{ "_id": "6ad319302c5c76d3dd0c9795", "Package": "TDbook", "Title": "Companion Package for the Book \"Data Integration, Manipulation\nand Visualization of Phylogenetic Trees\" by Guangchuang Yu\n(2022, ISBN:9781032233574, doi:10.1201/9781003279242)", "Version": "0.0.6", "Authors@R": "c(\nperson(\"Guangchuang\", \"Yu\", email = \"guangchuangyu@gmail.com\", role = c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0002-6485-8781\")),\nperson(\"Shuangbin\", \"Xu\", email = \"xshuangbin@163.com\", role = \"aut\", comment = c(ORCID=\"0000-0003-3513-5362\")),\nperson(\"Lin\", \"Li\", email = \"williamlee2220@qq.com\", role = \"aut\", comment = c(ORCID=\"0000-0002-6522-1889\"))\n)", "Description": "The companion package that provides all the datasets used\nin the book \"Data Integration, Manipulation and Visualization\nof Phylogenetic Trees\" by Guangchuang Yu (2022,\nISBN:9781032233574, doi:10.1201/9781003279242).", "License": "Artistic-2.0", "Encoding": "UTF-8", "URL": "https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/", "BugReports": "https://github.com/YuLab-SMU/TDbook/issues", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.1", "Repository": "https://yulab-smu.r-universe.dev", "Date/Publication": "2022-09-15 03:06:28 UTC", "RemoteUrl": "https://github.com/yulab-smu/tdbook", "RemoteRef": "HEAD", "RemoteSha": "60b2de7f8df45b440c93cc17513e868ee98c1496", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-17 06:39:37 UTC", "User": "root" }, "Author": "Guangchuang Yu [aut, cre, cph] (ORCID:\n),\nShuangbin Xu [aut] (ORCID: ),\nLin Li [aut] (ORCID: )", "Maintainer": "Guangchuang Yu ", "_user": "yulab-smu", "_type": "src", "_file": "TDbook_0.0.6.tar.gz", "_fileid": "https://r2.ropensci.org/b0445aa2ebde8496854e5acc247ab7e2a46ce2713d444f411f8145597b85e703", "_filesize": 3268250, "_sha256": "b0445aa2ebde8496854e5acc247ab7e2a46ce2713d444f411f8145597b85e703", "_expires": "2027-01-25T06:43:55.000Z", "_created": "2026-10-17T06:39:37.000Z", "_published": "2026-10-17T06:44:00.334Z", "_buildurl": "https://github.com/r-universe/yulab-smu/actions/runs/39010595980", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 117332578151, "time": 133, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12093126088" }, { "job": 117332578137, "time": 130, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12092693117" }, { "job": 117332578119, "time": 67, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12092757939" }, { "job": 117332578079, "time": 87, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12092592381" }, { "job": 117332168699, "time": 134, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12093220494" }, { "job": 117332578131, "time": 68, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12092427796" }, { "job": 117332578179, "time": 83, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12092872108" }, { "job": 117332578120, "time": 60, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12091799520" }, { "job": 117332578139, "time": 58, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12092178696" } ], "_upstream": "https://github.com/yulab-smu/tdbook", "_commit": { "id": "60b2de7f8df45b440c93cc17513e868ee98c1496", "author": "Guangchuang Yu ", "committer": "Guangchuang Yu ", "message": "add doi\n", "time": 1663211188 }, "_maintainer": { "name": "Guangchuang Yu", "email": "guangchuangyu@gmail.com", "login": "guangchuangyu", "twitter": "@guangchuangyu", "description": "Professor of Bioinformatics at Southern Medical University.", "uuid": 626539, "orcid": "0000-0002-6485-8781" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" } ], "_owner": "yulab-smu", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 13, "_contributors": [ { "user": "guangchuangyu", "count": 18, "uuid": 626539 }, { "user": "xiangpin", "count": 17, "uuid": 17870644 }, { "user": "sanl20", "count": 7, "uuid": 75999371 } ], "_userbio": { "uuid": 40430016, "type": "organization", "name": "Bioinformatics Group @ SMU", "followers": 727, "description": "Research group led by Prof. Guangchuang Yu in School of Basic Medical Sciences, Southern Medical University" }, "_downloads": { "count": 421, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/TDbook" }, "_devurl": "https://github.com/yulab-smu/tdbook", "_searchresults": 97, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/readme.html", "extra/readme.md", "extra/TDbook.html" ], "_homeurl": "https://github.com/yulab-smu/tdbook", "_realowner": "yulab-smu", "_cranurl": true, "_releases": [ { "version": "0.0.3", "date": "2021-10-28" }, { "version": "0.0.4", "date": "2021-11-03" }, { "version": "0.0.5", "date": "2022-03-03" }, { "version": "0.0.6", "date": "2022-08-13" } ], "_exports": [], "_datasets": [ { "name": "AA_sequence", "title": "Data set containing multiple sequence alignment information", "object": "AA_sequence", "class": [ "AAbin" ], "fields": [], "table": false, "tojson": false }, { "name": "df_alleles", "title": "Allele table", "object": "df_alleles", "class": [ "data.frame" ], "fields": [], "rows": 386, "table": true, "tojson": true }, { "name": "df_alltax_info", "title": "Data frame containing hierarchical relationship", "object": "df_alltax_info", "class": [ "data.frame" ], "fields": [ "Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species" ], "rows": 1351, "table": true, "tojson": true }, { "name": "df_bar_data", "title": "Trait data", "object": "df_bar_data", "class": [ "data.frame" ], "fields": [ "id", "dummy_bar_value" ], "rows": 386, "table": true, "tojson": true }, { "name": "df_barplot_attr", "title": "Data set of the abundance of microbes at the body sites of greatest prevalence", "object": "df_barplot_attr", "class": [ "data.frame" ], "fields": [ "ID", "Sites", "HigherAbundance" ], "rows": 332, "table": true, "tojson": true }, { "name": "df_Candidaauris_data", "title": "Population genetics data No.1", "object": "df_Candidaauris_data", "class": [ "data.frame" ], "fields": [ "ID", "Latitude", "Longitude", "CLADE", "CLADE__colour", "COUNTRY", "COUNTRY__colour", "year", "month", "day", "FCZ", "FCZ__colour", "AMB", "AMB__colour", "MCF", "MCF__colour", "ERG11", "ERG11__colour", "FKS1", "FKS1__colour" ], "rows": 305, "table": true, "tojson": true }, { "name": "df_difftax", "title": "Data frame containing taxa and factor information and pvalue", "object": "df_difftax", "class": [ "data.frame" ], "fields": [ "f", "DIAGNOSIS", "pvalue" ], "rows": 36, "table": true, "tojson": true }, { "name": "df_info", "title": "Sampling information data set", "object": "df_info", "class": [ "data.frame" ], "fields": [ "id", "location", "name", "country", "year", "X" ], "rows": 386, "table": true, "tojson": true }, { "name": "df_inode_data", "title": "Nodedata to be mapped to tree", "object": "df_inode_data", "class": [ "data.frame" ], "fields": [ "newick_label", "vernacularName", "infoURL", "rank", "bootstrap", "posterior" ], "rows": 6, "table": true, "tojson": true }, { "name": "df_NJIDqgsS", "title": "Population genetics data No.2", "object": "df_NJIDqgsS", "class": [ "data.frame" ], "fields": [ "id", "X__latitude", "X__longitude", "country", "country__shape", "country__colour", "year", "year__shape", "year__colour", "haplotype", "haplotype__shape", "haplotype__colour" ], "rows": 1832, "table": true, "tojson": true }, { "name": "df_ring_heatmap", "title": "Data set of the abundance and types of microbes", "object": "df_ring_heatmap", "class": [ "data.frame" ], "fields": [ "ID", "Sites", "Abundance" ], "rows": 2324, "table": true, "tojson": true }, { "name": "df_svl", "title": "Data frame containing slv information", "object": "df_svl", "class": [ "data.frame" ], "fields": [ "svl" ], "rows": 100, "table": true, "tojson": true }, { "name": "df_tip_data", "title": "Tipdata to be mapped to tree", "object": "df_tip_data", "class": [ "data.frame" ], "fields": [ "Newick_label", "vernacularName", "imageURL", "imageLicense", "imageAuthor", "infoURL", "mass_in_kg", "trophic_habit", "ncbi_taxid", "rank" ], "rows": 7, "table": true, "tojson": true }, { "name": "df_tippoint", "title": "Data set of the abundance and types of microbes", "object": "df_tippoint", "class": [ "data.frame" ], "fields": [ "ID", "Phylum", "Type", "Size" ], "rows": 332, "table": true, "tojson": true }, { "name": "dna_HPV58_aln", "title": "A DNAbin class to store the aligned sequnces of species of HPV58.tree", "object": "dna_HPV58_aln", "class": [ "DNAbin" ], "fields": [], "table": false, "tojson": false }, { "name": "text_RMI_tree", "title": "Tree to display with symbolic points indicating partitioned bootstrap values", "object": "text_RMI_tree", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "tree_anole", "title": "Tree