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             Returns or inspect parameters associated with a
                        data object
define.effects          define.effects()
define.effects.df       define.effects.df()
define.genome           Defines 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   Sets effect weights for all effects
effmap.remove           Removes a stored effect map
effmap.remove.all       Removes all stored effect maps
evaluate.all.loci       Evaluates all loci in a population
evaluate.allele         evaluate.allele()
evaluate.allele.freq    Calculates or return allele frequencies for
                        selected loci
evaluate.allele.freq2   evaluate.allele.freq2()
evaluate.allele2        evaluate.allele2()
evaluate.genome         evaluate.genome()
evaluate.genotype       evaluate.genotype()
evaluate.hap.calc       Calculates haplotype information for a pair of
                        loci
evaluate.hap.calc.d     Calculates a haplotype statistic for a pair of
                        loci
evaluate.hap.free       Releases or resets temporary
                        haplotype-evaluation state
evaluate.hap.init       Initializes haplotype evaluation for a
                        population
evaluate.hap.return.genotype
                        Returns genotype results from the current
                        haplotype evaluation
evaluate.hap.return.table
                        Returns the table produced by the current
                        haplotype evaluation
evaluate.haplotype      Evaluates haplotypes for selected loci in a
                        population
evaluate.ld             Evaluates linkage disequilibrium for a
                        population and genomic position
evaluate.locus          Evaluates selected loci in a population
evaluate.mdp            Evaluates marker-assisted donor-parent
                        information for populations
evaluate.population     Evaluates 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              Constructs 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
                        Returns 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    Returns the current genome parameters
genome.parameter.set    Sets genome parameters used by the simulation
                        code
genome.segments         Extracts or summarizes genome segments for
                        populations
genotype.population     genotype.population()
get.genome.par          get.genome.par()
get.map                 get.map()
get.mdp                 Returns the current marker-assisted
                        donor-parent information
get.population          get.population()
get.population.gvalue   Get genetic values from a simulation population
get.population.info     Returns 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              Builds the genomic-selection variance or
                        covariance matrix for a data set
gs.build.Z              gs.build.Z()
gs.build.esvs           Builds estimation and validation subsets from a
                        base data set
gs.build.tsps           Builds training and prediction subsets from a
                        base data set
gs.check.pvals          Checks whether p-values are available for a
                        genomic-selection data set
gs.compare.effects      gs.compare.effects()
gs.cross.eval.es        Evaluates Crosses by Expected Superior Progeny
                        Value
gs.cross.eval.gd        Evaluates Crosses by Genetic Distance
gs.cross.eval.gd.fct    Evaluates crosses using genetic-distance
                        function
gs.cross.eval.ma        Evaluates Crosses by Maximum Marker-Effect
                        Value
gs.cross.eval.mi        Evaluates Crosses by Minimum Marker-Effect
                        Value
gs.cross.eval.mu        Evaluates Crosses by Expected Progeny Mean
gs.cross.eval.va        Evaluates Crosses by Segregation Variance
gs.cross.info           Information for Evaluated Crosses
gs.cross.info.gd        Returns or write genetic-distance information
                        for crosses
gs.cross.validation     gs.cross.validation()
gs.esteff.lsq           Estimates marker effects using the LSQ method
gs.esteff.rmla          Estimates marker effects using the RMLA method
gs.esteff.rmlc          gs.esteff.rmlc()
gs.esteff.rmlr          Estimates marker effects using the RMLR method
gs.esteff.rmlv          gs.esteff.rmlv()
gs.esteff.rr            Estimates Marker Effects by Ridge Regression
gs.estimate.gv          Estimates genomic values for an estimation or
                        prediction data set
gs.get.V                Returns the genomic-selection variance or
                        covariance matrix for a data set
gs.get.Z                Returns the genomic-selection marker or design
                        matrix for a data set
gs.get.im               Returns the genomic-selection information
                        matrix for a data set
gs.get.info.level       Returns the genomic-selection information level
                        for a data set
gs.get.y                Returns the genomic-selection response vector
                        for a data set
