{ "_id": "6a19dba3ad7a21ec89460ea8", "Package": "MethEvolSIM", "Title": "Simulate DNA Methylation Dynamics on Different Genomic\nStructures along Genealogies", "Version": "0.3.0", "Authors@R": "c(\nperson('Sara', 'Castillo Vicente', , 'castillo@bio.lmu.de', role=c('aut', 'cre')),\nperson('Dirk', 'Metzler', , 'metzler@bio.lmu.de', role=c('aut', 'ths'))\n)", "Author": "Sara Castillo Vicente [aut, cre], Dirk Metzler [aut, ths]", "Maintainer": "Sara Castillo Vicente ", "Description": "DNA methylation is an epigenetic modification involved in\ngenomic stability, gene regulation, development and disease.\nDNA methylation occurs mainly through the addition of a methyl\ngroup to cytosines, for example to cytosines in a CpG\ndinucleotide context (CpG stands for a cytosine followed by a\nguanine). Tissue-specific methylation patterns lead to genomic\nregions with different characteristic methylation levels. E.g.\nin vertebrates CpG islands (regions with high CpG content) that\nare associated to promoter regions of expressed genes tend to\nbe unmethylated. 'MethEvolSIM' is a model-based simulation\nsoftware for the generation and modification of cytosine\nmethylation patterns along a given tree, which can be a\ngenealogy of cells within an organism, a coalescent tree of DNA\nsequences sampled from a population, or a species tree. The\nsimulations are based on an extension of the model of Grosser &\nMetzler (2020) and allows for\nchanges of the methylation states at single cytosine positions\nas well as simultaneous changes of methylation frequencies in\ngenomic structures like CpG islands.", "License": "GPL (>= 3)", "Encoding": "UTF-8", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.0.0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 18:26:54 UTC", "User": "root" }, "Repository": "https://sarisworld.r-universe.dev", "Date/Publication": "2026-05-29 15:10:02 UTC", "RemoteUrl": "https://github.com/cran/MethEvolSIM", "RemoteRef": "HEAD", "RemoteSha": "e4b141cbd0ebda0ddaa4de0ad2a96b4e8308208b", "MD5sum": "b93c0436ab6add555a022568220aff88", "_user": "sarisworld", "_type": "src", "_file": "MethEvolSIM_0.3.0.tar.gz", "_fileid": "6164d9f12ca03ad7f43b9ed8ad9540829699b4c3e3f5bfa301404d9cc71a51fc", "_filesize": 2583580, "_sha256": "6164d9f12ca03ad7f43b9ed8ad9540829699b4c3e3f5bfa301404d9cc71a51fc", "_created": "2026-05-29T18:26:54.000Z", "_published": "2026-05-29T18:32:03.490Z", "_distro": "noble", "_jobs": [ { "job": 78562324562, "time": 252, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7298160553" }, { "job": 78562324836, "time": 207, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7298145935" }, { "job": 78562324817, "time": 229, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7298142729" }, { "job": 78562324530, "time": 260, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7298150399" }, { "job": 78561663305, "time": 240, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7298075177" }, { "job": 78562324546, "time": 110, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7298112694" }, { "job": 78562324625, "time": 204, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7298144944" }, { "job": 78562324584, "time": 216, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7298148536" }, { "job": 78562324596, "time": 226, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7298151850" } ], "_buildurl": "https://github.com/r-universe/sarisworld/actions/runs/26654656709", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/MethEvolSIM", "_commit": { "id": "e4b141cbd0ebda0ddaa4de0ad2a96b4e8308208b", "author": "Sara Castillo Vicente ", "committer": "cran-robot ", "message": "version 0.3.0\n", "time": 1780067402 }, "_maintainer": { "name": "Sara Castillo Vicente", "email": "castillo@bio.lmu.de", "login": "sarisworld", "description": "", "uuid": 92255152 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "R6", "role": "Imports" }, { "package": "ape", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-22", "n": 1 } ], "_tags": [ { "name": "0.3.0", "date": "2026-05-29" } ], "_stars": 0, "_contributors": [ { "user": "sarisworld", "count": 11, "uuid": 92255152 } ], "_userbio": { "uuid": 92255152, "type": "user", "name": "sarisworld" }, "_downloads": { "count": 136, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/MethEvolSIM" }, "_searchresults": 11, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MethEvolSIM.