{ "_id": "6a1d674c1d7bb097a0a4d4c2", "Package": "ShellChron", "Title": "Builds Chronologies from Oxygen Isotope Profiles in Shells", "Version": "0.4.1", "Authors@R": "person(given = \"Niels\",\nfamily = \"de Winter\",\nrole = c(\"aut\", \"cre\"),\nemail = \"niels_de_winter@live.nl\",\ncomment = c(ORCID = \"0000-0002-1453-5407\"))", "Description": "Takes as input a stable oxygen isotope (d18O) profile\nmeasured in growth direction (D) through a shell +\nuncertainties in both variables (d18O_err & D_err). It then\nmodels the seasonality in the d18O record by fitting a\ncombination of a growth and temperature sine wave to\nyear-length chunks of the data (see Judd et al., (2018)\n). This modeling is carried\nout along a sliding window through the data and yields\nestimates of the day of the year (Julian Day) and local growth\nrate for each data point. Uncertainties in both modeling\nroutine and the data itself are propagated and pooled to obtain\na confidence envelope around the age of each data point in the\nshell. The end result is a shell chronology consisting of\nestimated ages of shell formation relative to the annual cycle\nwith their uncertainties. All formulae in the package serve\nthis purpose, but the user can customize the model (e.g. number\nof days in a year and the mineralogy of the shell carbonate)\nthrough input parameters.", "License": "GPL-3", "URL": "https://github.com/nielsjdewinter/ShellChron", "BugReports": "https://github.com/nielsjdewinter/ShellChron/issues", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.1", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nmake libicu-dev libssl-dev libproj-dev libsqlite3-dev\nlibudunits2-dev", "Repository": "https://nielsjdewinter.r-universe.dev", "Date/Publication": "2022-08-18 13:57:00 UTC", "RemoteUrl": "https://github.com/nielsjdewinter/shellchron", "RemoteRef": "HEAD", "RemoteSha": "ac2ecdddd0cd1616e60b3711f6b2cbca56abc411", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-01 10:56:59 UTC", "User": "root" }, "Author": "Niels de Winter [aut, cre] (ORCID:\n)", "Maintainer": "Niels de Winter ", "MD5sum": "e4ee8f473252625d9e783fa3dc5fb1f8", "_user": "nielsjdewinter", "_type": "src", "_file": "ShellChron_0.4.1.tar.gz", "_fileid": "f0fa88c50507d129abc0b9bf80108e11ae9623d1b09f14e6e819a303368f00c3", "_filesize": 1031691, "_sha256": "f0fa88c50507d129abc0b9bf80108e11ae9623d1b09f14e6e819a303368f00c3", "_created": "2026-06-01T10:56:59.000Z", "_published": "2026-06-01T11:04:44.122Z", "_distro": "noble", "_jobs": [ { "job": 78837629462, "time": 160, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7329725717" }, { "job": 78837629530, "time": 158, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7329725553" }, { "job": 78837629475, "time": 123, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7329783243" }, { "job": 78837629474, "time": 121, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7329806427" }, { "job": 78836975741, "time": 244, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7329673333" }, { "job": 78837629492, "time": 138, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7329718855" }, { "job": 78837629481, "time": 92, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7329704585" }, { "job": 78837629617, "time": 85, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7329702438" }, { "job": 78837629504, "time": 182, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7329732783" } ], "_buildurl": "https://github.com/r-universe/nielsjdewinter/actions/runs/26750493870", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/nielsjdewinter/shellchron", "_commit": { "id": "ac2ecdddd0cd1616e60b3711f6b2cbca56abc411", "author": "Niels J. de Winter ", "committer": "Niels J. de Winter ", "message": "Added functions to convert between d18Oc, d18Ow and T\n", "time": 1660831020 }, "_maintainer": { "name": "Niels de Winter", "email": "niels_de_winter@live.nl", "login": "nielsjdewinter", "twitter": "@NielsJdeWinter", "description": "Assistant professor Marine Geology and Paleoclimatology", "uuid": 32540829, "orcid": "0000-0002-1453-5407" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "rtop", "version": ">= 0.5.14", "role": "Imports" }, { "package": "zoo", "version": ">= 1.8.7", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.2.1", "role": "Imports" }, { "package": "ggpubr", "version": ">= 0.4.0", "role": "Imports" }, { "package": "tidyr", "version": ">= 1.1.1", "role": "Imports" }, { "package": "scales", "version": ">= 1.1.0", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "nielsjdewinter", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 3, "_contributors": [ { "user": "nielsjdewinter", "count": 74, "uuid": 32540829 }, { "user": "niklas-palaeo", "count": 5, "uuid": 