{ "_id": "6ad5c42743d630dc48a400aa", "Package": "serrsBayes", "Type": "Package", "Title": "Bayesian Modelling of Raman Spectroscopy", "Version": "0.6-1", "Date": "2026-10-05", "Authors@R": "c(\nperson(\"Matt\", \"Moores\", role = c(\"aut\", \"cre\"), email = \"mmoores@gmail.com\", comment = c(ORCID = \"0000-0003-4531-3572\")),\nperson(\"Jake\", \"Carson\", role=\"aut\", email=\"Jake.Carson@warwick.ac.uk\", comment = c(ORCID = \"0000-0002-7896-0971\")),\nperson(\"Dirk\", \"Eddelbuettel\", role = \"ctb\", comment = c(ORCID = \"0000-0001-6419-907X\")),\nperson(\"Benjamin\", \"Moskowitz\", role=\"ctb\", comment = c(ORCID = \"0000-0003-1005-8639\")),\nperson(\"Kirsten\", \"Gracie\", role=\"dtc\"),\nperson(\"Karen\", \"Faulds\", role=\"dtc\", comment = c(ORCID = \"0000-0002-5567-7399\")),\nperson(\"Duncan\", \"Graham\", role=\"dtc\", comment = c(ORCID = \"0000-0002-6079-2105\")),\nperson(\"Mark\", \"Girolami\", role=\"aut\", comment = c(ORCID = \"0000-0003-3008-253X\")),\nperson(\"Engineering and Physical Sciences Research Council\", role=\"fnd\", comment=\"EPSRC programme grant ref: EP/L014165/1\"),\nperson(\"University of Warwick\", role=\"cph\"))", "Description": "Sequential Monte Carlo (SMC) algorithms for fitting a\ngeneralised additive mixed model (GAMM) to surface-enhanced\nresonance Raman spectroscopy (SERRS), using the method of\nMoores et al. (2026) .\nMultivariate observations of SERRS are highly collinear and\nlend themselves to a reduced-rank representation. The GAMM\nseparates the SERRS signal into three components: a sequence of\nLorentzian, Gaussian, or pseudo-Voigt peaks; a smoothly-varying\nbaseline; and additive white noise. The parameters of each\ncomponent of the model are estimated iteratively using SMC. The\nposterior distributions of the parameters given the observed\nspectra are represented as a population of weighted particles.", "License": "GPL (>= 2) | file LICENSE", "URL": "https://github.com/mooresm/serrsBayes,\nhttps://mooresm.github.io/serrsBayes/", "BugReports": "https://github.com/mooresm/serrsBayes/issues", "LazyData": "true", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.1.0", "Repository": "https://mooresm.r-universe.dev", "Date/Publication": "2026-10-19 06:00:06 UTC", "RemoteUrl": "https://github.com/mooresm/serrsbayes", "RemoteRef": "HEAD", "RemoteSha": "bfbb8164308daa75d6e86218d4dde2a0a0fc2975", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-19 06:53:25 UTC", "User": "root" }, "Author": "Matt Moores [aut, cre] (ORCID: ),\nJake Carson [aut] (ORCID: ),\nDirk Eddelbuettel [ctb] (ORCID:\n),\nBenjamin Moskowitz [ctb] (ORCID:\n),\nKirsten Gracie [dtc],\nKaren Faulds [dtc] (ORCID: ),\nDuncan Graham [dtc] (ORCID: ),\nMark Girolami [aut] (ORCID: ),\nEngineering and Physical Sciences Research Council [fnd] (EPSRC\nprogramme grant ref: EP/L014165/1),\nUniversity of Warwick [cph]", "Maintainer": "Matt Moores ", "_user": "mooresm", "_type": "src", "_file": "serrsBayes_0.6-1.tar.gz", "_fileid": "https://r2.ropensci.org/9c972cd6fcbb4cce1a5de880a66627539e5fb8b833223702f7a98ca86dc71f30", "_filesize": 1900467, "_sha256": "9c972cd6fcbb4cce1a5de880a66627539e5fb8b833223702f7a98ca86dc71f30", "_expires": "2027-01-27T07:17:53.000Z", "_created": "2026-10-19T06:53:25.000Z", "_published": "2026-10-19T07:17:59.594Z", "_buildurl": "https://github.com/r-universe/mooresm/actions/runs/39211823180", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 117929195937, "time": 139, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12167859913" }, { "job": 117929195832, "time": 172, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12168341564" }, { "job": 