Plots tables of means from REML
(R.W. Payne).
Options
GRAPHICS = string token |
Type of graph (highresolution , lineprinter ); default high |
---|---|
METHOD = string token |
What to plot (points , means , linesandpoints , onlylines , data , barchart , splines ); default poin when XFACTOR is a factor, and only when it is a variate |
XFREPRESENTATION = string token |
How to label the x-axis (levels , labels ); default labe uses the XFACTOR labels, if available |
PSE = string token |
What to plot to represent variation when points are plotted at the means (differences , lsd , means , allmeans ); default diff |
LSDLEVEL = scalar |
Significance level (%) to use for approximate least significant differences; default 5 |
DFSPLINE = scalar |
Number of degrees of freedom to use when METHOD=splines |
YTRANSFORM = string tokens |
Transformed scale for additional axis marks and labels to be plotted on the right-hand side of the y-axis (identity , log , log10 , logit , probit , cloglog , square , exp , exp10 , ilogit , iprobit , icloglog , root ); default iden i.e. none |
PENYTRANSFORM = scalar |
Pen to use to plot the transformed axis marks and labels; default * selects a pen, and defines its properties, automatically |
SAVE = REML save structure |
Save structure to provide the table of means; default uses the save structure from the most recent REML |
Parameters
XFACTOR = factors or variates |
Provides the x-values for each plot; by default this is chosen automatically |
---|---|
GROUPS = factors or pointers |
Factor or factors identifying groups in each plot; by default chosen automatically |
TRELLISGROUPS = factors or pointers |
Factor or factors specifying the different plots of a trellis plot of a multi-way table |
PAGEGROUPS = factors or pointers |
Factor or factors specifying plots to be displayed on different pages |
NEWXLEVELS = variates |
Values to be used for XFACTOR ; default uses the existing levels if XFACTOR is a factor, and the minimum and maximum values if it is a variate |
TITLE = texts |
Title for the graph; default is to define a title automatically if GROUPS is set, or to have none if it is unset |
YTITLE = texts |
Title for the y-axis; default is to use the identifier of the y-variate, or to have no title if this is unnamed |
XTITLE = texts |
Title for the x-axis; default is to use the identifier of the XFACTOR |
PENS = variates |
Defines the pen to use to plot the points and/or line for each group defined by the GROUPS factors |
Description
VGRAPH
plots tables of predicted means from REML
. In its simplest form, the behaviour of VGRAPH
depends on the model. If the fixed model contains only main effects, it plots the means for the first factor in the fixed model. Otherwise, it looks for the first fixed term involving two factors; it then plots the means with one of these factors as the x-axis, and the second as a grouping factor with levels identified by different plotting colours and symbols.
By default, the means are from the most recent REML
. However, you can plot means from an earlier analysis, by using the SAVE
option of VGRAPH
to specify its save structure (saved using the SAVE
parameter of the REML
command that performed the analysis). VGRAPH
uses the VPREDICT
directive with default option settings to obtain the means. This should give the same means as those printed by REML
or VDISPLAY
. If you want to use VPREDICT
with other option settings, you can plot these using the DTABLE
procedure.
The GRAPHICS
option controls whether a high-resolution or a line-printer graph is plotted; by default GRAPHICS=high
.
The METHOD
option controls how the predicted means are plotted in high-resolution graphics, with settings:
points |
to plot a point at each mean; |
---|---|
means |
synonym of points ; |
linesandpoints |
to plot points and join them by lines; |
onlylines |
to draw lines between the means; |
data |
to draw lines between the means, and then also plot the original data values; |
barchart |
to plot the means as a barchart; |
splines |
to plot points at the means together with a smooth spline to show the trend over each group of means; the DFSPLINE specifies the degrees of freedom for the splines; if this is not set, 2 d.f. are used when there are up to 10 points, 3 if there are 11 to 20, and 4 for 21 or more. |
The default is to plot points
when XFACTOR
is a factor, and onlylines
when it is a variate. Only points
are available in line-printer graphics.
