{ "_id": "6a1ef537b401979e73416791", "Package": "Mangrove", "Type": "Package", "Title": "Risk Prediction on Trees", "Version": "1.21", "Date": "2017-02-22", "Author": "Luke Jostins", "Maintainer": "Luke Jostins ", "Description": "Methods for performing genetic risk prediction from\ngenotype data. You can use it to perform risk prediction for\nindividuals, or for families with missing data.", "License": "GPL (>= 2)", "LazyLoad": "yes", "Packaged": { "Date": "2026-05-19 06:53:57 UTC", "User": "root" }, "NeedsCompilation": "no", "Repository": "https://lowk.r-universe.dev", "Date/Publication": "2017-02-22 16:15:37 UTC", "RemoteUrl": "https://github.com/cran/Mangrove", "RemoteRef": "HEAD", "RemoteSha": "a302411add434c6056126a3fd3eded27339d47aa", "MD5sum": "854010a2e2acd348c6fe2fd91b090973", "_user": "lowk", "_type": "src", "_file": "Mangrove_1.21.tar.gz", "_fileid": "95fe1f43deabcfbe70bbba32bfc6c5f830637a6899e89712505664ff41bf921a", "_filesize": 376558, "_sha256": "95fe1f43deabcfbe70bbba32bfc6c5f830637a6899e89712505664ff41bf921a", "_created": "2026-05-19T06:53:57.000Z", "_published": "2026-06-02T15:22:31.678Z", "_distro": "noble", "_jobs": [ { "job": 79106865954, "time": 107, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7076788148" }, { "job": 79106866310, "time": 104, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7076787152" }, { "job": 79106866807, "time": 179, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7076798857" }, { "job": 79106866156, "time": 304, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7076798053" }, { "job": 79106865672, "time": 190, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7076757421" }, { "job": 79106864658, "time": 91, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7362089088" }, { "job": 79106866362, "time": 77, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7076779787" }, { "job": 79106868190, "time": 82, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7076781840" }, { "job": 79106866734, "time": 91, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7076784397" } ], "_buildurl": "https://github.com/r-universe/lowk/actions/runs/26081245172", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/Mangrove", "_commit": { "id": "a302411add434c6056126a3fd3eded27339d47aa", "author": "Luke Jostins ", "committer": "cran-robot ", "message": "version 1.21\n", "time": 1487780137 }, "_maintainer": { "name": "Luke Jostins", "email": "luke.jostins@kennedy.ox.ac.uk", "login": "lowk", "description": "", "uuid": 8233299 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "kinship2", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 1, "_contributors": [ { "user": "lukejostins", "count": 2, "uuid": 181030 }, { "user": "lowk", "count": 1, "uuid": 8233299 } ], "_userbio": { "uuid": 8233299, "type": "user", "name": "lowk" }, "_downloads": { "count": 576, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/Mangrove" }, "_mentions": 3, "_searchresults": 15, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/Mangrove.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "lowk", "_cranurl": false, "_releases": [ { "version": "1.0", "date": "2011-10-26" }, { "version": "1.1", "date": "2012-03-08" }, { "version": "1.21", "date": "2017-02-22" } ], "_exports": [ "applyBetas", "applyORs", "calcBetas", "calcORs", "getVarExp", "getVarExpSim", "initialiseTree", "plot.MangroveBetas", "plot.MangroveContPreds", "plot.MangroveORs", "plot.MangrovePed", "plot.MangroveRiskPreds", "plot.MangroveSample", "plot.MangroveTree", "plotNaivePrev", "plotSampledPrev", "print.MangroveBetas", "print.MangroveContPreds", "print.MangroveORs", "print.MangrovePed", "print.MangroveRiskPreds", "print.MangroveSample", "print.MangroveTree", "readBetas", "readORs", "readPed", "summary.MangroveBetas", "summary.MangroveContPreds", "summary.MangroveORs", "summary.MangrovePed", "summary.MangroveRiskPreds", "summary.MangroveSample", "summary.MangroveTree" ], "_datasets": [ { "name": "ccped", "title": "Example data for the Mangrove vignette", "object": "ccped", "file": "ccped.rda", "class": [ "MangrovePed", "data.frame" ], "fields": [ "Family", "ID", "Mother", "Father", "Sex", "Phenotype", "SNP1.1", "SNP1.2", "SNP2.1", "SNP2.2", "SNP3.1", "SNP3.2", "SNP4.1", "SNP4.2" ], "rows": 20000, "table": true, "tojson": true }, { "name": "contped", "title": "Example data for the Mangrove