DT_technow              Technow Hybrid Phenotype Data
Md_technow              Technow Dent Marker Data
Mf_technow              Technow Flint Marker Data
append.population       append.population()
be.quiet                Switch SelectionTools output to a quiet mode
concat.population       concat.population()
copy.population         copy.population()
cross                   cross()
data.params             Return or inspect parameters associated with a
                        data object
define.effects          define.effects()
define.effects.df       define.effects.df()
define.genome           Define a genome from a linkage map and optional
                        chromosome lengths
define.map              define.map()
deprecated              Issue information for a deprecated function or
                        object name
dh                      dh()
divide.population       divide.population()
effect.weight.set.all   Set effect weights for all effects
effmap.remove           Remove a stored effect map
effmap.remove.all       Remove all stored effect maps
evaluate.all.loci       Evaluate all loci in a population
evaluate.allele         evaluate.allele()
evaluate.allele.freq    Calculate or return allele frequencies for
                        selected loci
evaluate.allele.freq2   evaluate.allele.freq2()
evaluate.allele2        Evaluate allele information for selected loci
                        in a population
evaluate.genome         evaluate.genome()
evaluate.genotype       evaluate.genotype()
evaluate.genotype2      Evaluate genotype information for selected loci
                        in a population
evaluate.hap.calc       Calculate haplotype information for a pair of
                        loci
evaluate.hap.calc.d     Calculate a haplotype statistic for a pair of
                        loci
evaluate.hap.free       Release or reset temporary haplotype-evaluation
                        state
evaluate.hap.init       Initialize haplotype evaluation for a
                        population
evaluate.hap.return.genotype
                        Return genotype results from the current
                        haplotype evaluation
evaluate.hap.return.table
                        Return the table produced by the current
                        haplotype evaluation
evaluate.haplotype      Evaluate haplotypes for selected loci in a
                        population
evaluate.ld             Evaluate linkage disequilibrium for a
                        population and genomic position
evaluate.locus          Evaluate selected loci in a population
evaluate.mdp            Evaluate marker-assisted donor-parent
                        information for populations
evaluate.population     Evaluate genetic values for simulation
                        populations
gd.allele.frequencies   gd.allele.frequencies()
gd.allow.zero.frequencies
                        gd.allow.zero.frequencies()
gd.correct.missing      gd.correct.missing()
gd.data.parameters      gd.data.parameters()
gd.distance.similarity
                        Gd distance similarity
gd.dummy.populations    Molecular marker data for several dummy
                        populations
gd.genetic.distance     gd.genetic.distance()
gd.list.irregular       gd.list.irregular()
gd.list.missing         gd.list.missing()
gd.maize.aflp           51 maize lines analyzed with 462 AFLP markers.
gd.maize.lines          RFLP data from 50 maize lines
gd.maize.populations    SSR data from seven maize populations
gd.mk.matr              Construct a matrix from genetic-distance
                        results
gd.pcoa                 gd.pcoa()
gd.salad.aflp           Jasminas 44 salads analyzed with 108 AFLP
                        markers.