117929196187, "time": 261, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12168945101" }, { "job": 117929195960, "time": 289, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12167748780" }, { "job": 117929195844, "time": 114, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12168464703" }, { "job": 117929195978, "time": 301, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12168323251" }, { "job": 117929196042, "time": 123, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12169585958" }, { "job": 117929195909, "time": 341, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12167908724" }, { "job": 117926795841, "time": 469, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12168237246" }, { "job": 117929195969, "time": 277, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12168700577" }, { "job": 117929196039, "time": 399, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12168456659" }, { "job": 117929196064, "time": 158, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12168780433" }, { "job": 117929196034, "time": 119, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12167568974" }, { "job": 117929196114, "time": 383, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12168084125" }, { "job": 117929196054, "time": 272, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12167938144" } ], "_upstream": "https://github.com/mooresm/serrsbayes", "_commit": { "id": "bfbb8164308daa75d6e86218d4dde2a0a0fc2975", "author": "Matt Moores ", "committer": "Matt Moores ", "message": "check Google's Open Source Vulnerabilities database\n", "time": 1792389606 }, "_maintainer": { "name": "Matt Moores", "email": "mmoores@gmail.com", "login": "mooresm", "mastodon": "@MattMoores@fediscience.org", "linkedin": "in/matthewmoores", "orcid": "0000-0003-4531-3572", "twitter": "@MooresMt", "description": "I work on Bayesian computational methods for image analysis and Raman spectroscopy. I'm Docent in Computational Statistics at LUT University, Finland.", "uuid": 3189935 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Matrix", "role": "Depends" }, { "package": "truncnorm", "role": "Depends" }, { "package": "splines", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppEigen", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 0.11.3", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "Hmisc", "role": "Suggests" } ], "_owner": "mooresm", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-45", "n": 1 }, { "week": "2026-40", "n": 20 }, { "week": "2026-41", "n": 3 }, { "week": "2026-43", "n": 1 } ], "_tags": [ { "name": "v0.6-0", "date": "2026-10-03" } ], "_topics": [ "bayesian", "chemometrics", "raman", "sequential-monte-carlo", "spectroscopy", "cpp", "openmp" ], "_stars": 8, "_contributors": [ { "user": "mooresm", "count": 79, "uuid": 3189935 }, { "user": "eddelbuettel", "count": 2, "uuid": 673121 } ], "_userbio": { "uuid": 3189935, "type": "user", "name": "Matt", "followers": 21, "description": "I work on Bayesian computational methods for image analysis and Raman spectroscopy. I'm Docent in Computational Statistics at LUT University, Finland." }, "_downloads": { "count": 438, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/serrsBayes" }, "_devurl": "https://github.com/mooresm/serrsbayes", "_pkgdown": "https://mooresm.github.io/serrsBayes/", "_searchresults": 54, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/serrsBayes.html", "LICENSE" ], "_homeurl": "https://github.com/mooresm/serrsbayes", "_realowner": "mooresm", "_cranurl": true, "_releases": [ { "version": "0.3-10", "date": "2018-02-14" }, { "version": "0.3-11", "date": "2018-02-15" }, { "version": "0.3-12", "date": "2018-02-18" }, { "version": "0.3-13", "date": "2018-06-05" }, { "version": "0.4-0", "date": "2019-04-29" }, { "version": "0.4-1", "date": "2020-02-05" }, { "version": "0.4-2", "date": "2021-06-07" }, { "version": "0.5-0", "date": "2021-06-28" }, { "version": "0.6-0", "date": "2026-10-03" } ], "_exports": [ "computeLogLikelihood", "copyLogProposals", "effectiveSampleSize", "fitSpectraMCMC", "fitSpectraSMC", "fitVoigtIBIS", "fitVoigtPeaksSMC", "getBsplineBasis", "getVoigtParam", "marginalMetropolisUpdate", "mhUpdateVoigt", "mixedVoigt", "resampleParticles", "residualResampling", "reWeightParticles", "sumDexp", "sumDlogNorm", "sumDnorm", "weightedGaussian", "weightedLorentzian", "weightedMean", "weightedVariance" ], "_datasets": [ { "name": "lsTamra", "title": "Surface-enhanced Raman spectram of tetramethylrhodamine+DNA (T20)", "object": "lsTamra", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "methanol", "title": "Raman spectrum of methanol (CH3OH)", "object": "methanol", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "result", "title": "SMC particles for TAMRA+DNA (T20)", "object": "result", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "result2", "title": "SMC particles for methanol (CH3OH)", "object": "result2", "class": [ "list" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "serrsBayes-package", "title": "Bayesian modelling and quantification of Raman spectroscopy", "topics": [ "serrsBayes-package", "serrsBayes" ] }, { "page": "computeLogLikelihood", "title": "Compute the log-likelihood.", "topics": [ "computeLogLikelihood" ] }, { "page": "copyLogProposals", "title": "Initialise the vector of Metropolis-Hastings proposals.", "topics": [ "copyLogProposals" ] }, { "page": "effectiveSampleSize", "title": "Compute the effective sample size (ESS) of the particles.", "topics": [ "effectiveSampleSize" ] }, { "page": "fitSpectraMCMC", "title": "Fit the model using Markov chain Monte Carlo.", "topics": [ "fitSpectraMCMC" ] }, { "page": "fitSpectraSMC", "title": "Fit the model using Sequential Monte Carlo (SMC).", "topics": [ "fitSpectraSMC" ] }, { "page": "fitVoigtIBIS", "title": "Fit the model with Voigt peaks using iterated batch importance sampling (IBIS).", "topics": [ "fitVoigtIBIS" ] }, { "page": "fitVoigtPeaksSMC", "title": "Fit the model with Voigt peaks using Sequential Monte Carlo (SMC).", "topics": [ "fitVoigtPeaksSMC" ] }, { "page": "getBsplineBasis", "title": "Compute cubic B-spline basis functions for the given wavenumbers.", "topics": [ "getBsplineBasis" ] }, { "page": "getVoigtParam", "title": "Compute the pseudo-Voigt mixing ratio for each peak.", "topics": [ "getVoigtParam" ] }, { "page": "lsTamra", "title": "Surface-enhanced Raman spectram of tetramethylrhodamine+DNA (T20)", "topics": [ "lsTamra" ] }, { "page": "marginalMetropolisUpdate", "title": "Update all of the parameters using a single Metropolis-Hastings step.", "topics": [ "marginalMetropolisUpdate" ] }, { "page": "methanol", "title": "Raman spectrum of methanol (CH3OH)", "topics": [ "methanol" ] }, { "page": "mhUpdateVoigt", "title": "Update the parameters of the Voigt peaks using marginal Metropolis-Hastings.", "topics": [ "mhUpdateVoigt" ] }, { "page": "mixedVoigt", "title": "Compute the spectral signature using Voigt peaks.", "topics": [ "mixedVoigt" ] }, { "page": "resampleParticles", "title": "Resample in place to avoid expensive copying of data structures, using a permutation of the ancestry vector.", "topics": [ "resampleParticles" ] }, { "page": "residualResampling", "title": "Compute an ancestry vector for residual resampling of the SMC particles.", "topics": [ "residualResampling" ] }, { "page": "result", "title": "SMC particles for TAMRA+DNA (T20)", "topics": [ "result" ] }, { "page": "result2", "title": "SMC particles for methanol (CH3OH)", "topics": [ "result2" ] }, { "page": "reWeightParticles", "title": "Update the importance weights of each particle.", "topics": [ "reWeightParticles" ] }, { "page": "sumDexp", "title": "Sum log-likelihoods of i.i.d. exponential.", "topics": [ "sumDexp" ] }, { "page": "sumDlogNorm", "title": "Sum log-likelihoods of i.i.d. lognormal.", "topics": [ "sumDlogNorm" ] }, { "page": "sumDnorm", "title": "Sum log-likelihoods of Gaussian.", "topics": [ "sumDnorm" ] }, { "page": "weightedGaussian", "title": "Compute the spectral signature using Gaussian peaks.", "topics": [ "weightedGaussian" ] }, { "page": "weightedLorentzian", "title": "Compute the spectral signature using Lorentzian peaks.", "topics": [ "weightedLorentzian" ] }, { "page": "weightedMean", "title": "Compute the weighted arithmetic means of the particles.", "topics": [ "weightedMean" ] }, { "page": "weightedVariance", "title": "Compute the weighted variance of the particles.", "topics": [ "weightedVariance" ] } ], "_pkglogo": "https://github.com/mooresm/serrsbayes/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/mooresm/serrsbayes/raw/HEAD/README.md", "_rundeps": [ "lattice", "Matrix", "Rcpp", "RcppEigen", "truncnorm" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" }, { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_vignettes": [ { "source": "Introduction.Rmd", "filename": "Introduction.html", "title": "Introducing serrsBayes", "author": "Matt Moores", "engine": "knitr::rmarkdown", "headings": [ "Data", "Priors", "Computation", "Posterior Inference", "References" ], "created": "2018-02-18 19:07:24", "modified": "2026-10-02 07:33:14", "commits": 21 }, { "source": "Methanol.Rmd", "filename": "Methanol.html", "title": "Methanol example", "author": "Matt Moores, Benjamin Moskowitz and Karen Faulds", "engine": "knitr::rmarkdown", "headings": [ "Raw Data", "fitSpectraSMC", "fitVoigtPeaksSMC", "fitSpectraSMC, redux", "References" ], "created": "2019-04-11 07:03:39", "modified": "2021-06-06 21:31:04", "commits": 8 } ], "_score": 6.237543738142874, "_indexed": true, "_nocasepkg": "serrsbayes", "_universes": [ "mooresm" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.6-1", "date": "2026-10-19T06:55:38.000Z", "distro": "resolute", "arch": "aarch64", "commit": "bfbb8164308daa75d6e86218d4dde2a0a0fc2975", "fileid": "https://r2.ropensci.org/ac9d55352f9193597c240f19e3f53033da01f570047c93ab904a1ad5e0c8627e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mooresm/actions/runs/39211823180" }, { "r": "4.7.0", "os": "linux", "version": "0.6-1", "date": "2026-10-19T06:55:51.000Z", "distro": "resolute", "arch": "x86_64", "commit": "bfbb8164308daa75d6e86218d4dde2a0a0fc2975", "fileid": "https://r2.ropensci.org/2dee08bd9a16a0bca33247c394d5e62851c9ec1d1a6a27a92bca4e93448e3b2e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mooresm/actions/runs/39211823180" }, { "r": "4.6.1", "os": "linux", "version": "0.6-1", "date": "2026-10-19T06:57:41.000Z", "distro": "resolute", "arch": "aarch64", "commit": "bfbb8164308daa75d6e86218d4dde2a0a0fc2975", "fileid": "https://r2.ropensci.org/a6a8eeba2c726482e8ebdb7fde96d96470f9ec372d4033d9565684965765b6a6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mooresm/actions/runs/39211823180" }, { "r": "4.6.1", "os": "linux", "version": "0.6-1", "date": "2026-10-19T06:58:00.000Z", "distro": "resolute", "arch": "x86_64", "commit": "bfbb8164308daa75d6e86218d4dde2a0a0fc2975", "fileid": "https://r2.ropensci.org/31bdb5