### 1. Highlights

● produced in 2010

● 4 new directives, 29 new procedures, 6 new functions

● trellis plots of tables (`DTABLE`

)

● multiple correspondence analysis (`MCORANALYSIS`

)

● stepwise discriminant analysis (`SDISCRIMINATE`

)

● neural networks (`NNFIT`

, `NNDISPLAY`

, `NNPREDICT`

)

● random classification forests (`BCFOREST`

, `BCFIDENTIFY`

and `BCFDISPLAY`

)

● quantile nonlinear regression (`RQNONLINEAR`

)

● parallel anova and regression (`AYPARALLEL`

and `RYPARALLEL`

)

● easier prediction and plotting of predictions from unbalanced analysis of variance (`AUPREDICT`

and `AUGRAPH`

)

● multiple comparisons in unbalanced anova (`AUMCOMPARISON`

)

● plots of `REML`

effects (`VDEFFECTS`

)

● QTL analysis extensions – association mapping (`QASSOCIATION`

, `QEIGENANALYSIS`

), linkage disequilibrium (`QLDDECAY`

), descriptive statistics and diagnostic plots (`QMKDIAGNOSTICS`

), replacement of missing marker scores (`QMVREPLACE`

), percentage variance accounted for by QTLs (`QMVAF`

)

● positive semi-definite approximations non-positive semi-definite matrices (`POSSEMIDEFINITE`

)

● testing of individual fixed and random terms in hierarchical generalized linear models (`HGFTEST`

and `HGRTEST`

)

● stratified random samples (`SVSAMPLE`

)

● measures of association for circular data (`CASSOCIATION`

)

● tests for circular data with common mean direction or identical distributions (`CCOMPARE`

)

● spectra of spatial point patterns (`DPSPECTRALPLOT`

)

### 2. What’s new

**2.1 Directives**

`BIDENTIFY`

identifies specimens using a tree.

`NNDISPLAY`

displays output from a multi-layer perceptron neural network fitted by `NNFIT`

.

`NNFIT`

fits a multi-layer perceptron neural network.

`NNPREDICT`

forms predictions from a multi-layer perceptron neural network fitted by `NNFIT`

.

**2.2 Procedures**

`AUGRAPH`

plots tables of means from `AUNBALANCED`

.

`AUMCOMPARISON`

performs pairwise multiple comparison tests for means from an unbalanced analysis of variance, performed previously by `AUNBALANCED`

.

`AUPREDICT`

forms predictions from an unbalanced design (after `AUNBALANCED`

).

`AYPARALLEL`

does the same analysis of variance for several y-variates, and collates the output.

`BCFDISPLAY`

displays information about a random classification forest.

`BCFIDENTIFY`

identifies specimens using a random classification forest.

`BCFOREST`

constructs a random classification forest.

`CABIPLOT`

plots results from correspondence analysis or multiple correspondence analysis.

`CASSOCIATION`

calculates measures of association for circular data.

`CCOMPARE`

tests whether samples from circular distributions have a common mean direction or have identical distributions.

`DPSPECTRALPLOT`

calculates an estimate of the spectrum of a spatial point pattern.

`DTABLE`

plots tables.

`FVSTRING`

forms a string listing the identifiers of a set of data structures.

`HGFTEST`

calculates likelihood tests for fixed terms in a hierarchical generalized linear model.

`HGRTEST`

calculates likelihood tests for random terms in a hierarchical generalized linear model.

`MCORANALYSIS`

does multiple correspondence analysis.

`POSSEMIDEFINITE`

calculates a positive semi-definite approximation of a non-positive semi-definite symmetric matrix.

`QASSOCIATION`

(now `QSASSOCIATION`

) performs marker-trait association analysis in a genetically diverse population.

`QEIGENANALYSIS`

uses principal components analysis and the Tracy-Widom statistic to find the number of significant principal components to represent a set of variables.

`QLDDECAY`

estimates linkage disequilibrium (LD) decay along a chromosome.

`QMKDIAGNOSTICS`

generates descriptive statistics and diagnostic plots of molecular marker data.

`QMVAF`

calculates percentage variance accounted for by QTL effects in a multi-environment analysis.

`QMVREPLACE`

replaces missing marker scores with one of the scores of the most similar genotypes.

`RQNONLINEAR`

fits and plots quantile regressions for nonlinear models.

`RYPARALLEL`

fits the same regression model to several response variates, and collates the output.

`SDISCRIMINATE`

selects the best set of variates to discriminate between groups.

`SVSAMPLE`

constructs stratified random samples.

`T%CONTROL`

expresses tables as percentages of control cells.

`VDEFFECTS`

plots one- or two-way tables of effects estimated in a `REML`

analysis.

**2.3 Functions**

`COLBIND`

joins two matrices side by side.