gd.similarity.coefficient
                        gd.similarity.coefficient()
gd.splitdot             Split or transform marker labels used by
                        genetic-diversity routines
gd.status.zero.frequencies
                        Return status information concerning zero
                        allele frequencies
generate.effect.file    generate.effect.file()
generate.map.file       generate.map.file()
generate.population     generate.population()
genome.contribution     genome.contribution()
genome.parameter.get    Return the current genome parameters
genome.parameter.set    Set genome parameters used by the simulation
                        code
genome.segments         Extract or summarize genome segments for
                        populations
genotype.population     genotype.population()
get.genome.par          get.genome.par()
get.map                 get.map()
get.mdp                 Return the current marker-assisted donor-parent
                        information
get.population          get.population()
get.population.gvalue   Get genetic values from a simulation population
get.population.info     Return stored information for individuals in a
                        population
get.population.pvalue   Get phenotypic values from a simulation
                        population
get.population.size     get.population.size()
get.score               get.score()
gs.build.V              Build the genomic-selection variance or
                        covariance matrix for a data set
gs.build.Z              gs.build.Z()
gs.build.esvs           Build estimation and validation subsets from a
                        base data set
gs.build.tsps           Build training and prediction subsets from a
                        base data set
gs.check.pvals          Check whether p-values are available for a
                        genomic-selection data set
gs.compare.effects      gs.compare.effects()
gs.cross.eval.es        Evaluate crosses using expected selection
                        response
gs.cross.eval.gd        Evaluate crosses using genetic distance
gs.cross.eval.gd.fct    Evaluate crosses using genetic-distance
                        function
gs.cross.eval.ma        Evaluate crosses using marker effects
gs.cross.eval.mi        Evaluate crosses using marker information
gs.cross.eval.mu        Evaluate crosses using cross mean
gs.cross.eval.va        Evaluate crosses using cross variance
gs.cross.info           Return or write information for evaluated
                        crosses
gs.cross.info.gd        Return or write genetic-distance information
                        for crosses
gs.cross.validation     gs.cross.validation()
gs.esteff.lsq           Estimate marker effects using the LSQ method
gs.esteff.rmla          Estimate marker effects using the RMLA method
gs.esteff.rmlc          gs.esteff.rmlc()
gs.esteff.rmlr          Estimate marker effects using the RMLR method
gs.esteff.rmlv          gs.esteff.rmlv()
gs.esteff.rr            Estimate marker effects using the RR method
gs.estimate.gv          Estimate genomic values for an estimation or
                        prediction data set
gs.get.V                Return the genomic-selection variance or
                        covariance matrix for a data set
gs.get.Z                Return the genomic-selection marker or design
                        matrix for a data set
gs.get.im               Return the genomic-selection information matrix
                        for a data set
gs.get.info.level       Return the genomic-selection information level
                        for a data set
gs.get.y                Return the genomic-selection response vector
                        for a data set
gs.info                 Print or handle a genomic-selection information
                        message
gs.lambda.aov           Estimate or set genomic-selection lambda values
                        using the aov method
gs.lambda.const         Estimate or set genomic-selection lambda values
                        using the const method
gs.lambda.emstep        Estimate or set genomic-selection lambda values
                        using the emstep method
gs.lambda.hsq           Estimate or set genomic-selection lambda values
                        using the hsq method
gs.lambda.reg           Estimate or set genomic-selection lambda values
                        using the reg method
gs.lambda.rmla          Estimate or set genomic-selection lambda values
                        using the rmla method
gs.lambda.rmla.02       Estimate or set genomic-selection lambda values
                        using the rmla.02 method
gs.lambda.rmlc          Estimate or set genomic-selection lambda values
                        using the rmlc method
gs.lambda.rmlr          Estimate or set genomic-selection lambda values
                        using the rmlr method
gs.lambda.rmlv          Estimate or set genomic-selection lambda values
                        using the rmlv method
gs.lambda.rrblup        Estimate or set genomic-selection lambda values
