phylo_data {opm}R Documentation

Export phylogenetic data

Description

Create entire character matrix (include header and footer) in a file format suitable for exporting phylogenetic data. Return it or write it to a file. This function can also produce HTML tables and text paragraphs suitable for displaying PM data in taxonomic journals such as IJSEM.

Usage

  ## S4 method for signature 'OPMD_Listing'
phylo_data(object, html.args = html_args(), run.tidy = FALSE)
  ## S4 method for signature 'OPMS_Listing'
phylo_data(object, html.args = html_args(), run.tidy = FALSE)
  ## S4 method for signature 'XOPMX'
phylo_data(object, as.labels,
    subset = param_names("disc.name"), sep = " ", extract.args = list(),
    join = TRUE, discrete.args = list(range = TRUE, gap = TRUE), ...) 
  ## S4 method for signature 'data.frame'
phylo_data(object, as.labels = NULL,
    subset = "numeric", sep = " ", ...) 
  ## S4 method for signature 'matrix'
phylo_data(object,
    format = opm_opt("phylo.fmt"), outfile = "", enclose = TRUE, indent = 3L,
    paup.block = FALSE, delete = c("none", "uninf", "constant", "ambig"),
    join = FALSE, cutoff = 0, digits = opm_opt("digits"),
    comments = comment(object), html.args = html_args(),
    prefer.char = format == "html", run.tidy = FALSE, ...)

Arguments

object

Data frame, numeric matrix or OPMS or MOPMX object (with aggregated values). Currently only ‘integer’, ‘logical’, ‘double’ and ‘character’ matrix content is supported. The data-frame and OPMS methods first call extract and then the matrix method. The methods for OPMD_Listing and OPMS_Listing objects can be applied to the results of listing.

format

Character scalar determining the output format, either epf (Extended PHYLIP Format), nexus, phylip, hennig or html.

If NEXUS or ‘Hennig’ format is chosen, a non-empty comment attribute will be output together with the data (and appropriately escaped). In case of HTML format, a non-empty comment yields the title of the HTML document.

EPF or ‘extended PHYLIP’ is sometimes called ‘relaxed PHYLIP’. The main difference between EPF and PHYLIP is that the former can use labels with more than ten characters, but its labels must not contain whitespace. (These adaptations are done automatically with safe_labels.)

outfile

Character scalar. If a non-empty character scalar, resulting lines are directly written to this file. Otherwise, they are returned.

enclose

Logical scalar. Shall labels be enclosed in single quotes? Ignored unless format is ‘nexus’.

indent

Integer scalar. Indentation of commands in NEXUS format. Ignored unless format is ‘nexus’ (and a matter of taste anyway).

paup.block

Logical scalar. Append a PAUP* block with selected (recommended) default values? Has no effect unless ‘nexus’ is selected as ‘format’.

delete

Character scalar with one of the following values:

uninf

Columns are removed which are either constant (in the strict sense) or are columns in which some fields contain polymorphisms, and no pairs of fields share no character states.

ambig

Columns with ambiguities (multiple states in at least one single field) are removed.

constant

Columns which are constant in the strict sense are removed.

delete is currently ignored for formats other than HTML, and note that columns become rows in the final HTML output.

join

Logical scalar, vector or factor. Unless FALSE, rows of object are joined together, either according to the row names (if join is TRUE), or directly according to join. This can be used to deal with measurements repetitions for the same organism or treatment.

cutoff

Numeric scalar. If joining results in multiple-state characters, they can be filtered by removing all entries with a relative frequency less than ‘cutoff’. Makes not much sense for non-integer numeric data.

digits

Numeric scalar. Used for rounding, and thus ignored unless object is of mode ‘numeric’.

comments

Character vector. Comments to be added to the output (as title if HTML is chosen). Ignored if the output format does not allow for comments. If empty, a default comment is chosen.

html.args

List of arguments used to modify the generated HTML. See html_args for the supported list elements and their meaning.

prefer.char

Logical scalar indicating whether or not to use NA as intermediary character state. Has only an effect for ‘logical’ and ‘integer’ characters. A warning is issued if integers are not within the necessary range, i.e. either 0 or 1.

run.tidy

Logical scalar. Filter the resulting HTML through the Tidy program? Ignored unless format is html. Otherwise, if TRUE, it is an error if the Tidy executable is not found.

as.labels

Vector of data-frame indexes or OPMS metadata entries. See extract.

sep

Character scalar. See extract.

subset

Character scalar. For the OPMS method, passed to the OPMS method of extract. For the data-frame method, a selection of column classes to extract.

extract.args

Optional list of arguments passed to that method.

discrete.args

Optional list of arguments passed from the OPMS method to discrete. If set to NULL, discretisation is turned off. Ignored if stored discretised values are chosen by setting subset to param_names("disc.name").

