ASReml v4.0: Release Notes

ASReml Versions

  • ASReml 3.0 is the current released version
  • ASReml 4.0 contains extensions under development
  • Draft documentation is contained in the file doc/UpdateR4.pdf, also obtainable from the Beta downloads page

v4.0lm (28th October 2014)

  • Cumulative enhancements from internal version 4.0lb - 4.0lm
  • a4data Allow MODIFY to work on nrm(Animal .01 !GU)
  • !CONTINUE and !LAST problems following qualifiers
  • Allow multiple increases in workspace allocation
  • Change to Long Integer addressing for XFA setup
  • Fix crash in VWVG with XFA large memory
  • Fix failure to handle XLT internal function in loop when large memory
  • Convert Address from short to long (W20 crash Weights)
  • Test VPREDICT has 3rd field; so no CRASH
  • Fix bug that tabulate not honoured when it follows RESIDUAL
  • Fix error; mean lines reversed in !X !Y plots
  • Add LinePrinter version to .res file
  • Stop stripping wrapper from simple terms
  • SITE*6 now becomes SITE*8
  • If name given for residual, use it e.g. units;Residual
  • Allow lit;us[1:3] in VPREDICT
  • Fix bug reading xfa(fac,2).lit
  • Fix bug parsing XFA structural
  • Insert THRLEVELS in ARGlist c.f. lg/knwd (needed for Cheese example
  • Catch bug when logical table has more than 4225000000 cells
  • Delete erroneous position message for idv(A) variance structure
  • Recognise xxx.grr Factor
  • Change to us(T).xxx;us(T) naming of components.
  • Change !CENTRE options
  • Bug recognising GenVar when GenVar created Sire*4
  • Update syntax NOKEY => NOID etc.
  • !CENTRE activated
  • Fix bug in DenDF calculation for ANTE1 in grass.as
  • Extend .xml to .pvs output
  • Extend level labels for 3-way interaction when !SLNFORM is set
  • Enable !SMODE 32
  • convert mkr/mat to .grr
  • convert snp() to grr()
  • GRR file initializes Factor class names if GIDname matches an !A variable name
  • Allow VPREDICT to use labels
  • Allow !FINAL on data line
  • Review LofDet calc of GIV
  • Fix bug reporting variance parameters in .res
  • !AIF replaces !DIAG
  • !XML to request XML output
  • Grid infill now works for multiple sections
  • Add !XML Command Line qualifier
  • Fix bug in restoring label IDV_V
  • Fix bug to eport final itern seq when simple model
  • Add !FINAL
  • Hold repeated level lists more efficiently
  • Fix bug reading in DENSE GIV of order 3189
  • Extend mvs example to !ASUV
  • Correct fix for threshold model examples (Cheese)
  • Update to .mat input option
  • Fix bug parsing !LAST Identifier.us(Trait)
  • Fix problem labelling correlations of 0/1 variates
  • Fix weighted multivariate analysis failure
  • Fix bug parsing -pSMTTWNP_30 smt (2nd P confused it)
  • Fix wrongly applied US to spl(EWEAGE) in thr 4 model
  • Fix LogL for weighted multivariate analysis
  • Fix PREDICT EWE !PRESENT BFLOCK under threshold model
  • Modify sln header layout
  • Fix bug in writing bss.vvp
  • Adjust workspace check near line 2653
  • Refine NGAMMA count in bss.as job (SING)
  • Modify SITE from A6 to A8 so better labeling in plots
  • Modif SITE from A6 to A8
  • Change bgrm to sgrm to match documentation

v4.0lb (28th July 2014)

