From 93505924d1e615c24d36287b29d780c5b426523e Mon Sep 17 00:00:00 2001 From: Ward Wheeler Date: Thu, 19 Oct 2023 11:09:21 -0400 Subject: [PATCH] Added missingThreshold to docs --- doc/PhyG-User-Manual/PhyG-User-Manual.tex | 4 ++-- doc/PhyG-User-Manual/PhyG_Allcommands.tex | 7 ++++++- 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/doc/PhyG-User-Manual/PhyG-User-Manual.tex b/doc/PhyG-User-Manual/PhyG-User-Manual.tex index b2183a80f..88d52580c 100644 --- a/doc/PhyG-User-Manual/PhyG-User-Manual.tex +++ b/doc/PhyG-User-Manual/PhyG-User-Manual.tex @@ -554,7 +554,7 @@ \section*{Acknowledgments} %\newpage %\bibliography{big-refs-3.bib} - \bibliography{/Users/louise/DropboxAMNH/big-refs-3.bib} - %\bibliography{/home/ward/Dropbox/Work_stuff/manus/big-refs-3.bib} + %\bibliography{/Users/louise/DropboxAMNH/big-refs-3.bib} + \bibliography{/home/ward/Dropbox/Work_stuff/manus/big-refs-3.bib} %\bibliography{/users/ward/Dropbox/work_stuff/manus/big-refs-3.bib} \end{document} \ No newline at end of file diff --git a/doc/PhyG-User-Manual/PhyG_Allcommands.tex b/doc/PhyG-User-Manual/PhyG_Allcommands.tex index df504b63d..b235d60c3 100644 --- a/doc/PhyG-User-Manual/PhyG_Allcommands.tex +++ b/doc/PhyG-User-Manual/PhyG_Allcommands.tex @@ -1283,7 +1283,12 @@ \subsection{Set} \end{description} %\item[modelcomplexity] \hl{details} - + \item[missingThreshold:[Int]] Sets the maximum percentage of missing data in a terminal. + The default setting is 100, leaving all terminals in the data set. Terminal taxa + with more than the missing fraction are deleted. The \texttt{missingThreshold} value is determined + by the number of input blocks (files). Hence, a taxon with all missing values in a TNT file + will be counted as not missing for this purpose. + \item[multiTraverse:[BOOL]] Controls the multi-traverse character optimization option. If \texttt{True}, character trees are traversed from each edge as in \citep{VaronandWheeler2012,VaronandWheeler2013, POY4, POY5}, but