...

Optional arguments passed between the methods (i.e., from the other methods to the matrix method) or to hwrite from the hwriter package. Note that ‘table.summary’ is set via html.args and that ‘page’, ‘x’ and ‘div’ cannot be used.

Details

Exporting PM data in such formats allows one to either infer trees from the data under the maximum-likelihood and/or the maximum-parsimony criterion, or to reconstruct the evolution of PM characters on given phylogenetic trees, or to nicely display the data in HTML format.

For exporting NEXUS format, the matrix should normally be converted beforehand by applying discrete. Exporting HTML is optimised for data discretised with gap set to TRUE. For other data, the character.states argument should be modified, see html_args. The hennig (Hennig86) format is the one used by TNT; it allows continuous characters to be analysed as such. Regarding the meaning of ‘character’ as used here, see the ‘Details’ section of discrete.

The generated HTML is guaranteed to produce neither errors nor warnings if checked using the Tidy program. It deliberately contains no formatting instructions but a rich annotation with ‘class’ attributes which allows for CSS-based formatting. This annotation includes the naming of all sections and all kinds of textual content. Whether the characters show differences between at least one organism and the others is also indicated. For the CSS files that come with the package, see the examples below and opm_files.

Value

Character vector, each element representing a line in a potential output file, returned invisibly if outfile is given.

References

Berger, S. A., Stamatakis, A. 2010 Accuracy of morphology-based phylogenetic fossil placement under maximum likelihood. 8th ACS/IEEE International Conference on Computer Systems and Applications (AICCSA-10). Hammamet, Tunisia [analysis of phenotypic data with RAxML].

Felsenstein, J. 2005 PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Seattle: University of Washington, Department of Genome Sciences [the PHYLIP program].

Goloboff, P.A., Farris, J.S., Nixon, K.C. 2008 TNT, a free program for phylogenetic analysis. Cladistics 24, 774–786 [the TNT program].

Goloboff, P.A., Mattoni, C., Quinteros, S. 2005 Continuous characters analysed as such. Cladistics 22, 589–601.

Maddison, D. R., Swofford, D. L., Maddison, W. P. 1997 Nexus: An extensible file format for systematic information. Syst Biol 46, 590–621 [the NEXUS format].

Stamatakis, A. 2006 RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models Bioinformatics 22, 2688–2690. [the RAxML program].

Swofford, D. L. 2002 PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0 b10. Sunderland, Mass.: Sinauer Associates [the PAUP* program].

http://ijs.sgmjournals.org/ [IJSEM journal]

http://tidy.sourceforge.net/ [HTML Tidy]

See Also

base::comment base::write hwriter::hwrite

Other phylogeny-functions: html_args, safe_labels

Examples

# simple helper functions
echo <- function(x) write(substr(x, 1, 250), file = "")
is_html <- function(x) is.character(x) &&
  c("<html>", "<head>", "<body>", "</html>", "</head>", "</body>") %in% x
longer <- function(x, y) any(nchar(x) > nchar(y)) &&
  !any(nchar(x) < nchar(y))

## examples with a dummy data set
x <- matrix(c(0:9, letters[1:22]), nrow = 2)
colnames(x) <- LETTERS[1:16]
rownames(x) <- c("Ahoernchen", "Behoernchen") # Chip and Dale in German

# EPF is a comparatively restricted format
echo(y.epf <- phylo_data(x, format = "epf"))

## 2 16
## Ahoernchen   02468ACEGIKMOQSU
## Behoernchen  13579BDFHJLNPRTV

stopifnot(is.character(y.epf), length(y.epf) == 3)
stopifnot(identical(y.epf, phylo_data(as.data.frame(x), subset = "factor",
  format = "epf")))

# PHYLIP is even more restricted (shorter labels!)
echo(y.phylip <- phylo_data(x, format = "phylip"))

## 2 16
## Ahoernchen   02468ACEGIKMOQSU
## Behoernche   13579BDFHJLNPRTV

stopifnot((y.epf == y.phylip) == c(TRUE, FALSE, FALSE))

# NEXUS allows for more content; note the comment and the character labels
echo(y.nexus <- phylo_data(x, format = "nexus"))

