### 1. Highlights

● produced in 2008

● 7 new directives, 5 new functions and 26 new procedures

● REML least-significant differences and comparisons of means (`VLSD`

, `VMCOMPARISON`

)

● canonical correspondence analysis, with biplots and triplots (`CCA`

, `CRBIPLOT`

, `CRTRIPLOT`

)

● factor analysis (`FCA`

)

● easier specification of a wider range of graphics colours (`PEN`

)

● ability to put a box around the graphics frame and control the background colours inside title bars and around graphics windows (`FRAME`

)

● plots of bitmaps (`DBITMAP`

)

● construction of efficient factorial or fractional-factorial designs (`AGFACTORIAL`

, `AFMINABERRATION`

)

● Cochran-Armitage test for trend (`CATRENDTEST`

)

● Dunnett’s test (`AMDUNNETT`

)

● Steel’s test (`STEEL`

)

● mean-mean plots (`AMCOMPARISON`

, `VMCOMPARISON`

)

● plots of estimates from regression and generalized linear models (`RDESTIMATES`

)

● Wald tests for terms in regression and generalized linear models (`RWALD`

)

● Wald tests and plots of means for HGLMs (`HGGRAPH`

, `HGWALD`

)

● efficient fitting of HGLMs with large numbers of random effects (`HGANALYSE`

)

● self-organising maps (`SOM`

, `SOMADJUST`

, `SOMDESCRIBE`

, `SOMESTIMATE`

, `SOMIDENTIFY`

, `SOMPREDICT`

)

● nonparametric estimates of species richness (`ECNPESTIMATE`

)

● printing of tables of textual strings (`PRINT`

)

● tables of standard errors of skewness and kurtosis (`TABULATE`

)

● rejection sampling (`GREJECTIONSAMPLE`

)

● QR decomposition (`QRD`

)

● links to NAG Library algorithms (`NAG`

)

### 2. What’s new

**2.1 Directives**

`AFMINABERRATION`

forms minimum aberration factorial or fractional-factorial designs.

`DBITMAP`

plots a bit map of RGB colours.

`FARGUMENTS`

forms lists of arguments involved in an expression.

`FCA`

performs factor analysis.

`NAG`

calls an algorithm from the NAG Library.

`QRD`

calculates QR decompositions of matrices.

`RKESTIMATES`

saves estimates and other information about individual terms in a regression analysis.

**2.2 Procedures**

`ADETECTION`

calculates the minimum size of effect or contrast detectable in an analysis of variance.

`AGFACTORIAL`

generates minimum aberration block or fractional factorial designs.

`AMDUNNETT`

forms Dunnett’s simultaneous confidence interval around a control.

`CATRENDTEST`

calculates the Cochran-Armitage chi-square test for trend.

`CCA`

performs canonical correspondence analysis.

`CRBIPLOT`

plots correlation or distance biplots after `RDA`

, or ranking biplots after `CCA`

.

`CRTRIPLOT`

plots ordination biplots or triplots after `CCA`

or `RDA`

.

`ECNPESTIMATE`

calculates nonparametric estimates of species richness.

`FITMULTINOMIAL`

fits generalized linear models with multinomial distribution.

`GETRGB`

gets the RGB values of the standard graphics colours.

`GREJECTIONSAMPLE`

generates random samples using rejection sampling.

`HGGRAPH`

draws a graph to display the fit of an HGLM or DHGLM analysis.

`HGWALD`

prints or saves Wald tests for fixed terms in an HGLM.

`PRSPEARMAN`

calculates probabilities for Spearman’s rank correlation statistic.

`RDESTIMATES`

plots one- or two-way tables of regression estimates.

`RTCOMPARISONS`

calculates comparison contrasts within a multi-way table of means.

`RWALD`

calculates Wald and F tests for dropping terms from a regression.

`SOM`

declares a self-organizing map.

`SOMADJUST`

performs adjustments to the weights of a self-organizing map.

`SOMDESCRIBE`

summarizes values of variables at nodes of a self-organizing map.

`SOMESTIMATE`

estimates the weights for self-organizing maps.

`SOMIDENTIFY`

allocates samples to nodes of a self-organizing map.

`SOMPREDICT`

makes predictions using a self-organizing map.

