{ "_id": "6a4987e56d67900babdf951c", "Package": "aphid", "Type": "Package", "Title": "Analysis with Profile Hidden Markov Models", "Version": "1.3.6", "Authors@R": "person(\"Shaun\", \"Wilkinson\", email = \"shaunpwilkinson@gmail.com\",\nrole = c(\"aut\", \"cre\"))", "Author": "Shaun Wilkinson [aut, cre]", "Maintainer": "Shaun Wilkinson ", "Description": "Designed for the development and application of hidden\nMarkov models and profile HMMs for biological sequence\nanalysis. Contains functions for multiple and pairwise sequence\nalignment, model construction and parameter optimization, file\nimport/export, implementation of the forward, backward and\nViterbi algorithms for conditional sequence probabilities,\ntree-based sequence weighting, and sequence simulation.\nFeatures a wide variety of potential applications including\ndatabase searching, gene-finding and annotation, phylogenetic\nanalysis and sequence classification. Based on the models and\nalgorithms described in Durbin et al (1998, ISBN:\n9780521629713).", "License": "GPL-3", "URL": "https://github.com/shaunpwilkinson/aphid", "BugReports": "https://github.com/shaunpwilkinson/aphid/issues", "LazyData": "TRUE", "Encoding": "UTF-8", "SystemRequirements": "GNU make", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.1", "Config/pak/sysreqs": "make libjpeg-dev libssl-dev", "Repository": "https://phylotastic.r-universe.dev", "Date/Publication": "2026-01-23 02:04:50 UTC", "RemoteUrl": "https://github.com/shaunpwilkinson/aphid", "RemoteRef": "HEAD", "RemoteSha": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-22 07:22:07 UTC", "User": "root" }, "_user": "phylotastic", "_type": "src", "_file": "aphid_1.3.6.tar.gz", "_fileid": "https://r2.ropensci.org/7052502bd8e40bb66763d75169858e846298a96df6d6d95f40467b9290f6425c", "_filesize": 606636, "_sha256": "7052502bd8e40bb66763d75169858e846298a96df6d6d95f40467b9290f6425c", "_expires": "2026-10-12T22:23:31.000Z", "_created": "2026-06-22T07:22:07.000Z", "_published": "2026-07-04T22:23:33.204Z", "_jobs": [ { "job": 85171882889, "time": 159, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7785690325" }, { "job": 85171883036, "time": 155, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7785687627" }, { "job": 85171883051, "time": 201, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7785703237" }, { "job": 85171883083, "time": 165, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7785691127" }, { "job": 85171883102, "time": 140, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7785682666" }, { "job": 85171882894, "time": 190, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7785699693" }, { "job": 85171882997, "time": 144, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7785684314" }, { "job": 85171882897, "time": 194, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7785700324" }, { "job": 85171882915, "time": 217, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7785637829" }, { "job": 85171883091, "time": 115, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7785675242" }, { "job": 85171882820, "time": 151, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7785686882" }, { "job": 85171882893, "time": 130, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7785680143" }, { "job": 85171883026, "time": 155, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7785688003" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/phylotastic/actions/runs/27936208744", "_status": "success", "_upstream": "https://github.com/shaunpwilkinson/aphid", "_commit": { "id": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873", "author": "Shaun Wilkinson ", "committer": "GitHub ", "message": "Delete aphid.Rproj", "time": 1769133890 }, "_maintainer": { "name": "Shaun Wilkinson", "email": "shaunpwilkinson@gmail.com", "login": "shaunpwilkinson", "description": "Managing Director at Wilderlab", "uuid": 10361217 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "graphics", "role": "Imports" }, { "package": "openssl", "role": "Imports" }, { "package": "kmer", "version": ">= 1.0.0", "role": "Imports" }, { "package": "qpdf", "role": "Imports" }, { "package": "Rcpp", "version": ">= 0.12.5", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "ape", "version": ">= 4.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "shaunpwilkinson", "_selfowned": false, "_usedby": 3, "_updates": [ { "week": "2026-03", "n": 2 }, { "week": "2026-04", "n": 6 } ], "_tags": [], "_stars": 22, "_contributors": [ { "user": "shaunpwilkinson", "count": 216, "uuid": 10361217 } ], "_userbio": { "uuid": 1652822, "type": "organization", "name": "phylotastic", "followers": 5 }, "_downloads": { "count": 500, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/aphid" }, "_devurl": "https://github.com/shaunpwilkinson/aphid", "_searchresults": 50, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/aphid.