fed4656c74660da1d069ba4a8bb34f315f7f3f1cefcac0559a6ee5a2c1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mooresm/actions/runs/39211823180" }, { "r": "4.5.3", "os": "mac", "version": "0.6-1", "date": "2026-10-19T07:10:45.000Z", "arch": "aarch64", "commit": "bfbb8164308daa75d6e86218d4dde2a0a0fc2975", "fileid": "https://r2.ropensci.org/cc875933dad0e85fd21c53fc1b74d8cb60d6eed4bb5339bde620713a2447ad60", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mooresm/actions/runs/39211823180" }, { "r": "4.5.3", "os": "mac", "version": "0.6-1", "date": "2026-10-19T07:00:04.000Z", "arch": "x86_64", "commit": "bfbb8164308daa75d6e86218d4dde2a0a0fc2975", "fileid": "https://r2.ropensci.org/8fb0c9dc34061185f4e2a7262aafee5cad1ccfe6aa04a7c1b40b49627e335bd1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mooresm/actions/runs/39211823180" }, { "r": "4.6.1", "os": "mac", "version": "0.6-1", "date": "2026-10-19T07:16:36.000Z", "arch": "aarch64", "commit": "bfbb8164308daa75d6e86218d4dde2a0a0fc2975", "fileid": "https://r2.ropensci.org/22131bf41f79e8ccb46f52aa4e6edfac1c61af69fd0e205ec17a493ebfbadd12", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mooresm/actions/runs/39211823180" }, { "r": "4.6.1", "os": "mac", "version": "0.6-1", "date": "2026-10-19T06:59:20.000Z", "arch": "x86_64", "commit": "bfbb8164308daa75d6e86218d4dde2a0a0fc2975", "fileid": "https://r2.ropensci.org/65e7f0261203b39bac52f3b3ebb6c86e7dcd6723ed53468c95b92ed5fc1acadb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mooresm/actions/runs/39211823180" }, { "r": "4.6.0", "os": "wasm", "version": "0.6-1", "date": "2026-10-19T06:58:33.000Z", "arch": "emscripten", "commit": "bfbb8164308daa75d6e86218d4dde2a0a0fc2975", "fileid": "https://r2.ropensci.org/590866e5c3344cfb875f0ae06a8327989c6c8eb8c92821304c5b9504b23f78c0", "status": "success", "buildurl": "https://github.com/r-universe/mooresm/actions/runs/39211823180" }, { "r": "4.7.0", "os": "win", "version": "0.6-1", "date": "2026-10-19T06:59:09.000Z", "arch": "aarch64", "commit": "bfbb8164308daa75d6e86218d4dde2a0a0fc2975", "fileid": "https://r2.ropensci.org/f2b1b06c78e87bbb086ae3a61668faeb2126766e1acb9fc1c0f05d5ab4b0a020", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mooresm/actions/runs/39211823180" }, { "r": "4.7.0", "os": "win", "version": "0.6-1", "date": "2026-10-19T06:55:01.000Z", "arch": "x86_64", "commit": "bfbb8164308daa75d6e86218d4dde2a0a0fc2975", "fileid": "https://r2.ropensci.org/a30b6c56c6da107ec3abb86babf757c8c8fd54e001f93647a98bd71ea9fc12da", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mooresm/actions/runs/39211823180" }, { "r": "4.5.3", "os": "win", "version": "0.6-1", "date": "2026-10-19T06:54:57.000Z", "arch": "x86_64", "commit": "bfbb8164308daa75d6e86218d4dde2a0a0fc2975", "fileid": "https://r2.ropensci.org/53d5526c591359172d141ae665382511f4be41c231cbc86dfad8ddcfdbf99c7b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mooresm/actions/runs/39211823180" }, { "r": "4.6.1", "os": "win", "version": "0.6-1", "date": "2026-10-19T06:58:49.000Z", "arch": "aarch64", "commit": "bfbb8164308daa75d6e86218d4dde2a0a0fc2975", "fileid": "https://r2.ropensci.org/b0573b798955a5c241b92aa3282a5c100a45f516c4a0617e028fd41d41c5fb70", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mooresm/actions/runs/39211823180" }, { "r": "4.6.1", "os": "win", "version": "0.6-1", "date": "2026-10-19T06:57:29.000Z", "arch": "x86_64", "commit": "bfbb8164308daa75d6e86218d4dde2a0a0fc2975", "fileid": "https://r2.ropensci.org/e2d1ffca76ae84bbbf4dee99b730a8d68731188e30844d2d3c7a5b823c873dea", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mooresm/actions/runs/39211823180" } ] }