1. Highlights

● 32 new procedures

● density plots of large data sets (`DXYDENSITY`

)

● p-rep (i.e. partially-replicated) designs (`AFPREP`

, `CDNPREP`

)

● random regression forests (`BRFOREST`

. `BRFDISPLAY`

. `BRFPREDICT`

)

● checks of `REML`

residuals (`VCHECK`

)

● standard errors for `REML`

residuals and fitted values (`VFRESIDUALS`

)

● generalized heritability (`VHERITABILITY`

)

● line-by-tester analysis (`VALINEBYTESTER`

, `VLINEBYTESTER`

)

● nearest-neighbour analysis (`VNEARESTNEIGHBOUR`

)

● selection by genetic similarity with a target genotype, and calculation of selection indexes (`QBESTGENOTYPES`

, `QSELECTIONINDEX`

)

● recovery from unsuccessful model fitting in automatic `REML`

analysis (`VARECOVER`

)

● automatic export of `ANOVA`

output to R (`A2RDA`

)

2. What’s new

2.1 Directives

None yet

2.2 Procedures

`AFMEANS`

forms tables of means classified by `ANOVA`

treatment factors.

`AFPREP`

searches for an efficient partially-replicated design.

`ARETRIEVE`

retrieves an `ANOVA`

save structure from an external file.

`ASTORE`

stores an `ANOVA`

save structure in an external file.

`A2RDA`

saves results from an analysis of variance in R data frames.

`BCKEEP`

saves information from a classification tree.

`BKKEEP`

saves information from an identification key.

`BRFDISPLAY`

displays information about a random regression forest.

`BRFOREST`

constructs a random regression forest.

`BRFPREDICT`

makes predictions using a random regression forest.

`BRKEEP`

saves information from a regression tree.

`CDNPREP`

constructs a multi-location partially-replicated design using CycDesigN.

`DBINFORMATION`

loads information on the tables and columns in an ODBC database, PC Windows only.

`DXYDENSITY`

produces density plots for large data sets.

`FBETWEENGROUPVECTORS`

forms variates and classifying factors containing within-group summaries to use e.g. in a between-group analysis.

`FPARETOSET`

forms the Pareto optimal set of non-dominated groups.

`FREGULAR`

expands vectors onto a regular two-dimensional grid.

`FRTPRODUCTDESIGNMATRIX`

forms summation, or relationship, matrices for model terms.

`QBESTGENOTYPES`

sorts individuals of a segregating population by their genetic similarity with a defined target genotype, using the identity by descent (IBD) information at QTL positions for one or more traits.

`QSELECTIONINDEX`

calculates (molecular) selection indexes by using phenotypic information and/or molecular scores of multiple traits.

`QMVESTIMATE`

replaces missing molecular marker scores using conditional genotypic probabilities.

`TABINSERT`

inserts the contents of a sub-table into a table.

`VALINEBYTESTER`

provides combinabilities and deviances for a line-by-tester trial analysed by `VABLOCKDESIGN`

or `VAROWCOLUMNDESIGN`

.

`VARECOVER`

recovers when `REML`

, is unable to fit a model, by simplifying the random model.

`VASDISPLAY`

displays further output from an analysis by `VASERIES`

.

`VASKEEP`

copies information from an analysis by `VASERIES`

into GenStat data structures.

`VCHECK`

checks standardized residuals from a `REML`

analysis.

`VDFIELDRESIDUALS`

display residuals from a `REML`

analysis in field layout.

`VFRESIDUALS`

obtains residuals, fitted values and their standard errors from a `REML`

analysis.

`VHERITABILITY`

calculates generalized heritability for a random term in a `REML`

analysis.

`VLINEBYTESTER`

analyses a line-by-tester trial by `REML`

.

`VNEARESTNEIGHBOUR`

analyses a field trial using nearest neighbour analysis.

2.2 Functions

None.

3. What’s changed

Most of the changes are compatible with Release 16, 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 17 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 3.4.

3.1 Directives

`DEVICE`

now lets you control whether the plotting of each graph must be completed before on the device any other commands are executed.

`TXCONSTRUCT`

can now form texts from formulae.

3.2 Procedures

^{†}`AGRAPH`

now lets you include additional axis markings, transformed onto another scale, on the right-hand side of the y-axis.