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "sarisworld", "_cranurl": false, "_releases": [ { "version": "0.1", "date": "2024-04-18" }, { "version": "0.1.1", "date": "2024-04-30" }, { "version": "0.1.2", "date": "2024-05-24" }, { "version": "0.1.3", "date": "2024-07-20" }, { "version": "0.1.4", "date": "2024-07-30" }, { "version": "0.1.5", "date": "2024-08-16" }, { "version": "0.1.6", "date": "2024-09-09" }, { "version": "0.1.7", "date": "2024-09-22" }, { "version": "0.2", "date": "2025-03-17" }, { "version": "0.2.1", "date": "2025-04-11" }, { "version": "0.3.0", "date": "2026-05-29" } ], "_exports": [ "categorize_islandGlbSt", "categorize_siteMethSt", "compare_CherryFreqs", "compute_fitch", "compute_meanCor_i", "compute_meanCor_ni", "computeFitch_islandGlbSt", "countSites_cherryMethDiff", "freqSites_cherryMethDiff", "get_cherryDist", "get_islandMeanFreqM", "get_islandMeanFreqP", "get_islandSDFreqM", "get_islandSDFreqP", "get_meanMeth_islands", "get_nonislandMeanFreqM", "get_nonislandMeanFreqP", "get_nonislandSDFreqM", "get_nonislandSDFreqP", "get_parameterValues", "get_siteFChange_cherry", "mean_CherryFreqsChange_i", "mean_TreeFreqsChange_i", "MeanSiteFChange_cherry", "pValue_CherryFreqsChange_i", "simulate_evolData", "simulate_initialData" ], "_help": [ { "page": "categorize_islandGlbSt", "title": "Categorize Global States of CpG Islands", "topics": [ "categorize_islandGlbSt" ] }, { "page": "categorize_siteMethSt", "title": "Categorize Methylation Frequencies Based on Thresholds", "topics": [ "categorize_siteMethSt" ] }, { "page": "cftpStepGenerator", "title": "cftpStepGenerator", "topics": [ "cftpStepGenerator" ] }, { "page": "combiStructureGenerator", "title": "combiStructureGenerator", "topics": [ "combiStructureGenerator" ] }, { "page": "compare_CherryFreqs", "title": "Compare Methylation Frequencies Between Two Tips", "topics": [ "compare_CherryFreqs" ] }, { "page": "compute_fitch", "title": "Compute Fitch Parsimony for Methylation Categories", "topics": [ "compute_fitch" ] }, { "page": "compute_meanCor_i", "title": "Compute the Mean Correlation of Methylation State in Islands", "topics": [ "compute_meanCor_i" ] }, { "page": "compute_meanCor_ni", "title": "Compute the Mean Correlation of Methylation State in Non-islands", "topics": [ "compute_meanCor_ni" ] }, { "page": "computeFitch_islandGlbSt", "title": "Compute Fitch Parsimony for Global Methylation States at CpG Islands", "topics": [ "computeFitch_islandGlbSt" ] }, { "page": "count_upm", "title": "Count Methylation States", "topics": [ "count_upm" ] }, { "page": "countSites_cherryMethDiff", "title": "Count Methylation Differences Between Cherry Pairs", "topics": [ "countSites_cherryMethDiff" ] }, { "page": "freqSites_cherryMethDiff", "title": "Compute Methylation Frequency Differences Between Cherry Pairs", "topics": [ "freqSites_cherryMethDiff" ] }, { "page": "get_cherryDist", "title": "Get Cherry Pair Distances from a Phylogenetic Tree", "topics": [ "get_cherryDist" ] }, { "page": "get_islandMeanFreqM", "title": "Calculate the Mean Frequency of Methylated Sites in Islands", "topics": [ "get_islandMeanFreqM" ] }, { "page": "get_islandMeanFreqP", "title": "Calculate the Mean Frequency of Partially Methylated Sites in Islands", "topics": [ "get_islandMeanFreqP" ] }, { "page": "get_islandSDFreqM", "title": "Calculate