{ "_id": "6a227703cd65a98ecbd4b283", "Date": "2025-09-13", "Package": "chem16S", "Version": "1.2.0-6", "Title": "Chemical Metrics for Microbial Communities", "Authors@R": "c(\nperson(\"Jeffrey\", \"Dick\", , \"j3ffdick@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-0687-5890\"))\n)", "Author": "Jeffrey Dick [aut, cre] (0000-0002-0687-5890)", "Maintainer": "Jeffrey Dick ", "Description": "Combines taxonomic classifications of high-throughput 16S\nrRNA gene sequences with reference proteomes of archaeal and\nbacterial taxa to generate amino acid compositions of community\nreference proteomes. Calculates chemical metrics including\ncarbon oxidation state ('Zc'), stoichiometric oxidation and\nhydration state ('nO2' and 'nH2O'), H/C, N/C, O/C, and S/C\nratios, grand average of hydropathicity ('GRAVY'), isoelectric\npoint ('pI'), protein length, and average molecular weight of\namino acid residues. Uses precomputed reference proteomes for\narchaea and bacteria derived from the Genome Taxonomy Database\n('GTDB'). Also includes reference proteomes derived from the\nNCBI Reference Sequence ('RefSeq') database and manual mapping\nfrom the 'RDP Classifier' training set to 'RefSeq' taxonomy as\ndescribed by Dick and Tan (2023)\n. Processes taxonomic\nclassifications in 'RDP Classifier' format or OTU tables in\n'phyloseq-class' objects from the Bioconductor package\n'phyloseq'.", "Encoding": "UTF-8", "License": "GPL-3", "VignetteBuilder": "knitr", "URL": "https://github.com/jedick/chem16S", "Config/pak/sysreqs": "libglpk-dev libicu-dev libxml2-dev zlib1g-dev", "Repository": "https://jedick.r-universe.dev", "Date/Publication": "2025-09-13 10:43:42 UTC", "RemoteUrl": "https://github.com/jedick/chem16S", "RemoteRef": "HEAD", "RemoteSha": "df51f65f63e3cd091bcc55db25ca93dc4e1afc9e", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-05 07:09:00 UTC", "User": "root" }, "MD5sum": "a0e257cd663ac8399ebfd6bc713581c6", "_user": "jedick", "_type": "src", "_file": "chem16S_1.2.0-6.tar.gz", "_fileid": "7445d29c2290567045b769678731287b6d169f4fd0eed01a71af64f97f97c780", "_filesize": 4600360, "_sha256": "7445d29c2290567045b769678731287b6d169f4fd0eed01a71af64f97f97c780", "_created": "2026-06-05T07:09:00.000Z", "_published": "2026-06-05T07:13:07.879Z", "_distro": "noble", "_jobs": [ { "job": 79680969428, "time": 202, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7430869251" }, { "job": 79680969347, "time": 173, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7430861685" }, { "job": 79680969375, "time": 154, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7430856519" }, { "job": 79680969367, "time": 176, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7430862550" }, { "job": 79680425757, "time": 258, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7430815690" }, { "job": 79680969342, "time": 128, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7430849510" }, { "job": 79680969369, "time": 154, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7430856870" }, { "job": 79680969397, "time": 142, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7430853846" }, { "job": 79680969346, "time": 154, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7430856586" } ], "_buildurl": "https://github.com/r-universe/jedick/actions/runs/27000742094", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/jedick/chem16S", "_commit": { "id": "df51f65f63e3cd091bcc55db25ca93dc4e1afc9e", "author": "jedick ", "committer": "jedick ", "message": "Fix tests for ggplot2 4.0.0\n", "time": 1757760222 }, "_maintainer": { "name": "Jeffrey Dick", "email": "j3ffdick@gmail.com", "login": "jedick", "linkedin": "in/jeffrey-m-dick", "description": "Research data scientist | Genomics | Geochemistry | R - Python - NLP - GenAI", "uuid": 12667794, "orcid": "0000-0002-0687-5890" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "plyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "phyloseq", "role": "Imports" }, { "package": "canprot", "version": ">= 