to color with continuous state transition in edges", "object": "tree_anole", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "tree_boots", "title": "Tree to be mapped to data", "object": "tree_boots", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "tree_Candidaauris", "title": "Tree No.1 to display with visualized population genetics data", "object": "tree_Candidaauris", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "tree_hmptree", "title": "Tree to display with multiple graphs for multi-dimensional data", "object": "tree_hmptree", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "tree_HPV58", "title": "Tree to display with dot and line plots of pairwise nucleotide sequence distances", "object": "tree_HPV58", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "tree_long_branch_example", "title": "Tree to display with shrunk outlier long branch", "object": "tree_long_branch_example", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "tree_nex", "title": "Tree to display with silhouettes from Phylopic", "object": "tree_nex", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "tree_NJIDqgsS", "title": "Tree No.2 to display with visualized population genetics data", "object": "tree_NJIDqgsS", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "tree_nwk", "title": "Tree to display with sampling information, SNP and Trait data", "object": "tree_nwk", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "tree_seq_nwk", "title": "Tree to display with multiple sequence alignment", "object": "tree_seq_nwk", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "tree_treenwk_30.4.19", "title": "Tree to group and highlight", "object": "tree_treenwk_30.4.19", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "data-AA_sequence", "title": "Data set containing multiple sequence alignment information", "topics": [ "AA_sequence", "data-AA_sequence" ] }, { "page": "data-df_alleles.csv", "title": "Allele table", "topics": [ "data-df_alleles.csv", "df_alleles" ] }, { "page": "data-df_alltax_info", "title": "Data frame containing hierarchical relationship", "topics": [ "data-df_alltax_info", "df_alltax_info" ] }, { "page": "data-df_bar_data", "title": "Trait data", "topics": [ "data-df_bar_data", "df_bar_data" ] }, { "page": "data-df_barplot_attr", "title": "Data set of the abundance of microbes at the body sites of greatest prevalence", "topics": [ "data-df_barplot_attr", "df_barplot_attr" ] }, { "page": "data-df_Candidaauris_data", "title": "Population genetics data No.1", "topics": [ "data-df_Candidaauris_data", "df_Candidaauris_data" ] }, { "page": "data-df_difftax", "title": "Data frame containing taxa and factor information and pvalue", "topics": [ "data-df_difftax", "df_difftax" ] }, { "page": "data-df_info", "title": "Sampling information data set", "topics": [ "data-df_info", "df_info" ] }, { "page": "data-df_inode_data", "title": "Nodedata to be mapped to tree", "topics": [ "data-df_inode_data", "df_inode_data" ] }, { "page": "data-df_NJIDqgsS", "title": "Population genetics data No.2", "topics": [ "data-df_NJIDqgsS", "df_NJIDqgsS" ] }, { "page": "data-df_ring_heatmap", "title": "Data set of the abundance and types of microbes", "topics": [ "data-df_ring_heatmap", "df_ring_heatmap" ] }, { "page": "data-df_svl", "title": "Data frame containing slv information", "topics": [ "data-df_svl", "df_svl" ] }, { "page": "data-df_tip_data", "title": "Tipdata to be mapped to tree", "topics": [ "data-df_tip_data", "df_tip_data" ] }, { "page": "data-df_tippoint", "title": "Data set of the abundance and types of microbes", "topics": [ "data-df_tippoint", "df_tippoint" ] }, { "page": "data-dna_HPV58_aln", "title": "A DNAbin class to store the aligned sequnces of species of HPV58.tree", "topics": [ "data-dna_HPV58_aln", "dna_HPV58_aln" ] }, { "page": "data-text_RMI_tree", "title": "Tree to display with symbolic points indicating partitioned bootstrap values", "topics": [ "data-text_RMI_tree", "text_RMI_tree" ] }, { "page": "data-tree_anole", "title": "Tree to color with continuous state transition in edges", "topics": [ "data-tree_anole", "tree_anole" ] }, { "page": "data-tree_boots", "title": "Tree to be mapped to data", "topics": [ "data-tree_boots", "tree_boots" ] }, { "page": "data-tree_Candidaauris", "title": "Tree