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/shaunpwilkinson/aphid", "_realowner": "shaunpwilkinson", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2017-06-24" }, { "version": "1.0.1", "date": "2017-07-07" }, { "version": "1.1.0", "date": "2018-03-16" }, { "version": "1.2.0", "date": "2018-08-14" }, { "version": "1.3.0", "date": "2018-10-09" }, { "version": "1.3.1", "date": "2018-11-10" }, { "version": "1.3.2", "date": "2019-03-15" }, { "version": "1.3.3", "date": "2019-05-08" }, { "version": "1.3.5", "date": "2022-12-05" }, { "version": "1.3.6", "date": "2026-01-23" } ], "_exports": [ "align", "align.AAbin", "align.default", "align.DNAbin", "align.list", "backward", "backward.HMM", "backward.PHMM", "deriveHMM", "derivePHMM", "derivePHMM.AAbin", "derivePHMM.default", "derivePHMM.DNAbin", "derivePHMM.list", "forward", "forward.HMM", "forward.PHMM", "generate", "generate.HMM", "generate.PHMM", "logsum", "map", "plot.HMM", "plot.PHMM", "posterior", "posterior.HMM", "posterior.PHMM", "print.DPA", "print.HMM", "print.PHMM", "readPHMM", "train", "train.HMM", "train.PHMM", "unalign", "Viterbi", "Viterbi.default", "Viterbi.HMM", "Viterbi.PHMM", "weight", "weight.AAbin", "weight.default", "weight.dendrogram", "weight.DNAbin", "weight.list", "writePHMM" ], "_datasets": [ { "name": "casino", "title": "Dishonest casino.", "object": "casino", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "globins", "title": "Globin protein alignment.", "object": "globins", "class": [ "matrix", "array" ], "fields": {}, "rows": 7, "table": true, "tojson": true }, { "name": "substitution", "title": "Substitution matrices.", "object": "substitution", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "align", "title": "Multiple sequence alignment in R.", "topics": [ "align", "align.AAbin", "align.default", "align.DNAbin", "align.list" ] }, { "page": "aphid", "title": "The 'aphid' package for analysis with profile hidden Markov models.", "topics": [ "aphid-package", "aphid" ] }, { "page": "backward", "title": "The backward algorithm.", "topics": [ "backward", "backward.HMM", "backward.PHMM" ] }, { "page": "casino", "title": "Dishonest casino.", "topics": [ "casino" ] }, { "page": "deriveHMM", "title": "Derive a standard hidden Markov model from a set of sequences.", "topics": [ "deriveHMM" ] }, { "page": "derivePHMM", "title": "Derive a profile hidden Markov model from sequences.", "topics": [ "derivePHMM", "derivePHMM.AAbin", "derivePHMM.default", "derivePHMM.DNAbin", "derivePHMM.list" ] }, { "page": "forward", "title": "The forward algorithm.", "topics": [ "forward", "forward.HMM", "forward.PHMM" ] }, { "page": "generate", "title": "Generate random sequences from a model.", "topics": [ "generate", "generate.HMM", "generate.PHMM" ] }, { "page": "globins", "title": "Globin protein alignment.", "topics": [ "globins" ] }, { "page": "logsum", "title": "Sum of logged probabilities.", "topics": [ "logsum" ] }, { "page": "map", "title": "Optimized profile HMM construction.", "topics": [ "map" ] }, { "page": "plot.HMM", "title": "Plot standard hidden Markov models.", "topics": [ "plot.HMM" ] }, { "page": "plot.PHMM", "title": "Plot profile hidden Markov models.", "topics": [ "plot.PHMM" ] }, { "page": "posterior", "title": "Posterior decoding.", "topics": [ "posterior", "posterior.HMM", "posterior.PHMM" ] }, { "page": "print", "title": "Print summary methods.", "topics": [ "print", "print.DPA", "print.HMM", "print.PHMM" ] }, { "page": "readPHMM", "title": "Import profile hidden Markov models into R.", "topics": [ "readPHMM" ] }, { "page": "substitution", "title": "Substitution matrices.", "topics": [ "substitution" ] }, { "page": "train", "title": "Iterative model refinement.", "topics": [ "train", "train.HMM", "train.PHMM" ] }, { "page": "unalign", "title": "Deconstruct an alignment.", "topics": [ "unalign" ] }, { "page": "Viterbi", "title": "The Viterbi algorithm.", "topics": [ "Viterbi", "Viterbi.default", "Viterbi.HMM", "Viterbi.PHMM" ] }, { "page": "weight", "title": "Sequence weighting.", "topics": [ "weight", "weight.AAbin", "weight.default", "weight.dendrogram", "weight.DNAbin", "weight.list" ] }, { "page": "writePHMM", "title": "Export profile hidden Markov models as text.", "topics": [ "writePHMM" ] } ], "_readme": "https://github.com/shaunpwilkinson/aphid/raw/HEAD/README.md", "_rundeps": [ "ape", "askpass", "curl", "digest", "kmer", "lattice", "nlme", "openssl", "phylogram", "qpdf", "Rcpp", "sys" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "aphid-vignette.Rmd", "filename": "aphid-vignette.html", "title": "The 'aphid' package for analysis