## #NEXUS
## 
## [
## Characters exported by opm version 1.3.63
## ]
## 
## begin data;
##    dimensions ntax = 2 nchar = 16;
##    format datatype = standard missing = ?;
##    format symbols = "0123456789ABCDEFGHIJKLMNOPQRSTUV";
##    charlabels 'A' 'B' 'C' 'D' 'E' 'F' 'G' 'H' 'I' 'J' 'K' 'L' 'M' 'N' 'O' 'P';
##    matrix
## 'Ahoernchen'     02468ACEGIKMOQSU
## 'Behoernchen'    13579BDFHJLNPRTV
##    ;
## end;
## 
## begin assumptions;
##    typeset * default = ord : all;
## end;

nexus.len.1 <- length(y.nexus)
stopifnot(is.character(y.nexus), nexus.len.1 > 10)

# adding a PAUP* block with (hopefully useful) default settings
echo(y.nexus <- phylo_data(x, format = "nexus", paup.block = TRUE))

## #NEXUS
## 
## [
## Characters exported by opm version 1.3.63
## ]
## 
## begin data;
##    dimensions ntax = 2 nchar = 16;
##    format datatype = standard missing = ?;
##    format symbols = "0123456789ABCDEFGHIJKLMNOPQRSTUV";
##    charlabels 'A' 'B' 'C' 'D' 'E' 'F' 'G' 'H' 'I' 'J' 'K' 'L' 'M' 'N' 'O' 'P';
##    matrix
## 'Ahoernchen'     02468ACEGIKMOQSU
## 'Behoernchen'    13579BDFHJLNPRTV
##    ;
## end;
## 
## begin assumptions;
##    typeset * default = ord : all;
## end;
## 
## begin paup;
##    set torder=left tcompress taxlabels=full outroot=monophyl autoclose;
##    set maxtrees=1000 increase=auto autoinc=1000 storetreewts storebrlens;
##    set rootmethod=midpoint warnroot=no;
##    defaults nj bionj breakties=random;
##    defaults upgma bionj breakties=random;
##    defaults hsearch start=stepwise addseq=random randomize=addseq swap=tbr;
##    default hsearch multrees steepest=no;
##    defaults bootstrap grpfreq=no;
##    defaults contree grpfreq=no;
##    defaults savedist triangle=both;
##    defaults describetrees labelnode=no;
##    dset negbrlen=setzero dcollapse missdist=ignore;
##    pset opt=minf collapse=minbrlen mstaxa=uncertain;
## end;

stopifnot(is.character(y.nexus), length(y.nexus) > nexus.len.1)

# adding our own comment
comment(x) <- c("This is", "a test") # yields two lines
echo(y.nexus <- phylo_data(x, format = "nexus"))

## #NEXUS
## 
## [
## This is
## a test
## ]
## 
## begin data;
##    dimensions ntax = 2 nchar = 16;
##    format datatype = standard missing = ?;
##    format symbols = "0123456789ABCDEFGHIJKLMNOPQRSTUV";
##    charlabels 'A' 'B' 'C' 'D' 'E' 'F' 'G' 'H' 'I' 'J' 'K' 'L' 'M' 'N' 'O' 'P';
##    matrix
## 'Ahoernchen'     02468ACEGIKMOQSU
## 'Behoernchen'    13579BDFHJLNPRTV
##    ;
## end;
## 
## begin assumptions;
##    typeset * default = ord : all;
## end;

stopifnot(identical(length(y.nexus), nexus.len.1 + 1L))

# Hennig86/TNT also includes the comment
echo(y.hennig <- phylo_data(x, format = "hennig"))

## Warning: TNT will not accept less than 4 organisms

## nstates 32;
## xread
## '
## This is
## a test
## '
## 16 2
## &[numeric]
## Ahoernchen   02468ACEGIKMOQSU
## Behoernchen  13579BDFHJLNPRTV
## ;
## ccode - .;
## procedure /;

hennig.len.1 <- length(y.hennig)
stopifnot(is.character(y.hennig), hennig.len.1 > 10)

# without an explicit comment, the default one will be used
comment(x) <- NULL
echo(y.hennig <- phylo_data(x, format = "hennig"))

## Warning: TNT will not accept less than 4 organisms

## nstates 32;
## xread
## '
## Characters exported by opm version 1.3.63
## '
## 16 2
## &[numeric]
## Ahoernchen   02468ACEGIKMOQSU
## Behoernchen  13579BDFHJLNPRTV
## ;
## ccode - .;
## procedure /;

stopifnot(identical(length(y.hennig), hennig.len.1 - 1L))

