| append.population() | append.population |
| Switch SelectionTools output to a quiet mode | be.quiet |
| concat.population() | concat.population |
| copy.population() | copy.population |
| cross() | cross |
| Return or inspect parameters associated with a data object | data.params |
| define.effects() | define.effects |
| define.effects.df() | define.effects.df |
| Define a genome from a linkage map and optional chromosome lengths | define.genome |
| define.map() | define.map |
| Issue information for a deprecated function or object name | deprecated |
| dh() | dh |
| divide.population() | divide.population |
| Technow Hybrid Phenotype Data | DT_technow |
| Set effect weights for all effects | effect.weight.set.all |
| Remove a stored effect map | effmap.remove |
| Remove all stored effect maps | effmap.remove.all |
| Evaluate all loci in a population | evaluate.all.loci |
| evaluate.allele() | evaluate.allele |
| Calculate or return allele frequencies for selected loci | evaluate.allele.freq |
| evaluate.allele.freq2() | evaluate.allele.freq2 |
| evaluate.allele2() | evaluate.allele2 |
| evaluate.genome() | evaluate.genome |
| evaluate.genotype() | evaluate.genotype |
| Calculate haplotype information for a pair of loci | evaluate.hap.calc |
| Calculate a haplotype statistic for a pair of loci | evaluate.hap.calc.d |
| Release or reset temporary haplotype-evaluation state | evaluate.hap.free |
| Initialize haplotype evaluation for a population | evaluate.hap.init |
| Return genotype results from the current haplotype evaluation | evaluate.hap.return.genotype |
| Return the table produced by the current haplotype evaluation | evaluate.hap.return.table |
| Evaluate haplotypes for selected loci in a population | evaluate.haplotype |
| Evaluate linkage disequilibrium for a population and genomic position | evaluate.ld |
| Evaluate selected loci in a population | evaluate.locus |
| Evaluate marker-assisted donor-parent information for populations | evaluate.mdp |
| Evaluate genetic values for simulation populations | evaluate.population |
| 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 |
| Molecular marker data for several dummy populations | gd.dummy.populations |
| gd.genetic.distance() | gd.genetic.distance |
| gd.list.irregular() | gd.list.irregular |
| gd.list.missing() | gd.list.missing |
| 51 maize lines analyzed with 462 AFLP markers. | gd.maize.aflp maize.aflp |
| RFLP data from 50 maize lines | gd.maize.lines |
| SSR data from seven maize populations | gd.maize.populations |
| Construct a matrix from genetic-distance results | gd.mk.matr |
| gd.pcoa() | gd.pcoa |
| Jasminas 44 salads analyzed with 108 AFLP markers. | gd.salad.aflp |
| gd.similarity.coefficient() | gd.similarity.coefficient |
| Split or transform marker labels used by genetic-diversity routines | gd.splitdot |
| Return status information concerning zero allele frequencies | gd.status.zero.frequencies |
| generate.effect.file() | generate.effect.file |
| generate.map.file() | generate.map.file |
| generate.population() | generate.population |
| genome.contribution() | genome.contribution |
| Return the current genome parameters | genome.parameter.get |
| Set genome parameters used by the simulation code | genome.parameter.set |
| Extract or summarize genome segments for populations | genome.segments |
| genotype.population() | genotype.population |
| get.genome.par() | get.genome.par |
| get.map() | get.map |
| Return the current marker-assisted donor-parent information | get.mdp |
| get.population() | get.population |
| Get genetic values from a simulation population | get.population.gvalue |
| Return stored information for individuals in a population | get.population.info |
| Get phenotypic values from a simulation population | get.population.pvalue |
| get.population.size() | get.population.size |
| get.score() | get.score |
| Build estimation and validation subsets from a base data set | gs.build.esvs |
| Build training and prediction subsets from a base data set | gs.build.tsps |
| Build the genomic-selection variance or covariance matrix for a data set | gs.build.V |
| gs.build.Z() | gs.build.Z |
| Check whether p-values are available for a genomic-selection data set | gs.check.pvals |
| gs.compare.effects() | gs.compare.effects |
| Evaluate Crosses by Expected Superior Progeny Value | gs.cross.eval.es |