with profile hidden Markov models", "author": "Shaun Wilkinson", "engine": "knitr::rmarkdown", "headings": [ "Abstract", "Introduction", "The 'aphid' package", "Hidden Markov Models", "Deriving HMMs from sequence data", "Profile Hidden Markov Models", "File I/O", "Sequence Simulation", "Model Training", "Sequence Alignment", "Further Reading", "Acknowledgements", "References" ], "created": "2017-03-21 07:11:42", "modified": "2026-01-22 08:11:53", "commits": 15 } ], "_score": 6.99563519459755, "_indexed": false, "_nocasepkg": "aphid", "_universes": [ "phylotastic" ], "_indexurl": "https://shaunpwilkinson.r-universe.dev/aphid", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3.6", "date": "2026-06-22T07:24:41.000Z", "distro": "noble", "arch": "aarch64", "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873", "fileid": "https://r2.ropensci.org/48432758647e5127fe2bd36f103053160dc4c1a5b3573e11d00aa3612e93c9a0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/27936208744" }, { "r": "4.7.0", "os": "linux", "version": "1.3.6", "date": "2026-06-22T07:24:31.000Z", "distro": "noble", "arch": "x86_64", "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873", "fileid": "https://r2.ropensci.org/2715c2c8fdae2017e473af258e093e0ae215ed789fce8b72b0d521f12ea45a95", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/27936208744" }, { "r": "4.6.0", "os": "linux", "version": "1.3.6", "date": "2026-06-22T07:25:21.000Z", "distro": "noble", "arch": "aarch64", "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873", "fileid": "https://r2.ropensci.org/e8f3f6484a9634329fa8b5084514cd5697c25f8b810cd14971bf548fbe76f67f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/27936208744" }, { "r": "4.6.0", "os": "linux", "version": "1.3.6", "date": "2026-06-22T07:24:39.000Z", "distro": "noble", "arch": "x86_64", "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873", "fileid": "https://r2.ropensci.org/5b19f834de16114f94ee053f83e03ed4fa8a5c8c57542e110bb4aa500871f0bd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/27936208744" }, { "r": "4.5.3", "os": "mac", "version": "1.3.6", "date": "2026-06-22T07:24:16.000Z", "arch": "aarch64", "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873", "fileid": "https://r2.ropensci.org/d82fed1404103a06c07b836557d19067f8c68d1ca8587ec832ce6649be259e02", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/27936208744" }, { "r": "4.5.3", "os": "mac", "version": "1.3.6", "date": "2026-06-22T07:24:51.000Z", "arch": "x86_64", "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873", "fileid": "https://r2.ropensci.org/df74d641d110ce1919343abd04eb9955ff5b5983989fcfd2fc0ec0a5abcd2b5a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/27936208744" }, { "r": "4.6.0", "os": "mac", "version": "1.3.6", "date": "2026-06-22T07:24:14.000Z", "arch": "aarch64", "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873", "fileid": "https://r2.ropensci.org/ea4c79e63292247519d7ae07bfc89e5b8f8373572afd4d30f8b73cd1ae46719a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/27936208744" }, { "r": "4.6.0", "os": "mac", "version": "1.3.6", "date": "2026-06-22T07:24:51.000Z", "arch": "x86_64", "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873", "fileid": "https://r2.ropensci.org/20f02aa8d563cd47366da9d1e2a0f6a13ddcfab325252460a4257f5d47195395", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/27936208744" }, { "r": "4.6.0", "os": "wasm", "version": "1.3.6", "date": "2026-06-22T07:24:30.000Z", "arch": "emscripten", "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873", "fileid": "https://r2.ropensci.org/86a785d510b89f8bd223309dbfab3f32b17da8aef6b7d54c73e1bea8c3e6f6ce", "status": "success", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/27936208744" }, { "r": "4.7.0", "os": "win", "version": "1.3.6", "date": "2026-06-22T07:23:53.000Z", "arch": "x86_64", "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873", "fileid": "https://r2.ropensci.org/10937bb6cb3e8af2be98edc70365dbfd55d6b3b113ba338fc87d1ac98e7fa788", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/27936208744" }, { "r": "4.5.3", "os": "win", "version": "1.3.6", "date": "2026-06-22T07:23:39.000Z", "arch": "x86_64", "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873", "fileid": "https://r2.ropensci.org/28290bc84519101ba2a1608852d88588bb6db9c30469950c21053b58414d4a10", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/27936208744" }, { "r": "4.6.0", "os": "win", "version": "1.3.6", "date": "2026-06-22T07:23:56.000Z", "arch": "x86_64", "commit": "cd00a45ea36d9b26c02e68a33ffa7f5831aef873", "fileid": "https://r2.ropensci.org/870adec206253515ab28ce871525f31188b1bdb727593ce223941a17ea362560", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/27936208744" } ] }