gs.info                 Prints or handles a genomic-selection
                        information message
gs.lambda.aov           Estimates or sets genomic-selection lambda
                        values using the aov method
gs.lambda.const         Estimates or sets genomic-selection lambda
                        values using the const method
gs.lambda.emstep        Estimates or sets genomic-selection lambda
                        values using the emstep method
gs.lambda.hsq           Estimates or sets genomic-selection lambda
                        values using the hsq method
gs.lambda.reg           Estimates or sets genomic-selection lambda
                        values using the reg method
gs.lambda.rmla          Estimates or sets genomic-selection lambda
                        values using the rmla method
gs.lambda.rmla.02       Estimates or sets genomic-selection lambda
                        values using the rmla.02 method
gs.lambda.rmlc          Estimates or sets genomic-selection lambda
                        values using the rmlc method
gs.lambda.rmlr          Estimates or sets genomic-selection lambda
                        values using the rmlr method
gs.lambda.rmlv          Estimates or sets genomic-selection lambda
                        values using the rmlv method
gs.lambda.rrblup        Estimates or sets genomic-selection lambda
                        values using the rrblup method
gs.make.A               Constructs a genomic relationship matrix from
                        marker dosages
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              Builds or returns the right-hand side for
                        genomic-selection mixed-model equations
gs.mme.solve            Gs mme solve
gs.mmet.coeff           Builds or solves transformed mixed-model
                        equations (coeff)
gs.mmet.coeff.3         Builds or solves transformed mixed-model
                        equations (coeff.3)
gs.mmet.rhs             Builds or solves transformed mixed-model
                        equations (rhs)
gs.mmet.solve           Builds or solves transformed mixed-model
                        equations (solve)
gs.neg.effall           Sets or process all marker effects using the
                        negative-effect convention
gs.plot.effects         gs.plot.effects()
gs.plot.model.fit       Plots the Fit of a Genomic Prediction Model
gs.plot.validation      gs.plot.validation()
gs.pos.effall           Sets 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         Returns marker p-values for a genomic-selection
                        data set
gs.set.all.info.levels
                        Sets all info levels used by the
                        genomic-selection routines
gs.set.allele.codes     Sets allele codes used by the genomic-selection
                        routines
gs.set.effects          Sets effects used by the genomic-selection
                        routines
gs.set.info.level       Sets info level used by the genomic-selection
                        routines
gs.set.lambda           Sets lambda used by the genomic-selection
                        routines
gs.set.num.threads      Sets num threads used by the genomic-selection
                        routines
gs.set.performance.data
                        Sets performance data used by the
                        genomic-selection routines
gs.single.marker.aov    Performs single-marker analysis for a
                        genomic-selection data set
gs.single.marker.reg    Performs 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              Tests marker or model parameters used by
                        genomic-selection routines
gs.testeff.lsq          Tests estimated marker effects using the
                        indicated method
gs.testeff.rmlc         Tests estimated marker effects using the
                        indicated method
gs.testeff.rmlv         Tests estimated marker effects using the
                        indicated method
gs.vc.rrblup            Estimates variance components for
                        ridge-regression BLUP
gs.w.aov                Calculates weights or statistics used by the
                        genomic-selection ANOVA method
gs.write.pseff          Writes Marker Effects for the Simulation
                        Backend
homozygote              homozygote()
il.eval.library         Constructs or evaluates introgression-line
                        libraries
il.eval.lines           Constructs or evaluates introgression-line
                        libraries
il.ideal.library        Constructs or evaluates introgression-line
                        libraries
il.overlapping.library
                        Constructs or evaluates introgression-line
                        libraries
influence.st.lmm        Exact Deletion Influence and Predictive
                        Studentization
info                    Prints or handles an information message
info.cat                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            Calculates or summarize linkage drag
linkage.map.get         Get a linkage map used by the simulation
                        routines
