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CHANGELOG
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ver 3.1.14
Fixed bugs uncovered by Eric Archer
ver 3.1.12
Updated 2 functions to bring rmetasim into R 4.0 compliance
Added an option to skip is.landscape check on some locus functions.
Added in functions for allele frequency specification in populations and stages.
Changed the test for surv matrix norm 12/17/18
You can always use "install_github("stranda/rmetasim") to get the most up to date copy of rmetasim.
ver 3.1.2
found and fixed a memory leak in the sequence mutation routines
ver 3.1.1
dealt with issues with compining on clang-4. Also registered native calls. Made the rudimentary space stuff interface acceptable to CRAN
ver 3.1.0
Added rudimentary space. Basically x and y dimensions in the intparam component of the landscape object
ver 3.0.8
Added a test to 'is.landscape' that checks to make sure that loci have the correct type for the type of it's allele states
ver 3.0.7
Added in a test for adding more than the maximum allowed loci
ver 3.0.6
The versions between this and 3.0.1 updated the vignette system and vignette content.
It also implemented a bunch of fixes for solaris compilation issues.
ver 3.0.1
Even more UI changes. Changed interface for several functions to standardize: When using functions that are exported and take a landscape, the landscape is always the first parameter now. This allows the use of piping with magrittr. The functions that were modified are:
landscape.amova.locus
landscape.locus
landscape.locus.states
landscape.mismatchdist
landscape.states
Routines that call these functions and do not use explicit parameter names will need to be adjusted accordingly
ver 3.0.0
Significant changes. Eliminated all of the backend-implemented output routines
ver 1.1.14
fixed a lot of memory management issues
ver 1.1.13
backed out the generalization of memory management implemented in 1.1.10 which caused an ugly memory leak. In the process of
improving memory management.
ver 1.1.12
increased the length of DNA seqs from 500 to 1000
ver 1.1.11
1/23/10
Resolved a small problem with the Rd file for landscape.mismatchdist.
ver 1.1.10
1/22/10
Fixed gnu-specific C++ array allocation. Should now compile on Sun.
Also added a function 'landscape.mig.matrix' that automatically creates a migration
matrix among populations
ver 1.1.09
10/7/09
Fixed changed dependency on ape and added 'pegas' functions as well as
explicit call to ade4's amova function to distinguish it from the pegas version.
ver 1.1.08
10/4/09
Fixed problem assigning individual ids (Thanks to Karen Martien)
ver 1.1.07
3/4/09
repaired bug in landscape.sample()
ver 1.1.05
1/24/08
added code to interface with amova functions in ade4.
ver 1.1.02
11/22/07
removed landscape.new.epoch.island and landscape.new.epoch.step
They didn't work as advertised and there has been limited desire to
use them
ver 1.1.009
5/10/07
Reinstated the labelling of individuals, their mothers, and fathers in
the columns 4:6 in the individual sub-object of a landscape.
ver 1.1.006
12/16/06
Finally fixed "the bug" that Karen Martien pointed out last year.
This was very hard to find because it did not manifest on my
development platform (mac), nor in the way that I use the programs and
therefore the way that my testscript works.
ver 1.1.0
12/3/06 Fixed some stack imbalance problems. Updated the code to read in simcoal simulations
10/10/06 Eliminated out of date documentation. Need to develop a
Vignette for the package. This is High on the TODO list
9/29/06 Tried to make rmetasim function names more consistent by
appending 'lansdscape' to the front of them. This should reduce
naming collision problems with base and other packages in R
3/25/06 Fixed bug in conversion between rmetasim objects and internal
c++ representations. Added code to parse Arlequin files into rmetasim
objects
3/25/06 IMPORTANT!!! Added three columns to individuals object between
the demographic information and the genetic information. They store
an individuals unique ID, it's mothers unique ID and fathers unique
ID. This can be used to track family structure over multiple
generations. Right now, rmetasim does nothing but create and assign
these IDs properly. This change alters the text file structure of
rmetasim and will have dire repurcussions for anyone who directly
accesses the individual objects and does not account for the addtional
three columns. All of the rmetasim functions should work correctly.
If individuals are created outside of the c++ backend, they should be
given appropriate IDs Zero for mother and father indicates individuals
created de novo
Several new functions have been defined to work with these objects.
ver 1.0.5
11/16/05 To accomodate changes in R 2.2 that implemented the S3 base
'simulate', changed the central function simulate.landscape() to sim.landscape()
ver 1.0.2
1/11/04 Fixed problem with is.landscape() AES
1/5/05 Addded some update features to landscapes AES