62431307 } ], "_userbio": { "uuid": 32540829, "type": "user", "name": "Niels J. de Winter", "description": "Assistant professor Marine Geology and Paleoclimatology" }, "_downloads": { "count": 177, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ShellChron" }, "_devurl": "https://github.com/nielsjdewinter/shellchron", "_searchresults": 15, "_rbuild": "4.6.0", "_assets": [ "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", "extra/ShellChron.html", "manual.pdf" ], "_homeurl": "https://github.com/nielsjdewinter/shellchron", "_realowner": "nielsjdewinter", "_cranurl": true, "_releases": [ { "version": "0.2.8", "date": "2020-11-20" }, { "version": "0.4.0", "date": "2021-07-05" } ], "_exports": [ "%>%", "age_corr", "cumdy", "cumulative_day", "d18O_model", "d18Oc_from_T_d18Ow", "d18Ow_from_d18O_T", "data_import", "data_import_object", "export_results", "growth_model", "growth_rate_curve", "mc_err_form", "mc_err_orth", "mc_err_proj", "peakid", "run_model", "sd_wt", "sinreg", "T_from_d18O_d18Ow", "temperature_curve", "wrap_function" ], "_datasets": [ { "name": "Virtual_shell", "title": "Virtual input data for ShellChron", "object": "Virtual_shell", "class": [ "data.frame" ], "fields": [ "D", "d18Oc", "D_err", "d18Oc_err", "YEARMARKER" ], "rows": 80, "table": true, "tojson": true } ], "_help": [ { "page": "age_corr", "title": "Function that corrects chronologies for sudden jumps in time", "topics": [ "age_corr" ] }, { "page": "CumDY", "title": "Function to detect year transitions and calculate cumulative age of model results", "topics": [ "cumdy" ] }, { "page": "cumulative_day", "title": "Function to detect year transitions and calculate cumulative age of model results", "topics": [ "cumulative_day" ] }, { "page": "d18O_model", "title": "Function to convert SST data to d18O", "topics": [ "d18O_model" ] }, { "page": "d18Oc_from_T_d18Ow", "title": "Function to convert T data to d18O", "topics": [ "d18Oc_from_T_d18Ow" ] }, { "page": "d18Ow_from_d18O_T", "title": "Function BLATANTLY STOLEN FROM SHELLCHRON PACKAGE to convert d18O data to SST", "topics": [ "d18Ow_from_d18O_T" ] }, { "page": "data_import", "title": "Function to import d18O data and process yearmarkers and calculation windows", "topics": [ "data_import" ] }, { "page": "data_import_object", "title": "Function to prepare d18O data from a preexisting object and process yearmarkers and calculation windows", "topics": [ "data_import_object" ] }, { "page": "Export_results", "title": "Function to merge and export the results of the ShellChron model", "topics": [ "export_results" ] }, { "page": "growth_model", "title": "Function that models a d18O curve through SST and GR sinusoids", "topics": [ "growth_model" ] }, { "page": "growth_rate_curve", "title": "Function that creates a skewed sinusoidal growth rate (GR) curve from a list of parameters", "topics": [ "growth_rate_curve" ] }, { "page": "mc_err_form", "title": "Function that propagates measurement uncertainty through model results", "topics": [ "mc_err_form" ] }, { "page": "mc_err_orth", "title": "Function that propagates measurement uncertainty through model results", "topics": [ "mc_err_orth" ] }, { "page": "mc_err_proj", "title": "Function that propagates measurement uncertainty through model results", "topics": [ "mc_err_proj" ] }, { "page": "PeakID", "title": "Function that identifies peaks in a dataset", "topics": [ "peakid" ] }, { "page": "Run_model", "title": "Function that optimizes sinusoid parameters to fit d18O data", "topics": [ "run_model" ] }, { "page": "sd_wt", "title": "Function to calculate weighted standard deviation", "topics": [ "sd_wt" ] }, { "page": "sinreg", "title": "Function that carries out a sinusoidal regression", "topics": [ "sinreg" ] }, { "page": "T_from_d18O_d18Ow", "title": "Function BLATANTLY STOLEN FROM SHELLCHRON PACKAGE to convert d18O data to SST", "topics": [ "T_from_d18O_d18Ow" ] }, { "page": "temperature_curve", "title": "Function that creates a sinusoidal Sea Surface Temperature (SST) curve from a list of parameters", "topics": [ "temperature_curve" ] }, { "page": "Virtual_shell", "title": "Virtual input data for ShellChron", "topics": [ "Virtual_shell" ] }, { "page": "Wrap_function", "title": "Full ShellChron workflow wrapped in a single function", "topics": [ "wrap_function" ] } ], "_readme": "https://github.com/nielsjdewinter/shellchron/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "boot", "broom", "car", "carData", "class", "classInt", "cli", "colorspace", "corrplot", "cowplot", "cpp11", "DBI", "Deriv", "doBy", "dplyr", "e1071", "farver", "FNN", "forecast", "Formula", "fracdiff", "generics", "ggplot2", "ggpubr", "ggrepel", "ggsci", "ggsignif", "glue", 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