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only-lou committed Oct 27, 2023
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66 changes: 42 additions & 24 deletions doc/PhyG-User-Manual/PhyG_Allcommands.tex
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Expand Up @@ -636,9 +636,17 @@ \subsection{Refine}
\item[keep:INT] Limits the number of returned graphs to that as specified by the
integer value.
\item[maxnetedges:INT] Specifies the maximum number of network edges, as indicated
by the integer value. % The number of edges visited?
\item[maxnetedges:INT] Used in conjunction with the network edit operations
\texttt{netadd}, \texttt{netdel} and \texttt{netadddel}, this specifies the maximum
number of network edges involved in the edit operation. When used in conjunction
with \texttt{netadd}, the maximum number of network edges added to the graph,
is determined by the associated integer value. Note: when deciding the number of
maximum edges, the user should be aware that the addition of network edges
exponentially increases the time taken to optimize the graph
\cite{WheelerandWashburn2023}. In the case of \texttt{netdel}, a maximum of network
edges, as specified by the integer value, will be deleted from the input graphs.
When used with \texttt{netadddel} \hl{...}
\item[netadd] Adds network edges to existing input graphs at all possible positions
until no better cost graph is found.
Expand Down Expand Up @@ -682,7 +690,7 @@ \subsection{Refine}
of lower cost is found. During this operation, the network edit neighborhoods
are traversed at random. }
\item {\texttt{refine(netmove, atrandom, steepest)}\\
%\item {\texttt{refine(netmove, atrandom, steepest)}\\
%add ga and drift examples
\end{example}
Expand Down Expand Up @@ -772,10 +780,10 @@ \subsection{Report}
lengths follow the terminal labels. Compare with \texttt{nobranchlengths}.
This is the default.
\item[collapse] Specifies that zero length branches are collapsed. Compare
with the \texttt{nocollapse} argument. If a dotpdf graph is specified, the
branches are collapsed by default. If ASCII, Newick, eNewick and dot are
specified, the zero length branches are not collapsed by default.
\item[collapse] Specifies that zero length branches are collapsed. If a dotpdf
graph is specified, the branches are collapsed by default. If ASCII, Newick,
eNewick and dot are specified, the zero length branches are not collapsed by
default. Compare with the \texttt{nocollapse} argument.
\item[crossrefs] Reports whether data are present or absent for each terminal
in each of the imported data files. The argument will report a table with terminals
Expand All @@ -784,7 +792,9 @@ \subsection{Report}
indicates that it is absent. This provides a comprehensive visual overview of the
completeness of the data. It will highlight missing data, as well as inconsistencies
in the spelling of taxon names in different data files (see Figure \ref{crossrefs}).
The reported file is in csv format.
This information will be directed to a file, in csv format, if a file name (in quotes),
followed by a comma, is included in the argument list of report. If no file name is
specified, this information will be printed to the stderr.
\begin{figure}
\centering
Expand All @@ -794,9 +804,9 @@ \subsection{Report}
\label{crossrefs}
\end{figure}
\item[data] Outputs a summary of the input data and terminals. This file summarizes
information relating to the input data (number of terminals, number of input files,
number of character blocks and the total number of characters). It also provides
\item[data] Outputs a summary of the input data and terminals. Information relating
to the input data (number of terminals, number of input files, number of character
blocks and the total number of characters) is summariazed. It also provides
information relating to the terminal taxa included in the analysis, including the
names of the taxa, a list of the excluded taxa (if any), and whether any terminals
were renamed. In this file you will also see information relating to ``Index'', ``Block'',
Expand All @@ -809,13 +819,20 @@ \subsection{Report}
sequence character (e.g. amino acids) is to treated as prealigned or not,
``Alphabet'' the elements of a sequence character, ``TCM'' is the transition cost
matrix specifying costs among sequence elements and ``gap'' or insertion-deletion.
The reported file is in csv format.
This information will be directed to a file, in csv format, if a file name (in quotes),
followed by a comma, is included in the argument list of report. If no file name is
specified, this information will be printed to the stderr.
\item[diagnosis] Outputs graph diagnosis information such as vertex, states
and edge statistics. The reported file is in csv format.
and edge statistics. This information will be directed to a file, in csv format, if a
file name (in quotes), followed by a comma, is included in the argument list of
report. If no file name is specified, this information will be printed to the stderr.
\item[displaytrees] Reports graph information for softwired networks. The
`display' trees are output for each data block.
`display' trees are output for each data block. This information will be directed
to a file, \hl{in text format}, if a file name (in quotes), followed by a comma, is
included in the argument list of report. If no file name is specified, this information
will be printed to the stderr.
\item[dot] Outputs a graph in dot format. The dot file can be viewed (and
modified) in \textit{Graphviz} (see also \texttt{dotpdf}). In order to output pdf
Expand All @@ -833,8 +850,8 @@ \subsection{Report}
(length) of 0.
\item[graphs] Outputs a graph in the format specified by the other arguments
in the command. These are either Newick, eNewick, ASCII, dot, and depending
on the operating system, eps (on MacOS) or pdf (on Linux) formats.
in the command. These are either Newick, eNewick, ASCII, dot, and dotpdf,
which will output a graph in eps (on MacOS) or pdf (on Linux) format.
\item[htulabels] Labels the HTUs in the output files (compare with
\texttt{nohtulabels}). This is the default.
Expand Down Expand Up @@ -875,12 +892,13 @@ \subsection{Report}
\texttt{nobranchlengths} will override this default and branch lengths
of graphs are not reported.
\item[nocollapse] By default, if a dotpdf graph is specified, the zero-length
branches are collapsed. Compare with the \texttt{collapse} argument. If
ASCII, Newick, eNewick and dot are specified, the zero length branches are
not collapsed by default. If \texttt{nocollapse} is specified, zero length branches
are not collapsed for output graphs.
\item[nocollapse] Specifies that zero length branches are not collapsed.
If ASCII, Newick, eNewick and dot graphs are specified, the zero length
branches are not collapsed by default. In contrast, if a dotpdf graph is specified,
the zero-length branches are collapsed. Note: by specifying
a dotpdf file, this will by default output a dot file with zero length branches not
collapsed. Compare with the \texttt{collapse} argument.
\item[nohtulabels] Labels of the HTUs are not included in the output files.
This option can not be applied to eNewick graph. Compare with the argument
\texttt{htulabels}.
Expand Down Expand Up @@ -984,7 +1002,7 @@ \subsection{Report}
\end{description}
\subsubsection{Defaults}
\texttt{report(dot, append, branchlengths, htulabels, collapse)}
\texttt{report(append, branchlengths, collapse, dot, htulabels)}
The default graph representation is \texttt{dot}. A dot file will only be
reported if no other graph type is indicated. Branch lengths and HTU
labels are printed in the output files. Zero length branches are collapsed.
Expand Down

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