Release 16: new features

1. Highlights

●  2 new directives and 29 new procedures

●  Bland-Altman plots to assess the agreement between two variates (BLANDALTMAN).

●  procedures for automatic selection of REML random models for single trials, series of trials and meta analysis (VABLOCKDESIGN, VAMETA, VAOPTIONS, VARANDOM, VAROWCOLUMNDESIGN, VASERIES, VFMODEL, VFSTRUCTURE, VMODEL)

●  multi-dimensional power models for REML covariance structures, also the linear variance model and the spherical family of geostatistical models (VSTRUCTURE)

●  QTL extensions including genomic predictions (GPREDICTION) and analysis of multi-trait trials (QMTBACKSELECT, QMTESTIMATE, QMTQTLSCAN)

●  zero-inflated binomial models (R0INFLATED)

●  fitting and prediction from Michaelis-Menten curves (MICHAELISMENTEN, MMPREDICT)

●  Wald tests in generalized estimating equations (GEE)

●  analysis of distance of multivariate data (MVAOD)

●  ability to rename data structures (RENAME)

2. What’s new

2.1 Directives

QDIALOG produces a modal dialog box to obtain a response from the user.

RENAME assigns new identifiers to data structures.

2.2 Procedures

AFAUGMENTED forms an augmented design.

AUSPREADSHEET saves results from an analysis of an unbalanced design (by AUNBALANCED) in a spreadsheet.

BLANDALTMAN produces Bland-Altman plots to assess the agreement between two variates.

DREFERENCELINE adds reference lines to a graph.

EDDUNNETT calculates equivalent deviates for Dunnett’s simultaneous confidence interval around a control.

GPREDICTION produces genomic predictions (breeding values) using phenotypic and molecular marker information.

MICHAELISMENTEN fits the Michaelis-Menten equation for substrate concentration versus time data.

MMPREDICT predicts the Michaelis-Menten curve for a particular set of parameter values.

MVAOD does an analysis of distance of multivariate data.

PLINK prints a link to a graphics file into an HTML file.

QFLAPJACK creates a Flapjack project file from genotypic and phenotypic data.

QMTBACKSELECT performs a QTL backward selection for loci in multi-trait trials.

QMTESTIMATE calculates QTL effects in multi-trait trials.

QMTQTLSCAN performs a genome-wide scan for QTL effects (Simple and Composite Interval Mapping) in multi-trait trials.

QREPORT creates an HTML report from QTL linkage or association analysis results.

QUESTION obtains a response using a GenStat menu.

RFINLAYWILKINSON performs Finlay and Wilkinson’s joint regression analysis of genotype-by-environment data.

SETNAME sets the identifier of a data structure to be one specified in a text.

TCOMBINE combines several tables into a single table.

UTMCONVERSION converts between geographical latitude and longitude coordinates and UTM eastings and northings.

VABLOCKDESIGN analyses an incomplete-block design by REML, allowing automatic selection of random and spatial covariance models.

VAMETA performs a REML meta analysis of a series of trials.

VAOPTIONS defines options for the fitting of models by VARANDOM and associated procedures.

VARANDOM finds the best REML random model from a set of models defined by VFMODEL.

VAROWCOLUMNDESIGN analyses a row-and-column design by REML, with automatic selection of the best random and spatial covariance model.

VASERIES analyses a series of trials with incomplete-block or row-and-column designs by REML, automatically selecting the best random models.

VFMODEL forms a model-definition structure for a REML analysis.

VFSTRUCTURE adds a covariance-structure definition to a REML model-definition structure.

VMODEL specifies the model for a REML analysis using a model-definition structure defined by VFMODEL.

2.2 Functions

None.

3. What’s changed

Most of the changes are compatible with Release 15, 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 15 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

SET and GET have been extended to allow you to request the use of enhanced computing algorithms from the Intel® Math Kernel Library.

^†VSTRUCTURE now allows power models of order one to be defined for points in more than two dimensions, and includes the linear-variance model and the spherical family of geostatistical models.

3.2 Procedures

^†AFIELDRESIDUALS now allows you to reverse the direction of the y-axis, so that the lower coordinates are at the top.

^†AMMI has much improved graphics, including AMMI 2 plots.

