Release 8: new features

1. Highlights

●  produced in 2005

●  6 new directives, 28 new procedures and 16 new functions

●  “formatted” output in html (for use e.g. in web pages), rtf (for wordprocessors) or LaTeX (for scientific publications)

●  Cokriging (see COKRIGE)

●  Lin’s concordance coefficient (see LCONCORDANCE)

●  McNemar’s test (see MCNEMAR)

●  power calculations for analysis of variance, regression and generalized linear models (see APOWER and RPOWER)

●  sample-size calculations for analysis of variance (ASAMPLESIZE), t-tests (STTEST), correlation coefficients (SCORRELATION), sign tests (SSIGNTEST), Mann-Whitney tests (SMANNWHITNEY), binomial tests (SBNTEST), Lin’s concordance coefficient (SLCONCORDANCE), and McNemar’s test (SMCNEMAR)

●  sample-size calculations for tests for equivalence and tests for non-inferiority made by an analysis of variance (ASAMPLESIZE) or a t-test (STTEST)

●  enhanced facilities for fitting proportional-hazards models, allowing sequences of models to be studied by adding or dropping terms (see RPHFIT)

●  generation of complete and quasi-complete Latin squares – used for experiments where treatment effects may carry over to adjacent plots (see AGQLATIN)

●  Nelder-Mead simplex algorithm for optimization – the target function may be calculated using expressions or by a GenStat procedure thus allowing any GenStat command to be involved (see SIMPLEX)

●  calculation of effective standard errors, for tables of means from an unbalanced analysis of variance, that give good approximations to the standard errors of differences (see SED2ESE)

●  algorithms for interactive identification e.g. of plants or animals (see IDENTIFY)

●  irredundant test sets, used e.g. for constructing efficient identification schemes (see IRREDUNDANT)

2. What’s new

2.1 Directives

CAPTION prints captions in standardized formats.

COKRIGE calculates kriged estimates using a model fitted to the sample variograms and cross variograms of a set of variates.

FCOVARIOGRAM forms a covariogram structure containing auto-variograms of individual variates and cross-variograms for pairs from a list of variates.

IRREDUNDANT forms irredundant test sets for the efficient identification of a set of objects.

MCOVARIOGRAM fits models to sets of variograms and cross variograms.

REFORMULATE modifies a formula or an expression to operate on a different set of data structures.

2.2 Procedures

AGQLATIN generates complete and quasi-complete Latin squares.

APOWER calculates the power (probability of detection) for terms in an analysis of variance.

ASAMPLESIZE finds the replication to detect a treatment effect or contrast.

FDRMIXTURE estimates false discovery rates using mixture distributions.

FVCOVARIANCE forms the variance-covariance matrix for a list of variates.

IDENTIFY identifies an unknown specimen from a defined set of objects.

LCONCORDANCE calculates Lin’s concordance correlation coefficient.

MCNEMAR performs McNemar’s test for the significance of changes.

NCONVERT converts integers between base 10 and other bases.

PRCORRELATION calculates probabilities for product moment correlations.

RMGLM fits a model where different units follow different generalized linear models.

RPHCHANGE modifies a proportional hazards model fitted by RPHFIT.

RPHDISPLAY prints output for a proportional hazards model fitted by RPHFIT.

RPHFIT fits the proportional hazards model to survival data as a generalized linear model.

RPHKEEP saves information from a proportional hazards model fitted by RPHFIT.

RPHVECTORS forms vectors for fitting proportional hazards data as a generalized linear model.

RPOWER calculates the power (probability of detection) for regression models.

SBNTEST calculates the sample size for binomial tests.

SCORRELATION calculates the sample size to detect specified correlations.

SED2ESE calculates effective standard errors that give good approximate standard errors of differences.

SIMPLEX searches for the minimum of a function using the Nelder-Mead simplex algorithm.

SLCONCORDANCE calculates the sample size for Lin’s concordance coefficient.

SMANNWHITNEY calculates sample sizes for the Mann-Whitney test.

SMCNEMAR calculates sample sizes for McNemar’s test.

SPRECISION calculates the sample size to obtain a specified precision.

SSIGNTEST calculates the sample size for a sign test.

STTEST calculates the sample size for t-tests (including equivalence tests).

VMATRIX copies values and row/column labels from a matrix to variates or texts.

