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CHANGELOG
Version 1.3-2 Fixed check issue with "lost braces"
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.