`STEEL`

performs Steel’s many-one rank test.

`VLSD`

prints approximate least significant differences for `REML`

means.

`VMCOMPARISON`

performs pairwise comparisons between `REML`

means.

**2.2 Functions**

`BLUE`

calculates the blue components of RGB colour values.

`GRAY`

or `GREY`

calculates RGB colour values for values on the gray (grey) scale.

`GREEN`

calculates the green components of RGB colour values.

`RED`

calculates the red components of RGB colour values.

`RGB`

calculates RGB colour values from red, green and blue components.

### 3. What’s changed

The representation of colours in graphics has been changed in Release 11 to allow you to use standard colour names. So virtually all options and parameters of the directives and library procedures that define colours will now take strings or texts as their settings. At the same time the use of colour numbers has been modified to allow you to define a colour directly by its RGB value, instead of requiring you first to redefine one of the 256 standard GenStat colours. Now instead of putting e.g.

`COLOUR 3; RED=50; GREEN=205; BLUE=50`

`PEN 3; COLOUR=3`

to define pen 3 as lime green, you can put either

`PEN 3; COLOUR='limegreen'`

or, if you still want to set individual RGB values, you can use the `RGB`

function

`PEN3; COLOUR=RGB(50; 205; 50)`

For details of the new colours; see the description of the `PEN`

directive.

This may cause incompatibilities in existing programs as, if you supply a number as the setting of a colour option or parameter, GenStat will now interpret it as an RGB value instead of as the number of a standard colour.

The `COLOUR`

directive thus need no longer be used, although it will be retained for use in old programs, together with the old standard colours numbers. If you have programs and procedures that rely on the old way of specifying the colours, you can use the `SET`

directive to request that number settings for colour options and parameters be interpreted in the old way rather than as RGB values. Also, the `GET`

directive can find out the current colour method (as, for example, inside a procedure), and `the RESTORE`

option of the `PROCEDURE`

directive can be set to restore the colour method automatically on exit from a procedure.

To convert programs, the colour names corresponding to the initial default settings of the old colours in Release 10 were as follows:

0 White

1 Black

2 Red

3 LimeGreen

4 Blue

5 Aqua

6 Fuchsia

7 Yellow

8 DarkOrange

9 Chartreuse

10 SpringGreen

11 DodgerBlue

12 BlueViolet

13 DeepPink

14 DimGray

15 DarkGray

16 IndianRed

17 YellowGreen

18 LimeGreen

19 Turquoise

20 MediumSlateBlue

21 MediumOrchid

22 DarkRed

23 Green

24 Navy

25 Salmon

26 PaleGreen

27 MediumSlateBlue

28 DarkSlateGray

29 DimGray

30 Gray

31 Gainsboro

32 White

These colours were then recycled over colours 33-64, 65-96, 97-128, 129-160, 161-192, 193-224 and 225-256.

Most of the other changes are compatible with Release 10, the previous release. There are a few commands, however, where new options or parameters have been inserted into the existing lists. These may cause problems in statements where option or parameter names have been omitted or abbreviated (see Section 1.7.1 of Part 1 of the *Guide to the GenStat Command Language* for details). To avoid any difficulty, the name of the option/parameter after the new option/parameter should be given explicitly, and not abbreviated to fewer than four characters.

Any command, where changes in Release 11 may cause incompatibilities in existing programs, is marked in Sections 3.1 and 3.2 by the symbol ^{†}. The full details are given in Section 3.3.

**3.1 Directives**

`ASSIGN`

can control the number that a dummy setting of the `STRUCTURE`

parameter is substituted before it is assigned (useful for procedure writers).

^{†}`BARCHART`

now allows you to set the lower heights of the error bars to be different from the upper heights, and you can control the scale used to label the y-axis.

`DGRAPH`

allows you to control the appearance of vertical or horizontal error bars, and to specify explicitly the order in which items are plotted.

`FACROTATE`

can now save communalities.

`FCLASSIFICATION`

now allows you to include only terms that can be dropped individually from the formula.

^{†}`FRAME`

can now put a box around the whole frame, and control the background colours for the windows, their frames and title bars.

^{†}`FVARIOGRAM`

now provides robust methods to estimate the variogram, but it will no longer estimate cross variograms as this can now be done by `FCOVARIOGRAM`

.

