Description Usage Arguments Details Value Author(s) References See Also
A coordinate plot which maps each element in the probability transition matrix (of any order) as a line, where each line is weighted by probability. Users can apply filters to emphasize the most (or least) probable state sequences overall, or by initial state. Various color palettes using the Hue-Chroma-Luminance color scheme can be easily selected by the user. Input is an object of class march.Dcmm
which is the output of march.dcmm.construct
.
1 2 3 4 5 6 7 | ## For class 'march.Dcmm'
march.Dcmm.trmatplot ( d, seed = NULL, type = "hidden", hstate = 1,
cspal = NULL, cpal = NULL, main = NULL, xlab = NULL,
ylab = NULL, ylim = NULL, xtlab = NULL, ytlab = NULL,
pfilter = NULL, shade.col = "grey80", num = NULL, hide.col = NULL,
lorder = NULL, plot = TRUE, verbose = FALSE, ...)
|
d |
Object to be plotted. A |
seed |
A single value, interpreted as an integer, or |
type |
Character string. Can be specified as either |
hstate |
Numeric. Valid when |
cspal |
A color palette that can be specified as one of: |
cpal |
Color palette vector when coloring probability sequences. The |
main |
Title for the graphic. Default is Probability Transition Matrix. |
xlab |
Label for the x axis. Default is Time. |
ylab |
Label for the y axis. Default is States. |
ylim |
Numeric vector of length 2 giving the y coordinates range. |
xtlab |
Label for the x axis ticks. Default is time (t, t+1,...). |
ytlab |
Labels for the y axis ticks. |
pfilter |
Probability filter. Can be specified as one of |
shade.col |
The color for sequences shaded out using the |
num |
Numeric. The number of sequences to be highlighted, a whole number from 1 to |
hide.col |
The color for sequences shaded out using the |
lorder |
Line order. Either |
plot |
Logical. Should the object be plotted. Default is |
verbose |
Logical. Reports extra information on progress. Default is |
... |
Additional arguments, such as graphical parameters, to be passed on. See |
Setting a seed
allows the graphic to be replicated.
The pfilter
argument serves to highlight probability sequences that are either most probable while shading out those that are less probable in shade.col
and vice-versa.
The four options for pfilter
are described below, and are illustrated in Examples in trmatplot
.
"smax"
For each initial state the most probable next state is highlighed.
"smin"
For each initial state the least probable next state is highlighed.
"tmax"
The sequence of states with the highest probability overall is highlighed. To highlight the n most probable sequences of states, set num = n
.
"tmin"
The sequence of states with the lowest probability overall is highlighed. To highlight the n least probable sequences of states, set num = n
.
The filter
and hide.col
arguments are inherent in and may be passed on to seqpcplot
.
The filter
argument serves to specify filters to gray less interesting patterns.
The filtered-out patterns are displayed in the hide.col
color.
The filter argument expects a list with at least elements type
and value
.
Most relevant within the context of probabilities is type = "sequence"
, which highlights the specific pattern.
See Examples in trmatplot
.
trmatplot
returns an object of class trmatplot
. Some of the arguments are inherent in par
and seqpcplot
.
Pauline Adamopoulou
Buergin, R. and G. Ritschard (2014), "A decorated parallel coordinate plot for categorical longitudinal data", The American Statistician. Vol. 68(2), pp. 98-103.
Zeileis, A.; Hornik, K. and P. Murrell (2009), "Escaping RGBland: Selecting Colors for Statistical Graphics", Computational Statistics & Data Analysis. Vol. 53, pp. 3259-3270.
trmatplot
,
trmatplot.default
,
trmatplot.depmix.fitted
,
trmatplot.array
,
seqpcplot
,
par
.
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