linkage.map.load        Loads a linkage map used by the simulation
                        routines
linkage.map.save        Saves a linkage map used by the simulation
                        routines
list.effects            list.effects()
list.populations        list.populations
load.effmap             load.effmap()
load.internal.effmap    Loads 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             Runs and Compares 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
masbc.input             Input Files for Marker-Assisted Backcrossing
                        Examples
optimize.population     Optimize a population using the package
                        selection routines
ph.linkage.map.create   Creates a linkage map for phenotype or
                        simulation use
phenotype.population    Generates phenotypic values for a simulation
                        population
plabsim                 Performs the SelectionTools operation "plabsim"
plabsim.R.date          Performs the SelectionTools operation "plabsim
                        R date"
plabsim.R.version       Performs the SelectionTools operation "plabsim
                        R version"
plabsim.init            Initializes the PLABSIM simulation state
plabsim.version         Performs the SelectionTools operation "plabsim
                        version"
plant                   Creates or process a plant object in the
                        simulation framework
population.append       Appends 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        Checks whether a simulation population exists
population.individual.remove
                        Individual remove a population or population
                        data
population.info.get     Returns stored information for an individual
population.info.set     Sets 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
                        Loads a population from PLABSIM-style data
population.plabsim.save
                        Saves a population in PLABSIM-style format
population.remove       Removes a population or population data
population.remove.all   Removes all simulation populations
population.rename       Rename a simulation population
population.resize       Resize a population or population data
population.sample       Sample a simulation population
population.size.get     Returns 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
propsd                  Proportional Loss of Expected Sample Standard
                        Deviation
read.vcf                Reads a Beagle-Oriented VCF into SelectionTools
remove.all.populations
                        remove.all.populations()
remove.effmaps          remove.effmaps()
remove.evaluate.population
                        Removes genetic and phenotypic evaluation
                        values
remove.genotype.population
                        Removes cached genotype information from a
                        population
remove.map              Removes 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               Returns or display resource information used by
                        SelectionTools
return.population       return.population()
rng.choose              Chooses the simulation random-number generator
                        state
rng.info                Info the simulation random-number generator
                        state
rng.init                Initializes the random-number generators
rng.list                List the simulation random-number generator
                        state
sample.population       sample.population()
save.linkage.map        Saves a linkage map
sdev                    Calculates a standard-deviation quantity used
                        by the simulation code
sel.target.define       Defines a selection target
select.all.best         Selects all individuals in the best value
                        classes
select.all.best.intern
                        Determines the best value classes in a sorted
                        population
select.genotypes        Selects specific allele combinations from
                        populations
select.n.best           Selects a fixed number of best individuals
select.n.best.segments
                        Selects the best genome segments according to
                        the requested criterion
set.NoLociInit          Sets the initial segment capacity used by the
                        simulation
set.co.freq             Sets crossover-frequency information
set.eff.weight          set.eff.weight()
set.genome.par          set.genome.par()
set.info.level          set.info.level()
set.mdp                 Sets marker-assisted donor-parent information
set.population.gvalue   Sets genetic selection values for a simulation
                        population
set.population.info     Sets population information used by the
                        simulation routines
show.phase              Display a Compact Statistical Phasing Summary
single.cross            Creates 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            Plots 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   Converts Compact STvcf Data to a VCF-Like Data
                        Frame