  • Cumulative enhancements from internal version 4.0ks - 4.0lb
  • Get start values xfa(A,1) ==> us(A)
  • Fixed bug parsing !SUBSET Tr123 Trait 1 2 3 0 0
  • Fixed bug in forming PEV of Selection Index
  • Fixed crash when invalid model term specified
  • Fixed SE reported when Singular component
  • Adjust switching from 1 to multiple factor update
  • Exclude factors from XFA eigen analysis
  • Fixed confusion parsing xfa(F,k)
  • Insert default initial values for XFA structures
  • Fixed confusion when user specifies ?sv file to read
  • Fixed bug: not opening .rsv file
  • Extended VPREDICT syntax
  • Better scaling in .vvp
  • Fixed bug parsing xfa2(Trait)
  • Fixed bug in reading named .tsv file
  • Adjustment so GDENSE works with singular GRM
  • Fixed to avoid crash when RES/PV is NaN
  • Inserted heading into .sln file
  • Fixed to avoid crash on diagnostic print when few (<40) equations
  • Adjusted format of diagnostic print
  • Fixed to print warning when $string undefined
  • Fixed new bug in !ASSIGN testing
  • Fixed new bug in testing for partial matches
  • Fix to disallow special characters in new factor names
  • Fixed format 2470, change condition
  • Prevented MKR BLUP overwriting KCV
  • Test factor labels of SUBSET better
  • Test Assign labels better
  • Increased space for GRM matrix
  • Report correct name of .rsv file used
  • Changed logical units to avoid conflict when CYCLE HOLD
  • Reduce XFAIF when MAXIT=1 (assume near solution)
  • PEV of marker blups (mkr/grm): now works
  • Extended VPREDICT to S X C D functions
  • Fixed .vvp for XFA on gamma scale
  • Fixed bug parsing labels on marker file when not many of them
  • Replaced SMIGE with SMISG so Singular GRM allowed
  • Added !PSD qualifier to declare number of singularities in GRM
  • Added !HOLD qualifier to !CYCLE so it only reads data and mkr file first cycle
  • Made !ASUV default for BINNOR model
  • Made !SPECIALCHAR parsing more robust
  • TPREDICT hyb !AVE xfa1(site) !ONLY xfa1(site).hyb
  • Allowed negative pivot in Dense equations (e.g. GRM)
  • Report more characteristics of GRM
  • Enabled reading labels from .mkr files
  • Improved histogram for mkr file report
  • Fixed bug when long line splits as NA*
  • Increase size of CCOL/CVAL work vectors to avoid overflow with and()
  • Fixed failure to parse and(Lhyb.xfa1(Loc),-0.2)
  • Added notice for MODIFY sat(Trial)... case
  • Revamped TSV/RSV/CONTINUE
  • Fixed bug reading .rsv when two xfa model terms
  • !FOLDER can now appear before variable definitions
  • Class names file may be in FOLDER
  • Added !SUBSECTION diagnostic warning if too many sections
  • Updated Data Sort parameters; modified report of 'size' of units
  • Fixed bug when and() term IGNORED
  • Added warning if !SUBSECTION result is suspicious
  • Added code to fix class names appearing as NA
  • Let !SECTION !ROW !COL inform record sorting if residual model does not
  • Fixed bug labelling XFA factors
  • Inserted code for if class levels NA
  • Fixed bug Recognise !A !L ../filename
  • Fixed bug in '!CONTINUE !OUTFOLDER'
  • Check CONTRAST basis variable: warning
  • Implemented new ASReml license
  • Fixed bug: failed to sort xfa.ped equations
  • Increased default space for sorting under !ROWFAC !COLFAC
  • Increased HELPFL to 200 characters
  • Fixed check of at() str too long; allow 190 rather than 90
  • Clear extra characters when expanded length > 1000
  • Changed LogDet calc message to Notice
  • In !L file, allowed "Chap 5" ==> 'Chap_5'
  • More robust LDET of sparse GIV
  • Fixed bug opening named Scratch file
  • Fixed bug when Scratch file not large enough
  • Fixed misreading long lines (character dropped)

40 kr 26 Mar 2014

  • Fixed format bug; truncated counts when NREC<99999
  • Fixed bug reporting XFA matrix in .asr when some PSI zero.
  • Fixed LongInt addressing Bug reporting spl trend with Huge workspace
  • Fixed bug producing Predict PLOT with !PARALEL qualifier

v4.0kq (16th March 2014)

  • Tighten model parsing checks and( , 0.2)
  • Allow residual units.mthr(Trait)
  • remove IF rgmstr==4 so .msv has same structure as .tsv
  • moved 'CALL StructureCheck' so ARCOL.as 18 now runs
  • modified StructureCheck to insert missing V parameter in G structures
  • Bug reporting pedigree conflict fixed, !UPPER added
  • !UPPERCASE added
  • Implement !GINDEX as TPREDICT
  • Added message when US not PD
  • Cancelled trying to reuse previous equation order: failing

v4.0kp (5th March 2014)

