ssp: Define Arguments for Plotting Multichannel Sequences and/or Most Probable Paths from Hidden Markov Models

Description

Function ssp defines the arguments for plotting with plot.ssp() or gridplot().

Usage

ssp(
  x,
  hidden.paths = NULL,
  plots = "obs",
  type = "d",
  tlim = 0,
  sortv = NULL,
  sort.channel = 1,
  dist.method = "OM",
  with.missing = FALSE,
  missing.color = NULL,
  title = NA,
  title.n = TRUE,
  cex.title = 1,
  title.pos = 1,
  with.legend = "auto",
  ncol.legend = "auto",
  with.missing.legend = "auto",
  legend.prop = 0.3,
  cex.legend = 1,
  hidden.states.colors = "auto",
  hidden.states.labels = "auto",
  xaxis = TRUE,
  xlab = NA,
  xtlab = NULL,
  xlab.pos = 1,
  ylab = "auto",
  hidden.states.title = "Hidden states",
  yaxis = FALSE,
  ylab.pos = "auto",
  cex.lab = 1,
  cex.axis = 1,
  withlegend,
  respect_void = TRUE,
  ...
)

Value

Object of class ssp.

Arguments

x: Either a hidden Markov model object of class hmm or a state sequence object of class stslist (created with the TraMineR::seqdef()) function) or a list of state sequence objects.
hidden.paths: Output from hidden_paths() function. Optional, if x is a hmm object or if type = "obs".
plots: What to plot. One of "obs" for observations (the default), "hidden.paths" for most probable paths of hidden states, or "both" for observations and hidden paths together.
type: The type of the plot. Available types are "I" for sequence index plots and "d" for state distribution plots (the default). See TraMineR::seqplot() for details.
tlim: Indexes of the subjects to be plotted (the default is 0, i.e. all subjects are plotted). For example, tlim = 1:10 plots the first ten subjects in data.
sortv: A sorting variable or a sort method (one of "from.start", "from.end", "mds.obs", or "mds.hidden") for type = "I". The value "mds.hidden" is only available when hidden paths are available. Options "mds.obs" and "mds.hidden" automatically arrange the sequences according to the scores of multidimensional scaling (using stats::cmdscale()) for the observed data or hidden states paths. MDS scores are computed from distances/dissimilarities using a metric defined in argument dist.method. See TraMineR::plot.stslist() for more details on "from.start" and "from.end".
sort.channel: The number of the channel according to which the "from.start" or "from.end" sorting is done. Sorting according to hidden states is called with value 0. The default value is 1 (the first channel).
dist.method: The metric to be used for computing the distances of the sequences if multidimensional scaling is used for sorting. One of "OM" (optimal matching, the default), "LCP" (longest common prefix), "RLCP" (reversed LCP, i.e. longest common suffix), "LCS" (longest common subsequence), "HAM" (Hamming distance), and "DHD" (dynamic Hamming distance). Transition rates are used for defining substitution costs if needed. See TraMineR::seqdef() for more information on the metrics.
with.missing: Controls whether missing states are included in state distribution plots (type = "d"). The default is FALSE.
missing.color: Alternative color for representing missing values in the sequences. By default, this color is taken from the missing.color attribute of the sequence object.
title: Main title for the graphic. The default is NA: if title.n = TRUE, only the number of subjects is plotted. FALSE prints no title, even when title.n = TRUE.
title.n: Controls whether the number of subjects (in the first channel) is printed in the title of the plot. The default is TRUE: n is plotted if title is anything but FALSE.
cex.title: Expansion factor for setting the size of the font for the title. The default value is 1. Values lesser than 1 will reduce the size of the font, values greater than 1 will increase the size.
title.pos: Controls the position of the main title of the plot. The default value is 1. Values greater than 1 will place the title higher.
with.legend: Defines if and where the legend for the states is plotted. The default value "auto" (equivalent to TRUE and "right") creates separate legends for each requested plot and positions them on the right-hand side of the plot. Other possible values are "bottom", "right.combined", and "bottom.combined", of which the last two create a combined legend in the selected position. FALSE prints no legend.
ncol.legend: (A vector of) the number of columns for the legend(s). The default "auto" determines number of columns depending on the position of the legend.
with.missing.legend: If set to "auto" (the default), a legend for the missing state is added automatically if one or more of the sequences in the data/channel contains missing states and type = "I". If type = "d" missing states are omitted from the legends unless with.missing = TRUE. With the value TRUE a legend for the missing state is added in any case; equivalently FALSE omits the legend for the missing state.
legend.prop: Sets the proportion of the graphic area used for plotting the legend when with.legend is not FALSE. The default value is 0.3. Takes values from 0 to 1.
cex.legend: Expansion factor for setting the size of the font for the labels in the legend. The default value is 1. Values lesser than 1 will reduce the size of the font, values greater than 1 will increase the size.
hidden.states.colors: A vector of colors assigned to hidden states. The default value "auto" uses the colors assigned to the stslist object (created with TraMineR::seqdef()) if hidden.paths is given; otherwise colors from colorpalette() are automatically used.
hidden.states.labels: Labels for the hidden states. The default value "auto" uses the names provided in x$state_names if x is an hmm object; otherwise the number of the hidden state.
xaxis: Controls whether an x-axis is plotted below the plot at the bottom. The default value is TRUE.
xlab: An optional label for the x-axis. If set to NA, no label is drawn.
xtlab: Optional labels for the x-axis tick labels. If unspecified, the column names of the seqdata sequence object are used (see TraMineR::seqdef()).
xlab.pos: Controls the position of the x-axis label. The default value is 1. Values greater than 1 will place the label further away from the plot.
ylab: Labels for the channels shown as labels for y-axes. A vector of names for each channel (observations). The default value "auto" uses the names provided in x$channel_names if x is an hmm object; otherwise the names of the list in x if given, or the number of the channel if names are not given. FALSE prints no labels.
hidden.states.title: Optional label for the hidden state plot (in the y-axis). The default is "Hidden states".
yaxis: Controls whether or not to plot the y-axis. The default is FALSE.
ylab.pos: Controls the position of the y axis labels (labels for channels and/or hidden states). Either "auto" or a numerical vector indicating how far away from the plots the titles are positioned. The default value "auto" positions all titles on line 1. Shorter vectors are recycled.
cex.lab: Expansion factor for setting the size of the font for the axis labels. The default value is 1. Values lesser than 1 will reduce the size of the font, values greater than 1 will increase the size.
cex.axis: Expansion factor for setting the size of the font for the x-axis tick labels. The default value is 1. Values lesser than 1 will reduce the size of the font, values greater than 1 will increase the size.
withlegend: Deprecated. Use with.legend instead.
respect_void: If TRUE (default), states at the time points corresponding to TraMineR's void in the observed sequences are set to void in the hidden state sequences as well.
...: Other arguments to be passed on to TraMineR::seqplot().

Details

This function is deprecated, use stacked_sequence_plot() instead.