The PSE
option specifies the type of error bar to be plotted, when points are plotted for the means, with settings:
differences |
average standard error of difference; |
---|---|
lsd |
average approximate least significant difference (calculated using the VLSD procedure); |
means |
average effective standard error for the means; |
allmeans |
plots plus and minus the effective standard error around every mean. |
The LSDLEVEL
option sets the significance level (%) to use for the approximate least significant differences (default 5). The allmeans
setting is often unsuitable for plots other than barcharts when there are GROUPS
, as the plus/minus e.s.e. bars may overlap each other.
You can define the table of means to plot explicitly, by specifying its classifying factors using the XFACTOR
, GROUPS
, TRELLISGROUPS
and PAGEGROUPS
parameters. The XFACTOR
parameter can define a factor against whose levels the means are plotted. It can also specify a variate, and VPREDICT
then sets up a factor automatically, to classify the table, with levels at the values specified by the NEWXLEVELS
parameter. With a multi-way table, there will be a plot of means against the XFACTOR
levels for every combination of levels of the factors specified by the GROUPS
, TRELLISGROUPS
and PAGEGROUPS
parameters. The GROUPS
parameter specifies factors whose levels are to be included in a single window of the graph. So, for example, if you specify
VGRAPH [METHOD=line] XFACTOR=A; GROUPS=B
VGRAPH
will produce plot the means in a single window with factor A
on the x-axis, and a line for each level of the factor B
. You can set GROUPS
to a pointer to specify several factors to define groups. For example
POINTER [VALUES=B,C] Groupfactors
VGRAPH [METHOD=line] XFACTOR=A; GROUPS=Groupfactors
to plot a line for every combination of the levels of factors B
and C
. Similarly, the TRELLISGROUPS
option can specify one or more factors to define a trellis plot. For example,
VGRAPH [METHOD=line] XFACTOR=A; GROUPS=B; TRELLISGROUPS=C
will produce a plot for each level of C
, in a trellis arrangement; each plot will again have factor A
on the x-axis, and a line for each level of the factor B
. Likewise, the PAGEGROUPS
parameter can specify factors whose combinations of levels are to be plotted on different pages. So
VGRAPH [METHOD=line] XFACTOR=A; GROUPS=B; PAGEGROUPS=C
will produce a plot for each level of C
, but now on separate pages. Multi-way tables can plotted even if the corresponding model term was not in the REML
analysis. For example you can plot a two-way table even if the analysis contained only the main effects of the two factors; however, the lines will then all be parallel and no LSDs can be included.
The NEWXLEVELS
parameter allows different levels to be supplied for an XFACTOR
factor, if its existing levels are unsuitable. If the factor has labels, these are used to label the x-axis unless you set option XFREPRESENTATION=levels
. When XFACTOR
is a variate, NEWXLEVELS
can specify the values where the predictions are to be made. By default, they are made at its minimum and maximum values.
Note that the values predicted by VPREDICT
, for an XFACTOR
variate, will not include any spline effects, nor can it take account of any relationships between different variates in the model. (For example, the model may include a variate and its square.) To take account of relationships like these, you should use VPREDICT
directly, specifying the linked variables with the PARALLEL
parameter. Save the table of predictions, and then plot it using DTABLE
.
The TITLE
, YTITLE
and XTITLE
parameters can supply titles for the graph, the y-axis and the x-axis, respectively. The symbols, colours and line styles that are used in a high-resolution plot are usually set up by VGRAPH
automatically. If you want to control these yourself, you should use the PEN
directive to define a pen with your preferred symbol, colour and line style, for each of the groups defined by combinations of the GROUPS
factors. The pen numbers should then be supplied to VGRAPH
, in a variate with a value for each group, using the PENS
parameter.
The YTRANSFORM
option allows you to include additional axis markings, transformed onto another scale, on the right-hand side of the y-axis. Suppose, for example, suppose you have analysed a variate of percentages that have been transformed to logits. You might then set YTRANSFORM=ilogit
(the inverse-logit transformation) to include markings in percentages alongside the logits. The settings are the same as those of the TRANSFORM
parameter of AXIS
(which is used to add the markings). You can control the colours of the transformed marks and labels, by defining a pen with the required properties, and specifying it with the PENYTRANSFORM
option. Otherwise, the default is to plot them in blue.