                        using the rrblup method
gs.mme.coeff            Gs mme coeff
gs.mme.invcoeff         Gs mme invcoeff
gs.mme.restcoeff        Gs mme restcoeff
gs.mme.restrhs          Gs mme restrhs
gs.mme.rhs              Build or return the right-hand side for
                        genomic-selection mixed-model equations
gs.mme.solve            Gs mme solve
gs.mmet.coeff           Build or solve transformed mixed-model
                        equations (coeff)
gs.mmet.coeff.3         Build or solve transformed mixed-model
                        equations (coeff.3)
gs.mmet.rhs             Build or solve transformed mixed-model
                        equations (rhs)
gs.mmet.solve           Build or solve transformed mixed-model
                        equations (solve)
gs.neg.effall           Set or process all marker effects using the
                        negative-effect convention
gs.plot.effects         gs.plot.effects()
gs.plot.model.fit       gs.plot.model.fit()
gs.plot.validation      gs.plot.validation()
gs.pos.effall           Set or process all marker effects using the
                        positive-effect convention
gs.predict.genotypes    gs.predict.genotypes()
gs.reset                Reset genomic-selection data and settings
gs.restrict.marker.data.01
                        Restrict marker data using the package
                        genomic-selection interface
gs.return.effects       gs.return.effects()
gs.return.pvals         Return marker p-values for a genomic-selection
                        data set
gs.set.all.info.levels
                        Set all info levels used by the
                        genomic-selection routines
gs.set.allele.codes     Set allele codes used by the genomic-selection
                        routines
gs.set.effects          Set effects used by the genomic-selection
                        routines
gs.set.info.level       Set info level used by the genomic-selection
                        routines
gs.set.lambda           Set lambda used by the genomic-selection
                        routines
gs.set.num.threads      Set num threads used by the genomic-selection
                        routines
gs.set.performance.data
                        Set performance data used by the
                        genomic-selection routines
gs.single.marker.aov    Perform single-marker analysis for a
                        genomic-selection data set
gs.single.marker.reg    Perform single-marker analysis for a
                        genomic-selection data set
gs.start.timer          Start or stop the genomic-selection timing
                        helper
gs.stop.timer           Start or stop the genomic-selection timing
                        helper
gs.test.mp              Test marker or model parameters used by
                        genomic-selection routines
gs.testeff.lsq          Test estimated marker effects using the
                        indicated method
gs.testeff.rmlc         Test estimated marker effects using the
                        indicated method
gs.testeff.rmlv         Test estimated marker effects using the
                        indicated method
gs.vc.rrblup            Estimate variance components for
                        ridge-regression BLUP
gs.w.aov                Calculate weights or statistics used by the
                        genomic-selection ANOVA method
gs.write.pseff          Write Marker Effects for the Simulation Backend
homozygote              homozygote()
il.eval.library         Construct or evaluate introgression-line
                        libraries
il.eval.lines           Construct or evaluate introgression-line
                        libraries
il.ideal.library        Construct or evaluate introgression-line
                        libraries
il.overlapping.library
                        Construct or evaluate introgression-line
                        libraries
info                    Print or handle an information message
info.cat                Emit information-level-controlled status output
init.population         init.population()
lib00.map1              Linkage Map for Marker-Assisted Backcrossing
                        Examples
lib00.map1a             Reduced Linkage Map for Marker-Assisted
                        Backcrossing Examples
lib00.map2              Linkage Map for Three-Stage Marker-Assisted
                        Backcrossing
linkage.drag            Calculate or summarize linkage drag
linkage.map.get         Get a linkage map used by the simulation
                        routines
linkage.map.load        Load a linkage map used by the simulation
                        routines
linkage.map.save        Save a linkage map used by the simulation
                        routines
list.effects            list.effects()
list.populations        list.populations
load.effmap             load.effmap()
load.internal.effmap    Load an internal effect map
load.linkage.map        load.linkage.map()
mab.Examples            mab.Examples
mab.Input.files         Structure of input files for the optimize-mab
                        routines.