## examples with real data and HTML

# setting the CSS file that comes with opm as default
opm_opt(css.file = opm_files("css")[[1]])

# see discrete() for the conversion and note the OPMS example below: one
# could also get the results directly from OPMS objects
x <- extract(vaas_4[, , 1:10], as.labels = list("Species", "Strain"),
  in.parens = FALSE)
x <- discrete(x, range = TRUE, gap = TRUE)
echo(y <- phylo_data(x, format = "html",
  html.args = html_args(organisms.start = "Strains: ")))

## <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
## <html>
## <head>
## <title>Characters exported by opm version 1.3.63</title>
## <meta name="generator" content="opm version 1.3.63">
## <meta name="date" content="2016-04-14T14:04:37+0100">
## <!-- user-defined CSS file(s) -->
## <link rel="stylesheet" type="text/css" href="file:///usr/local/lib/R/library/opm/auxiliary/styles_1.css">
## </head>
## <body>
## <div class="headline" title="headline">Characters exported by opm version 1.3.63</div>
## <div class="table-legend" title="table-legend"><span class="organism-list-head" title="organism-list-head">Strains: </span> <span class="organism-index" title="organism-index">1</span>, <span class="organism-name" title="organism-name">Escherichia co
## <div class="table-legend" title="table-legend"><span class="character-state-list-head" title="character-state-list-head">Symbols: </span> <span class="state-1" title="state-1">-</span>, <span class="character-state-name" title="character-state-name">
## <div class="main-table">
## <table summary="character matrix" border="1">
## <tr>
## <td></td><td><span class="organism-index" title="organism-index">1</span></td><td><span class="organism-index" title="organism-index">2</span></td><td><span class="organism-index" title="organism-ind
## </div>
## </body>
## </html>

# this yields HTML with the usual tags, a table legend, and the table itself
# in a single line; the default 'organisms.start' could also be used
stopifnot(is_html(y))

# now with joining of the results per species (and changing the organism
# description accordingly)
x <- extract(vaas_4[, , 1:10], as.labels = list("Species"),
  in.parens = FALSE)

## Warning in .local(object, ...): duplicated label: Escherichia coli

x <- discrete(x, range = TRUE, gap = TRUE)
echo(y <- phylo_data(x, format = "html", join = TRUE,
  html.args = html_args(organisms.start = "Species: ")))

## <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
## <html>
## <head>
## <title>Characters exported by opm version 1.3.63</title>
## <meta name="generator" content="opm version 1.3.63">
## <meta name="date" content="2016-04-14T14:04:37+0100">
## <!-- user-defined CSS file(s) -->
## <link rel="stylesheet" type="text/css" href="file:///usr/local/lib/R/library/opm/auxiliary/styles_1.css">
## </head>
## <body>
## <div class="headline" title="headline">Characters exported by opm version 1.3.63</div>
## <div class="table-legend" title="table-legend"><span class="organism-list-head" title="organism-list-head">Species: </span> <span class="organism-index" title="organism-index">1</span>, <span class="organism-name" title="organism-name">Escherichia co
## <div class="table-legend" title="table-legend"><span class="character-state-list-head" title="character-state-list-head">Symbols: </span> <span class="state-1" title="state-1">-</span>, <span class="character-state-name" title="character-state-name">
## <div class="main-table">
## <table summary="character matrix" border="1">
## <tr>
## <td></td><td><span class="organism-index" title="organism-index">1</span></td><td><span class="organism-index" title="organism-index">2</span></td></tr>
## <tr>
## <td><div class="character-name" title="ch
## </div>
## </body>
## </html>

stopifnot(is_html(y))
# Here and in the following examples note the highlighting of the variable
# (uninformative or informative) characters. The uninformative ones are those
# that are not constant but show overlap regarding the sets of character
# states between all organisms. The informative ones are those that are fully
# distinct between all organisms.

# 'OPMS' method, yielding the same results than above but directly
echo(yy <- phylo_data(vaas_4[, , 1:10], as.labels = "Species",
  format = "html", join = TRUE, extract.args = list(in.parens = FALSE),
  html.args = html_args(organisms.start = "Species: ")))

## <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
## <html>
## <head>
## <title>Characters exported by opm version 1.3.63</title>
## <meta name="generator" content="opm version 1.3.63">
## <meta name="date" content="2016-04-14T14:04:37+0100">
## <!-- user-defined CSS file(s) -->
## <link rel="stylesheet" type="text/css" href="file:///usr/local/lib/R/library/opm/auxiliary/styles_1.css">
## </head>
## <body>
## <div class="headline" title="headline">Characters exported by opm version 1.3.63</div>
## <div class="table-legend" title="table-legend"><span class="organism-list-head" title="organism-list-head">Species: </span> <span class="organism-index" title="organism-index">1</span>, <span class="organism-name" title="organism-name">Escherichia co
## <div class="table-legend" title="table-legend"><span class="character-state-list-head" title="character-state-list-head">Symbols: </span> <span class="state-1" title="state-1">-</span>, <span class="character-state-name" title="character-state-name">
## <div class="main-table">
## <table summary="character matrix" border="1">
## <tr>
## <td></td><td><span class="organism-index" title="organism-index">1</span></td><td><span class="organism-index" title="organism-index">2</span></td></tr>
## <tr>
## <td><div class="character-name" title="ch
## </div>
## </body>
## </html>