st.calc.ld              Calculates Linkage Disequilibrium from Marker
                        Data
st.calc.ld.2            Calculates linkage disequilibrium from marker
                        data
st.calc.q               Calculates the package-specific Q statistic or
                        quantity
st.calc.rf              Calculates recombination fractions
st.calculate.enrichment
                        Calculates Haplotype Enrichment and Selects
                        Donor Genotypes
st.chrom.stats          Returns chromosome statistics for a data set
st.compact.data.set     Compacts a Marker Data Set and Repacks Allele
                        Storage
st.copy.marker.data     st.copy.marker.data()
st.cross.allocate       Integer Progeny Allocation to Fixed Crosses
st.cross.plan           Optimum Cross Selection with Integer Families
st.cross.plan.execute   Executes Named Families from a Cross Plan
st.data.combine         Combine Individuals from Marker Data Sets
st.data.set.list        List SelectionTools Marker Data Sets
st.data.set.remove      Removes a SelectionTools Marker Data Set
st.data.set.remove.all
                        Removes All SelectionTools Marker Data Sets
st.datadir              Constructs a path in the SelectionTools data
                        directory
st.dataframe.to.STvcf   Converts a VCF-Like Data Frame to Compact STvcf
                        Format
st.dd                   Constructs a path in the SelectionTools data
                        directory
st.def.hblocks          Defines Haplotype Blocks
st.destroy.phase        Randomizes the Stored Phase of a Marker Data
                        Set
st.detect.core          Detect a Haplotype Core Collection
st.diallel.cross        Identify Unordered Diallel Crosses
st.genetic.distances    Genetic Distances and Population Plots
st.genetic.distances.02
                        Calculates genetic distances from
                        SelectionTools marker data
st.genetic.distances.fct
                        Calculates genetic distances from
                        SelectionTools marker data
st.get.A                Constructs a genomic relationship matrix from a
                        SelectionTools data set
st.get.info.level       Returns the current SelectionTools information
                        level
st.get.map              Returns the linkage map for a SelectionTools
                        data set
st.get.num.threads      Reports the computational thread configuration
st.get.simpop           Returns Simulation-Population Data in
                        SelectionTools Format
st.get.simpop.perfdata
                        Returns simulation-population data in
                        SelectionTools format
st.get.simpop2          Returns Simulation-Population Marker Data
                        without a Linkage Map
st.gwas                 Single-Marker Association Scans with Mixed
                        Models
st.hybrid.data.set      supported Hybrid Data Sets
st.id                   Constructs a path in the SelectionTools input
                        directory
st.indir                Constructs a path in the SelectionTools input
                        directory
st.info                 Prints or handles a SelectionTools information
                        message
st.keep.intersection.markers
                        Keeps the Marker Intersection of Two
                        SelectionTools Data Sets
st.kernel.structure     Verify Kronecker structure in a relationship
                        kernel
st.lmm                  Gaussian Linear Mixed Models
st.lmm.allfit           Compares Gaussian mixed-model optimizers and
                        starting values
st.lmm.bootstrap        Bootstrap Statistics from Gaussian Linear Mixed
                        Models
st.lmm.by               Fits Independent Gaussian Models to Groups of
                        Observations
st.lmm.compare          Likelihood Comparisons and Fixed-Term Deletion
                        for Mixed Models
st.lmm.components       Components and Random-Coefficient Covariance
                        Diagnostics of a Fitted Model
st.lmm.diagnostics      Leverage and Residual Diagnostics for Gaussian
                        Mixed Models
st.lmm.model            Model Information and Updates for Gaussian
                        Mixed Models
st.lmm.profile          ML Likelihood Profiles for Gaussian Mixed
                        Models
st.lmm.refit            Refits a Retained Gaussian Model and Evaluates
                        Its Likelihood
st.lmm.simulate         Simulates Gaussian linear mixed-model responses
st.load.performance.data
                        Loads Performance Data from an R Data Set
st.load.vcf.data        Loads Compact STvcf Marker Data with an
                        Optional Linkage Map
st.lsm                  Least-squares means, contrasts and fixed-effect
                        hypotheses
st.lsm-hypotheses       Fixed-Effect Hypotheses Through st.lsm
st.mark.alleles         Identify markers by effect and replace selected
                        marker alleles in marker data
st.marker.data.statistics
                        Summarizes a SelectionTools Marker Data Set
st.markerdata.to.STvcf