^{†}`PEN`

now allows you to control whether missing x- or y-values cause a break when drawing splines through the points. You can also control the positioning of labels by the points, and set the thickness of error bars.

`PRINT`

can now print tables of textual strings.

^{†}`SET`

can reset the current `REML`

model definitions, as specified by `VCOMPONENTS`

and `VSTRUCTURE`

(and `GET`

can access them using the `SPECIAL`

option, and `PROCEDURE`

can restore them).

`TABULATE`

can form tables of standard errors of skewness and kurtosis.

^{†}`TXCONSTRUCT`

allows you to control how to represent missing values in numerical structures. Also the `LASTSEPARATOR`

option has been modified so that it takes its default from the setting of the `SEPARATOR`

option (the previous default was not what most users seemed to expect).

**3.2 Procedures**

`AMCOMPARISON`

can now produce mean-mean plots.

`AREPMEASURES`

can now save the expanded factors, for example, to allow you to produce mean plots (using `AGRAPH`

).

`DBARCHART`

can now plot error bars.

`DISCRIMINATE`

can produce canonical correlation coefficients.

`DSCATTER`

can produce matrix plots of one set of variables against another set.

`FRESTRICTEDSET`

can save a variate with each unit set to 1 or 0 according to whether or not that unit is restricted in any of the input vectors.

`HGANALYSE`

allows you to specify a random term whose factor combinations should be used as a groups factor during the fitting of the augmented mean model; this allows models with large numbers of random effects to be fitted much more efficiently.

^{†}`HGDISPLAY`

allows you to print information from the analysis of the dispersion parameter of a random term.

^{†}`HGKEEP`

allows you to specify which method to use for the adjusted profile likelihood when calculating the likelihood statistics (as in `HGDISPLAY`

), and to save the numbers of fixed and random parameters in the mean and dispersion models.

`MANNWHITNEY`

now compares each group against a control group (specified by a new `CONTROL`

option) when there are more than 2 groups.

^{†}`RDA`

can now perform partial redundancy analysis, and also allows you to control the scaling of species and site scores.

`SVTABULATE`

can now provide bootstrap quantiles and confidence.

^{†}`SVSTRATIFIED`

and `SVGLM`

allow you to form bootstrap confidence intervals using t-statistics instead of percentiles.

**3.3 Functions**

^{†}`NEWLEVELS`

gives ordinals (1, 2 …) if the second argument omitted (previously this was undefined).

**3.4 Incompatibilities**

`BARCHART` directive |
option `YSCALING` inserted before `OUTLINE` ; parameters `LOWERERRORBARS` and `GROUPS` inserted before `PEN` . |
---|---|

`FRAME` directive |
option `BOXFRAME` inserted before `RESET` ; parameters `CINTERIOR` , `CFRAME` and `CTITLE` inserted before `SAVE` . |

`FVARIOGRAM` directive |
option `METHOD` inserted before `DIRECTIONS` ; parameter `CROSSCOMPARISON` deleted. |

`HGDISPLAY` procedure |
Option `DISPERSION` inserted before `SAVE` . |

`HGKEEP` procedure |
option `DMETHOD` inserted before `SAVE` . |

`PEN` directive |
options `YMISSING` , `XMISSING` , `YLPOSITION` , `XLPOSITION` , `BARTHICKNESS` , `BARCAPWIDTH` and `DESCRIPTION` inserted before `SAVE` . |

`RDA` procedure |
option `SCALING` inserted before `TOLERANCE` ; parameter `Z` inserted before `LRV` , and `SPECIESSCORES` inserted before `SITESCORES` ; `BIPLOT` option removed (use `CRBIPLOT` and `CRTRIPLOT` instead). |

`SET` directive |
option `VCOMPONENTS` inserted before `WORDLENGTH` . Also the action of the `SEED` option has been changed so that its use matches the way in which the `SEED` option of `CALCULATE` operates; this may change the output of some existing programs. |

`SVSTRATIFIED` procedure |
option `CIMETHOD` inserted before `COMPACT` . |

`TXCONSTRUCT` directive |
the `LASTSEPARATOR` option now takes its default from the setting of the `SEPARATOR` option. |