
Frequently Answered Questions:
 Why won’t the newest version of COMPARE run on my computer?
 How can I save my results to file?
 How can I deal with missing data in COMPARE?
 Why am I still getting a message that there is an error in my phylogeny?
It works in xxxx!
 Can I use COMPARE to analyze categorical data or to run an ANOVA?
 There are no branch lengths on my phylogeny, what do I do?
 How do I get a pvalue for a correlation coefficient from COMPARE?
 Why won’t the newest version of COMPARE
run on my computer? Make sure you have a modern web browser
(e.g., Internet Explorer or Netscape) and that you have recently downloaded
and installed the Java Virtual Machine (http://www.java.com). COMPARE
was written in JAVA and can be run directly from your browser without
being downloaded or installed. It works well on PCs, Macs, and UNIX
machines, with Internet Explorer and Netscape. You can also download
an executable version or compile it yourself from the source code.
 How can I save my results to file?
Although, COMPARE does not write to or read from your hard drive, you
can transfer your results with copy/paste (use the shortcut keys and
right mouse button) to another file.
 How can I deal with missing data in COMPARE?
COMPARE assumes that each data set is complete. To handle missing data,
create one or more reduced data sets and phylogenies. You can do this
easily using the "Draw Phylogeny" button/window to delete
taxa and save a new reduced tree.
 Why am I still getting a message that
there is an error in my phylogeny? It works in xxxx! If it's
not a missing parentheses or comma, there is probably a polytomy in
your phylogeny. Try using Phylodendron or some other program to draw
the phylogeny to find it. For hard polytomies (representing rapid diversification
rather than ignorance) insert very tiny branch lengths so that the phylogeny
is actually bifurcating. For soft polytomies (representing ignorance),
consider using the Generate Phylogenies page to create several possible
phylogenies.
 Can I use COMPARE to analyze categorical
data or to run an ANOVA? Most of the analysis routines in COMPARE
are set up as regressions. Hence, they work best when at least the Y
variable is continuous. Categorical predictor (x) variables can be included,
if you first code each variable as a set of dichotomous "dummy"
variables. A oneway ANOVA with three levels is equivalent to a regression
of y on two x variables (yes/no level 1, yes/no level 2). Look at a
good regression textbook for further explanation.
 There are no branch lengths on my phylogeny,
what do I do? All phylogenetic analyses either use or assume
branch lengths of one form or another. Most phylogenetic methods require
that branch lengths be in units of the expected amount of phenotypic
change for the character of interest, quantities that are almost never
known. Lots of partial solutions have been proposed, including plots,
statistical transformations, and randomization tests. My own preference
is to use methods (e.g., PGLS, PMM) which estimate an extra parameter
which automatically stretches and shrinks branch lengths to fit the
data and phylogeny. In COMPARE, you can also generate 1000s of possible
branch lengths for a known phylogeny, analyze your data on each and
combine the results to calculate a confidence interval that takes your
uncertainty into account.
 How do I get a pvalue for a correlation
coefficient from COMPARE? Many correlation coefficients (e.g.,
for Felsenstein contrasts) can be tested against standard statistical
tables. In other cases, it is difficult to know the distribution of
correlation coefficients, making it even more difficult to calculate
pvalues. Instead, COMPARE reports regression slopes (b) and standard
errors. If the error term in the regression model is independent, normally
distributed, and homoscedastic, you can estimate a rough 95% confidence
interval for a regression slope as +/ 1.96 standard errors. The correlation
coefficient is directly related to the regression slopes. In a bivariate
regression, if the regression slope differs significantly from zero,
the correlation coefficient will too.
