{ "_id": "6ac8c01ede46216d5edd67a6", "Package": "simplePHENOTYPES", "Date": "2026-09-29", "Type": "Package", "Version": "2.0.0.9003", "Title": "Simulation of Pleiotropic, Linked and Epistatic Phenotypes", "Description": "The number of studies involving correlated traits and the\navailability of tools to handle this type of data has increased\nconsiderably in the last decade. With such a demand, we need\ntools for testing hypotheses related to single and multi-trait\n(correlated) phenotypes based on many genetic settings. Thus,\nwe implemented various options for simulation of pleiotropy and\nLinkage Disequilibrium under additive, dominance and epistatic\nmodels. The simulation currently takes a marker data set as an\ninput and then uses it for simulating multiple traits as\ndescribed in Fernandes and Lipka (2020)\n.", "Authors@R": "c(\nperson(\"Samuel\", \"Fernandes\", email = \"fernandessb101@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-8269-535X\")),\nperson(\"Alexander\", \"Lipka\", email = \"alipka@illinois.edu\" , role = \"aut\",\ncomment = c(ORCID = \"0000-0003-1571-8528\"))\n)", "License": "MIT + file LICENSE", "Copyright": "The package authors, except the Rust crates vendored in\nsrc/rust/vendor.tar.xz; see file inst/COPYRIGHTS for their\nauthors and licences.", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "URL": "https://github.com/samuelbfernandes/simplePHENOTYPES", "BugReports": "https://github.com/samuelbfernandes/simplePHENOTYPES/issues", "NeedsCompilation": "yes", "Config/rextendr/version": "0.5.0", "Config/testthat/edition": "3", "SystemRequirements": "Cargo (Rust's package manager), rustc >= 1.71.0, xz", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "xz-utils libclang-dev", "Repository": "https://samuelbfernandes.r-universe.dev", "Date/Publication": "2026-10-09 06:30:42 UTC", "RemoteUrl": "https://github.com/samuelbfernandes/simplephenotypes", "RemoteRef": "HEAD", "RemoteSha": "3c000630a5e566640b5eadfd429d0fcbfd5349b9", "Packaged": { "Date": "2026-10-09 09:30:07 UTC", "User": "root" }, "Author": "Samuel Fernandes [aut, cre] (ORCID:\n),\nAlexander Lipka [aut] (ORCID: )", "Maintainer": "Samuel Fernandes ", "_user": "samuelbfernandes", "_type": "src", "_file": "simplePHENOTYPES_2.0.0.9003.tar.gz", "_fileid": "https://r2.ropensci.org/3862ec8869a244c393728f2a4d83fc0a24add77a39c1c43cc61de3051bda9695", "_filesize": 4632771, "_sha256": "3862ec8869a244c393728f2a4d83fc0a24add77a39c1c43cc61de3051bda9695", "_expires": "2027-01-17T10:21:16.000Z", "_created": "2026-10-09T09:30:07.000Z", "_published": "2026-10-09T10:21:18.754Z", "_buildurl": "https://github.com/r-universe/samuelbfernandes/actions/runs/37911109043", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 113758325572, "time": 1254, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11607394693" }, { "job": 113758325550, "time": 1334, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11607598750" }, { "job": 113758325746, "time": 1209, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11608770867" }, { "job": 113758325554, "time": 1366, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11608736221" }, { "job": 113758325358, "time": 1293, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11610860036" }, { "job": 113758325211, "time": 2366, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11610140286" }, { "job": 113758325278, "time": 1099, "config": 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{ "version": "1.3.0", "date": "2021-01-20" }, { "version": "1.3.1", "date": "2026-10-05" } ], "_exports": [ "a_matrix", "additive", "additive_value", "as_numeric", "as_population", "breed_composition", "bulk", "coheritability", "combining_ability", "complex_phenotypes", "cor_ar1", "create_phenotypes", "cross", "cross_usefulness", "crossbreed", "dominance", "dosages", "double_haploid", "epistasis", "families", "filter_geno", "founders_coalescent", "g_matrix", "genetic_values", "genotypic_value", "gxe_value", "haplotypes", "heterosis", "liability_threshold", "mabc_select", "marker_select", "mate", "mating_design", "mediation_split", "n_individuals", "observe_counts", "optimum_contribution", "parentage", "pedigree", "phenotype_value", "phenotypes_long", "phenotypes_wide", "population_from_haplotypes", "population_trait", "predict_ebv", "prediction_accuracy", "progeny_test", "qtn_table", "recurrent_parent_recovery", "recurrent_selection", "sample_parents", "select_ind", "selection_methods", "selfcross", "simulate_phenotype", "simulate_transcriptome", "single_seed_descent", "synthetic_map", "template_effects", "transcriptome", "vqtl", "write_phenotypes", "write_qtn_table" ], "_datasets": [ { "name": "SNP55K_maize282_maf04", "title": "Genotypic data for 282 inbred association panel using the 55K SNP array (filtered by MAF>0.4 to reduce file size). Reference: Cook et al. 2012. Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels. Plant Physiology 158:824-834", "object": "SNP55K_maize282_maf04", "class": [ "data.frame" ], "fields": [], "rows": 10650, "table": true, "tojson": true } ], "_help": [ { "page": "sub-.Population", "title": "Subset the individuals of a Population", "topics": [ "[.Population" ] }, { "page": "a_matrix", "title": "Numerator relationship matrix from the recorded pedigree", "topics": [ "a_matrix" ] }, { "page": "additive", "title": "Add an additive variance component", "topics": [ "additive" ] }, { "page": "additive_value", "title": "Additive genetic value on a fixed, cross-generational scale", "topics": [ "additive_value" ] }, { "page": "as_numeric", "title": "Convert genotypes to numeric coding", "topics": [ "as_numeric" ] }, { "page": "as_population", "title": "Create a population of phased individuals from genotype data", "topics": [ "as_population" ] }, { "page": "breed_composition", "title": "Expected breed composition from the pedigree", "topics": [ "breed_composition" ] }, { "page": "bulk", "title": "Bulk advance", "topics": [ "bulk" ] }, { "page": "c.Population", "title": "Pool populations that share a genetic map", "topics": [ "c.Population" ] }, { "page": "coheritability", "title": "Co-heritability between traits", "topics": [ "coheritability" ] }, { "page": "combining_ability", "title": "Combining ability: GCA, SCA and testcross merit", "topics": [ "combining_ability" ] }, { "page": "complex_phenotypes", "title": "Combine single-architecture models under a common heritability", "topics": [ "complex_phenotypes" ] }, { "page": "cor_ar1", "title": "AR(1) correlation matrix", "topics": [ "cor_ar1" ] }, { "page": "create_phenotypes", "title": "Simulation of single/multiple traits under different models and genetic architectures.", "topics": [ "create_phenotypes" ] }, { "page": "cross", "title": "Cross two individuals", "topics": [ "cross" ] }, { "page": "cross_usefulness", "title": "Predict the usefulness of candidate crosses", "topics": [ "cross_usefulness" ] }, { "page": "crossbreed", "title": "Crossbreeding systems", "topics": [ "crossbreed" ] }, { "page": "dominance", "title": "Add a dominance variance component", "topics": [ "dominance" ] }, { "page": "dosages", "title": "Dosage matrix of a Population", "topics": [ "dosages" ] }, { "page": "double_haploid", "title": "Produce doubled haploids from an individual", "topics": [ "double_haploid" ] }, { "page": "epistasis", "title": "Add an epistatic variance component", "topics": [ "epistasis" ] }, { "page": "families", "title": "Family groupings from the recorded pedigree", "topics": [ "families" ] }, { "page": "filter_geno", "title": "Filter a genotype object by MAF, heterozygosity and LD", "topics": [ "filter_geno" ] }, { "page": "founders_coalescent", "title": "Founder haplotypes from a coalescent with recombination", "topics": [ "founders_coalescent" ] }, { "page": "g_matrix", "title": "Genomic relationship matrix (VanRaden 2008)", "topics": [ "g_matrix" ] }, { "page": "genetic_values", "title": "Genetic values behind the simulated phenotypes", "topics": [ "genetic_values" ] }, { "page": "genotypic_value", "title": "Total genotypic value on a fixed, cross-generational scale", "topics": [ "genotypic_value" ] }, { "page": "gxe_value", "title": "Genotype-by-environment slope on a fixed, cross-generational scale", "topics": [ "gxe_value" ] }, { "page": "haplotypes", "title": "The phased haplotypes of a population", "topics": [ "haplotypes" ] }, { "page": "heterosis", "title": "Heterosis on a frozen additive + dominance architecture", "topics": [ "heterosis" ] }, { "page": "liability_threshold", "title": "Categorical phenotypes from a liability-threshold model", "topics": [ "liability_threshold" ] }, { "page": "mabc_select", "title": "Marker-assisted backcross selection", "topics": [ "mabc_select" ] }, { "page": "marker_select", "title": "Marker-assisted selection and gene pyramiding", "topics": [ "marker_select" ] }, { "page": "mate", "title": "Execute a mating plan", "topics": [ "mate" ] }, { "page": "mating_design", "title": "Build a mating plan", "topics": [ "mating_design" ] }, { "page": "mediation_split", "title": "Genetic-mediated vs environmental split of a derived transcriptome component", "topics": [ "mediation_split" ] }, { "page": "n_individuals", "title": "Number of individuals in a Population", "topics": [ "n_individuals" ] }, { "page": "observe_counts", "title": "Draw RNA-seq counts from a simulated transcriptome", "topics": [ "observe_counts" ] }, { "page": "optimum_contribution", "title": "Optimum contribution selection", "topics": [ "optimum_contribution" ] }, { "page": "parentage", "title": "Parentage of a Population's individuals", "topics": [ "parentage" ] }, { "page": "pedigree", "title": "Pedigree selection", "topics": [ "pedigree" ] }, { "page": "phenotype_value", "title": "Phenotype on a fixed, cross-generational scale", "topics": [ "phenotype_value" ] }, { "page": "phenotypes_long", "title": "Realized phenotypes in long format", "topics": [ "phenotypes_long" ] }, { "page": "phenotypes_wide", "title": "Realized phenotypes in wide format", "topics": [ "phenotypes_wide" ] }, { "page": "plot.phenotype_sim", "title": "Diagnostic plots for a simulated phenotype", "topics": [ "plot.phenotype_sim" ] }, { "page": "population_from_haplotypes", "title": "Create a population from phased haplotypes", "topics": [ "population_from_haplotypes" ] }, { "page": "population_trait", "title": "The trait a Population carries", "topics": [ "population_trait" ] }, { "page": "predict_ebv", "title": "Predicted breeding values by BLUP with known variance components", "topics": [ "predict_ebv" ] }, { "page": "predict.transcriptome_sim", "title": "Apply a fixed transcriptome architecture to a new population", "topics": [ "predict.transcriptome_sim" ] }, { "page": "prediction_accuracy", "title": "Accuracy of predicted breeding values", "topics": [ "prediction_accuracy" ] }, { "page": "progeny_test", "title": "Progeny test: score parents by the mean of their progeny", "topics": [ "progeny_test" ] }, { "page": "qtn_table", "title": "The QTNs behind a simulation, with their effects", "topics": [ "qtn_table" ] }, { "page": "recurrent_parent_recovery", "title": "Marker-observed recovery of the recurrent-parent genome", "topics": [ "recurrent_parent_recovery" ] }, { "page": "recurrent_selection", "title": "Recurrent selection", "topics": [ "recurrent_selection" ] }, { "page": "sample_parents", "title": "Draw parents for mating in proportion to OCS contributions", "topics": [ "sample_parents" ] }, { "page": "select_ind", "title": "Select individuals from a simulated population", "topics": [ "select_ind" ] }, { "page": "selection_methods", "title": "The engine's selection operators, as a manifest", "topics": [ "selection_methods" ] }, { "page": "selfcross", "title": "Self-pollinate an individual", "topics": [ "selfcross" ] }, { "page": "simulate_phenotype", "title": "Start a phenotype simulation (v2 grammar foundation)", "topics": [ "simulate_phenotype" ] }, { "page": "simulate_transcriptome", "title": "Simulate a genetically controlled transcriptome", "topics": [ "simulate_transcriptome" ] }, { "page": "single_seed_descent", "title": "Single seed descent", "topics": [ "single_seed_descent" ] }, { "page": "synthetic_map", "title": "Build a synthetic genetic map from physical marker positions", "topics": [ "synthetic_map" ] }, { "page": "template_effects", "title": "Realized-scale additive and dominance effects of a simulation", "topics": [ "template_effects" ] }, { "page": "transcriptome", "title": "Transcriptome layer: a phenotype component driven by gene expression", "topics": [ "transcriptome" ] }, { "page": "vqtl-layer", "title": "Add a variance-QTL (vQTL) component", "topics": [ "vqtl" ] }, { "page": "write_phenotypes", "title": "Write realized phenotypes to disk", "topics": [ "write_phenotypes" ] }, { "page": "write_qtn_table", "title": "Write the QTN table of a simulation to disk", "topics": [ "write_qtn_table" ] } ], "_readme": "https://github.com/samuelbfernandes/simplephenotypes/raw/HEAD/README.md", "_rundeps": [ "data.table", "mvtnorm", "rlang" ], "_vignettes": [ { "source": "complete-reference.Rmd", "filename": "complete-reference.html", "title": "Complete reference: every option in one place", "engine": "knitr::rmarkdown", "headings": [ "1. Genotype input", "Converting from other formats", "Filtering markers with filter_geno()", "2. The genetic map", "3. The simulation grammar", "Every layer", "Layer options", "Replications and per-trait proportions", "One call instead of a pipe", "Fine control: fixed loci, phase, means, subsets", "4. Genetic architectures", "Independent", "Pleiotropy with a target genetic correlation", "Linkage disequilibrium", "Combining architectures", "5. Breeding populations", "Crossing, selfing, doubled haploids", "Recurrent selfing", "Reproducibility", "Phenotyping a pedigree", "6. Inspecting a simulation", "7. Output", "In memory", "Written to disk", "8. Transcriptome and expression-mediated phenotypes", "Simulating expression", "A phenotype from expression", "Genetic and environmental mediation", "Without genotypes", "Reusing an architecture in a new population", "Calibrating to observed expression", "RNA-seq counts", "9. 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"Residual correlation", "Not yet in the grammar" ], "created": "2026-09-10 15:39:50", "modified": "2026-10-03 04:08:17", "commits": 4 }, { "source": "simplePHENOTYPES.Rmd", "filename": "simplePHENOTYPES.html", "title": "Original implementation of create_phenotypes", "author": "simplePHENOTYPES v 1.3 (r Sys.Date())", "engine": "knitr::rmarkdown", "headings": [ "Load Sample Data set", "Single Trait", "Multiple Traits: Pleiotropy Architecture", "Multiple Traits: Partial Pleiotropy Architecture", "Multiple Traits: Spurious Pleiotropy Architecture", "Multiple Traits: Partial Pleiotropy Architecture with other useful parameters", "Using Selected Markers to be QTN", "Using Multiple Marker Data Files" ], "created": "2019-09-26 15:55:11", "modified": "2026-09-10 22:18:00", "commits": 19 }, { "source": "breeding-populations.Rmd", "filename": "breeding-populations.html", "title": "Simulating breeding populations", "author": "simplePHENOTYPES", "engine": "knitr::rmarkdown", "headings": [ "Before 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