| Evaluate Crosses by Genetic Distance | gs.cross.eval.gd |
| Evaluate crosses using genetic-distance function | gs.cross.eval.gd.fct |
| Evaluate Crosses by Maximum Marker-Effect Value | gs.cross.eval.ma |
| Evaluate Crosses by Minimum Marker-Effect Value | gs.cross.eval.mi |
| Evaluate Crosses by Expected Progeny Mean | gs.cross.eval.mu |
| Evaluate Crosses by Segregation Variance | gs.cross.eval.va |
| Return or write information for evaluated crosses | gs.cross.info |
| Return or write genetic-distance information for crosses | gs.cross.info.gd |
| gs.cross.validation() | gs.cross.validation |
| Estimate marker effects using the LSQ method | gs.esteff.lsq |
| Estimate marker effects using the RMLA method | gs.esteff.rmla |
| gs.esteff.rmlc() | gs.esteff.rmlc |
| Estimate marker effects using the RMLR method | gs.esteff.rmlr |
| gs.esteff.rmlv() | gs.esteff.rmlv |
| Estimate Marker Effects by Ridge Regression | gs.esteff.rr |
| Estimate genomic values for an estimation or prediction data set | gs.estimate.gv |
| Return the genomic-selection information matrix for a data set | gs.get.im |
| Return the genomic-selection information level for a data set | gs.get.info.level |
| Return the genomic-selection variance or covariance matrix for a data set | gs.get.V |
| Return the genomic-selection response vector for a data set | gs.get.y |
| Return the genomic-selection marker or design matrix for a data set | gs.get.Z |
| Print or handle a genomic-selection information message | gs.info |
| Estimate or set genomic-selection lambda values using the aov method | gs.lambda.aov |
| Estimate or set genomic-selection lambda values using the const method | gs.lambda.const |
| Estimate or set genomic-selection lambda values using the emstep method | gs.lambda.emstep |
| Estimate or set genomic-selection lambda values using the hsq method | gs.lambda.hsq |
| Estimate or set genomic-selection lambda values using the reg method | gs.lambda.reg |
| Estimate or set genomic-selection lambda values using the rmla method | gs.lambda.rmla |
| Estimate or set genomic-selection lambda values using the rmla.02 method | gs.lambda.rmla.02 |
| Estimate or set genomic-selection lambda values using the rmlc method | gs.lambda.rmlc |
| Estimate or set genomic-selection lambda values using the rmlr method | gs.lambda.rmlr |
| Estimate or set genomic-selection lambda values using the rmlv method | gs.lambda.rmlv |
| Estimate or set genomic-selection lambda values using the rrblup method | gs.lambda.rrblup |
| Gs mme coeff | gs.mme.coeff |
| Gs mme invcoeff | gs.mme.invcoeff |
| Gs mme restcoeff | gs.mme.restcoeff |
| Gs mme restrhs | gs.mme.restrhs |
| Build or return the right-hand side for genomic-selection mixed-model equations | gs.mme.rhs |
| Gs mme solve | gs.mme.solve |
| Build or solve transformed mixed-model equations (coeff) | gs.mmet.coeff |
| Build or solve transformed mixed-model equations (coeff.3) | gs.mmet.coeff.3 |
| Build or solve transformed mixed-model equations (rhs) | gs.mmet.rhs |
| Build or solve transformed mixed-model equations (solve) | gs.mmet.solve |
| Set or process all marker effects using the negative-effect convention | gs.neg.effall |
| gs.plot.effects() | gs.plot.effects |
| Plot the Fit of a Genomic Prediction Model | gs.plot.model.fit |
| gs.plot.validation() | gs.plot.validation |
| Set or process all marker effects using the positive-effect convention | gs.pos.effall |
| gs.predict.genotypes() | gs.predict.genotypes |
| Reset genomic-selection data and settings | gs.reset |
| Restrict marker data using the package genomic-selection interface | gs.restrict.marker.data.01 |
| gs.return.effects() | gs.return.effects |
| Return marker p-values for a genomic-selection data set | gs.return.pvals |
| Set all info levels used by the genomic-selection routines | gs.set.all.info.levels |
| Set allele codes used by the genomic-selection routines | gs.set.allele.codes |
| Set effects used by the genomic-selection routines | gs.set.effects |
| Set info level used by the genomic-selection routines | gs.set.info.level |
| Set lambda used by the genomic-selection routines | gs.set.lambda |
| Set num threads used by the genomic-selection routines | gs.set.num.threads |
| Set performance data used by the genomic-selection routines | gs.set.performance.data |