  • Cumulative enhancements from internal version 4.0kn - 4.0ko
  • Fixed Bug parsing long data lines
  • SLASHSLASH restricted to .as file
  • Parent/Non-Parent labeling in aif file
  • NPD US message updated
  • GDENSE default
  • failed on at(parity).units.us(Trait)
  • Stop if more geno than markers
  • Add processing of decimal markers
  • leave log() and sqrt() wrappers
  • Fixed Bug getting DET of GIV with Groups

v4.0km (9th January 2014)

  • Cumulative enhancements from internal version 4.0kk - 4.0kl
  • Fixed Bug parsing !FOR $LIST !DO command
  • Fixed Bug reading binary MBF file
  • Fix Bug creating design for row and(col)
  • !SIGMAP to allow the Sigma parameterization
  • No longer strip v from idv(units) under gamma parameterization
  • Fix Bug processing nrm(animal !INIT .25); fill in STRUC 14,16
  • Fix Bug processing idv(units.Trait) (!ASUV)
  • Added KEEP (ASUV flag) to SETSTR arg list
  • Do not create MODIFY lines for '-idv' terms
  • Set !SIGMAP for xxh() Rstructure models
  • Fix BUG in RCOV address (orange spl() error)
  • Fix fault Pedigree sort failure with Genetic Groups

v4.0kj (17th January 2014)

  • Fix so !SUBSET Trait 3 4 5 0 0 has factor size 3
  • Fix misspelling of constraint
  • Comment out debugging statement
  • Fix Bug resetting RSVFILE with !WORK
  • Fix Bug parsing !CONTINUE rsvfile
  • Extend !AIPENALTY
  • small changes to bsfx, mssyfa1, xfab
  • Fix Bug switching back to all factors when 2 XFA terms!
  • Moved !DOPART $1 to top command line!
  • Increased Rstring and Selectstrg to *24
  • Inserted factor namr in title of VG plot

v4.0ki (7th January 2014)

  • Cumulative enhancements from internal version 4.0kb - 4.0kh
  • Give heading for ar1v() term in component table
  • Fixed Bug parsing at(Age):ar1(Row):ar1(Col):us(Trait)
  • Fixed bug arising from new VC table labelling.
  • Needed to convert I4 to I8 integers KPLUSW, MEMORY
  • Long LXBASE+AIOPT in airhat call
  • Modified format 2133 and rearranged WRITEs using it
  • Fixed bug reporting conflicting pedigree (labelling)
  • Fixed bug parsing when reading pedigree
  • Modified variance components table at request of Robin extensive output changes.
  • Bug: inserted MOD() for case of -ve mdel term
  • Extended functionality of VCM for Christ Brien
  • Extended VCM statement to allow list of parameters in place [VCB]
  • reordered so license check before prompts
  • Do not set space for data sorting if not required
  • Do not zero sln(EQN,2) as it sometimes crashes asreml-r
  • Change base 16000 to 17500 so can have more than 1000 loadings
  • Allow I9 for counts if MROW > 99999 (else I6)
  • !PRECISION 1 2 3 === 6 5 4
  • Assume random for nrm, grm and vs structures
  • !SAVE equivalent/alternative to !GIV
  • !L filename !SKIP equivalent to !LSKIP
  • Accommodate spurious leading BLANKS
  • Allow blank lines in files being merged
  • Notify if no Trait with !MULTINOMIAL
  • Changed comment
  • Changed LU=8 to LU=13 so TABULATE works!
  • Revampted Variance component table.
  • Bug adjusting arh(row)
  • Adjusted MP absorption so return correct Fincr
  • Fixed bug parsing ped col labels ANIMAL,SIRE,DAM
  • Improved error messages
  • Inserted links for !SUBSECTION in new syntax
  • Avoided bad memory reference
  • Fix format bug
  • Allow '*' on next line parsing old format Structure lines
  • Bug parsing !CONT 3
  • Bug reporting restart from .msv
  • Bug parsing str(row
  • Added RSVFILE
  • Allowed filename arg to !CONTINUE for .rsv file
  • Added warnings in two places where // notation fails.
  • Fix labelling of Matern parameters - Matern.as

v4.0ka (08th October 2013)

