validationplot          package:pls          R Documentation(latin1)

_V_a_l_i_d_a_t_i_o_n _P_l_o_t_s

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

     Functions to plot validation statistics, such as RMSEP or R^2, as
     a function of the number of components.

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

     validationplot(object, val.type = c("RMSEP", "MSEP", "R2"), estimate,
                    newdata, ncomp, comps, intercept, ...)
     ## S3 method for class 'mvrVal':
     plot(x, nCols, nRows, type = "l", lty = 1:nEst, lwd = NULL,
                pch = 1:nEst, cex = NULL, col = 1:nEst, legendpos,
                xlab = "number of components", ylab = x$type, main, ...)

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

  object: an 'mvr' object.

val.type: character.  What type of validation statistic to plot.

estimate: character.  Which estimates of the statistic to calculate. 
          See 'RMSEP'.

 newdata: data frame.  Optional new data used to calculate statistic.

ncomp, comps: integer vector.  The model sizes to compute the statistic
          for.  See 'RMSEP'.

intercept: logical.  Whether estimates for a model with zero components
          should be calculated as well.

       x: an 'mvrVal' object.  Usually the result of a 'RMSEP', 'MSEP'
          or 'R2' call.

nCols, nRows: integers.  The number of coloumns and rows the plots will
          be laid out in.  If not specified, 'plot.mvrVal' tries to be
          intelligent.

    type: character.  What type of plots to create.  Defaults to '"l"'
          (lines).  Alternative types include '"p"' (points) and '"b"'
          (both).  See 'plot' for a complete list of types.

     lty: vector of line types (recycled as neccessary).  Line types
          can be specified as integers or character strings (see 'par'
          for the details).

     lwd: vector of positive numbers (recycled as neccessary), giving
          the width of the lines.

     pch: plot character.  A character string or a vector of single
          characters or integers (recycled as neccessary).  See
          'points' for all alternatives.

     cex: numeric vector of character expansion sizes (recycled as
          neccessary) for the plotted symbols.

     col: character or integer vector of colors for plotted lines and
          symbols (recycled as neccessary).  See 'par' for the details.

legendpos: Legend position.  Optional.  If present, a legend is drawn
          at the given position.  The position can be specified
          symbolically (e.g., 'legendpos = "topright"').  This requires
          R >= 2.1.0.  Alternatively, the position can be specified
          explicitly ('legendpos = t(c(x,y))') or interactively
          ('legendpos = locator()').  This only works well for plots of
          single-response models.

xlab,ylab: titles for x and y axes.  Typically character strings, but
          can be expressions (e.g., 'expression(R^2)' or lists.  See
          'title' for details.

    main: optional main title for the plot.  See Details.

     ...: Further arguments sent to underlying plot functions.

_D_e_t_a_i_l_s:

     'validationplot' calls the proper validation function (currently
     'MSEP', 'RMSEP' or 'R2') and plots the results with 'plot.mvrVal'.
      'validationplot' can be called through the 'mvr' plot method, by
     specifying 'plottype = "validation"'.

     'plot.mvrVal' creates one plot for each response variable in the
     model, laid out in a rectangle.  It uses 'matplot' for performing
     the actual plotting.  If 'legendpos' is given, a legend is drawn
     at the given position.

     The argument 'main' can be used to specify the main title of the
     plot.  It is handled in a non-standard way.  If there is only on
     (sub) plot, 'main' will be used as the main title of the plot.  If
     there is _more_ than one (sub) plot, however, the presence of
     'main' will produce a corresponding 'global' title on the page. 
     Any graphical parametres, e.g., 'cex.main', supplied to 'coefplot'
     will only affect the 'ordinary' plot titles, not the 'global' one.
      Its appearance can be changed by setting the parameters with
     'par', which will affect _both_ titles.  (To have different
     settings for the two titles, one can override the 'par' settings
     with arguments to the plot function.)

_N_o_t_e:

     'legend' has many options.  If you want greater control over the
     appearance of the legend, omit the 'legendpos' argument and call
     'legend' manually.

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

     Ron Wehrens and Bjrn-Helge Mevik

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

     'mvr', 'plot.mvr', 'RMSEP', 'MSEP', 'R2', 'matplot', 'legend'

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

     data(oliveoil)
     mod <- plsr(sensory ~ chemical, data = oliveoil, validation = "LOO")
     ## Not run: 
     ## These three are equivalent:
     validationplot(mod, estimate = "all")
     plot(mod, "validation", estimate = "all")
     plot(RMSEP(mod, estimate = "all"))
     ## Plot R2:
     plot(mod, "validation", val.type = "R2")
     ## Plot R2, with a legend:
     plot(mod, "validation", val.type = "MSEP", legendpos = "top") # R >= 2.1.0
     ## End(Not run)

