Simulation and Data Analysis for Plant Breeders

Documentation for package ‘SelectionTools’ version 26.3

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A B C D E G H I L M O P R S T V W

-- A --

append.population

append.population()

-- B --

be.quiet

Switch SelectionTools output to a quiet mode

-- C --

concat.population	concat.population()
copy.population	copy.population()
cross	cross()

-- D --

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()
DT_technow	Technow Hybrid Phenotype Data

-- E --

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

-- G --

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.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.build.V	Build the genomic-selection variance or covariance matrix for a data set
gs.build.Z	gs.build.Z()
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.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.V	Return the genomic-selection variance or covariance matrix for a data set
gs.get.y	Return the genomic-selection response vector for a data set
gs.get.Z	Return the genomic-selection marker or design matrix 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

-- H --

homozygote

homozygote()

-- I --

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()

-- L --

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()

-- M --

mab.compare	Run and Compare a Series of Marker-Assisted Backcrossing Simulations
mab.df	Helper used by the marker-assisted backcross simulation routines
mab.Examples	mab.Examples
mab.Input.files	Structure of input files for the optimize-mab 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
maize.aflp	51 maize lines analyzed with 462 AFLP markers.
Md_technow	Technow Dent Marker Data
Mf_technow	Technow Flint Marker Data

-- O --

optimize.population

Optimize a population using the package selection routines

-- P --

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.init	Initialize the PLABSIM simulation state
plabsim.R.date	Perform the SelectionTools operation "plabsim R date"
plabsim.R.version	Perform the SelectionTools operation "plabsim R version"
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

-- R --

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

-- S --

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.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.NoLociInit	Set the initial number of loci used by the simulation
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.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.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.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.STvcf.to.dataframe	Convert Compact STvcf Data to a VCF-Like Data Frame
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

-- T --

talk.to.me

Enable or control SelectionTools console output

-- V --

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
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

-- W --

write.version.2

Write version information in the package-specific format