2.0.0", "role": "Imports" }, { "package": "tinytest", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "patchwork", "role": "Suggests" }, { "package": "ggpmisc", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "jedick", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-37", "n": 2 } ], "_tags": [], "_topics": [ "16s-rrna", "carbon-oxidation-state", "chemical-metrics", "genomic-adaptation", "microbial-communities" ], "_stars": 4, "_contributors": [ { "user": "jedick", "count": 117, "uuid": 12667794 } ], "_userbio": { "uuid": 12667794, "type": "user", "name": "Jeffrey Dick", "description": "Research data scientist | Genomics | Geochemistry | R - Python - NLP - GenAI" }, "_downloads": { "count": 184, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/chem16S" }, "_devurl": "https://github.com/jedick/chem16s", "_rbuild": "4.6.0", "_assets": [ "extra/chem16S.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/jedick/chem16s", "_realowner": "jedick", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2023-07-17" }, { "version": "1.1.0", "date": "2024-07-01" }, { "version": "1.2.0", "date": "2025-01-17" } ], "_exports": [ "chemlab", "get_metadata", "get_metric_byrank", "get_metrics", "map_taxa", "plot_metrics", "plot_ps_metrics", "plot_ps_metrics2", "ps_metrics", "ps_taxacounts", "read_RDP" ], "_datasets": [ { "name": "mouse.GTDB_220", "title": "'phyloseq-class' objects generated using the DADA2 Pipeline Tutorial", "object": "mouse.GTDB_220", "file": "mouse.GTDB_220.rda", "class": [ "phyloseq" ], "fields": [], "table": false, "tojson": false }, { "name": "mouse.RDP", "title": "'phyloseq-class' objects generated using the DADA2 Pipeline Tutorial", "object": "mouse.RDP", "file": "mouse.RDP.rda", "class": [ "phyloseq" ], "fields": [], "table": false, "tojson": false }, { "name": "mouse.silva", "title": "'phyloseq-class' objects generated using the DADA2 Pipeline Tutorial", "object": "mouse.silva", "file": "mouse.silva.rda", "class": [ "phyloseq" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "chem16S-package", "title": "Chemical metrics for microbial communities", "topics": [ "chem16S-package", "chem16S" ] }, { "page": "chem16S-data", "title": "`phyloseq-class` objects generated using the DADA2 Pipeline Tutorial", "topics": [ "chem16S-data", "mouse.GTDB_220", "mouse.RDP", "mouse.silva" ] }, { "page": "chemlab", "title": "Formatted labels for chemical metrics", "topics": [ "chemlab" ] }, { "page": "get_metadata", "title": "Template function for metadata", "topics": [ "get_metadata" ] }, { "page": "get_metric_byrank", "title": "Chemical metrics for taxa aggregated to a given rank", "topics": [ "get_metric_byrank" ] }, { "page": "get_metrics", "title": "Calculate chemical metrics of community reference proteomes", "topics": [ "get_metrics" ] }, { "page": "map_taxa", "title": "Map taxonomic names to NCBI or GTDB taxonomy", "topics": [ "map_taxa" ] }, { "page": "phyloseq_integration", "title": "Process `phyloseq-class` objects to calculate chemical metrics", "topics": [ "physeq", "plot_ps_metrics", "plot_ps_metrics2", "ps_metrics", "ps_taxacounts" ] }, { "page": "plot_metrics", "title": "Plot chemical metrics of community reference proteomes", "topics": [ "plot_metrics" ] }, { "page": "read_RDP", "title": "Read and filter RDP Classifier output", "topics": [ "read_RDP" ] } ], "_readme": "https://github.com/jedick/chem16S/raw/HEAD/README.md", "_rundeps": [ "ade4", "ape", "Biobase", "BiocGenerics", "biomformat", "Biostrings", "canprot", "cli", "cluster", "codetools", "cpp11", "crayon", "data.table", "digest", "farver", "foreach", "generics", "ggplot2", "glue", "gtable", "igraph", "IRanges", "isoband", "iterators", "jsonlite", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "mgcv", "multcompView", "multtest", "nlme", "permute", "phyloseq", "pixmap", "pkgconfig", "plyr", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "reshape2", "rlang", "S4Vectors", "S7", "scales", "Seqinfo", "sp", "stringi", "stringr", "survival", "vctrs", "vegan", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "metrics.Rmd", "filename": "metrics.html", "title": "Chemical metrics of reference