^{†}`AMCOMPARISON`

, ^{†}`AUMCOMPARISON`

and ^{†}`VMCOMPARISON`

can now save the differences between the pairs of means, and the widths of their confidence intervals.

^{†}`AREPMEASURES`

now lets you control the orders of the contrasts that are fitted.

^{†}`ASPREADSHEET`

now lets you specify factors within the tables of means whose levels are assumed to be equal for the two means, when calculating effective standard errors, and can save standardized residuals.

^{†}`ASTATUS`

can now save the weight variate from the most recent `ANOVA`

.

^{†}`AUGRAPH`

now lets you include additional axis markings, transformed onto another scale, on the right-hand side of the y-axis.

^{†}`BCIDENTIFY`

can now provide identifications for specimens with some of the necessary x-values missing or unavailable, and you can now specify the values to use for the explanatory variables.

`BCFIDENTIFY`

now lets you specify the values to use for the explanatory variables.

`BIPLOT`

now lets you save more than 2 dimensions.

^{†}`BREGRESSION`

now lets you define a stopping rule based on the number of observations at a node.

^{†}`BRPREDICT`

can now provide predictions for units when some of the necessary x-values are missing or unavailable, and you can now specify the values to use for the explanatory variables.

^{†}`CDNBLOCKDESIGN`

and ^{†}`CDNROWCOLUMNDESIGN`

now allow you to specify how to weight the importance of the information in the design, and to set different seeds for the design search and randomization.

^{†}`CSPRO`

now creates the data structures locally when called within a procedure, instead of in the main program. You can still create the structures in the main program, by setting option `SCOPE=global`

.

`DBARCHART`

now allows you omit any levels where there are only missing values.

`DTABLE`

now lets you plot lines between the data values without any points at the data values themselves. Also, you can now include additional axis markings, transformed onto another scale, on the right-hand side of the y-axis.

`GGEBIPLOT`

now lets you to specify or save the groups used for the `megaenvironment`

setting of `SCPLOT`

.

`HGGRAPH`

– when plotting on the scale of the linear predictor, you can now include axis markings, back-transformed onto the natural scale, on the right-hand side of the y-axis.

`HGPREDICT`

now lets you provide identifiers for the new factors that are defined when `LEVELS`

are specified.

^{†}`IMPORT`

now creates the data structures locally when called within a procedure, instead of in the main program. You can still create the structures in the main program, by setting option `SCOPE=global`

.

`MOVINGAVERAGE`

can now plot predictions, with the Holt-Winters method, and save their upper and lower confidence limits.

^{†}`PROBITANALYSIS`

can now save the estimates of the lethal doses, and their confidence intervals.

`RGRAPH`

– when plotting on the scale of the linear predictor, you can now include axis markings, back-transformed onto the natural scale, on the right-hand side of the y-axis.

`RPHKEEP`

can save, and `RPHDISPLAY`

and `RPHCHANGE`

can print, the number of degrees of freedom in the model.

`SETDEVICE`

now lets you control whether the plotting of each graph must be completed on the device before any other commands are executed.

`SUBSET`

has a new option `NULL`

to indicate if the subset contains no units. If this is set, `SUBSET`

suppresses the fault that it normally gives for an empty subset.

`TRELLIS`

now lets you control whether the same or different pens are used to plot each y-variate.

^{†}`VABLOCKDESIGN`

has a new setting of the `RSTRATEGY`

option that tries to fit the full random model and then, if that fails, tries simpler models until it finds one that can be fitted successfully; this is now the default. You can also control the terms whose effects and means are printed, and the type of standard errors that are presented.

^{†}`VAMETA`

now lets you request that a simpler random model is fitted, if `REML`

is unable to fit the random model that has been specified. You can also control the terms whose effects and means are printed, and the type of standard errors that are presented.

^{†}`VARANDOM`

now lets you exclude models with bound or aliased variance parameters. You can also control the terms whose effects and means are printed, and the type of standard errors that are presented.

^{†}`VAROWCOLUMNDESIGN`

has new settings of the `RSTRATEGY`

option that try simpler models if the full random model or a user-specified random model fails; the default is now to try the full model, and then simpler models if that fails. You can also control the terms whose effects and means are printed, and the type of standard errors that are presented.