^†BOXPLOT now allows you to control the ordering of the boxes when they are plotted horizontally. Also the ORIENTATION option has new settings horizontal and vertical, as synonyms of across and down, to provide better compatibility with other graphics commands, such as DHISTOGRAM and BARCHART.

^†DBIPLOT and GGEBIPLOT now allow you to supply your own title.

^†DMSCATTER now allows you to supply an overall title.

^†DQMKSCORES can now produce plots for backcross inbred lines, and the ordering of the COLOURS and TITLE options has been changed to be consistent with the ordering elsewhere (COLOURS before TITLE).

^†DQMQTLSCAN and ^†DQSQTLSCAN can now plot dominance effects and additive 2 effects.

^†DOTHISTOGRAM can now plot the individual dots in different colours, and allows you to control the order of the histograms when they are plotted horizontally.

^†GEE can now print Wald tests, and has a FACTORIAL option to control the complexity of the model to be fitted.

^†GESTABILITY has several more stability coefficients, and can also produce plots of the coefficients against the genotype means.

^†HGFTEST now provides more control over the refitting of the models.

^†LVARMODEL now allows the structure of the experiment to be specified more conveniently, by supplying block and plot-within-block factors.

META can now save the statistic Q for the test of heterogeneity across trials and its number of degrees of freedom, also the random effect variance.

^†MOVINGAVERAGE now provides the Holt-Winters method.

^†RCOMPARISONS and ^†RTCOMPARISONS now provides more control over the way in which the predictions are formed for generalized linear models.

^†RNEGBINOMIAL can now save the standard error of the aggregation parameter.

^†RSEARCH allows you to define a critical value for the probabilities of the terms in a model for that model to be printed.

^†R0INFLATED can now fit zero-inflated binomial models, and allows within-group regressions to be done, to save time and space with very large models.

^†QEIGENANALYSIS now allows you to specify the number of principal components to retain, and to save the number of effective number of columns of the marker data matrix.

^†QMBACKSELECT, ^†QMESTIMATE, ^†QMQTLSCAN, ^†QSBACKSELECT, ^†QSESTIMATE and ^†QSQTLSCAN can now analyse backcross inbred lines.

^†QSASSOCIATION has five new options and four new parameters, with enhancements including several methods to define a threshold for significance, the ability to form a kinship matrix, and more efficient analysis of very large data sets.

R0KEEP can now save the Akaike and Schwarz (Bayesian) information coefficients.

TABSORT now allows you to take a subset of the table, selecting only the best levels of the factors that are being sorted.

^†TTEST now allows you to make a permutation test using differences between means rather than t-statistics.

VTCOMPARISONS now provides tests of comparisons, combined over groups.

3.3 Functions

None.

