R alphasimr

Author: ndyk

August undefined, 2024

WebbBreeding Programme Modelling with AlphaSimR. Breeding programmes are key to the genetic improvement of plant varieties and animal breeds used in agriculture. This … Webb9 feb. 2024 · AlphaSimR is a highly flexible software package able to simulate a wide range of plant and animal breeding programs for diploid and autopolyploid species. AlphaSimR …

R: Make designed crosses

Webbthe trait for selection. Either a number indicating a single trait or a function returning a vector of length nInd. use. select on genetic values ( gv, default), estimated breeding values ( ebv ), breeding values ( bv ), or phenotypes ( pheno) p. the proportion of individuals selected. selectTop. selects highest values if true. WebbAlphaSimR-package: AlphaSimR: Breeding Program Simulations; attrition: Lose individuals at random; bv: Breeding value; calcGCA: Calculate GCA; cChr: Combine MapPop … bridal boot camp exercise tv

GitHub - gaynorr/AlphaSimR: R package for breeding program simulatio…

WebbAlphaSimR is a highly flexible software package able to simulate a wide range of plant and animal breeding programs for diploid and autopolyploid species. AlphaSimR is ideal for testing the overall strategy and detailed design of breeding programs. WebbMethods (by generic) [: Extract Pop by index or id c(Pop): Combine multiple Pops show(Pop): Show population summary Slots id. an individual's identifier. iid. an individual's internal identifier. mother. the identifier of the individual's mother WebbAlphaSimR users do not directly observe nor set the value of the environmental covariate. Instead, they indirectly set its value by providing a randomly sampled p-value for each environment. Users should note that p-values follow a uniform distribution over the range of zero to one, so it is recommended that users randomly generate p-values using R’s … canterbury masonic charitable trust

AlphaSimR: an R package for breeding program simulations

Webblibrary(AlphaSimR) # Step 1 ---- # Load in founder haplotypes. # This requires a genetic map and phased genotypes # Load the genetic map in the below format # Format: Marker name, Chromosome, Position (in Morgans) # Modeling 10 chromosomes with 10 loci each # Loci are equally space along 1 Morgan chromosomes Webb14 jan. 2024 · To make this task easier, AlphaSimR has been designed as a package for the R software environment. AlphaSimR provides its users with functions that match common operations undertaken in a breeding program, such as crossing and selection, so that users can build simulations by writing short scripts. canterbury - marlowe theatreWebb15 mars 2024 · AlphaSimR is a package for performing stochastic simulations of plant and animal breeding programs. It is the successor to the AlphaSim software for breeding … canterbury mattress review

"WebbFieldSimR is an R package to enable simulation of plot data in field trials for multiple traits across multiple environments. ... provides wrapper functions to simulate genetic values for multiple traits across multiple environments using the R package AlphaSimR. Installation. FieldSimR is available on CRAN. To install use: install.packages ... " - R alphasimr

R alphasimr

WebbDetails on how ‘AlphaSimR’ simulates additive and non-additive biological effects can be found in the “Traits in AlphaSimR” vignette. It should be noted, however, that a simple additive genetic model will be sufficient to answer most experimental questions and may be preferred to more complex models, especially if data to tune the simulation model is … Webb31 mars 2024 · AlphaSimR-package: AlphaSimR: Breeding Program Simulations; attrition: Lose individuals at random; bv: Breeding value; calcGCA: Calculate GCA; cChr: Combine …

Did you know?

Webb20 okt. 2024 · AlphaSimR: Breeding Program Simulations. The successor to the 'AlphaSim' software for breeding program simulation [Faux et al. (2016) … WebbSimParam {AlphaSimR} R Documentation: Simulation parameters Description. Container for global simulation parameters. Saving this object as SP will allow it to be accessed by function defaults. Public fields. nThreads. number of threads used on platforms with OpenMP support. snpChips.

WebbDownload AlphaSimR is available on CRAN. To install use: install.packages ('AlphaSimR') The development version of AlphaSimR (potentially unstable) can be accessed from the … Webb31 mars 2024 · AlphaSimR-package: AlphaSimR: Breeding Program Simulations; attrition: Lose individuals at random; bv: Breeding value; calcGCA: Calculate GCA; cChr: Combine …

AlphaSimR: Breeding Program Simulations. The successor to the 'AlphaSim' software for breeding program simulation [Faux et al. (2016) ]. Used for stochastic simulations of breeding programs to the level of DNA sequence for every individual. WebbSets phenotypes for all traits by adding random error from a multivariate normal distribution.

Webb20 okt. 2024 · These functions allow for constructing simulations of highly complex plant and animal breeding programs via scripting in the R software environment. Such simulations can be used to evaluate overall breeding program performance and conduct research into breeding program design, such as implementation of genomic selection. canterbury mattressWebbThe development version of AlphaSimR (potentially unstable) can be accessed from the devel branch on GitHub. To install use: devtools::install_github … canterbury medical practice emailWebbAlphaSimR/R/AlphaSimR.R Go to file Cannot retrieve contributors at this time 30 lines (29 sloc) 1.57 KB Raw Blame #' @useDynLib AlphaSimR, .registration = TRUE #' @import Rcpp #' @importFrom methods new validObject is .hasSlot #' @importFrom methods show classLabel #' @importFrom stats aggregate rnorm qnorm var canterbury mazdaWebb7 dec. 2024 · This paper introduces AlphaSimR, an R package for stochastic simulations of plant and animal breeding programs. Stochastic simulation is a powerful tool for design … bridal boot camp lifetime movieWebb13 okt. 2024 · Last week’s post just happened to use MCMCglmm as an example of an R package that can get confused by tibble-style data frames. To make that example, I simulated some pedigree and trait data. Just for fun, let’s look at the simulation code, and use MCMCglmm and AnimalINLA to get heritability estimates. First, here is some … bridal boot camp movie onlineWebb31 mars 2024 · AlphaSimR-package: AlphaSimR: Breeding Program Simulations; attrition: Lose individuals at random; bv: Breeding value; calcGCA: Calculate GCA; cChr: Combine … canterbury medical practice ct4 5blWebbBy default, 'AlphaSimR' does not support complex models for GxE interaction. However, its functionality to simulate correlated genetic values can be utilised for this purpose by providing the required variance structures. compsym_asr_input is a wrapper function to construct the variance structures required to simulate GxE interaction in 'AlphaSimR' … canterbury medical practice doctors