| Perform single-marker analysis for a genomic-selection data set | gs.single.marker.aov |
| Perform single-marker analysis for a genomic-selection data set | gs.single.marker.reg |
| Start or stop the genomic-selection timing helper | gs.start.timer |
| Start or stop the genomic-selection timing helper | gs.stop.timer |
| Test marker or model parameters used by genomic-selection routines | gs.test.mp |
| Test estimated marker effects using the indicated method | 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 |
| Estimate variance components for ridge-regression BLUP | gs.vc.rrblup |
| Calculate weights or statistics used by the genomic-selection ANOVA method | gs.w.aov |
| Write Marker Effects for the Simulation Backend | gs.write.pseff |
| homozygote() | homozygote |
| Construct or evaluate introgression-line libraries | 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 |
| Print or handle an information message | info |
| Emit information-level-controlled status output | info.cat |
| init.population() | init.population |
| Linkage Map for Marker-Assisted Backcrossing Examples | lib00.map1 |
| Reduced Linkage Map for Marker-Assisted Backcrossing Examples | lib00.map1a |
| Linkage Map for Three-Stage Marker-Assisted Backcrossing | lib00.map2 |
| Calculate or summarize linkage drag | linkage.drag |
| Get a linkage map used by the simulation routines | linkage.map.get |
| Load a linkage map used by the simulation routines | linkage.map.load |
| Save a linkage map used by the simulation routines | linkage.map.save |
| list.effects() | list.effects |
| list.populations | list.populations |
| load.effmap() | load.effmap |
| Load an internal effect map | load.internal.effmap |
| load.linkage.map() | load.linkage.map |
| Run and Compare a Series of Marker-Assisted Backcrossing Simulations | mab.compare |
| Helper used by the marker-assisted backcross simulation routines | mab.df |
| mab.Examples | mab.Examples |
| Structure of input files for the optimize-mab routines. | mab.Input.files |
| Loads the data of a simulation | mab.load.data |
| Helper used by the marker-assisted backcross simulation routines | mab.save.inds |
| Simulates a marker-assisted backcrossing program | mab.simulate |
| Tabulate the results of a series of simulations | mab.tabulate |
| Input Files for Marker-Assisted Backcrossing Examples | masbc.input |
| Technow Dent Marker Data | Md_technow |
| Technow Flint Marker Data | Mf_technow |
| Optimize a population using the package selection routines | optimize.population |
| Create a linkage map for phenotype or simulation use | ph.linkage.map.create |
| Generate phenotypic values for a simulation population | phenotype.population |
| Perform the SelectionTools operation "plabsim" | plabsim |
| Initialize the PLABSIM simulation state | plabsim.init |
| Perform the SelectionTools operation "plabsim R date" | plabsim.R.date |
| Perform the SelectionTools operation "plabsim R version" | plabsim.R.version |
| Perform the SelectionTools operation "plabsim version" | plabsim.version |
| Create or process a plant object in the simulation framework | plant |
| Append a copy of a simulation population | population.append |
| Concatenate Simulation Populations | population.concat |
| Copy a simulation population | population.copy |
| Divide a simulation population | population.divide |
| Check whether a simulation population exists | population.exist |
| Individual remove a population or population data | population.individual.remove |
| Return stored information for an individual | population.info.get |
| Set stored information for an individual | population.info.set |
| List a population or population data | population.list |
| Matrix load a population or population data | population.matrix.load |
| Matrix save a population or population data | population.matrix.save |
| Swap the names of two simulation populations | population.name.swap |
| Optimize storage for simulation populations | population.optimize |
| Load a population from PLABSIM-style data | population.plabsim.load |
| Save a population in PLABSIM-style format | population.plabsim.save |
| Remove a population or population data | population.remove |
| Remove all a population or population data | population.remove.all |
| Rename a simulation population | population.rename |
| Resize a population or population data | population.resize |
