ClineFit 2.0a

This is a first-release, pre-publication, beta version



ClineFit fits genotypic and morphological data to the classical, equilibrium cline models developed by Nick Barton in the 1980's -90's.  It uses a numerical maximum likelihood algorithm, and returns maximum-likelihood estimates of parameter values and 2-unit support limits.  It supports cline shapes of varying complexity, for example clines with or without introgressing tails.  It supports disequibrium estimation for data having multiple genetic markers, and uses that information along with cline shape data to estimate dispersal, selection and other parameters.  It supports customization of your models so you can compare
shapes and test hypotheses.

ClineFit uses the methods published in Evolution (Porter et al. 1997), which in turn follows Barton's methods very closely. Its main difference is that it fits genotypes to the cline shape directly, rather than fitting transformed data to a linearized model; this isn't such a big difference. 

ClineFit v2.0a replaces ClineFit v0.2, an antique that runs on older and increasingly hard to find versions of the Mac OS.  It was built using an obsolete compiler, so I can therefore no longer support it and don't recommend you use it anymore.


New and improved features in this version


 Support for data of (almost) all inheritance types:
Codominant markers
Dominant markers
Sex-linked/haplodiploid codominant markers
Sex-linked/haplodiploid dominant markers
Cytoplasmic markers inherited through females (e.g., mtDNA, cpDNA)
Cytoplasmic markers inherited through males (e.g., Y chromosomes)
Quantitative traits
Threshold traits (e.g., color morphs)
X/Y and W/Z sex determination

Disequilibrium estimation:
Uses all the data on the transect, instead of populations in a user-defined central region.  This gives more statistical power.
Supports estimation within and between genetic markers of all inheritance types.
Cline orientation:
Traits with higher values at either the left or right ends of the cline are supported.
Parameters such as width and tail shape can be co-estimated within and between traits of either orientation.
Considerable power to customize:
Turn parameters on or off to include or exclude them from the model.
Co-estimate vs. separately estimate parameters for arbitrary sets of traits (and use model selection to see if clines or parts of clines differ among them).
Comparison among transects:
Data from multiple transects can be estimated together
Among locations
Within or among groups of individuals (e.g., life stages)
Among years (e.g., look for evidence of movement)
Among species
Construct customized models to compare parameter combinations shared within and among transects simultaneously.

Not yet supported:  models that include disequilibrium
Model selection:
Reports AIC as well as log-likelihood scores, to compare customized models properly.
Estimate only the best fitting model under your settings, or
choose to include 2-unit support limits.
Improved MCMC algorithm:
Modified Gibbs sampler makes fitting and sampling for support much more efficient with large numbers of parameters.
Better able to escape blind alleys that appear when large numbers of parameters are estimated under customized models.
Better user control over the rate of approach to the maximum-likelihood cline shape.
Control over the number of cycles between saved parameter sets during sampling for support. 
More output files:
Output files suitable for making graphics.
Pairwise disequilibrium tables for all populations.
User's manual & sample files:
Instructions for creating the data files.
Step by step instructions for using each option.
Background on the models used in the program.
Explanations of each of the parameters.
Implications of the assumptions made in implementing the models and interpreting the results.
Background on maximum-likelihood estimation and model selection.
Ideas to try if your results look funky.
Graphics:
A Mathematica notebook for creating graphics (you still have to get your hands on a copy of Mathematica).
(No R package is available.)





Operating system


ClineFit 2.0a runs only on Mac OS X, versions 10.7 at least up to v.10.8.4.  It runs in the Terminal application as a command-line program.






User's group

I'm moderating a Google group on ClineFit. 

https://groups.google.com/forum/#!forum/clinefit
Join (or lurk).
Post your questions and insights.  I'll answer and others can too.
Help:   Report glitches ahead of my release of the full version.
Others depend on you.


 

Updates and bug fixes:


Version 2.0 beta02 -

August 29, 2013
New features:
- Threshold traits (those with 2 alternative states, for example 'red' and 'black') are now supported.
Bug fixes
- This version should run on Mac OS 10.7 and 10.8.
Manual:
- Information on formatting data for threshold traits.

- Commentary on subtlties in the interpretation of cline widths and associated dispersal estimates for clines in continuous and threshold traits.  In the section on Limits ot Interpretation.

Version 2.0
beta01 -

August 20, 2013
This is the first release
 

Downloads:




This is a pre-release, beta version, so you might run into more problems than normal.  I'm collecting suggestions for improvements.  I expect to be replacing versions at a reasonable rate as bugs are exposed, and as I add new features.  Join the User's Group to stay in the loop on those changes.

Latest version:  28 August 2013.
ClineFit v2.0 beta-02       (.zip format)
ClineFit Manual   (pdf)
At the next window, double-click the name of the file you want and it will download.

The operating system may block you from opening downloaded applications it hasn't seen before.  (It may also try to block the download, having identified that it contains an application.) After it downloads and you uncompress it, try Control-Click, then on the menu, Open.  You might still need system administrator authority to open it the first time.

Sample data:
SampleClineData1.txt
SampleClineDataNoQ.txt
SampleClineDataQonly.txt
SampleClineDataQ1only.txt
Sample2ClineData.txt
Sample2ClineDataNoQ.txt
Graphics:   
ClineFit Graphics.nb    (.zip format.  - 107MB.  A Mathematica notebook with some graphing functions)

These were used to generate the example graphics images:
SampleClineDataNoQOut_shape1.txt
SampleClineDataNoQOut_HI.txt

SampleClineDataQ1onlyOut_shape1.txt
SampleClineDataQ1phenotypes.txt



Older versions:




This is a pre-release, beta version, so you might run into more problems than normal.  I'm collecting suggestions for improvements.
ClineFit v2.0-beta-01       (.zip format) -- originally released: 20 August 2013
ClineFit Manual   (pdf) -- originally released: 20 August 2013



Questions?

Problems getting it to work? 
The user's group might be the best place to post.

Something else?


Adam Porter
Biology Dept.
UMass Amherst
aporter@bio.umass.edu






Page updated:
21 August 2013, A. Porter