################################################################################ CHANGELOG Version 1.3-1 Fixed issue with plot methods which was causing build error, and tidied up reference links and keywords sections. Version 1.3-0 Added S4 class, methods and generics for projections. This does everything the S3 classes used to do, and more, but with a stricter and more accessible structure. See ?Projection-class for methods for handling the new classes and ?Projection-plot for display and plot methods. Changes to 'project' function: - removed dependency on markovchain package and added a bespoke markov chain simulation function (.rmc) to handle that (thanks to Steve Ellner). - Changes to output new S4 Projection object Added a package Vignette which runs through (most) of the functionality of the package. See browseVignettes("popdemo") - new Polar bear data included for stochastics examples - updates to documentation to keep pace with CRAN Version 1.2-1 Bug fix ('project' function markov chain simulation not working) Version 1.2-0 Added functionality to 'project' function to perform stochastic projections Added 'eigs' function for calculating dominant eigendata Added 'stoch' function for calculating stochastic growth parameters (mean / variance) Version 1.1-1 - Bug fixes to S3 plot method for projections: now fully supports user-defined parameters, e.g. points instead of lines, colours, log axes, and more (without returning warnings). - Fixed bugs which caused certain S3 methods to not register properly. - Fixed a bug which meant not all deprecated functions were registering properly. Now all older versions of functions will work (with a warning to redirect to the new function). - Added support for simultaneously projecting multiple user-specified population vectors, with plotting support. - Small changes to documentation Version 1.1-0 Updates to 'project' function and its S3 method to facilitate projection of dirichlet draws of population structures. Version 1.0-0: 'devtools' now used to check and build the package. Changes to documentation, renaming of lots of functions. DOCUMENTATION Big changes to documentation. 1. Move to 'devtools' means the package source now uses 'roxygen2' for documentation. 2. Updates to contents of nearly all documentation files for better clarity and updated nomenclature. 3. Links between documentation now handled mostly by function families. 4. Merging of documentation for some S3 plot methods. FUNCTIONS 1. Deprecated functions Many functions in popdemo have been renamed in version 1.0-0. The old names are now deprecated. The old names will work for now, but may be removed completely in future versions! Most of the changes are to remove periods from function names: in previous versions the use of periods in names gave rise to the possibility for confusion between functions and S3 methods. The renamed functions are: 'Cohen.cumulative' now 'CohenD' 'convergence.time' now 'convt' 'inertia.tfa' now 'tfa_inertia' 'inertia.tfamatrix' now 'tfam_inertia' 'inertia.tfsens' now 'tfs_inertia' 'inertia.tfsensmatrix' now 'tfsm_inertia' 'is.matrix_ergodic' now 'isErgodic' 'is.matrix_irreducible' now 'isIrreducible' 'is.matrix_primitive' now 'isPrimitive' 'Keyfitz.delta' now 'KeyfitzD' 'projection.distance' now 'projectionD' Other functions have been renamed to keep consistency with new functions, and also to further avoid problems with S3 methods by making sure functions and classes don't have the same name: 'tfa' now 'tfa_lambda' 'tfamatrix' now 'tfam_lambda' 'tfsens now 'tfs_lambda 'tfsensmatrix' now 'tfsm_lambda' Some functions have been made internal, as they were only ever intended to be used by other popdemo functions: 'tf' now '.tf' 'minCS' now '.minCS' Two functions have been merged: 'reactivity','firststepatt' now 'reac' 2. New functions 'reac' replaces 'reactivity' and 'firststepatt'. Version 0.2-3: Further changes to DESCRIPTION file to keep CRAN happy Version 0.2-2: Changed title and description fields in DESCRIPTION file to align more closely with CRAN guidelines Version 0.2-1: Fixed bug in sens and elas functions where complex conjugates of left eigenvector were not properly calculated, which would have resulted in incorrect sensitivity and elasticity calculations for eigenvalues with nonzero imaginary components in version 0.1-4 and earlier. This does not affect results for sensitivity and elasticity analyses of the dominant eigenvalue of irreducible matrices (i.e. sensitivity and elasticity of asymptotic population growth in ergodic models). Version 0.1-4: Fixed maintainer email address Version 0.1-3: Tortoise matrix included as data Version 0.1-2: Bugs in demos sorted.