trellisplots              package:coda              R Documentation

_T_r_e_l_l_i_s _p_l_o_t_s _f_o_r _m_c_m_c _o_b_j_e_c_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     These methods use the Trellis framework as implemented in the
     'lattice' package to produce space-conserving diagnostic plots
     from '"mcmc"' and '"mcmc.list"' objects.  The 'xyplot' methods
     produce trace plots.  The 'densityplot' methods and 'qqmath'
     methods produce empirical density and probability plots.  The
     'levelplot' method depicts the correlation of the series.  The
     'acfplot' methods plot the auto-correlation in the series.

_U_s_a_g_e:

     ## S3 method for class 'mcmc':
     densityplot(x, data,
                  outer, aspect = "xy",
                  default.scales = list(relation = "free"),
                  start = 1, thin = 1,
                  main = attr(x, "title"),
                  xlab = "",
                  plot.points = "rug",
                  ...,
                  subset)
     ## S3 method for class 'mcmc.list':
     densityplot(x, data,
                  outer = FALSE, groups = !outer,
                  aspect = "xy",
                  default.scales = list(relation = "free"),
                  start = 1, thin = 1,
                  main = attr(x, "title"),
                  xlab = "",
                  plot.points = "rug",
                  ...,
                  subset)
     ## S3 method for class 'mcmc':
     levelplot(x, data, main = attr(x, "title"),
                  start = 1, thin = 1,
                  ...,
                  xlab = "", ylab = "",
                  cuts = 10, at,
                  col.regions = topo.colors(100),
                  subset)
     ## S3 method for class 'mcmc':
     qqmath(x, data,
                  outer, aspect = "xy",
                  default.scales = list(y = list(relation = "free")),
                  prepanel = prepanel.qqmathline,
                  start = 1, thin = 1,
                  main = attr(x, "title"),
                  ylab = "",
                  ...,
                  subset)
     ## S3 method for class 'mcmc.list':
     qqmath(x, data,
                  outer = FALSE, groups = !outer,
                  aspect = "xy",
                  default.scales = list(y = list(relation = "free")),
                  prepanel = prepanel.qqmathline,
                  start = 1, thin = 1,
                  main = attr(x, "title"),
                  ylab = "",
                  ...,
                  subset)
     ## S3 method for class 'mcmc':
     xyplot(x, data,
                  outer, layout = c(1, ncol(x)),
                  default.scales = list(y = list(relation = "free")),
                  type = 'l',
                  start = 1, thin = 1,
                  ylab = "", 
                  xlab = "Iteration number",
                  main = attr(x, "title"),
                  ...,
                  subset)
     ## S3 method for class 'mcmc.list':
     xyplot(x, data, outer = FALSE, groups = !outer,
                  aspect = "xy", layout = c(1, ncol(x[[1]])),
                  default.scales = list(y = list(relation = "free")),
                  type = 'l',
                  start = 1, thin = 1,
                  main = attr(x, "title"),
                  ylab = "",
                  ...,
                  subset)
     acfplot(x, data, ...)
     ## S3 method for class 'mcmc':
     acfplot(x, data, outer,
                  prepanel, panel, 
                  type = 'h',
                  aspect = "xy",
                  start = 1, thin = 1,
                  lag.max = NULL,
                  ylab = "Autocorrelation",
                  xlab = "Lag",
                  main = attr(x, "title"),
                  ...,
                  subset)
     ## S3 method for class 'mcmc.list':
     acfplot(x, data, outer = FALSE, groups = !outer,
                  prepanel, panel,
                  type = if (groups) 'b' else 'h',
                  aspect = "xy",
                  start = 1, thin = 1,
                  lag.max = NULL,
                  ylab = "Autocorrelation",
                  xlab = "Lag",
                  main = attr(x, "title"),
                  ...,
                  subset)

_A_r_g_u_m_e_n_t_s:

       x: an '"mcmc"' or '"mcmc.list"' object. 

    data: ignored, present for consistency with generic. 

   outer: for the '"mcmc.list"' methods, a logical flag to control
          whether multiple runs of a series are displayed in the same
          panel (they are if 'FALSE', not if 'TRUE').  If specified in
          the '"mcmc"' methods, this argument is ignored with a
          warning.  

  groups: for the '"mcmc.list"' methods, a logical flag to control
          whether the underlying 'lattice' call will be supplied a
          'groups' arguments indicating which run a data point
          originated from.  The panel function is responsible for
          handling such an argument, and will usually differentiate
          runs within a panel by using different graphical parameters. 
          When 'outer=FALSE', the default of 'groups' is 'TRUE' if the
          corresponding default panel function is able to make use of
          such information. When 'outer=FALSE', 'groups=TRUE' will be
          ignored with a warning.  

  aspect: controls the physical aspect ratio of the panel.  See
          'xyplot' for details.  The default for these methods is
          chosen carefully - check what the default plot looks like
          before changing this parameter.

default.scales: this parameter provides a reasonable default value of
          the 'scales' parameter for the method. It is unlikely that a
          user will wish to change this parameter.  Pass a value for
          'scales' (see 'xyplot') instead, which will override values
          specified here.  

    type: a character vector that determines if lines, points, etc. are
          drawn on the panel.  The default values for the methods are
          carefully chosen.  See 'panel.xyplot' for possible values. 

    thin: an optional thinning interval that is applied before the plot
          is drawn.

   start: an optional value for the starting point within the series. 
          Values before the starting point are considered part of the
          "burn-in" of the series and dropped.

plot.points: character argument giving the style in which points are
          added to the plot.  See 'panel.densityplot' for details. 

  layout: a method-specific default for the 'layout' argument to the
          lattice functions.

xlab,ylab,main: Used to provide default axis annotations and plot
          labels.

cuts, at: defines number and location of values where colors change 

col.regions: color palette used 

 lag.max: maximum lag for which autocorrelation is computed.  By
          default, the value chosen by 'acf' is used 

prepanel,panel: suitable prepanel and panel functions for 'acfplot'. 
          The prepanel function omits the lag-0 auto-correlation (which
          is always 1) from the range calculations.  

     ...: other arguments, passed to the lattice function.
          Documentation of the corresponding generics in the 'lattice'
          package should be consulted for possible arguments. 

  subset: indices of the subset of the series to plot.  The default is
          constructed from the 'start' and 'thin' arguments.

_V_a_l_u_e:

     An object of class '"trellis"'. The relevant 'update' method can
     be used to update components of the object and the 'print' method
     (usually called by default) will plot it on an appropriate
     plotting device.

_A_u_t_h_o_r(_s):

     Deepayan Sarkar Deepayan.Sarkar@R-project.org

_S_e_e _A_l_s_o:

     'Lattice' for a brief introduction to lattice displays and links
     to further documentation.

_E_x_a_m_p_l_e_s:

     data(line)
     xyplot(line)
     xyplot(line[[1]], start = 10)
     densityplot(line, start = 10)
     qqmath(line, start = 10)
     levelplot(line[[2]])
     acfplot(line, outer = TRUE)