2.3 Functions

BJ0	Bessel function J0.
BJ1	Bessel function J1.
BI0	modified Bessel function I0.
BI1	modified Bessel function I1.
MCENTRE	doubly centres a matrix so that its rows and columns have mean zero.
MEXP	matrix exponential.
MPOWER	matrix power.
MSQRT	matrix square root.
RANGE	range of values.
STANDARDIZE	standardizes the values.
TCOLUMN	converts a one-way table into a column matrix.
TDIAGONAL	converts a one-way table into a diagonal matrix.
TMATRIX	converts a two-way table into a matrix.
TPROJECT	converts a table into a variate.
TROW	converts a one-way table into a row matrix.
VRANGE	range of values across a pointer of variates.

3. What’s changed

Most of the changes are completely compatible with Release 7, 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 8 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

^†AKEEP can now save effective degrees of freedom for combined means and effects, and codes indicating the properties of the design and the model terms in the analysis.

ANOVA can now save a codes indicating the properties of the design.

CALCULATE has a new INDEX option, which is useful if the calculation has a list of structures before the assignment operator (=). The option is set to a scalar which will indicate the position within the list of the structure currently being evaluated.

ENQUIRE can save details of the output styles currently in use.

FPSEUDOFACTORS can save the resolution number of the design.

KRIGE has a new SAVE parameter too allow model information to be supplied more conveniently from MVARIOGRAM.

OPEN allows you to set the style of an output channel (as either plain-text, html, rtf or LaTeX).

OUTPUT allows you to set the style (plain-text or formatted) for future output to an output channel.

^†PEN has a new option setting METHOD=spline to plot a smoothing spline fitted through the points; the new DFSPLINE sets the number of degrees of freedom.

PRINT has a new parameter HEADING which allows you to specify column headings to be used for vectors instead of their identifiers, and a new option STYLE to request use of plain-text when printing to output files opened in html, rtf or LaTeX styles.

PROCEDURE has an extra setting, outstyle, for its RESTORE option to allow you to restore the style of output.

^†RKEEP can now save standard errors for the linear predictor.

SKIP allows you to specify whether to use plain-text or formatted styles when skipping lines in output.

TERMS has a new option MVINCLUDE to specify that units with missing values in an explanatory variable should not be omitted; instead the variable should make no contribution to the fitted values for these units.

3.2 Procedures

AUNBALANCED and AUDISPLAY can now print approximate effective standard errors of means, and AUKEEP can save them.

^†DISCRIMINATE – new version with enhanced output including plots.

FSTRING has an extra parameter to specify characters to go at the end of the string.

FTEXT can now generate a text from any numerical structure, and has additional parameters to control the display of factor levels and missing values.

KAPLANMEIER can now produce means and quantiles.

MVARIOGRAM has a new SAVE parameter too allow model information to be supplied more conveniently to KRIGE.

^†PRMANNWHITNEYU can calculate the exact probabilities when the data include tied values in many GenStat implementations (including MS Windows).

QLIST has a new option HELP to provide help information for the question.

^†RSURVIVAL now also covers the log-logistic and lognormal distributions, and can save their shape parameter sigma as well as the estimates of the survivor function.

SPCAPABILITY can produce histograms.

^†SVSTRATIFIED can produce ratio estimates when Y contains only the response data.

TALLY can use weights in its tabulations, and it can include quantiles in the graphs.

VTABLE can generate labels indicating the factor values corresponding to each unit of the generated variate.

In addition, the Library procedures have been modified where possible to use the new CAPTION directive and the new HEADING parameter and STYLE option of PRINT, so that their output is displayed correctly in GenStat’s new formatted output styles (see the OUTPUT directive). The procedures that cannot generate formatted output correctly have been modified to switch the output style to plain text by the command

OUTPUT [STYLE=plaintext]

and then restore the original style by including the setting outstyle in the settings of the RESTORE option in the PROCEDURE command.

3.3 Incompatibilities

AKEEP directive	option EXIT inserted before SAVE; parameter DFCMEANS inserted before CBEFFECTS, and parameter DFCEFFECTS inserted before CBCEFFICIENCY.
AUKEEP procedure	parameter ESEMEANS inserted before LSD.
DISCRIMINATE procedure	new parameter ALLOCATION inserted before MEANS.
PEN directive	new parameter DFSPLINE inserted before SAVE.
PRMANNWHITNEYU procedure	new parameter TIES inserted before CLPROBABILITY.
REPLICATION procedure	option MINREPLICATION inserted before MAXREPLICATION, and TMETHOD inserted before SAVE. Note, however, that this procedure is superceded by ASAMPLESIZE; it will be phased out in a future release.
RKEEP directive	parameter SELINEARPREDICTOR inserted before INFLATION.
RSURVIVAL procedure	options SIGMA, SURVIVOR and PARAMETERIZATION inserted before MAXCYCLE.
SVSTRATIFIED procedure	parameter XTOTALS inserted before TOTALS.