function mean.list to get the mean matrix from a list of matrices. changes in version 1.1.6 (2008-01-14) * changed ltre to LTRE * added plots to vitalsens example changes in version 1.1.5 (2008-01-05) * added ltre function for fixed LTRE. A random design is included in the example * added Calathea dataset for tropical understory herb in Horvitz and Schemske (1995) * fixed damping ratio in eigen.analysis. Now the function finds the second largest modulus and not just modulus of the second eigenvalue ( in case of eigenvalues with equal magnitudes in imprimitive matrices). Also, added which.max to find dominant eigenvalue instead of which(Re(ev$values)==max(Re(ev$values))) which may return two or more indexes in some cases changes in version 1.1.4 (2007-11-13) * fixed error in image plot on teasel example after loading to CRAN changes in version 1.1.3 (2007-11-13) * added function vitalsens for vital rate sensitivities and elasticities * added matplots to teasel example * changed name of lambda to lambda1 in eigen.analysis output to match package demogR (in case demogR is loaded after popbio, then functions using eigen.analysis should still work with some exceptions, eg, if matrix is singular) changes in version 1.1.2 (2007-09-13) * fixed undefined nyrs variable in varEst * added checks to head2 function to work with matrix or dataframe input only * removed extra brackets, foreign language encodings (Akcakaya) in .Rd files requested by JSS editors changes in version 1.1.1 (2007-08-25) * added pfister.plot to create log-log plots of variance vs. sensitivity and CV vs. elasticity * added more plotting examples (fig 9.3, 9.4, 9.11) from chap 9 in Caswell to teasel and tortoise datasets * added age-specific survival and fertility curves (fig 5.1 and 5.2) to whale dataset * corrected errors in hudcorr matrices and vitalsim function suggested by Doak in email dated 8/4/07. * added plot based on fig 8.3 to vitalsim function and code (not run) to simulate no correlations or only within-year correlations * changed colors in stage.vector.plot to rainbow(8) * added column names to boot.transitions (vector and matrix output, e.g., a11, a21, a31 a12, ...) and pop.projection output * changed stage.vector.plot examples to project matrix in example 2.1 in Caswell and create figure 2.3. ################### changes in version 1.1 (2007-07-28) * added new functions and datasets contirubted by Patrick Nantel * added default row and column names (if missing) to stage.vector.plot, checks for matrix with 2 or more stages, and repeats colors if necessary * now checking if matrix is singular in eigen.analysis. If matrix is singular, NA values are used instead of exiting with a warning. This is useful for bootstrapping that may create singular matrices * added print statements on long loops used in all three stochastic growth functions to track progress * now rounding stages first in vector before checking extinction probability in stoch.quasi.ext. Now if vector is (.3,.4,.4) and ext prob=1 then rounding stages sets n=0.