# the timestamps might differ, but otherwise the result is as above
stopifnot(length(y) == length(yy) && length(which(y != yy)) < 2)

# appending user-defined sections
echo(yy <- phylo_data(vaas_4[, , 1:10], as.labels = "Species",
  format = "html", join = TRUE, extract.args = list(in.parens = FALSE),
  html.args = html_args(organisms.start = "Species: ",
  append = list(section.1 = "additional text", section.2 = "more text"))))

## <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
## <html>
## <head>
## <title>Characters exported by opm version 1.3.63</title>
## <meta name="generator" content="opm version 1.3.63">
## <meta name="date" content="2016-04-14T14:04:37+0100">
## <!-- user-defined CSS file(s) -->
## <link rel="stylesheet" type="text/css" href="file:///usr/local/lib/R/library/opm/auxiliary/styles_1.css">
## </head>
## <body>
## <div class="headline" title="headline">Characters exported by opm version 1.3.63</div>
## <div class="table-legend" title="table-legend"><span class="organism-list-head" title="organism-list-head">Species: </span> <span class="organism-index" title="organism-index">1</span>, <span class="organism-name" title="organism-name">Escherichia co
## <div class="table-legend" title="table-legend"><span class="character-state-list-head" title="character-state-list-head">Symbols: </span> <span class="state-1" title="state-1">-</span>, <span class="character-state-name" title="character-state-name">
## <div class="main-table">
## <table summary="character matrix" border="1">
## <tr>
## <td></td><td><span class="organism-index" title="organism-index">1</span></td><td><span class="organism-index" title="organism-index">2</span></td></tr>
## <tr>
## <td><div class="character-name" title="ch
## </div>
## <!-- user-appended-sections -->
## <div class="user-appended-section" title="user-appended-section">
##   <div class="section.1" title="section.1">
##     additional text
##   </div>
##   <div class="section.2" title="section.2">
##     more text
##   </div>
## </div>
## 
## </body>
## </html>

stopifnot(length(y) < length(yy), length(which(!y %in% yy)) < 2)
# note the position -- there are also 'prepend' and 'insert' arguments

# effect of deletion
echo(y <- phylo_data(x, "html", delete = "none", join = FALSE))

## <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
## <html>
## <head>
## <title>Characters exported by opm version 1.3.63</title>
## <meta name="generator" content="opm version 1.3.63">
## <meta name="date" content="2016-04-14T14:04:37+0100">
## <!-- user-defined CSS file(s) -->
## <link rel="stylesheet" type="text/css" href="file:///usr/local/lib/R/library/opm/auxiliary/styles_1.css">
## </head>
## <body>
## <div class="headline" title="headline">Characters exported by opm version 1.3.63</div>
## <div class="table-legend" title="table-legend"><span class="organism-list-head" title="organism-list-head">Organisms: </span> <span class="organism-index" title="organism-index">1</span>, <span class="organism-name" title="organism-name">Escherichia 
## <div class="table-legend" title="table-legend"><span class="character-state-list-head" title="character-state-list-head">Symbols: </span> <span class="state-1" title="state-1">-</span>, <span class="character-state-name" title="character-state-name">
## <div class="main-table">
## <table summary="character matrix" border="1">
## <tr>
## <td></td><td><span class="organism-index" title="organism-index">1</span></td><td><span class="organism-index" title="organism-index">2</span></td><td><span class="organism-index" title="organism-ind
## </div>
## </body>
## </html>

echo(y.noambig <- phylo_data(x, "html", delete = "ambig", join = FALSE))