Options: GRAPHICS
, METHOD
, XFREPRESENTATION
, PSE
, LSDLEVEL
, DFSPLINE
, YTRANSFORM
, PENYTRANSFORM
, SAVE
.
Parameters: XFACTOR
, GROUPS
, TRELLISGROUPS
, PAGEGROUPS
, NEWXLEVELS
, TITLE
, YTITLE
, XTITLE
, PENS
.
See also
Procedures: VDEFFECTS
, AGRAPH
, DTABLE
, RGRAPH
, RDESTIMATES
.
Commands for: REML analysis of linear mixed models.
Example
CAPTION 'VGRAPH example','Guide Part 2, Example 5.3.5a'; STYLE=meta,plain FACTOR [NVALUES=322; LEVELS=27] Dam & [LEVELS=18] Pup FACTOR [LEVELS=2; LABELS=!T('M','F')] Sex FACTOR [LEVELS=3; LABELS=!T('C','Low','High')] Dose VARIATE [NVALUES=322] Littersize,Weight READ Dose,Sex,Littersize,Dam,Pup,Weight;\ FREPRESENTATION=2(labels),4(levels) C M 12 1 1 6.60 C M 12 1 2 7.40 C M 12 1 3 7.15 C M 12 1 4 7.24 C M 12 1 5 7.10 C M 12 1 6 6.04 C M 12 1 7 6.98 C M 12 1 8 7.05 C F 12 1 9 6.95 C F 12 1 10 6.29 C F 12 1 11 6.77 C F 12 1 12 6.57 C M 14 2 1 6.37 C M 14 2 2 6.37 C M 14 2 3 6.90 C M 14 2 4 6.34 C M 14 2 5 6.50 C M 14 2 6 6.10 C M 14 2 7 6.44 C M 14 2 8 6.94 C M 14 2 9 6.41 C F 14 2 10 5.92 C F 14 2 11 6.04 C F 14 2 12 5.82 C F 14 2 13 6.04 C F 14 2 14 5.96 C M 4 3 1 7.50 C M 4 3 2 7.08 C F 4 3 3 7.57 C F 4 3 4 7.27 C M 14 4 1 6.25 C M 14 4 2 6.93 C M 14 4 3 6.80 C M 14 4 4 6.69 C M 14 4 5 6.28 C M 14 4 6 6.27 C M 14 4 7 6.27 C M 14 4 8 6.47 C F 14 4 9 6.29 C F 14 4 10 5.98 C F 14 4 11 6.32 C F 14 4 12 6.28 C F 14 4 13 5.65 C F 14 4 14 5.57 C M 13 5 1 7.96 C M 13 5 2 6.84 C M 13 5 3 7.00 C M 13 5 4 8.10 C M 13 5 5 6.52 C M 13 5 6 7.23 C M 13 5 7 6.10 C M 13 5 8 7.31 C F 13 5 9 7.16 C F 13 5 10 7.09 C F 13 5 11 7.14 C F 13 5 12 5.02 C F 13 5 13 6.04 C M 9 6 1 8.26 C M 9 6 2 7.73 C M 9 6 3 8.33 C M 9 6 4 6.14 C M 9 6 5 7.75 C M 9 6 6 6.96 C F 9 6 7 7.26 C F 9 6 8 6.58 C F 9 6 9 3.68 C M 18 7 1 6.29 C M 18 7 2 6.32 C M 18 7 3 6.28 C M 18 7 4 6.24 C M 18 7 5 6.78 C M 18 7 6 6.63 C M 18 7 7 6.27 C M 18 7 8 6.29 C M 18 7 9 6.06 C F 18 7 10 6.16 C F 18 7 11 5.96 C F 18 7 12 6.26 C F 18 7 13 5.83 C F 18 7 14 6.11 C F 18 7 15 6.45 C F 18 7 16 6.25 C F 18 7 17 6.31 C F 18 7 18 5.74 C M 17 8 1 6.04 C M 17 8 2 5.84 C M 17 8 3 6.77 C M 17 8 4 5.59 C M 17 8 5 5.52 C M 17 8 6 6.42 C M 17 8 7 5.97 C M 17 8 8 6.34 C F 17 8 9 6.23 C F 17 8 10 5.95 C F 17 8 