| Sample a simulation population | population.sample |
| Return the size and allocated capacity of a simulation population | population.size.get |
| Sort a simulation population by genetic or phenotypic value | population.sort |
| Swap simulation population names | population.swap.name |
| Transfer a population or population data | population.transfer |
| Read a Beagle-Oriented VCF into SelectionTools | read.vcf |
| remove.all.populations() | remove.all.populations |
| remove.effmaps() | remove.effmaps |
| Remove genetic and phenotypic evaluation values | remove.evaluate.population |
| Remove cached genotype information from a population | remove.genotype.population |
| Remove the linkage map from the simulation | remove.map |
| remove.population() | remove.population |
| rename.population() | rename.population |
| reset.all() | reset.all |
| Reset marker-assisted donor-parent information | reset.mdp |
| Resize a population | resize.population |
| Return or display resource information used by SelectionTools | resources |
| return.population() | return.population |
| Choose the simulation random-number generator state | rng.choose |
| Info the simulation random-number generator state | rng.info |
| Initialize the random-number generators | rng.init |
| List the simulation random-number generator state | rng.list |
| sample.population() | sample.population |
| Save a linkage map | save.linkage.map |
| Calculate a standard-deviation quantity used by the simulation code | sdev |
| Define a selection target | sel.target.define |
| Select all individuals in the best value classes | select.all.best |
| Determine the best value classes in a sorted population | select.all.best.intern |
| Select specific allele combinations from populations | select.genotypes |
| Select a fixed number of best individuals | select.n.best |
| Select the best genome segments according to the requested criterion | select.n.best.segments |
| Set crossover-frequency information | set.co.freq |
| set.eff.weight() | set.eff.weight |
| set.genome.par() | set.genome.par |
| set.info.level() | set.info.level |
| Set marker-assisted donor-parent information | set.mdp |
| Set the initial number of loci used by the simulation | set.NoLociInit |
| Set genetic selection values for a simulation population | set.population.gvalue |
| Set population information used by the simulation routines | set.population.info |
| Display a Compact Statistical Phasing Summary | show.phase |
| Create or evaluate a single cross | single.cross |
| Start or stop the simulation timing helper | sm.start.timer |
| Start or stop the simulation timing helper | sm.stop.timer |
| Split a data object according to the package-specific convention | splitdt |
| ssd.mating() | ssd.mating |
| Fit a mixed linear model | st_mixed |
| Calculate Linkage Disequilibrium from Marker Data | st.calc.ld |
| Calculate linkage disequilibrium from marker data | st.calc.ld.2 |
| Calculate the package-specific Q statistic or quantity | st.calc.q |
| Calculate recombination fractions | st.calc.rf |
| Calculate Haplotype Enrichment and Select Donor Genotypes | st.calculate.enrichment st.select.enrichment |
| Return chromosome statistics for a data set | st.chrom.stats |
| Compact a SelectionTools Marker Data Set | st.compact.data.set |
| st.copy.marker.data() | st.copy.marker.data |
| List SelectionTools Marker Data Sets | print.st.data.set.list st.data.set.list |
| Remove a SelectionTools Marker Data Set | st.data.set.remove |
| Remove All SelectionTools Marker Data Sets | st.data.set.remove.all |
| Construct a path in the SelectionTools data directory | st.datadir |
| Convert a VCF-Like Data Frame to Compact STvcf Format | st.dataframe.to.STvcf |
| Construct a path in the SelectionTools data directory | st.dd |
| Define Haplotype Blocks | st.def.hblocks |
| Randomize the Stored Phase of a Marker Data Set | st.destroy.phase |
| st.genetic.distances() | st.genetic.distances |
| Calculate genetic distances from SelectionTools marker data | st.genetic.distances.02 |
| Calculate genetic distances from SelectionTools marker data | st.genetic.distances.fct |
| Return the current SelectionTools information level | st.get.info.level |
| Return the linkage map for a SelectionTools data set | st.get.map |
| Return the configured number of computational threads | st.get.num.threads |