## <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
## <html>
## <head>
## <title>Characters exported by opm version 1.3.63</title>
## <meta name="generator" content="opm version 1.3.63">
## <meta name="date" content="2016-04-14T14:04:37+0100">
## <!-- user-defined CSS file(s) -->
## <link rel="stylesheet" type="text/css" href="file:///usr/local/lib/R/library/opm/auxiliary/styles_1.css">
## </head>
## <body>
## <div class="headline" title="headline">Characters exported by opm version 1.3.63</div>
## <div class="table-legend" title="table-legend"><span class="organism-list-head" title="organism-list-head">Organisms: </span> <span class="organism-index" title="organism-index">1</span>, <span class="organism-name" title="organism-name">Escherichia 
## <div class="table-legend" title="table-legend"><span class="character-state-list-head" title="character-state-list-head">Symbols: </span> <span class="state-1" title="state-1">-</span>, <span class="character-state-name" title="character-state-name">
## <div class="main-table">
## <table summary="character matrix" border="1">
## <tr>
## <td></td><td><span class="organism-index" title="organism-index">1</span></td><td><span class="organism-index" title="organism-index">2</span></td><td><span class="organism-index" title="organism-ind
## </div>
## </body>
## </html>

stopifnot(length(which(y != y.noambig)) < 2) # timestamps might differ
# ambiguities are created only by joining
echo(y <- phylo_data(x, "html", delete = "none", join = TRUE))

## <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
## <html>
## <head>
## <title>Characters exported by opm version 1.3.63</title>
## <meta name="generator" content="opm version 1.3.63">
## <meta name="date" content="2016-04-14T14:04:37+0100">
## <!-- user-defined CSS file(s) -->
## <link rel="stylesheet" type="text/css" href="file:///usr/local/lib/R/library/opm/auxiliary/styles_1.css">
## </head>
## <body>
## <div class="headline" title="headline">Characters exported by opm version 1.3.63</div>
## <div class="table-legend" title="table-legend"><span class="organism-list-head" title="organism-list-head">Organisms: </span> <span class="organism-index" title="organism-index">1</span>, <span class="organism-name" title="organism-name">Escherichia 
## <div class="table-legend" title="table-legend"><span class="character-state-list-head" title="character-state-list-head">Symbols: </span> <span class="state-1" title="state-1">-</span>, <span class="character-state-name" title="character-state-name">
## <div class="main-table">
## <table summary="character matrix" border="1">
## <tr>
## <td></td><td><span class="organism-index" title="organism-index">1</span></td><td><span class="organism-index" title="organism-index">2</span></td></tr>
## <tr>
## <td><div class="character-name" title="ch
## </div>
## </body>
## </html>

echo(y.noambig <- phylo_data(x, "html", delete = "ambig", join = TRUE))

## <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
## <html>
## <head>
## <title>Characters exported by opm version 1.3.63</title>
## <meta name="generator" content="opm version 1.3.63">
## <meta name="date" content="2016-04-14T14:04:37+0100">
## <!-- user-defined CSS file(s) -->
## <link rel="stylesheet" type="text/css" href="file:///usr/local/lib/R/library/opm/auxiliary/styles_1.css">
## </head>
## <body>
## <div class="headline" title="headline">Characters exported by opm version 1.3.63</div>
## <div class="table-legend" title="table-legend"><span class="organism-list-head" title="organism-list-head">Organisms: </span> <span class="organism-index" title="organism-index">1</span>, <span class="organism-name" title="organism-name">Escherichia 
## <div class="table-legend" title="table-legend"><span class="character-state-list-head" title="character-state-list-head">Symbols: </span> <span class="state-1" title="state-1">-</span>, <span class="character-state-name" title="character-state-name">
## <div class="main-table">
## <table summary="character matrix" border="1">
## <tr>
## <td></td><td><span class="organism-index" title="organism-index">1</span></td><td><span class="organism-index" title="organism-index">2</span></td></tr>
## <tr>
## <td><div class="character-name" title="ch
## </div>
## </body>
## </html>

stopifnot(longer(y, y.noambig))
echo(y.nouninf <- phylo_data(x, "html", delete = "uninf", join = TRUE))

## <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
## <html>
## <head>
## <title>Characters exported by opm version 1.3.63</title>
## <meta name="generator" content="opm version 1.3.63">
## <meta name="date" content="2016-04-14T14:04:37+0100">
## <!-- user-defined CSS file(s) -->
## <link rel="stylesheet" type="text/css" href="file:///usr/local/lib/R/library/opm/auxiliary/styles_1.css">
## </head>
## <body>
## <div class="headline" title="headline">Characters exported by opm version 1.3.63</div>
## <div class="table-legend" title="table-legend"><span class="organism-list-head" title="organism-list-head">Organisms: </span> <span class="organism-index" title="organism-index">1</span>, <span class="organism-name" title="organism-name">Escherichia 
## <div class="table-legend" title="table-legend"><span class="character-state-list-head" title="character-state-list-head">Symbols: </span> <span class="state-1" title="state-1">-</span>, <span class="character-state-name" title="character-state-name">
## <div class="main-table">
## <table summary="character matrix" border="1">
## <tr>
## <td></td><td><span class="organism-index" title="organism-index">1</span></td><td><span class="organism-index" title="organism-index">2</span></td></tr>
## <tr>
## <td><div class="character-name" title="ch
## </div>
## </body>
## </html>

stopifnot(longer(y, y.nouninf))
echo(y.noconst <- phylo_data(x, "html", delete = "const", join = TRUE))