11 6.16 C F 17 8 12 6.19 C F 17 8 13 5.32 C F 17 8 14 5.00 C F 17 8 15 6.30 C F 17 8 16 5.00 C F 17 8 17 5.56 C M 17 9 1 5.37 C M 17 9 2 5.58 C M 17 9 3 5.51 C M 17 9 4 5.19 C M 17 9 5 5.34 C M 17 9 6 5.77 C M 17 9 7 5.17 C M 17 9 8 4.57 C M 17 9 9 5.39 C M 17 9 10 5.62 C M 17 9 11 5.40 C M 17 9 12 5.77 C M 17 9 13 5.24 C F 17 9 14 5.37 C F 17 9 15 5.33 C F 17 9 16 5.44 C F 17 9 17 5.14 C M 13 10 1 7.30 C M 13 10 2 6.60 C M 13 10 3 6.58 C M 13 10 4 6.68 C M 13 10 5 6.46 C M 13 10 6 6.38 C F 13 10 7 6.44 C F 13 10 8 6.67 C F 13 10 9 6.43 C F 13 10 10 6.53 C F 13 10 11 5.92 C F 13 10 12 6.52 C F 13 10 13 6.44 Low M 16 11 1 6.65 Low M 16 11 2 5.78 Low M 16 11 3 6.23 Low M 16 11 4 5.70 Low M 16 11 5 5.73 Low M 16 11 6 6.10 Low M 16 11 7 5.55 Low M 16 11 8 5.71 Low M 16 11 9 5.81 Low M 16 11 10 6.10 Low F 16 11 11 5.54 Low F 16 11 12 5.72 Low F 16 11 13 5.50 Low F 16 11 14 5.64 Low F 16 11 15 5.42 Low F 16 11 16 5.42 Low F 2 12 1 6.89 Low F 2 12 2 7.73 Low M 12 13 1 5.83 Low M 12 13 2 5.97 Low M 12 13 3 6.39 Low M 12 13 4 5.69 Low M 12 13 5 5.69 Low M 12 13 6 5.97 Low M 12 13 7 6.04 Low M 12 13 8 5.46 Low F 12 13 9 6.09 Low F 12 13 10 5.39 Low F 12 13 11 5.89 Low F 12 13 12 5.14 Low M 15 14 1 5.92 Low M 15 14 2 5.75 Low M 15 14 3 6.22 Low M 15 14 4 5.96 Low M 15 14 5 5.59 Low M 15 14 6 5.79 Low M 15 14 7 6.23 Low M 15 14 8 5.88 Low M 15 14 9 6.02 Low F 15 14 10 5.66 Low F 15 14 11 5.76 Low F 15 14 12 5.73 Low F 15 14 13 5.33 Low F 15 14 14 5.58 Low F 15 14 15 5.88 Low M 13 15 1 6.00 Low M 13 15 2 6.11 Low M 13 15 3 6.40 Low M 13 15 4 6.06 Low M 13 15 5 6.39 Low M 13 15 6 6.09 Low M 13 15 7 6.32 Low F 13 15 8 5.96 Low F 13 15 9 6.32 Low F 13 15 10 5.83 Low F 13 15 11 5.97 Low F 13 15 12 5.87 Low F 13 15 13 5.67 Low M 13 16 1 6.43 Low M 13 16 2 6.13 Low M 13 16 3 5.87 Low F 13 16 4 6.09 Low F 13 16 5 5.63 Low F 13 16 6 5.84 Low F 13 16 7 6.20 Low F 13 16 8 6.42 Low F 13 16 9 5.90 Low F 13 16 10 5.62 Low F 13 16 11 6.23 Low F 13 16 12 5.85 Low F 13 16 13 5.89 Low M 14 17 1 5.81 Low M 14 17 2 5.44 Low M 14 17 3 5.65 Low M 14 17 4 5.25 Low M 14 17 5 5.45 Low M 14 17 6 5.32 Low M 14 17 7 5.89 Low F 14 17 8 5.63 Low F 14 17 9 5.12 Low F 14 17 10 5.65 Low F 14 17 11 5.29 Low F 14 17 12 5.13 