{ "_id": "6a1ed588b401979e7340e63b", "Package": "LMMsolver", "Type": "Package", "Title": "Linear Mixed Models with Sparse Matrix Methods and Smoothing", "Description": "Provides tools for fitting linear mixed models using\nsparse matrix methods and variance component estimation.\nApplications include spline-based modeling of spatial and\ntemporal trends using penalized splines (Boer, 2023)\n.", "Version": "1.0.13", "Date": "2026-05-18", "Authors@R": "c(person(given = \"Martin\", \nfamily = \"Boer\",\nemail = \"martin.boer@wur.nl\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-1879-4588\")),\nperson(given = \"Bart-Jan\",\nfamily = \"van Rossum\",\nemail = \"bart-jan.vanrossum@wur.nl\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-8673-2514\")))", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "VignetteBuilder": "knitr", "URL": "https://biometris.github.io/LMMsolver/index.html,\nhttps://github.com/Biometris/LMMsolver/", "BugReports": "https://github.com/Biometris/LMMsolver/issues", "Config/roxygen2/version": "8.0.0", "Repository": "https://biometris.r-universe.dev", "Date/Publication": "2026-05-20 08:14:01 UTC", "RemoteUrl": "https://github.com/biometris/lmmsolver", "RemoteRef": "HEAD", "RemoteSha": "5d278027b9d09e541953f6b67e8f79282fae990b", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-20 10:34:43 UTC", "User": "root" }, "Author": "Martin Boer [aut] (ORCID: ),\nBart-Jan van Rossum [aut, cre] (ORCID:\n)", "Maintainer": "Bart-Jan van Rossum ", "MD5sum": "ab63a22dfe3883a30899bf4de881bb07", "_user": "biometris", "_type": "src", "_file": "LMMsolver_1.0.13.tar.gz", "_fileid": "77cc167cc1cf188e7a141573c0ae1552d794ebccac71d035f7e620256f2f4b04", "_filesize": 8908675, "_sha256": "77cc167cc1cf188e7a141573c0ae1552d794ebccac71d035f7e620256f2f4b04", "_created": "2026-05-20T10:34:43.000Z", "_published": "2026-06-02T13:07:20.482Z", "_distro": "noble", "_jobs": [ { "job": 79077341072, "time": 157, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7107703845" }, { "job": 79077340796, "time": 155, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7107703061" }, { "job": 79077341694, "time": 133, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7107696068" }, { "job": 79077341203, "time": 159, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7107704612" }, { "job": 79077341707, "time": 93, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7107752080" }, { "job": 79077342070, "time": 255, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7107772974" }, { "job": 79077341614, "time": 114, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7107692203" }, { "job": 79077340742, "time": 331, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7107810323" }, { "job": 79077340531, "time": 237, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7107648738" }, { "job": 79077340181, "time": 140, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7358499875" }, { "job": 79077340652, "time": 135, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7107696434" }, { "job": 79077341374, "time": 133, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7107695910" }, { "job": 79077340774, "time": 128, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7107693759" } ], "_buildurl": "https://github.com/r-universe/biometris/actions/runs/26156844153", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/biometris/lmmsolver", "_commit": { "id": "5d278027b9d09e541953f6b67e8f79282fae990b", "author": "Bart-Jan van Rossum ", "committer": "Bart-Jan van Rossum ", "message": "Added missing imports\n", "time": 1779264841 }, "_maintainer": { "name": "Bart-Jan van Rossum", "email": "bart-jan.vanrossum@wur.nl", "login": "bartjanvanrossum", "description": "", "uuid": 28725410, "orcid": "0000-0002-8673-2514" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Matrix", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "Rcpp", "version": ">= 