## <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
## <html>
## <head>
## <title>Characters exported by opm version 1.3.63</title>
## <meta name="generator" content="opm version 1.3.63">
## <meta name="date" content="2016-04-14T14:04:37+0100">
## <!-- user-defined CSS file(s) -->
## <link rel="stylesheet" type="text/css" href="file:///usr/local/lib/R/library/opm/auxiliary/styles_1.css">
## </head>
## <body>
## <div class="headline" title="headline">Characters exported by opm version 1.3.63</div>
## <div class="table-legend" title="table-legend"><span class="organism-list-head" title="organism-list-head">Organisms: </span> <span class="organism-index" title="organism-index">1</span>, <span class="organism-name" title="organism-name">Escherichia 
## <div class="table-legend" title="table-legend"><span class="character-state-list-head" title="character-state-list-head">Symbols: </span> <span class="state-1" title="state-1">-</span>, <span class="character-state-name" title="character-state-name">
## <div class="main-table">
## <table summary="character matrix" border="1">
## <tr>
## <td></td><td><span class="organism-index" title="organism-index">1</span></td><td><span class="organism-index" title="organism-index">2</span></td></tr>
## <tr>
## <td><div class="character-name" title="ch
## </div>
## </body>
## </html>

stopifnot(longer(y.noconst, y.nouninf))

# getting real numbers, not discretised ones
echo(yy <- phylo_data(vaas_4[, , 1:10], as.labels = "Species",
  format = "html", join = TRUE, extract.args = list(in.parens = FALSE),
  subset = "A", discrete.args = NULL,
  html.args = html_args(organisms.start = "Species: ")))

## <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
## <html>
## <head>
## <title>Characters exported by opm version 1.3.63</title>
## <meta name="generator" content="opm version 1.3.63">
## <meta name="date" content="2016-04-14T14:04:37+0100">
## <!-- user-defined CSS file(s) -->
## <link rel="stylesheet" type="text/css" href="file:///usr/local/lib/R/library/opm/auxiliary/styles_1.css">
## </head>
## <body>
## <div class="headline" title="headline">Characters exported by opm version 1.3.63</div>
## <div class="table-legend" title="table-legend"><span class="organism-list-head" title="organism-list-head">Species: </span> <span class="organism-index" title="organism-index">1</span>, <span class="organism-name" title="organism-name">Escherichia co
## <div class="main-table">
## <table summary="character matrix" border="1">
## <tr>
## <td></td><td><span class="organism-index" title="organism-index">1</span></td><td><span class="organism-index" title="organism-index">2</span></td></tr>
## <tr>
## <td><div class="character-name" title="ch
## </div>
## </body>
## </html>

stopifnot(is_html(yy), length(yy) == length(y) - 1) # no symbols list
# the highlighting is also used here, based on the following heuristic:
# if mean+/-2*sd does not overlap, the character is informative; else
# if mean+/-sd does not overlap, the character is uninformative; otherwise
# it is constant

# this can also be used for formats other than HTML (but not all make sense)
echo(yy <- phylo_data(vaas_4[, , 1:10], as.labels = "Species",
  format = "hennig", join = TRUE, extract.args = list(in.parens = FALSE),
  subset = "A", discrete.args = NULL))

## Warning: TNT will not accept less than 4 organisms

## nstates cont;
## xread
## '
## Characters exported by opm version 1.3.63
## '
## 10 2
## &[continuous]
## Escherichia_coli          14.3184- 9.7684 35.1843-17.2980 29.5878-35.8790 28.9383-32.5378 17.0109-22.9759 27.9727-39.2608 17.3777-24.2689 14.2196-19.0965 14.9447-19.5719 64.3279- 0.9505
## Pseudomonas_aeruginosa     7.5970- 0.8327 10.1221- 1.3439  2.8619- 4.0473  6.8192- 0.3000  4.2421- 2.4183  3.8125- 4.3329  3.2008- 4.0699  3.4809- 3.1850  4.2189- 4.4522 60.8540- 0.0274
## ;
## ccode - .;
## procedure /;

stopifnot(is.character(yy), length(yy) > 10)