mab.compare             Run and Compare a Series of Marker-Assisted
                        Backcrossing Simulations
mab.df                  Helper used by the marker-assisted backcross
                        simulation routines
mab.load.data           Loads the data of a simulation
mab.save.inds           Helper used by the marker-assisted backcross
                        simulation routines
mab.simulate            Simulates a marker-assisted backcrossing
                        program
mab.tabulate            Tabulate the results of a series of simulations
optimize.population     Optimize a population using the package
                        selection routines
ph.linkage.map.create   Create a linkage map for phenotype or
                        simulation use
phenotype.population    Generate phenotypic values for a simulation
                        population
plabsim                 Perform the SelectionTools operation "plabsim"
plabsim.R.date          Perform the SelectionTools operation "plabsim R
                        date"
plabsim.R.version       Perform the SelectionTools operation "plabsim R
                        version"
plabsim.init            Initialize the PLABSIM simulation state
plabsim.version         Perform the SelectionTools operation "plabsim
                        version"
plant                   Create or process a plant object in the
                        simulation framework
population.append       Append a copy of a simulation population
population.concat       Concatenate simulation populations
population.copy         Copy a simulation population
population.divide       Divide a simulation population
population.exist        Check whether a simulation population exists
population.individual.remove
                        Individual remove a population or population
                        data
population.info.get     Return stored information for an individual
population.info.set     Set stored information for an individual
population.list         List a population or population data
population.matrix.load
                        Matrix load a population or population data
population.matrix.save
                        Matrix save a population or population data
population.name.swap    Swap the names of two simulation populations
population.optimize     Optimize storage for simulation populations
population.plabsim.load
                        Load a population from PLABSIM-style data
population.plabsim.save
                        Save a population in PLABSIM-style format
population.remove       Remove a population or population data
population.remove.all   Remove all a population or population data
population.rename       Rename a simulation population
population.resize       Resize a population or population data
population.sample       Sample a simulation population
population.size.get     Return the size and allocated capacity of a
                        simulation population
population.sort         Sort a simulation population by genetic or
                        phenotypic value
population.swap.name    Swap simulation population names
population.transfer     Transfer a population or population data
remove.all.populations
                        remove.all.populations()
remove.effmaps          remove.effmaps()
remove.evaluate.population
                        Remove genetic and phenotypic evaluation values
remove.genotype.population
                        Remove cached genotype information from a
                        population
remove.map              Remove the linkage map from the simulation
remove.population       remove.population()
rename.population       rename.population()
reset.all               reset.all()
reset.mdp               Reset marker-assisted donor-parent information
resize.population       Resize a population
resources               Return or display resource information used by
                        SelectionTools
return.population       return.population()
rng.choose              Choose the simulation random-number generator
                        state
rng.info                Info the simulation random-number generator
                        state
rng.init                Init the simulation random-number generator
                        state
rng.list                List the simulation random-number generator
                        state
sample.population       sample.population()
save.linkage.map        Save a linkage map
sdev                    Calculate a standard-deviation quantity used by
                        the simulation code
sel.target.define       Define a selection target
select.all.best         Select all individuals in the best value
                        classes
select.all.best.intern
                        Determine the best value classes in a sorted
                        population
select.genotypes        Select specific allele combinations from
                        populations
select.n.best           Select a fixed number of best individuals
select.n.best.segments
                        Select the best genome segments according to
                        the requested criterion
set.NoLociInit          Set the initial number of loci used by the
                        simulation
set.co.freq             Set crossover-frequency information
set.eff.weight          set.eff.weight()
set.genome.par          set.genome.par()
set.info.level          set.info.level()
set.mdp                 Set marker-assisted donor-parent information
set.population.gvalue   Set genetic selection values for a simulation
                        population
set.population.info     Set population information used by the
                        simulation routines
single.cross            Create or evaluate a single cross
sm.start.timer          Start or stop the simulation timing helper
sm.stop.timer           Start or stop the simulation timing helper
splitdt                 Split a data object according to the
                        package-specific convention
ssd.mating              ssd.mating()
st.LDheatmap            Plot a Linkage Disequilibrium Heat Map
st.LDplot.ld            Prepare linkage-disequilibrium information for