                        Converts a SelectionTools Marker Data Set to
                        STvcf
st.ocs                  Optimum Parental Contributions
st.od                   Constructs a path in the SelectionTools output
                        directory
st.oma                  OMA: Optimum Mate Allocation
st.outdir               Constructs a path in the SelectionTools output
                        directory
st.phase                Cohort and Reference-Assisted Phasing of
                        Diploid Genotypes
st.plot.corr            Plots correlation information from
                        SelectionTools results
st.plot.corr.l          Plots correlation information from
                        SelectionTools results
st.plot.gene.diversity
                        st.plot.gene.diversity()
st.plot.ggt             Plots Graphical Genotypes
st.plot.ggt.src         Plots Graphical Genotypes from Map and Genotype
                        Objects
st.predict              Predict Random Effects and Combined Level Means
st.read.map             st.read.map()
st.read.map.df          Loads a marker map from a data frame or matrix
st.read.marker.data     st.read.marker.data()
st.read.marker.data.df
                        Loads marker data from an R data frame or
                        matrix
st.read.performance.data
                        st.read.performance.data()
st.recode.hbc           st.recode.hbc()
st.recode.hil           Recode Defined Haplotype Blocks as Marker Loci
st.recode.ref           Recode Marker Alleles Relative to a Reference
                        Individual
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
                        Returns performance data from a SelectionTools
                        data set
st.select.phen          Selects individuals using phenotypic
                        information
st.set.hblocks          Sets haplotype-block information
st.set.info.level       Sets info level used by SelectionTools
st.set.matrix.ops       Sets matrix ops used by SelectionTools
st.set.num.threads      Sets the computational thread budget
st.set.openblas.threads
                        Sets openblas threads used by SelectionTools
st.set.sim.ef           Transfer Marker Effects to the Simulation
                        Backend
st.set.sim.gp           Sets sim gp used by SelectionTools
st.set.sim.mp           Sets sim mp used by SelectionTools
st.set.sim.pp           Transfer a Marker Population to the Simulation
                        Backend
st.set.simpop           Initializes the Simulation Backend from a
                        SelectionTools Data Set
st.start.timer          Start or stop the SelectionTools timing helper
st.stop.timer           Start or stop the SelectionTools timing helper
st.switch.error         Calculates Switch Error against Known Phase
st.write.map            Writes linkage-map information for a
                        SelectionTools data set
st.write.marker.data    st.write.marker.data()
summarize.gvalue        summarize.gvalue()
swap.population.name    Swap population names
talk.to.me              Enables or controls SelectionTools console
                        output
v-dentmaize-vcf         STvcf Marker Data for Dent Maize Parents
v-dentmaize2-vcf        Mapped Common-Marker Data for Dent Maize
                        Parents
v-flintmaize-vcf        STvcf Marker Data for Flint Maize Parents
v-flintmaize2-vcf       Mapped Common-Marker Data for Flint Maize
                        Parents
v-hybmaize-phe          Phenotype Data for Maize Hybrids
v-hybmaize2-phe         Hybrid Phenotypes for the Mapped Maize Parental
                        Data
v-lmm-climate           Balanced Climate and Variety Experiment
v-lmm-corn              Corn Yield for a One-Sample Analysis
v-lmm-data              Datasets for Linear Mixed Models
v-lmm-fertilizer-regression
                        Fertilizer Dose and Yield for Linear Regression
v-lmm-fertilizer-replicated
                        Replicated Fertilizer Doses for a Regression
                        Lack-of-Fit Test
v-lmm-halfdiallel       Maize Half Diallel for Shared Parental GCA and
                        Cross SCA
v-lmm-iris              Iris Measurements for MANOVA
v-lmm-iris-two          Two Iris Species for Hotelling's Test
v-lmm-machines          Machine and Operator Experiment
v-lmm-mtcars            Motor Trend Car Measurements for Regression
v-lmm-rats              Rats for Partial and Sequential Regression
                        Tests
v-lmm-tomato            Tomato Plant Heights for Linear Hypotheses
v-lmm-tropmaize         Constructed Tropical Maize Complete-Block Trial
v-lmm-tropmaize-lattice
                        Tropical Maize Alpha-Lattice Trials in Five
                        Environments
v-rapeseed              Rapeseed Marker and Flowering-Time Data for the
                        GWAS Vignette
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         Compacts STvcf Genotype and Genetic-Map Data
                        for Tropical Maize
write.vcf               Writes SelectionTools Marker Data for Beagle
write.version.2         Writes version information in the
                        package-specific format