^{†}`VASERIES`

now has an `RSTRATEGY`

option to allow you to select the strategy to use to determine the random model. You can also control the terms whose effects and means are printed, and the type of standard errors that are presented.

`VFMODEL`

now lets you avoid overwriting the original model structure when making changes, and to set the experiments factor for a meta analysis.

^{†}`VGRAPH`

can now plot predicted means at the values of a variate as the x-dimension of the plot, and it now uses `VPREDICT`

, instead of `VKEEP`

, to obtain the means and their standard errors. Also, you can now include additional axis markings, transformed onto another scale, on the right-hand side of the y-axis.

^{†}`VFSTRUCTURE`

now lets you define residual models for experiments in a meta analysis.

^{†}`VLSD`

and ^{†}`VMCOMPARISON`

now allow you to specify the number of degrees of freedom to use to calculate the t-statistics and tests.

`VPLOT`

can now plot standardized residuals.

3.3 Functions

None.

3.4 Incompatibilities

`AGRAPH` procedure |
option `YTRANSFORM` inserted before `SAVE` . |
---|---|

`AMCOMPARISON` procedure |
parameter `DIFFERENCES` inserted before `LABELS` . |

`AREPMEASURES` procedure |
options `CONTRASTS` and `DEVIATIONS` inserted before `FPROBABILITY` . |

`AUMCOMPARISON` procedure |
parameter `DIFFERENCES` inserted before `LABELS` . |

`AUGRAPH` procedure |
option `YTRANSFORM` inserted before `SAVE` . |

`ASPREADSHEET` procedure |
options `EQFACTORS` and `RMETHOD` and inserted before `SPREADSHEET` . |

`ASTATUS` procedure |
parameter `WEIGHTS` inserted before `SAVE` . |

`BCIDENTIFY` procedure |
option `TERMINALNODES` now saves a pointer, instead of a variate, to allow for the fact that several nodes may have been used to form the identification when some x-values are missing or unavailable. Restrictions are now ignored. |

`BREGRESSION` procedure |
option `NSTOP` inserted before `OWNBSELECT` . |

`BRPREDICT` procedure |
option `TERMINALNODES` now saves a pointer, instead of a variate, to allow for the fact that several nodes may have been used to calculate the prediction when some x-values are missing or unavailable. Restrictions are now ignored. |

`CDNBLOCKDESIGN` procedure |
option `WEIGHTS` inserted before `SEED` . |

`CDNROWCOLUMNDESIGN` procedure |
options `WEIGHTS` and `RCWEIGHTS` inserted before `SEED` . |

`CSPRO` procedure |
default of `SCOPE` option changed to `local` instead of `global` . |

`IMPORT` procedure |
default of `SCOPE` option changed to `local` instead of `global` . |

`PROBITANALYSIS` procedure |
option of `CIPROBABIITY` inserted before `LOGBASE` ; this replaces the previously, and erroneously, undocumented option `%CONFIDENCE` (also just before `LOGBASE` ). |

`VABLOCKDESIGN` procedure |
options `PTERMS` and `PSE` inserted before `MVINCLUDE` ; new default, `allfeasible` , for the `RSTRATEGY` option. |

`VAMETA` procedure |
options `PTRY` and `PRECOVERY` inserted before `FIXED` ; parameter `EXIT` inserted before `SAVE` . |

`VARANDOM` procedure |
options `PTERMS` and `PSE` inserted before `MVINCLUDE` . |

`VAROWCOLUMNDESIGN` procedure |
options `PTERMS` and `PSE` inserted before `MVINCLUDE` ; new default, `allfeasible` , for the `RSTRATEGY` option. |

`VASERIES` procedure |
options `PTERMS` and `PSE` inserted before `MVINCLUDE` ; option `RSTRATEGY` inserted before `METHOD` ; parameter `EXIT` inserted before `SAVE` . |

`VFSTRUCTURE` procedure |
option `EXPERIMENT` inserted before `TERMS` . |

`VGRAPH` procedure |
option `YTRANSFORM` inserted before `SAVE` . |

`VMCOMPARISON` procedure |
options `DFMETHOD` , `DFGIVEN` and `FMETHOD` inserted before `SAVE` ; parameter `DIFFERENCES` inserted before `LABELS` . |

`VLSD` procedure |
options `DFMETHOD` , `DFGIVEN` and `FMETHOD` inserted before `SAVE` . |