No.1 to display with visualized population genetics data", "topics": [ "data-tree_Candidaauris", "tree_Candidaauris" ] }, { "page": "data-tree_hmptree", "title": "Tree to display with multiple graphs for multi-dimensional data", "topics": [ "data-tree_hmptree", "tree_hmptree" ] }, { "page": "data-tree_HPV58", "title": "Tree to display with dot and line plots of pairwise nucleotide sequence distances", "topics": [ "data-tree_HPV58", "tree_HPV58" ] }, { "page": "data-tree_long_branch_example", "title": "Tree to display with shrunk outlier long branch", "topics": [ "data-tree_long_branch_example", "tree_long_branch_example" ] }, { "page": "data-tree_nex", "title": "Tree to display with silhouettes from Phylopic", "topics": [ "data-tree_nex", "tree_nex" ] }, { "page": "data-tree_NJIDqgsS", "title": "Tree No.2 to display with visualized population genetics data", "topics": [ "data-tree_NJIDqgsS", "tree_NJIDqgsS" ] }, { "page": "data-tree_nwk", "title": "Tree to display with sampling information, SNP and Trait data", "topics": [ "data-tree_nwk", "tree_nwk" ] }, { "page": "data-tree_seq_nwk", "title": "Tree to display with multiple sequence alignment", "topics": [ "data-tree_seq_nwk", "tree_seq_nwk" ] }, { "page": "data-tree_treenwk_30.4.19", "title": "Tree to group and highlight", "topics": [ "data-tree_treenwk_30.4.19", "tree_treenwk_30.4.19" ] } ], "_readme": "https://github.com/yulab-smu/tdbook/raw/HEAD/README.md", "_rundeps": [], "_score": 5.100715086573082, "_indexed": true, "_nocasepkg": "tdbook", "_universes": [ "yulab-smu", "guangchuangyu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.0.6", "date": "2026-10-17T06:41:50.000Z", "distro": "resolute", "commit": "60b2de7f8df45b440c93cc17513e868ee98c1496", "fileid": "https://r2.ropensci.org/d7985b84f51c26773eb4c69990f0f7145c91b56e8f5e0c661c6658d78b1ffc2c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yulab-smu/actions/runs/39010595980" }, { "r": "4.6.1", "os": "linux", "version": "0.0.6", "date": "2026-10-17T06:41:53.000Z", "distro": "resolute", "commit": "60b2de7f8df45b440c93cc17513e868ee98c1496", "fileid": "https://r2.ropensci.org/cc9a5cc09268b23e7186c33d16049aa02fe192ca991feffc7be01d140e2ec14c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yulab-smu/actions/runs/39010595980" }, { "r": "4.5.3", "os": "mac", "version": "0.0.6", "date": "2026-10-17T06:43:31.000Z", "commit": "60b2de7f8df45b440c93cc17513e868ee98c1496", "fileid": "https://r2.ropensci.org/cde427f6e4ecb5d13ac8965cf0901eee9a62dec5760fcb8107b32ddd2303213d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yulab-smu/actions/runs/39010595980" }, { "r": "4.6.1", "os": "mac", "version": "0.0.6", "date": "2026-10-17T06:43:08.000Z", "commit": "60b2de7f8df45b440c93cc17513e868ee98c1496", "fileid": "https://r2.ropensci.org/2e19f96bd8ce7bf9144a66a12b45f4e80ea3bdfe6d0ad54085834ff4dd3ca177", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yulab-smu/actions/runs/39010595980" }, { "r": "4.6.0", "os": "wasm", "version": "0.0.6", "date": "2026-10-17T06:41:02.000Z", "commit": "60b2de7f8df45b440c93cc17513e868ee98c1496", "fileid": "https://r2.ropensci.org/700764110eb9208652580661bb864469c712421db40f4aff6947b2d62170f8f5", "status": "success", "buildurl": "https://github.com/r-universe/yulab-smu/actions/runs/39010595980" }, { "r": "4.7.0", "os": "win", "version": "0.0.6", "date": "2026-10-17T06:40:56.000Z", "commit": "60b2de7f8df45b440c93cc17513e868ee98c1496", "fileid": "https://r2.ropensci.org/274174880a0ea364ed8b48fa067c568f3a5c919f28f9871f58134c4595942fdb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yulab-smu/actions/runs/39010595980" }, { "r": "4.5.3", "os": "win", "version": "0.0.6", "date": "2026-10-17T06:40:39.000Z", "commit": "60b2de7f8df45b440c93cc17513e868ee98c1496", "fileid": "https://r2.ropensci.org/dd2c3be3ca29c6f471842523adfcb0608e6d451f49a01dcb2ab07511309ceda0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yulab-smu/actions/runs/39010595980" }, { "r": "4.6.1", "os": "win", "version": "0.0.6", "date": "2026-10-17T06:40:37.000Z", "commit": "60b2de7f8df45b440c93cc17513e868ee98c1496", "fileid": "https://r2.ropensci.org/a9d6790d1e93106321fc1822330f00c3c3388ef42d248b17ee95688d15273a25", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/yulab-smu/actions/runs/39010595980" } ] }