3.4 Incompatibilities

AFIELDRESIDUALS procedure	option YORIENTATION inserted before PENCONTOUR.
AMMI procedure	new option PLOT replaces the graph setting of PRINT, and the GRAPHICS option is deleted (only high-resolution graphics is now available).
BOXPLOT procedure	new option YORIENTATION inserted after ORIENTATION, and options reordered (for compatibility) to move SCREEN to come after METHOD.
DBIPLOT procedure	option TITLE inserted before WINDOW.
DMSCATTER procedure	new parameter TITLE added, and parameters reordered (for compatibility) to become Y, X, TITLE, YTITLES, XTITLES, YMARKS, XMARKS.
DQMKSCORES procedure	ordering of the COLOURS and TITLE options has been changed, to put COLOURS before TITLE.
DQMQTLSCAN procedure	option POPULATIONTYPE inserted before METHOD and THRESHOLD (whose order has been reversed), option COLOURS moved to come just before TITLE, and parameter IDEFFECTS inserted before IDPARENTS.
DQSQTLSCAN procedure	option POPULATIONTYPE inserted before METHOD and THRESHOLD (whose order has been reversed), option COLOURS moved to come just before TITLE, and parameter IDEFFECTS inserted before IDPARENTS.
DOTHISTOGRAM procedure	new option YORIENTATION inserted after ORIENTATION, and options reordered (for compatibility) to move SCREEN to come after YORIENTATION.
GEE procedure	option FACTORIAL inserted before AGGREGATION.
GESTABILITY procedure	options PLOT, NBEST and DIRECTION inserted before PERCENTQUANTILES.
HGFTEST procedure	option LMETHOD inserted before DMETHOD, option EMETHOD, inserted before MLAPLACEORDER, option DLAPLACEORDER inserted before MAXCYCLE, and options EXIT, TOLERANCE, and ETOLERANCE inserted before SAVE.
LVARMODEL procedure	parameter NROWS deleted, and new parameters BLOCKS and UNITS inserted before EFFECTS.
MOVINGAVERAGE procedure	option PRINT inserted before NSAMPLES.
QMAP procedure	option TITLE moved to come just before OUTFILENAME.
QEIGENANALYSIS procedure	option NROOTS inserted before PLOT, parameter NEFFECTIVE inserted before %VARIANCE, and default of SCALING option changed to none
QMBACKSELECT procedure	option POPULATIONTYPE inserted before ALPHALEVEL.
QMESTIMATE procedure	options NGENERATIONS, NBACKCROSSES and NSELFINGS, inserted before VCMODEL.
QMKDIAGNOSTICS procedure	options NBACKCROSSES and NSELFINGS, inserted before DCHROMOSOMES.
QMQTLSCAN procedure	option POPULATIONTYPE inserted before ALPHALEVEL, option COLOURS inserted before TITLE, option YLABEL deleted, parameters IDEFFECTS and IDPARENTS inserted before QSTATISTICS (which is the new name for STATISTICS).
QRECOMBINATIONS procedure	option TITLE moved to the end.
QSASSOCIATION procedure	the options are now PRINT, PLOT, RELATIONSHIPMODEL, SCORES, METHOD, ALPHALEVEL, THRMETHOD, THRESHOLD, DISTANCE, MINORALLELE, KMATRIX, KMETHOD, SUBPOPULATIONS, MODELPART, SCALING, STANDARDIZE, COLOURS, TITLE, YTITLE, XTITLE, and the parameters are TRAIT, GENOTYPES, MKSCORES, CHROMOSOMES, POSITIONS, MKNAMES, IDMGENOTYPES, GENFILENAME, MAPFILENAME, WALDSTATISTICS, NDF, MINLOG10P, LAMBDA, QSAVE, DFILENAME (with the new or reordered options and parameters shown in italics).
QSBACKSELECT procedure	option POPULATIONTYPE inserted before ALPHALEVEL.
QSESTIMATE procedure	options NGENERATIONS, NBACKCROSSES and NSELFINGS, inserted before FIXED.
QSIMULATE procedure	options ADD2EFFECTS and DOMINANCEEFFECTS inserted before QTLCHROMOSOMES.
QMQTLSCAN procedure	option POPULATIONTYPE inserted before ALPHALEVEL, option COLOURS inserted before TITLE, parameters IDEFFECTS and IDPARENTS inserted before QSTATISTICS (which is the new name for STATISTICS).
QTHRESHOLD procedure	option POPULATIONTYPE inserted before THRMETHOD, parameters ADD2PREDICTORS and DOMINANCEPREDICTORS inserted before THRESHOLD.
QUESTION	The QUESTION directive has been replaced by the QDIALOG directive, with updated facilities appropriate to the more recent computing environments. The new QUESTION procedure uses QDIALOG to duplicate most of the facilities of the directive, so that existing programs can still run. The main difference is that the SAVE option and the option settings MODE=e and MODE=f are no longer supported.
RCOMPARISONS procedure	options WEIGHTS, OFFSET, METHOD, ALIASING, BACKTRANSFORM, SCOPE, NOMESSAGE, DISPERSION, DMETHOD and NBINOMIAL inserted before LSDLEVEL.
RNEGBINOMIAL procedure	option SEAGGREGATION inserted before MAXCYCLE.
RSEARCH procedure	option PPROBABILITY inserted before FINALMODELS.
RTCOMPARISONS procedure	options WEIGHTS, OFFSET, METHOD, ALIASING, BACKTRANSFORM, SCOPE, NOMESSAGE, DISPERSION, DMETHOD, and NBINOMIAL inserted before LSDLEVEL.
R0INFLATED procedure	options XGROUPS and ZGROUPS inserted before MAXCYCLE; parameter NBINOMIAL inserted before RESIDUALS.
TTEST procedure	option PLOT inserted before NTIMES, and option PERMMETHOD inserted before SEED.
VSTRUCTURE directive	parameters DISTANCES and COORDINATES inserted before INITIAL.