  • Cumulative enhancements from internal version 4.0jy - 4.0jz
  • Extended code to permit residual diag().ar1().ar1()
  • Inserted 'Notice:' in diagnostic message
  • Fixed bug in Peppers job by moving VSOLN(EQN)=XD
  • Modified labelling of pedigree counts table.
  • Fixed bug wrt flevel(quadGF) when quadGF is zero
  • Treat MKR data outside -2,2 as missing.
  • Faster parsing of marker file values 0,1,2
  • Fixed bug in default skipping of first field of .mkr file
  • Fixed bug making file names for !out option with !RENAME cycling
  • Fixed bug when Insert Exit path when !A !L labels file not present.
  • Read error diagnostic print added
  • Added links for !EXCLUDE and !KCV
  • Added actions for !EXCLUDE
  • Added reading !EXCLUDE and !KCV qualifiers
  • Added KCV functionality
  • Added KCV and ExCLUDE variables
  • Fixed bug due to unset variable KS.

v4.0jx (08th September 2013)

  • Cumulative enhancements from internal version 4.0ju - 4.0jw
  • Fixed bug in LogL calc for NSECT>1 when NSPAT>1

    [Modifies reported LogL in dhglm, az06, binnor] [Forum query re spatial LogL]

  • Fixed bug with string overflow when parsing CALC statements (ININTR)
  • Get GLMM weights in correct order when data records sorted
  • Suppress erroneous messages parsing pedigree with !MGS option
  • Take PARENT Labels from 1st line of ped file where provided.
  • Move .msv file to logical unit 18.
  • Adjust XFA update cycling parameters.
  • Fixed bug when GLMM and !{ !} fixed.
  • Revise XFAIF to incorporate !AIPENALTY
  • Adjusted limits for pi in !FBB
  • Tidy up some labeling of VC table

    This affects most .asr files as the 'Variance' label has been changed to 'Residual'

  • Adjust model label strings
  • !MAXIT -1 aborts run after parsing job and writing .tsv
  • Added !TSV and !MSV as alternatives to !CONTINUE 2/3
  • RPscale defaults to 1.0 if supplied as zero
  • Supply better start values for US residual in !ASUV case
  • Fixed bug in processing singular VCM matrix
  • Changed reporting and reading of unset RP fields
  • Changed so !MAXIT 0 just parses the .as file, writes .tsv
  • Added !FBB pi to explore Bayes B like models
  • Changed output heading to Variance Component table affects all jobs
  • Changed output labeling of components affects SpatialModel jobs
  • Modified XFA update rules changes Factor Analytic jobs
  • Modified contents of .tsv affects all jobs
  • New .msv file for all jobs

v4.0jt (8th July 2013)

  • fixed license problem in ASReml-W

v4.0jt (2nd July 2013)

  • fixed bug reporting Boundary parameter as S
  • fixed bug reading !SPATIAL
  • fixed bug failing to properly initialize some parameters
  • fixed Test for label 1E-8
  • fixed TXTFORM wrong for multiple tabulates
  • fixed correlation close to boundary
  • fixed bug plotting residuals from AR.AR.US model
  • fixed bug parsing residual AR1(R).ar1(C).us(Tr)
  • fixed bug making predict design for dev(Year).us(Trait)

v4.0js (14th June 2013)

  • Cumulative enhancements from internal version 4.0jf - 4.0jr
  • Fixed problem when bivariate weighted used !TOT !WT
  • Fixed problem of at(Trait,2).X anulling Y for other traits when X missing
  • Added warning when CSV file has less fields than expected
  • Allowed qualifiers on idv() terms
  • Allow !PART list to extend beyond character 80
  • Honour !VARSCALE for 'residual units' and allow on model line
  • Fix bug parsing at(evt,'SFM_138)
  • Fix bug fixing ORDER parsing at(evt,'SFM_138)
  • Extend !CONTINUE 2 to read .tsv file
  • Get better default initial values for XFA models
  • Fix bug in format of MODIFY error message
  • Fix bug putting AINV structure on geno in loc.geno
  • Fix bug sorting data for spatial residual multi sections
  • !PRECISION ; adjust singularity detection threshold in GRM inversion
  • Change default init var under variance scale
  • Added !GDENSE qualifier to process GRM() densly
  • Add !OUTFOLDER qualifier to top command line
  • Fix bugs processing cholkc() wrapper function
  • Fixed bugs parsing spherical and circular models
  • Changed scatter plot to grid base when > 10000 points
  • Added Mean Axes to XYG scatter plot
  • Honour !GU after at(G,1).parc
  • Fix bug in reading G structure terms from new format .rsv file.
  • Add message when explicit V in R structure removed
  • Add !CENTRE qualifier, revise weight expression

v4.0je (29th May 2013)

  • Fixed some license problems.

v4.0jd (4th March 2013)

  • Beta release of ASReml 4.


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