## 'OPMD_Listing' method
echo(x <- phylo_data(listing(vaas_1, NULL)))

## Positive for dextrin, D-maltose, D-trehalose, beta-gentiobiose, positive control, pH 6, pH 5, alpha-D-lactose, D-melibiose, beta-methyl-D-glucoside, N-acetyl-D-glucosamine, N-acetyl-beta-D-mannosamine, N-acetyl-D-galactosamine, N-acetyl-neuraminic ac

stopifnot(is.character(x), length(x) == 1)
echo(x <- phylo_data(listing(vaas_1, NULL, html = TRUE)))

## <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
## <html>
## <head>
## <title>Character listing exported by opm version 1.3.63</title>
## <meta name="generator" content="opm version 1.3.63">
## <meta name="date" content="2016-04-14T14:04:37+0100">
## <!-- user-defined CSS file(s) -->
## <link rel="stylesheet" type="text/css" href="file:///usr/local/lib/R/library/opm/auxiliary/styles_1.css">
## </head>
## <body>
## <div>Positive for dextrin, <small>D</small>-maltose, <small>D</small>-trehalose, &beta;-gentiobiose, positive control, pH 6, pH 5, &alpha;-<small>D</small>-lactose, <small>D</small>-melibiose, &beta;-methyl-<small>D</small>-glucoside, <i>N</i>-acetyl
## <div>Negative for negative control, <small>D</small>-arabitol, gelatin, <small>L</small>-histidine, <small>L</small>-pyroglutamic acid, pectin, glucuronamide, mucic acid, quinic acid, <small>D</small>-saccharic acid, <i>p</i>-hydroxy-phenylacetic aci
## <div>Ambiguous for <small>D</small>-cellobiose, sucrose, turanose, stachyose, <small>D</small>-raffinose, <small>D</small>-salicin, 3-<i>O</i>-methyl-<small>D</small>-glucose, <small>D</small>-fucose, myo-inositol, <small>D</small>-aspartic acid, <sm
## </body>
## </html>

stopifnot(is.character(x), length(x) > 1)

## 'OPMS_Listing' method
echo(x <- phylo_data(listing(vaas_4, as.groups = "Species")))

## Positive for positive control, pH 6, pH 5, 1% NaCl, 4% NaCl, 8% NaCl, 1% sodium lactate, fusidic acid, D-glucose-6-phosphate, D-fructose-6-phosphate, D-serine #1, troleandomycin, rifamycin SV, minocycline, gly-pro, L-alanine, L-aspartic acid, L-serin
## Positive for positive control, pH 6, pH 5, 1% NaCl, 4% NaCl, 8% NaCl, 1% sodium lactate, fusidic acid, troleandomycin, rifamycin SV, minocycline, gly-pro, L-alanine, L-arginine, L-aspartic acid, L-glutamic acid, L-histidine, L-pyroglutamic acid, linc

stopifnot(is.character(x), length(x) == 2, !is.null(names(x)))
echo(x <- phylo_data(listing(vaas_4, as.groups = "Species", html = TRUE)))

## <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
## <html>
## <head>
## <title>Character listings exported by opm version 1.3.63</title>
## <meta name="generator" content="opm version 1.3.63">
## <meta name="date" content="2016-04-14T14:04:37+0100">
## <!-- user-defined CSS file(s) -->
## <link rel="stylesheet" type="text/css" href="file:///usr/local/lib/R/library/opm/auxiliary/styles_1.css">
## </head>
## <body>
## <div class="headline" title="headline"><span class="organism-name" title="organism-name">Escherichia coli</span></div>
## <div>Positive for positive control, pH 6, pH 5, 1% NaCl, 4% NaCl, 8% NaCl, 1% sodium lactate, fusidic acid, <small>D</small>-glucose-6-phosphate, <small>D</small>-fructose-6-phosphate, <small>D</small>-serine #1, troleandomycin, rifamycin SV, minocyc
## <div class="headline" title="headline"><span class="organism-name" title="organism-name">Pseudomonas aeruginosa</span></div>
## <div>Positive for positive control, pH 6, pH 5, 1% NaCl, 4% NaCl, 8% NaCl, 1% sodium lactate, fusidic acid, troleandomycin, rifamycin SV, minocycline, gly-pro, <small>L</small>-alanine, <small>L</small>-arginine, <small>L</small>-aspartic acid, <smal
## </body>
## </html>

stopifnot(is.character(x), length(x) > 2, is.null(names(x)))
[Package opm version 1.3.63 Index]