proteomes for taxa", "author": "Jeffrey M. Dick", "engine": "knitr::rmarkdown", "headings": [ "Required packages", "Reference proteomes for taxa", "r Zc for genera in selected phyla and classes", "Prokaryotic genera, aggregated to phylum", "Prokaryotic genera, aggregated to class", "Stoichiometric hydration state (r nH2O)", "Viruses and prokaryotes", "Other metrics", "Take-home messages", "References" ], "created": "2023-07-06 03:09:58", "modified": "2024-12-02 01:35:35", "commits": 12 }, { "source": "phyloseq.Rmd", "filename": "phyloseq.html", "title": "Integration of chem16S with phyloseq", "author": "Jeffrey M. Dick", "engine": "knitr::rmarkdown", "headings": [ "Load required packages", "Mouse microbiome data", "Lowest-level taxa", "Taxonomic mapping", "From taxonomy to amino acid composition", "From taxonomy to chemical metrics", "Using GTDB for reference proteomes", "Take-home messages", "References" ], "created": "2023-07-06 03:09:58", "modified": "2024-12-02 01:35:35", "commits": 15 }, { "source": "plotting.Rmd", "filename": "plotting.html", "title": "Plotting two chemical metrics", "author": "Jeffrey M. Dick", "engine": "knitr::rmarkdown", "headings": [ "Load required packages", "GlobalPatterns", "Humboldt Sulfuretum (Marine Sediment)", "Qinghai-Tibet Plateau (Hot Springs)", "Comparing more datasets", "Take-home messages", "References" ], "created": "2023-07-06 03:09:58", "modified": "2024-12-02 01:35:35", "commits": 14 } ], "_score": 5.079181246047625, "_indexed": true, "_nocasepkg": "chem16s", "_universes": [ "jedick" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.2.0-6", "date": "2026-06-05T07:11:43.000Z", "distro": "noble", "commit": "df51f65f63e3cd091bcc55db25ca93dc4e1afc9e", "fileid": "c570f99717042c5724b5439e21f3724ba1880dc5fbcdf410686f50b617636d39", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jedick/actions/runs/27000742094" }, { "r": "4.6.0", "os": "linux", "version": "1.2.0-6", "date": "2026-06-05T07:11:29.000Z", "distro": "noble", "commit": "df51f65f63e3cd091bcc55db25ca93dc4e1afc9e", "fileid": "156f8c043c6433d859382e7ca22a82535d33ab41de7206e74c5e312290694691", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jedick/actions/runs/27000742094" }, { "r": "4.5.3", "os": "mac", "version": "1.2.0-6", "date": "2026-06-05T07:11:05.000Z", "commit": "df51f65f63e3cd091bcc55db25ca93dc4e1afc9e", "fileid": "ecb7a87aafeb972c5ecb59e799c92a516f4d6f2549d197461d7e705c0854ea0b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jedick/actions/runs/27000742094" }, { "r": "4.6.0", "os": "mac", "version": "1.2.0-6", "date": "2026-06-05T07:11:15.000Z", "commit": "df51f65f63e3cd091bcc55db25ca93dc4e1afc9e", "fileid": "18cbad3e915b511154df395191be3c5cd50c24e268554e32c7e8096eefc7ca58", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jedick/actions/runs/27000742094" }, { "r": "4.6.0", "os": "wasm", "version": "1.2.0-6", "date": "2026-06-05T07:11:37.000Z", "commit": "df51f65f63e3cd091bcc55db25ca93dc4e1afc9e", "fileid": "6eddbfe97e053b2465baa5fccc031943f473c44d36e103714e0ee6c43cc84315", "status": "success", "buildurl": "https://github.com/r-universe/jedick/actions/runs/27000742094" }, { "r": "4.7.0", "os": "win", "version": "1.2.0-6", "date": "2026-06-05T07:10:47.000Z", "commit": "df51f65f63e3cd091bcc55db25ca93dc4e1afc9e", "fileid": "c166c9e6eea4f755c87cccd441fb7dbec0bc28546b5efed030f3d1d5cce67682", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jedick/actions/runs/27000742094" }, { "r": "4.5.3", "os": "win", "version": "1.2.0-6", "date": "2026-06-05T07:10:39.000Z", "commit": "df51f65f63e3cd091bcc55db25ca93dc4e1afc9e", "fileid": "36680944146403a1c9fe5ed481e9067c85d8bcfce493c9deb0e4fb3d672075ae", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jedick/actions/runs/27000742094" }, { "r": "4.6.0", "os": "win", "version": "1.2.0-6", "date": "2026-06-05T07:10:44.000Z", "commit": "df51f65f63e3cd091bcc55db25ca93dc4e1afc9e", "fileid": "9d1698e96554d92d43ee3b5924687e96f5f6315bfc8d2d72796187eeba76f336", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jedick/actions/runs/27000742094" } ] }