the Mean Standard Deviation of Methylated Sites in Islands", "topics": [ "get_islandSDFreqM" ] }, { "page": "get_islandSDFreqP", "title": "Calculate the Mean Standard Deviation of Partially Methylated Sites in Islands", "topics": [ "get_islandSDFreqP" ] }, { "page": "get_meanMeth_islands", "title": "Compute the Mean Methylation of CpG Islands", "topics": [ "get_meanMeth_islands" ] }, { "page": "get_nonislandMeanFreqM", "title": "Calculate the Mean Frequency of Methylated Sites in Non-Islands", "topics": [ "get_nonislandMeanFreqM" ] }, { "page": "get_nonislandMeanFreqP", "title": "Calculate the Mean Frequency of Partially Methylated Sites in Non-Islands", "topics": [ "get_nonislandMeanFreqP" ] }, { "page": "get_nonislandSDFreqM", "title": "Calculate the Mean Standard Deviation of Methylated Sites in Non-Islands", "topics": [ "get_nonislandSDFreqM" ] }, { "page": "get_nonislandSDFreqP", "title": "Calculate the Mean Standard Deviation of Partially Methylated Sites in Non-Islands", "topics": [ "get_nonislandSDFreqP" ] }, { "page": "get_parameterValues", "title": "Get Default Parameter Values", "topics": [ "get_parameterValues" ] }, { "page": "get_siteFChange_cherry", "title": "Compute Site Frequency of Methylation Changes per Cherry", "topics": [ "get_siteFChange_cherry" ] }, { "page": "mean_CherryFreqsChange_i", "title": "Mean Number of Significant Methylation Frequency Changes per Island in Cherries", "topics": [ "mean_CherryFreqsChange_i" ] }, { "page": "mean_TreeFreqsChange_i", "title": "Mean Number of Significant Frequency Changes per Island Across all Tree Tips", "topics": [ "mean_TreeFreqsChange_i" ] }, { "page": "MeanSiteFChange_cherry", "title": "Compute the Mean Site Frequency of Methylation Changes per Cherry", "topics": [ "MeanSiteFChange_cherry" ] }, { "page": "pValue_CherryFreqsChange_i", "title": "Compute p-Values for Methylation Frequency Changes in Cherries", "topics": [ "pValue_CherryFreqsChange_i" ] }, { "page": "simulate_evolData", "title": "Simulate Data Evolution along a Tree", "topics": [ "simulate_evolData" ] }, { "page": "simulate_initialData", "title": "Simulate Initial Data", "topics": [ "simulate_initialData" ] }, { "page": "singleStructureGenerator", "title": "singleStructureGenerator", "topics": [ "singleStructureGenerator" ] }, { "page": "treeMultiRegionSimulator", "title": "treeMultiRegionSimulator", "topics": [ "treeMultiRegionSimulator" ] }, { "page": "validate_data_cherryDist", "title": "Validate Structure of Input Data for Cherry Distance Computation", "topics": [ "validate_data_cherryDist" ] }, { "page": "validate_dataAcrossTips", "title": "Validate Data Structure Across Tips", "topics": [ "validate_dataAcrossTips" ] }, { "page": "validate_structureIndices", "title": "Validate Structure Indices for Island and Non-Island Data", "topics": [ "validate_structureIndices" ] }, { "page": "validate_tree", "title": "Validate and Parse a Phylogenetic Tree", "topics": [ "validate_tree" ] } ], "_readme": "https://github.com/cran/MethEvolSIM/raw/HEAD/README.md", "_rundeps": [ "ape", "digest", "lattice", "nlme", "R6", "Rcpp" ], "_vignettes": [ { "source": "CFTP_method-vignette.Rmd", "filename": "CFTP_method-vignette.html", "title": "CFTP Method", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Use examples", "Convergence and Convergence Approximations", "Visual Examples", "Reproducibility", "Workflow Requirements", "Steps in the Workflow", "References" ], "created": "2025-03-17 07:31:17", "modified": "2025-03-17 07:31:17", "commits": 1 }, { "source": "intro-vignette.Rmd", "filename": "intro-vignette.html", "title": "Introduction to MethEvolSIM", "engine": "knitr::rmarkdown", "headings": [ "A first example", "Model parameters", "Initial methylation state distribution", "DNA methylation evolution processes", "Island-wide events (IWEs)", "Single-site events (SSEs)", "Simulation Setup", "Structural distribution of CpG sites", "Parameter values", "Simulation of DNA Methylation Data", "Simulation of Initial Data", "Exploration of Initial Data", "Simulation of Data Evolution", "References" ], "created": "2024-04-19 02:35:02", "modified": "2025-03-17 07:31:17", "commits": 4 }, { "source": "sumstats-vignette.Rmd", "filename": "sumstats-vignette.html", "title": "Summary Statistics", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Summary Statistics", "Frequency of Methylation States per Genomic Structure Type", "Global Mean", "Mean SD of Observed Frequencies per Structure Type at Tree Tips", "Mean Correlation of a Central Segment of Methylation States per Genomic Structure Type", "Comparison of tree tips", "Mean Frequency of Methylation State Changes at Single Sites per Structure Type", "Fitch Parsimony Estimate for Minimum Global Methylation State Changes at CpG Islands", "Mean Number of Significant Methylation Frequency Changes per Island and Cherry", "Mean Number of Significant Methylation Frequency Changes per Island Across All Tree Tips", "References" ], "created": "2025-03-17 07:31:17", "modified": "2025-03-17 07:31:17", "commits": 1 } ], "_score": 3.2174839442139063, "_indexed": true, "_nocasepkg": "methevolsim", "_universes": [ "sarisworld" ], "_previous": "0.2.1", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.3.0", "date": "2026-05-29T18:30:03.000Z", "distro": "noble", "commit": "e4b141cbd0ebda0ddaa4de0ad2a96b4e8308208b", "fileid": "77ec80853a9908b5f9b1b1bb0b417f41208d66d94d459cc7564867587a20ac4d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sarisworld/actions/runs/26654656709" }, { "r": "4.6.0", "os": "linux", "version": "0.3.0", "date": "2026-05-29T18:29:07.000Z", "distro": "noble", "commit": "e4b141cbd0ebda0ddaa4de0ad2a96b4e8308208b", "fileid": "19d96bc4b7b5ee28bbc12be8b2cd567c6b3a726c9fe6591ba85556576f8ddeee", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sarisworld/actions/runs/26654656709" }, { "r": "4.5.3", "os": "mac", "version": "0.3.0", "date": "2026-05-29T18:29:12.000Z", "commit": "e4b141cbd0ebda0ddaa4de0ad2a96b4e8308208b", "fileid": "382c30b130e60aba7e119a7a431c053538f135d64a91804bdd4de658f8e2c57c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sarisworld/actions/runs/26654656709" }, { "r": "4.6.0", "os": "mac", "version": "0.3.0", "date": "2026-05-29T18:29:36.000Z", "commit": "e4b141cbd0ebda0ddaa4de0ad2a96b4e8308208b", "fileid": "706cdff8518e897dda054f3629451159588268a8894c1222edd977421a09e723", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sarisworld/actions/runs/26654656709" }, { "r": "4.6.0", "os": "wasm", "version": "0.3.0", "date": "2026-05-29T18:29:09.000Z", "commit": "e4b141cbd0ebda0ddaa4de0ad2a96b4e8308208b", "fileid": "a3ed12f28d03c442242d0922a4de3df2772f72a1667561d85a48cd918ae2ca26", "status": "success", "buildurl": "https://github.com/r-universe/sarisworld/actions/runs/26654656709" }, { "r": "4.7.0", "os": "win", "version": "0.3.0", "date": "2026-05-29T18:28:27.000Z", "commit": "e4b141cbd0ebda0ddaa4de0ad2a96b4e8308208b", "fileid": "47ff311b54affc56f93c99edab7ea9f57a5c7a60b170feefd47848ac3c634b1b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sarisworld/actions/runs/26654656709" }, { "r": "4.5.3", "os": "win", "version": "0.3.0", "date": "2026-05-29T18:28:14.000Z", "commit": "e4b141cbd0ebda0ddaa4de0ad2a96b4e8308208b", "fileid": "05fc63ed1a0766f56bd7e03dfc8d2278066dcac7195709cebdaa9cea6ccde2a8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sarisworld/actions/runs/26654656709" }, { "r": "4.6.0", "os": "win", "version": "0.3.0", "date": "2026-05-29T18:28:13.000Z", "commit": "e4b141cbd0ebda0ddaa4de0ad2a96b4e8308208b", "fileid": "92b19bd07509c74c00cc3342b8bd5fbc6b3d66ad4d18dc85c723cf48582b69e8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sarisworld/actions/runs/26654656709" } ] }