0.10.4", "role": "Imports" }, { "package": "spam", "role": "Imports" }, { "package": "splines", "role": "Imports" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "tinytest", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "maps", "role": "Suggests" }, { "package": "sf", "role": "Suggests" } ], "_owner": "biometris", "_selfowned": true, "_usedby": 7, "_updates": [ { "week": "2025-23", "n": 1 }, { "week": "2025-33", "n": 28 }, { "week": "2025-34", "n": 8 }, { "week": "2025-39", "n": 6 }, { "week": "2025-40", "n": 5 }, { "week": "2025-46", "n": 11 }, { "week": "2025-47", "n": 3 }, { "week": "2025-48", "n": 10 }, { "week": "2025-49", "n": 11 }, { "week": "2025-52", "n": 4 }, { "week": "2026-04", "n": 5 }, { "week": "2026-05", "n": 4 }, { "week": "2026-09", "n": 7 }, { "week": "2026-10", "n": 2 }, { "week": "2026-12", "n": 8 }, { "week": "2026-14", "n": 6 }, { "week": "2026-15", "n": 13 }, { "week": "2026-16", "n": 7 }, { "week": "2026-17", "n": 1 }, { "week": "2026-18", "n": 11 }, { "week": "2026-19", "n": 7 }, { "week": "2026-20", "n": 8 }, { "week": "2026-21", "n": 2 } ], "_tags": [ { "name": "v.1.0.11", "date": "2025-08-19" }, { "name": "v.1.0.12", "date": "2025-12-04" } ], "_topics": [ "mixed-models", "splines", "cpp" ], "_stars": 18, "_contributors": [ { "user": "martinboer", "count": 847, "uuid": 10836537 }, { "user": "bartjanvanrossum", "count": 282, "uuid": 28725410 }, { "user": "dbustoskorts", "count": 5, "uuid": 42030790 } ], "_userbio": { "uuid": 60092315, "type": "organization", "name": "Wageningen Universtiy & Research, Biometris", "description": "Biometris develops statistical and mathematical methods for the quantification of biological processes and processes in our living environment." }, "_downloads": { "count": 690, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/LMMsolver" }, "_devurl": "https://github.com/biometris/lmmsolver", "_searchresults": 97, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/LMMsolver.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/biometris/lmmsolver", "_realowner": "biometris", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2021-11-02" }, { "version": "1.0.1", "date": "2022-03-28" }, { "version": "1.0.2", "date": "2022-04-21" }, { "version": "1.0.3", "date": "2022-08-19" }, { "version": "1.0.4", "date": "2022-12-15" }, { "version": "1.0.5", "date": "2023-04-14" }, { "version": "1.0.6", "date": "2023-11-27" }, { "version": "1.0.7", "date": "2024-04-16" }, { "version": "1.0.8", "date": "2024-08-26" }, { "version": "1.0.9", "date": "2025-01-17" }, { "version": "1.0.10", "date": "2025-05-14" }, { "version": "1.0.11", "date": "2025-08-20" }, { "version": "1.0.12", "date": "2025-12-11" } ], "_exports": [ "as.ginverse", "diagnosticsMME", "displayMME", "effDim", "getHeritability", "LMMsolve", "LMMsolveObject", "makeGrid", "mLogLik", "multinomial", "obtainSmoothTrend", "spl1D", "spl2D", "spl3D" ], "_datasets": [ { "name": "APSIMdat", "title": "Simulated Biomass as function of time using APSIM wheat.", "object": "APSIMdat", "class": [ "data.frame" ], "fields": [ "env", "geno", "das", "biomass" ], "rows": 121, "table": true, "tojson": true }, { "name": "barley.uniformity.trial", "title": "Uniformity trial of barley", "object": "barley.uniformity.trial", "class": [ "data.frame" ], "fields": [ "row", "col", "yield" ], "rows": 1076, "table": true, "tojson": true }, { "name": "multipop", "title": "Simulated QTL mapping data set", "object": "multipop", "class": [ "data.frame" ], "fields": [ "cross", "ind", "pA", "pB", "pC", "pheno" ], "rows": 180, "table": true, "tojson": true }, { "name": "oats.data", "title": "Alpha lattice design of spring oats", "object": "oats.data", "class": [ "data.frame" ], "fields": [ "plot", "rep", "block", "gen", "yield", "row", "col" ], "rows": 72, "table": true, "tojson": true }, { "name": "SeaSurfaceTemp", "title": "Sea Surface Temperature", "object": "SeaSurfaceTemp", "class": [ "data.frame" ], "fields": [ "lon", "lat", "sst", "type" ], "rows": 15607, "table": true, "tojson": true } ], "_help": [ { "page": "APSIMdat", "title": "Simulated Biomass as function of time using APSIM wheat.", "topics": [ "APSIMdat" ] }, { "page": "as.ginverse", "title": "Construct a ginverse Object from Precision Matrices", "topics": [ "as.ginverse" ] }, { "page": "barley.uniformity.trial", "title": "Uniformity trial of barley", "topics": [ "barley.uniformity.trial" ] }, { "page": "coef.LMMsolve", "title": "Coefficients from the mixed model equations of an LMMsolve object.", "topics": [ "coef.LMMsolve" ] }, { "page": "deviance.LMMsolve", "title": "Deviance of an LMMsolve object", "topics": [ "deviance.LMMsolve" ] }, { "page": "diagnosticsMME", "title": "Give diagnostics for mixed model coefficient matrix C and the cholesky decomposition", "topics": [ "diagnosticsMME" ] }, { "page": "displayMME", "title": "Display the sparseness of the mixed model coefficient matrix", "topics": [ "displayMME" ] }, { "page": "effDim", "title": "Function to get the Effective Dimensions.", "topics": [ "effDim" ] }, { "page": "fitted.LMMsolve", "title": "Fitted values of an LMMsolve object.", "topics": [ "fitted.LMMsolve" ] }, { "page": "getHeritability", "title": "Generalized heritability of a random term", "topics": [ "getHeritability" ] }, { "page": "LMMsolve", "title": "Solve Linear Mixed Models", "topics": [ "LMMsolve" ] }, { "page": "LMMsolveObject", "title": "Fitted LMMsolve Object", "topics": [ "LMMsolveObject" ] }, { "page": "logLik.LMMsolve", "title": "Log-likelihood of an LMMsolve object", "topics": [ "logLik.LMMsolve" ] }, { "page": "makeGrid", "title": "Create a data frame for use in making predictions.", "topics": [ "makeGrid" ] }, { "page": "mLogLik", "title": "Function to obtain restricted log-likelihood and the first derivatives of the log-likelihood, given values for the penalty parameters", "topics": [ "mLogLik" ] }, { "page": "multinomial", "title": "Family Object for Multinomial Model", "topics": [ "multinomial" ] }, { "page": "multipop", "title": "Simulated QTL mapping data set", "topics": [ "multipop" ] }, { "page": "oats.data", "title": "Alpha lattice design of spring oats", "topics": [ "oats.data" ] }, { "page": "obtainSmoothTrend", "title": "Obtain Smooth Trend.", "topics": [ "obtainSmoothTrend" ] }, { "page": "predict.LMMsolve", "title": "Predict function", "topics": [ "predict.LMMsolve" ] }, { "page": "residuals.LMMsolve", "title": "Residuals of an LMMsolve object.", "topics": [ "residuals.LMMsolve" ] }, { "page": "SeaSurfaceTemp", "title": "Sea Surface Temperature", "topics": [ "SeaSurfaceTemp" ] }, { "page": "spl1D", "title": "Fit P-splines", "topics": [ "spl1D", "spl2D", "spl3D" ] }, { "page": "summary.LMMsolve", "title": "Summarize Linear Mixed Model fits", "topics": [ "print.summary.LMMsolve", "summary.LMMsolve" ] } ], "_pkglogo": "https://github.com/biometris/lmmsolver/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/biometris/lmmsolver/raw/HEAD/README.md", "_rundeps": [ "dotCall64", "lattice", "Matrix", "Rcpp", "spam" ], "_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": "Solving_Linear_Mixed_Models.Rmd", "filename": "Solving_Linear_Mixed_Models.html", "title": "Mixed Models and Smoothing", "engine": "knitr::rmarkdown", "headings": [ "The LMMsolver package", "Introduction", "Linear Regression", "Fitting a non-linear function.", "Smoothing combining two experiments", "Smooth trends in two dimensions", "US precipitation example", "Sea Surface Temperatures", "Generalized Linear Mixed Models.", "Modelling count data using Poisson model.", "Binomial distribution", "Multinomial distribution", "Examples in Quantitative Genetics and Agriculture", "Linear Variance model oats data", "Generalized Heritability", "Modelling longitudinal data", "QTL mapping using IBDs", "References" ], "created": "2021-09-28 14:43:01", "modified": "2026-05-17 20:26:51", "commits": 60 } ], "_score": 8.925991370121062, "_indexed": true, "_nocasepkg": "lmmsolver", "_universes": [ "biometris", "bartjanvanrossum" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.13", "date": "2026-05-20T10:37:19.000Z", "distro": "noble", "arch": "aarch64", "commit": "5d278027b9d09e541953f6b67e8f79282fae990b", "fileid": "c5444aeff7647d9288d3466253afbf7f2247b1f84be811fb494ab510ca97d1b5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biometris/actions/runs/26156844153" }, { "r": "4.7.0", "os": "linux", "version": "1.0.13", "date": "2026-05-20T10:37:12.000Z", "distro": "noble", "arch": "x86_64", "commit": "5d278027b9d09e541953f6b67e8f79282fae990b", "fileid": "b9981776222263f30dcbf54de2eef1aeb1f7bb24f7417237890561d87e1d26fb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biometris/actions/runs/26156844153" }, { "r": "4.6.0", "os": "linux", "version": "1.0.13", "date": "2026-05-20T10:36:58.000Z", "distro": "noble", "arch": "aarch64", "commit": "5d278027b9d09e541953f6b67e8f79282fae990b", "fileid": "512a931d71b07cd5812beeabde9644f880dc68e3f044e0ce01d8ceb9da192272", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biometris/actions/runs/26156844153" }, { "r": "4.6.0", "os": "linux", "version": "1.0.13", "date": "2026-05-20T10:37:16.000Z", "distro": "noble", "arch": "x86_64", "commit": "5d278027b9d09e541953f6b67e8f79282fae990b", "fileid": "28314a85120244e0c768a1a43e8041b77ae7b85ea41763c41173852cbcf2b10f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biometris/actions/runs/26156844153" }, { "r": "4.5.3", "os": "mac", "version": "1.0.13", "date": "2026-05-20T10:39:54.000Z", "arch": "aarch64", "commit": "5d278027b9d09e541953f6b67e8f79282fae990b", "fileid": "94739edb0e3ffd0dbfe773aa7eb37d7ead5ca054eff9d9f422d3c3fd7f0c042d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biometris/actions/runs/26156844153" }, { "r": "4.5.3", "os": "mac", "version": "1.0.13", "date": "2026-05-20T10:40:03.000Z", "arch": "x86_64", "commit": "5d278027b9d09e541953f6b67e8f79282fae990b", "fileid": "3fae05c44bb9fbcc0f817e03d5cf5476b2769a10c13f440180321572f02d76ce", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biometris/actions/runs/26156844153" }, { "r": "4.6.0", "os": "mac", "version": "1.0.13", "date": "2026-05-20T10:36:50.000Z", "arch": "aarch64", "commit": "5d278027b9d09e541953f6b67e8f79282fae990b", "fileid": "9749084e153849fe491b41908b8cd9124d6f9d4e83ddef1a7efbf69c383f3d3e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biometris/actions/runs/26156844153" }, { "r": "4.6.0", "os": "mac", "version": "1.0.13", "date": "2026-05-20T10:41:18.000Z", "arch": "x86_64", "commit": "5d278027b9d09e541953f6b67e8f79282fae990b", "fileid": "2a7689bc146af2703754fc7aa05716d74c613354ebdb35d587efb9cfae534dc5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biometris/actions/runs/26156844153" }, { "r": "4.7.0", "os": "win", "version": "1.0.13", "date": "2026-05-20T10:36:25.000Z", "arch": "x86_64", "commit": "5d278027b9d09e541953f6b67e8f79282fae990b", "fileid": "09884d64d69bf1e4dcb0a932bab889eeb111e0672036a9a41cc63191f4985516", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biometris/actions/runs/26156844153" }, { "r": "4.5.3", "os": "win", "version": "1.0.13", "date": "2026-05-20T10:36:22.000Z", "arch": "x86_64", "commit": "5d278027b9d09e541953f6b67e8f79282fae990b", "fileid": "93a9b3472c80d905227268600114436a2922e5ada89af95c629d7a1de3ee8e62", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biometris/actions/runs/26156844153" }, { "r": "4.6.0", "os": "win", "version": "1.0.13", "date": "2026-05-20T10:36:19.000Z", "arch": "x86_64", "commit": "5d278027b9d09e541953f6b67e8f79282fae990b", "fileid": "c278f69e1e8f533530cebe7868767a5b766d2f2cf47a5b213c6a49646a070c5c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biometris/actions/runs/26156844153" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.13", "date": "2026-06-02T13:06:22.000Z", "arch": "emscripten", "commit": "5d278027b9d09e541953f6b67e8f79282fae990b", "fileid": "22ab0ceb8851f610aa9c0a3f745b81c0b211c609ee54c75fc72982380faf448f", "status": "success", "buildurl": "https://github.com/r-universe/biometris/actions/runs/26156844153" } ] }