AGRAPH procedure

Plots tables of means from ANOVA (R.W. Payne).

 

Options

GRAPHICS = string token Type of graph (highresolution, lineprinter); default high
METHOD = string token What to plot (means, lines, data, barchart, splines); default mean
XFREPRESENTATION = string token How to label the x-axis (levels, labels); default labels uses the XFACTOR labels, if available
PSE = string token What to plot to represent variation (differences, lsd, means, allmeans); default diff
LSDLEVEL = scalar Significance level (%) to use for 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 = ANOVA or regression save structure Save structure to provide the table of means; default uses the save structure from the most recent ANOVA

 

Parameters

XFACTOR = factors Factor providing the x-values for each plot
GROUPS = factors or pointers Factor or factors identifying groups of points 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 instead of its existing levels
TITLE = texts Title for the graph; default defines a title automatically
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

AGRAPH plots tables of means from an ANOVA analysis. In its simplest form, the behaviour of AGRAPH depends on the model. If the treatment model contains only main effects, it plots the means for the first factor in the model. Otherwise it looks for the first treatment 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 ANOVA. However, you can plot means from an earlier analysis, by using the SAVE option of AGRAPH to specify its save structure (saved using the SAVE parameter of the ANOVA command that performed the analysis).

Usually, each mean is represented by a point. However, with high-resolution plots, the METHOD option can be set to lines to draw lines between the points, or data to draw just the lines and then also plot the original data values, or barchart to plot the means as a barchart, or splines to plot the points together with a smooth spline to show the trend over each group of points. 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 GRAPHICS option controls whether a high-resolution or a line-printer graph is plotted; by default GRAPHICS=high.

The PSE option specifies the type of error bar to be plotted with the means, with settings:

    differences average standard error of difference;
    lsd average least significant difference;
    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 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 defines the factor against whose levels the means are plotted. 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

AGRAPH [METHOD=line] XFACTOR=A; GROUPS=B

AGRAPH will produce a plot of 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

AGRAPH [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,

AGRAPH [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

AGRAPH [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 ANOVA 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 standard errors or LSDs can be included.

The NEWXLEVELS parameter enables different levels to be supplied for XFACTOR if the existing levels are unsuitable. If XFACTOR has labels, these are used to label the x-axis unless you set option XFREPRESENTATION=levels.

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 AGRAPH 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 AGRAPH, in a variate with a value for each group, using the PENS parameter.

The YTRANSFORM option lets you 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.

For compatibility with previous releases, AGRAPH lets you plot predicted means from an analysis by the AUNBALANCED procedure (which uses the Genstat regression commands). However, procedure AUGRAPH (new in Release 13) is now recommended instead. Also, in Release 13, a new procedure DTABLE was included to plot a user-supplied table. Previously this could be done using the MEANS parameter of AGRAPH, which has now been withdrawn.

Options: GRAPHICS, METHOD, XFREPRESENTATION, PSE, LSDLEVEL, DFSPLINE, YTRANSFORM, PENYTRANSFORM, SAVE.

Parameters: XFACTOR, GROUPS, TRELLISGROUPS, PAGEGROUPS, NEWXLEVELS, TITLE, YTITLE, XTITLE, PENS.

 

See also

Directive: ANOVA.

Procedures: APLOT, AUGRAPH, RGRAPH, VGRAPH.

Commands for: Analysis of variance.

Example

CAPTION  'AGRAPH example',!t('Split plot design, see the',\
         'Guide to Genstat, Part 2, Section 4.2.1.'); STYLE=meta,plain
FACTOR   [NVALUES=72; LEVELS=6] Blocks
&        [LEVELS=3] Wplots
&        [LEVELS=4] Subplots
GENERATE Blocks,Wplots,Subplots
FACTOR   [LABELS=!T('0 cwt','0.2 cwt','0.4 cwt','0.6 cwt')] Nitrogen
&        [LABELS=!T(Victory,'Golden rain',Marvellous)]      Variety
VARIATE  Yield; DECIMALS=2; EXTRA=' of oats in cwt. per acre'
READ     [SERIAL=yes] Nitrogen,Variety,Yield
 4 3 2 1 1 2 4 3 1 2 3 4 3 1 2 4 4 1 2 3 2 1 3 4
 2 3 4 1 4 2 3 1 1 4 2 3 3 4 1 2 1 3 4 2 2 3 4 1
 4 1 3 2 3 4 1 2 3 4 2 1 3 1 4 2 4 3 1 2 1 2 3 4 :
 3 3 3 3 1 1 1 1 2 2 2 2 3 3 3 3 1 1 1 1 2 2 2 2
 2 2 2 2 3 3 3 3 1 1 1 1 3 3 3 3 2 2 2 2 1 1 1 1
 2 2 2 2 1 1 1 1 3 3 3 3 1 1 1 1 2 2 2 2 3 3 3 3 :
156 118 140 105 111 130 174 157 117 114 161 141
104  70  89 117 122  74  89  81 103  64 132 133
108 126 149  70 144 124 121  96  61 100  91  97
109  99  63  70  80  94 126  82  90 100 116  62
 96  60  89 102 112  86  68  64 132 124 129  89
118  53 113  74 104  86  89  82  97  99 119 121 :
" Convert yields to cwt per acre."
CALCULATE  Yield=(Yield*80)/(112*4)
" Define the treatment structure: factorial effects of V and N."
TREATMENTS Variety*Nitrogen
" Subplots nested within whole-plots nested within blocks."
BLOCK      Blocks/Wplots/Subplots
ANOVA      [PRINT=means] Yield
AGRAPH
Updated on January 10, 2018

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