`MINSERT`

inserts a matrix into another matrix.

`ROWBIND`

joins (i.e. stacks) two matrices vertically.

`RQOBJECTIVE`

calculates the objective function from fitting a quantile linear regression.

`VPERCENTILES`

calculates percentiles across a set of variates.

`VQUANTILES`

calculates quantiles across a set of variates.

### 3. What’s changed

Most of the changes are compatible with Release 12, 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 13 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**

^{†}`AXIS`

, ^{†}`XAXIS`

, ^{†}`YAXIS`

and ^{†}`ZAXIS`

now allow you to use scientific or engineering format for numbers, and to rotate axis labels.

`FITCURVE`

can now fit the emax and generalized emax growth curves.

emax | y = α + γ / (1 + exp(-β × (log(x) – μ)) ) + ε |
---|---|

gemax | y = α + γ / (1 + τ × exp(-β × (log(x) – μ)))^{1/τ} + ε |

These are similar to the logistic and generalized logistic curves, except that their equations involve log(*x*) instead of *x*. They are usually used to model decreasing relationships (i.e. the parameter β in the equation is negative), but GenStat will allow increasing relationships with these curves too.

^{†}`PEN`

can now use bitmaps as symbols, and define transparent colours.

In `PREDICT`

and `VPREDICT`

, you can now supply identifiers for the factors that need to be created to index the tables of predictions when `LEVELS`

are specified.

`TXFIND`

can now insist the subtexts to be found must occur within a single line of the target text; it can also save the column and line of the last character of the subtext within the target text.

**3.2 Procedures**

^{†}`AGRAPH`

can now split the plots across different pages and can draw smooth curves through the points; in addition, the procedure has been simplified following the inclusion of `AUGRAPH`

and `DTABLE`

, which should now be used for plots from unbalanced analysis of variance or plots of general tables.

^{†}`AGSQLATTICE`

can now form lattice square designs.

`ANTORDER`

, `ANTTEST`

and `AREPMEASURES`

now allow the data to be specified in a single variate (with a time factor to identify when each observation was made).

^{†}`APOLYNOMIAL`

can now form the equations of polynomials at various levels of other factors (when their interactions with the polynomial factor have been included in the analysis).

`BCIDENTIFY`

can now form a matrix with the probabilities that the specimens belong to each group.

`BOXPLOT`

now allows the widths and positions of the boxes along the x-axis to be controlled.

^{†}`CORANALYSIS`

has been updated to provide the method and outputs described in Greenacre (2007), *Correspondence Analysis in Practice, second edition*.

^{†}`DBIPLOT`

now plots arrows on the biplot axes to represent their loadings (or inverse loadings); the loadings show the approximate contribution of each variable in the first two dimensions.

^{†}`DCORRELATION`

can now include axes (and labels) in the plots.

`DSCATTER`

includes a key in the plots when there are groups.

`FILEREAD`

parameter `FGROUPS`

has two new settings `form`

and `leave`

, that should be used in future instead of `yes`

and `no`

to specify explicitly whether each structure should or should not be defined automatically as a factor. This is to remove the confusion arising from the fact that the default for `FGROUPS`

is `check`

, whereas other options and parameters that have no as a setting, use `no`

as their default. However, for compatibility with earlier programs, the settings `yes`

and `no`

will continue to be recognised as synonyms for `form`

and `leave`

.

^{†}`FFRAME`

allows you specify the starting number of the windows, and to save the list of numbers.

`GRTHIN`

allows you to save an indicator indicating whether each point was included or excluded.

^{†}`MAANOVA`

can now save residuals and fitted values.

^{†}`RPROPORTIONAL`

has been rewritten to fit the model by a direct maximization of the likelihood, using NAG algorithm `G12BAF`

; this is much more efficient for large data sets than the alternative method, used in procedure `RPHFIT`

, which fits a generalized linear model to an expanded data set.

`R2LINES`

can save the intercepts.

`SAGRAPES`

option `SCALING`

has two new settings `equal`

and `none`

, that should be used in future instead of `yes`

and `no`

to specify whether or not to have equal scaling for x and y axes on Drift-Unreliability and Discrimination-Disagreement graphs. However, for compatibility with earlier programs, the settings `yes`

and `no`

will continue to be recognised as synonyms for `equal`

and `none`

.

`VMCOMPARISON`

now allows Bonferroni or Sidak adjustments to be made to the critical probability values.

^{†}`VGRAPH`

can produce trellis plots, split over pages and can draw smooth curves through the points.