Low F 14 17 13 5.60 Low F 14 17 14 5.08 Low M 15 18 1 6.77 Low M 15 18 2 7.13 Low M 15 18 3 6.85 Low F 15 18 4 6.49 Low F 15 18 5 6.09 Low F 15 18 6 6.09 Low F 15 18 7 5.99 Low F 15 18 8 6.01 Low F 15 18 9 6.11 Low F 15 18 10 6.15 Low F 15 18 11 4.75 Low F 15 18 12 5.69 Low F 15 18 13 6.19 Low F 15 18 14 5.72 Low F 15 18 15 6.14 Low M 10 19 1 6.72 Low M 10 19 2 6.34 Low M 10 19 3 6.48 Low M 10 19 4 5.74 Low F 10 19 5 6.11 Low F 10 19 6 5.71 Low F 10 19 7 6.41 Low F 10 19 8 6.21 Low F 10 19 9 6.11 Low F 10 19 10 5.81 Low M 16 20 1 5.90 Low M 16 20 2 6.22 Low M 16 20 3 6.67 Low M 16 20 4 6.23 Low M 16 20 5 6.24 Low M 16 20 6 6.26 Low M 16 20 7 6.38 Low M 16 20 8 6.05 Low M 16 20 9 5.89 Low M 16 20 10 6.29 Low F 16 20 11 6.12 Low F 16 20 12 5.40 Low F 16 20 13 5.50 Low F 16 20 14 5.46 Low F 16 20 15 5.97 Low F 16 20 16 6.11 High M 14 21 1 5.09 High M 14 21 2 5.57 High M 14 21 3 5.69 High M 14 21 4 5.50 High M 14 21 5 5.45 High M 14 21 6 5.24 High M 14 21 7 5.36 High M 14 21 8 5.26 High M 14 21 9 5.36 High M 14 21 10 5.01 High M 14 21 11 5.03 High F 14 21 12 5.23 High F 14 21 13 5.13 High F 14 21 14 4.48 High M 10 22 1 5.30 High M 10 22 2 5.40 High M 10 22 3 5.55 High M 10 22 4 6.02 High M 10 22 5 5.27 High F 10 22 6 5.19 High F 10 22 7 5.42 High F 10 22 8 5.40 High F 10 22 9 5.12 High F 10 22 10 5.40 High M 3 23 1 7.70 High F 3 23 2 7.68 High F 3 23 3 6.33 High M 12 24 1 6.28 High M 12 24 2 5.74 High M 12 24 3 6.29 High F 12 24 4 5.68 High F 12 24 5 5.76 High F 12 24 6 6.03 High F 12 24 7 5.30 High F 12 24 8 5.55 High F 12 24 9 6.53 High F 12 24 10 5.76 High F 12 24 11 5.77 High F 12 24 12 5.49 High M 8 25 1 6.50 High M 8 25 2 7.10 High M 8 25 3 7.00 High M 8 25 4 7.00 High M 8 25 5 5.85 High F 8 25 6 6.10 High F 8 25 7 6.63 High F 8 25 8 6.33 High M 9 26 1 7.00 High M 9 26 2 6.15 High F 9 26 3 6.22 High F 9 26 4 6.20 High F 9 26 5 5.76 High F 9 26 6 6.21 High F 9 26 7 6.42 High F 9 26 8 6.42 High F 9 26 9 6.30 High M 9 27 1 5.64 High M 9 27 2 6.06 High M 9 27 3 6.56 High M 9 27 4 6.29 High M 9 27 5 5.69 High M 9 27 6 6.36 High F 9 27 7 5.93 High F 9 27 8 5.74 High F 9 27 9 5.74 : VCOMPONENTS [FIXED=Littersize+Dose*Sex] RANDOM=Dam/Pup REML Weight VGRAPH [METHOD=lines] Dose; GROUPS=Sex