| Return Simulation-Population Data in SelectionTools Format | st.get.simpop |
| Return simulation-population data in SelectionTools format | st.get.simpop.perfdata |
| Return Simulation-Population Marker Data without a Linkage Map | st.get.simpop2 |
| Construct a path in the SelectionTools input directory | st.id |
| Construct a path in the SelectionTools input directory | st.indir |
| Print or handle a SelectionTools information message | st.info |
| Keep the Marker Intersection of Two SelectionTools Data Sets | st.keep.intersection.markers |
| Plot a Linkage Disequilibrium Heat Map | st.LDheatmap |
| Prepare linkage-disequilibrium information for plotting | st.LDplot.ld |
| Prepare linkage-disequilibrium information for plotting | st.LDplot.map |
| Load Performance Data from an R Data Set | st.load.performance.data |
| Load Compact STvcf Marker and Linkage-Map Data | st.load.vcf.data |
| Identify markers by effect and replace selected marker alleles in marker data | st.mark.alleles |
| Summarize a SelectionTools Marker Data Set | st.marker.data.statistics |
| Convert a SelectionTools Marker Data Set to STvcf | st.markerdata.to.STvcf |
| Fit the package multi-kernel mixed-model routine | st.mxd |
| Construct a path in the SelectionTools output directory | st.od |
| Construct a path in the SelectionTools output directory | st.outdir |
| Cohort and Reference-Assisted Phasing of Diploid Genotypes | st.phase |
| Statistical Phasing and Missing-Genotype Imputation of Diploid Marker Data | st.phase.v1 |
| Plot correlation information from SelectionTools results | st.plot.corr |
| Plot correlation information from SelectionTools results | st.plot.corr.l |
| st.plot.gene.diversity() | st.plot.gene.diversity |
| Plot Graphical Genotypes | st.plot.ggt |
| Plot Graphical Genotypes from Map and Genotype Objects | st.plot.ggt.src |
| st.read.map() | st.read.map |
| Load a marker map from a data frame or matrix | st.read.map.df |
| st.read.marker.data() | st.read.marker.data |
| Load marker data from an R data frame or matrix | st.read.marker.data.df |
| st.read.performance.data() | st.read.performance.data |
| st.recode.hbc() | st.recode.hbc |
| Recode Defined Haplotype Blocks as Marker Loci | st.recode.hil |
| Recode Marker Alleles Relative to a Reference Individual | st.recode.ref |
| Recode reference-marker information using the package-specific convention | st.recode.ref.2 |
| Reset SelectionTools data and settings | st.reset |
| st.restrict.marker.data() | st.restrict.marker.data |
| Return performance data from a SelectionTools data set | st.return.performance.data |
| Select individuals using phenotypic information | st.select.phen |
| Set haplotype-block information | st.set.hblocks |
| Set info level used by SelectionTools | st.set.info.level |
| Set matrix ops used by SelectionTools | st.set.matrix.ops |
| Set num threads used by SelectionTools | st.set.num.threads |
| Set openblas threads used by SelectionTools | st.set.openblas.threads |
| Transfer Marker Effects to the Simulation Backend | st.set.sim.ef |
| Set sim gp used by SelectionTools | st.set.sim.gp |
| Set sim mp used by SelectionTools | st.set.sim.mp |
| Transfer a Marker Population to the Simulation Backend | st.set.sim.pp |
| Initialize the Simulation Backend from a SelectionTools Data Set | st.set.simpop |
| Start or stop the SelectionTools timing helper | st.start.timer |
| Start or stop the SelectionTools timing helper | st.stop.timer |
| Convert Compact STvcf Data to a VCF-Like Data Frame | st.STvcf.to.dataframe |
| Calculate Switch Error against Known Phase | print.st.switch.error st.switch.error |
| Write linkage-map information for a SelectionTools data set | st.write.map |
| st.write.marker.data() | st.write.marker.data |
| summarize.gvalue() | summarize.gvalue |
| Swap population names | swap.population.name |
| Enable or control SelectionTools console output | talk.to.me |
| Genetic Map for Tropical Maize | v-tropmaize-map v.tropmaize.map |
| Phenotypic Data for Tropical Maize | v-tropmaize-phe v.tropmaize.phe |
| Genotype Data for Tropical Maize | v-tropmaize-pop v.tropmaize.pop |
| Compact STvcf Genotype and Genetic-Map Data for Tropical Maize | v-tropmaize-vcf v.tropmaize.vcf |
| Write SelectionTools Marker Data for Beagle | write.vcf |
| Write version information in the package-specific format | write.version.2 |