                        plotting
st.LDplot.map           Prepare linkage-disequilibrium information for
                        plotting
st.STvcf.to.dataframe   Convert Compact STvcf Data to a VCF-Like Data
                        Frame
st.calc.ld              Calculate linkage disequilibrium from marker
                        data
st.calc.ld.2            Calculate linkage disequilibrium from marker
                        data
st.calc.q               Calculate the package-specific Q statistic or
                        quantity
st.calc.rf              Calculate recombination fractions
st.chrom.stats          Return chromosome statistics for a data set
st.copy.marker.data     st.copy.marker.data()
st.datadir              Construct a path in the SelectionTools data
                        directory
st.dataframe.to.STvcf   Convert a VCF-Like Data Frame to Compact STvcf
                        Format
st.dd                   Construct a path in the SelectionTools data
                        directory
st.def.hblocks          st.def.hblocks()
st.genetic.distances    st.genetic.distances()
st.genetic.distances.02
                        Calculate genetic distances from SelectionTools
                        marker data
st.genetic.distances.fct
                        Calculate genetic distances from SelectionTools
                        marker data
st.get.info.level       Return the current SelectionTools information
                        level
st.get.map              Return the linkage map for a SelectionTools
                        data set
st.get.num.threads      Return the configured number of computational
                        threads
st.get.simpop           Return Simulation-Population Data in
                        SelectionTools Format
st.get.simpop.perfdata
                        Return simulation-population data in
                        SelectionTools format
st.get.simpop2          Return Simulation-Population Marker Data
                        without a Linkage Map
st.id                   Construct a path in the SelectionTools input
                        directory
st.indir                Construct a path in the SelectionTools input
                        directory
st.info                 Print or handle a SelectionTools information
                        message
st.load.performance.data
                        Load Performance Data from an R Data Set
st.load.vcf.data        Load Compact STvcf Marker and Linkage-Map Data
st.mark.alleles         Identify markers by effect and replace selected
                        marker alleles in marker data
st.marker.data.statistics
                        st.marker.data.statistics()
st.markerdata.to.STvcf
                        Convert a SelectionTools Marker Data Set to
                        STvcf
st.mxd                  Fit the package multi-kernel mixed-model
                        routine
st.od                   Construct a path in the SelectionTools output
                        directory
st.outdir               Construct a path in the SelectionTools output
                        directory
st.plot.corr            Plot correlation information from
                        SelectionTools results
st.plot.corr.l          Plot correlation information from
                        SelectionTools results
st.plot.gene.diversity
                        st.plot.gene.diversity()
st.plot.ggt             st.plot.ggt()
st.plot.ggt.src         Create a graphical genotype plot from
                        SelectionTools source data
st.read.map             st.read.map()
st.read.marker.data     st.read.marker.data()
st.read.marker.data.df
                        Read marker data from a data frame into
                        SelectionTools
st.read.performance.data
                        st.read.performance.data()
st.recode.hbc           st.recode.hbc()
st.recode.hil           st.recode.hil()
st.recode.ref           st.recode.ref()
st.recode.ref.2         Recode reference-marker information using the
                        package-specific convention
st.reset                Reset SelectionTools data and settings
st.restrict.marker.data
                        st.restrict.marker.data()
st.return.performance.data
                        Return performance data from a SelectionTools
                        data set
st.select.phen          Select individuals using phenotypic information
st.set.hblocks          Set haplotype-block information
st.set.info.level       Set info level used by SelectionTools
st.set.matrix.ops       Set matrix ops used by SelectionTools
st.set.num.threads      Set num threads used by SelectionTools
st.set.openblas.threads
                        Set openblas threads used by SelectionTools
st.set.sim.ef           Transfer Marker Effects to the Simulation
                        Backend
st.set.sim.gp           Set sim gp used by SelectionTools
st.set.sim.mp           Set sim mp used by SelectionTools
st.set.sim.pp           Transfer a Marker Population to the Simulation
                        Backend
st.set.simpop           Initialize the Simulation Backend from a
                        SelectionTools Data Set
st.simple.ggt.plot      Create a simple graphical genotype plot
st.start.timer          Start or stop the SelectionTools timing helper
st.stop.timer           Start or stop the SelectionTools timing helper
st.write.map            Write linkage-map information for a
                        SelectionTools data set
st.write.marker.data    st.write.marker.data()
st_mixed                Fit a single-kernel mixed model using the
                        SelectionTools native implementation
summarize.gvalue        summarize.gvalue()
swap.population.name    Swap population names
talk.to.me              Enable or control SelectionTools console output
v-tropmaize-map         Genetic Map for Tropical Maize
v-tropmaize-phe         Phenotypic Data for Tropical Maize
v-tropmaize-pop         Genotype Data for Tropical Maize
v-tropmaize-vcf         Compact STvcf Genotype and Genetic-Map Data for
                        Tropical Maize
write.version.2         Write version information in the
                        package-specific format