**3.3 Functions**

The existing functions are all unchanged.

|**3.4 Incompatibilities**

`AGRAPH` procedure |
options `COMBINATIONS` and `ADJUSTMENT` deleted; option `DFSPLINE` inserted before `SAVE` ; parameters `MEANS` , `BAR` and `BARDESCRIPTION` deleted; parameter `PAGEGROUPS` inserted before `NEWXLEVELS` . |
---|---|

`AGSQLATTICE` procedure |
parameters `ROWS` and `COLUMNS` inserted before `UNITS` . |

`APOLYNOMIAL` procedure |
parameter `GROUPS` inserted before `COEFFICIENTS` . |

`AXIS` directive |
parameter `LROTATION` inserted before `NSUBTICKS` ; parameter `VREPRESENTATION` inserted before `SAVE` . |

`BASSESS` directive |
option `SELECTION` renamed `SELECTED` (to remove clash the usage in `FIT` , `DESCRIBE` etc) |

`CORANALYSIS` procedure |
now uses the method of Greenacre (2007, Correspondence Analysis in Practice, second edition) by default, instead of the method of Digby & Kempton (1987, Multivariate Analysis of Ecological Communities). |

`DBIPLOT` procedure |
option `MULTIPLIER` inserted before `WINDOW` . |

`DCORRELATION` procedure |
option `SHOW` inserted before `NCOLOURS` . |

`DQMQTLSCAN` procedure |
options `METHOD` and `DCHROMOSOMES` inserted before `TITLE` , and `YAXUPPER` inserted before `YLABEL` . |

`DQSQTLSCAN` procedure |
options `METHOD` and `DCHROMOSOMES` inserted before `WINDOW` , and `YUPPER` inserted before `SCREEN` . |

`EXPORT` procedure |
option `PRINT` added before `OUTFILE` . |

`FILEREAD` procedure |
parameter `FGROUPS` has two new settings `form` and `leave` , that should be used in future instead of `yes` and `no` (although `yes` and `no` will continue to be recognised). |

`FFRAME` procedure |
options `STARTWINDOW` and `TESTGRAPH` inserted before `NUMBERING` ; parameter `SWINDOW` inserted before `SYLOWER` . |

`KERNELDENSITY` procedure |
options `PLOT` and `TITLE` inserted before `WINDOW` . |

`MAANOVA` procedure |
parameters `RESIDUALS` and `FITTEDVALUES` inserted before `MEANS` . |

`MOVINGAVERAGE` procedure |
option `PLOT` , with setting `movingaverages` , replaces the `GRAPHICS` option . |

`PEN` directive |
parameters `TSYMBOL` , `TLINE` , `TFILL` and `TAREA` inserted before `SAVE` . |

`QSBACKSELECT` procedure |
parameters `ADD2PREDICTORS` and `DOMINANCEPREDICTORS` inserted before `CHROMOSOMES` , and `DOMSELECTED` inserted before `WALDSTATISTICS` . |

`QSQTLSCAN` procedure |
parameters `ADD2PREDICTORS` and `DOMINANCEPREDICTORS` inserted before `CHROMOSOMES` . |

`RQLINEAR` procedure |
parameters reordered to match `RKEEP` : new order is `Y` , `PRQUANTILES` , `RESIDUALS` , `FITTEDVALUES` , `ESTIMATES` , `SE` , `VCOVARIANCE` , `DF` , `LOWER` , `UPPER` , `LOWFITTEDVALUES` , `UPPFITTEDVALUES` , `OBJECTIVE` , `EXIT` . |

`RPROPORTIONAL` procedure |
completely rewritten (but the old procedure is currently still available, as `OLDRPROPORTIONAL` ). |

`R2LINES` procedure |
parameter `INTERCEPTS` inserted before `LOWER` . |

`RQSMOOTH` procedure |
`RESIDUALS` parameter moved to come before `FITTEDVALUES` to match `RKEEP` etc. |

`RSURVIVAL` procedure |
option `PLOT` (with setting `survivorfunction` ) inserted before `GRAPHICS` to control whether any plots are done. |

`SAGRAPES` procedure |
option `SCALING` has two new settings `equal` and `none` , that should be used in future instead of `yes` and `no` (although `yes` and `no` will continue to be recognised). |

`VGRAPH` procedure |
options `LSDLEVEL` and `DFSPLINE` inserted before `SAVE` ; parameters `MEANS` , `BAR` and `BARDESCRIPTION` deleted; parameters `TRELLISGROUPS` and `PAGEGROUPS` inserted before `NEWXLEVELS` . |

`XAXIS` directive |
parameter `LROTATION` inserted before `NSUBTICKS` ; parameter `VREPRESENTATION` inserted before `YOMETHOD` . |

`YAXIS` directive |
parameter `LROTATION` inserted before `NSUBTICKS` ; parameter `VREPRESENTATION` inserted before `XOMETHOD` . |

`ZAXIS` directive |
parameter `LROTATION` inserted before `NSUBTICKS` ; parameter `VREPRESENTATION` inserted before `XOMETHOD` . |