vignette", "object": "contped", "file": "contped.rda", "class": [ "MangrovePed", "data.frame" ], "fields": [ "Family", "ID", "Father", "Mother", "Sex", "Phenotype", "rs2284746.1", "rs2284746.2", "rs1738475.1", "rs1738475.2", "rs4601530.1", "rs4601530.2", "rs7532866.1", "rs7532866.2", "rs2154319.1", "rs2154319.2", "rs17391694.1", "rs17391694.2", "rs6699417.1", "rs6699417.2", "rs10874746.1", "rs10874746.2", "rs9428104.1", "rs9428104.2", "rs11205277.1", "rs11205277.2", "rs17346452.1", "rs17346452.2", "rs1325598.1", "rs1325598.2", "rs1046934.1", "rs1046934.2", "rs10863936.1", "rs10863936.2", "rs6684205.1", "rs6684205.2", "rs11118346.1", "rs11118346.2", "rs10799445.1", "rs10799445.2", "rs4665736.1", "rs4665736.2", "rs6714546.1", "rs6714546.2", "rs17511102.1", "rs17511102.2", "rs2341459.1", "rs2341459.2", "rs12474201.1", "rs12474201.2", "rs3791675.1", "rs3791675.2", "rs11684404.1", "rs11684404.2", "rs7567288.1", "rs7567288.2", "rs7567851.1", "rs7567851.2", "rs1351164.1", "rs1351164.2", "rs12470505.1", "rs12470505.2", "rs2629046.1", "rs2629046.2", "rs2580816.1", "rs2580816.2", "rs12694997.1", "rs12694997.2", "rs2597513.1", "rs2597513.2", "rs13088462.1", "rs13088462.2", "rs2336725.1", "rs2336725.2", "rs9835332.1", "rs9835332.2", "rs17806888.1", "rs17806888.2", "rs9863706.1", "rs9863706.2", "rs6439167.1", "rs6439167.2", "rs9844666.1", "rs9844666.2", "rs724016.1", "rs724016.2", "rs572169.1", "rs572169.2", "rs720390.1", "rs720390.2", "rs2247341.1", "rs2247341.2", "rs6449353.1", "rs6449353.2", "rs17081935.1", "rs17081935.2", "rs7697556.1", "rs7697556.2", "rs788867.1", "rs788867.2", "rs10010325.1", "rs10010325.2", "rs7689420.1", "rs7689420.2", "rs955748.1", "rs955748.2", "rs1173727.1", "rs1173727.2", "rs11958779.1", "rs11958779.2", "rs10037512.1", "rs10037512.2", "rs13177718.1", "rs13177718.2", "rs1582931.1", "rs1582931.2", "rs274546.1", "rs274546.2", "rs526896.1", "rs526896.2", "rs4282339.1", "rs4282339.2", "rs12153391.1", "rs12153391.2", "rs889014.1", "rs889014.2", "rs422421.1", "rs422421.2", "rs6879260.1", "rs6879260.2", "rs3812163.1", "rs3812163.2", "rs1047014.1", "rs1047014.2", "rs806794.1", "rs806794.2", "rs3129109.1", "rs3129109.2", "rs2256183.1", "rs2256183.2", "rs6457620.1", "rs6457620.2", "rs2780226.1", "rs2780226.2", "rs6457821.1", "rs6457821.2", "rs9472414.1", "rs9472414.2", "rs9360921.1", "rs9360921.2", "rs310405.1", "rs310405.2", "rs7759938.1", "rs7759938.2", "rs1046943.1", "rs1046943.2", "rs961764.1", "rs961764.2", "rs1490384.1", "rs1490384.2", "rs6569648.1", "rs6569648.2", "rs7763064.1", "rs7763064.2", "rs543650.1", "rs543650.2", "rs9456307.1", "rs9456307.2", "rs798489.1", "rs798489.2", "rs4470914.1", "rs4470914.2", "rs12534093.1", "rs12534093.2", "rs1708299.1", "rs1708299.2", "rs6959212.1", "rs6959212.2", "rs42235.1", "rs42235.2", "rs822552.1", "rs822552.2", "rs2110001.1", "rs2110001.2", "rs1013209.1", "rs1013209.2", "rs7460090.1", "rs7460090.2", "rs6473015.1", "rs6473015.2", "rs6470764.1", "rs6470764.2", "rs12680655.1", "rs12680655.2", "rs7864648.1", "rs7864648.2", "rs11144688.1", "rs11144688.2", "rs7853377.1", "rs7853377.2", "rs8181166.1", "rs8181166.2", "rs2778031.1", "rs2778031.2", "rs9969804.1", "rs9969804.2", "rs1257763.1", "rs1257763.2", "rs473902.1", "rs473902.2", "rs7027110.1", "rs7027110.2", "rs1468758.1", "rs1468758.2", "rs751543.1", "rs751543.2", "rs7466269.1", "rs7466269.2", "rs7849585.1", "rs7849585.2", "rs7909670.1", "rs7909670.2", "rs2145998.1", "rs2145998.2", "rs11599750.1", "rs11599750.2", "rs2237886.1", "rs2237886.2", "rs7926971.1", "rs7926971.2", "rs1330.1", "rs1330.2", "rs10838801.1", "rs10838801.2", "rs1814175.1", "rs1814175.2", "rs5017948.1", "rs5017948.2", "rs3782089.1", "rs3782089.2", "rs7112925.1", "rs7112925.2", "rs634552.1", "rs634552.2", "rs494459.1", "rs494459.2", "rs654723.1", "rs654723.2", "rs2856321.1", "rs2856321.2", "rs10770705.1", "rs10770705.2", "rs2638953.1", "rs2638953.2", "rs2066807.1", "rs2066807.2", "rs1351394.1", "rs1351394.2", "rs10748128.1", "rs10748128.2", "rs11107116.1", "rs11107116.2", "rs7971536.1", "rs7971536.2", "rs11830103.1", "rs11830103.2", "rs7332115.1", "rs7332115.2", "rs3118905.1", "rs3118905.2", "rs7319045.1", "rs7319045.2", "rs1950500.1", "rs1950500.2", "rs2093210.1", "rs2093210.2", "rs1570106.1", "rs1570106.2", "rs862034.1", "rs862034.2", "rs7155279.1", "rs7155279.2", "rs16964211.1", "rs16964211.2", "rs7178424.1", "rs7178424.2", "rs10152591.1", "rs10152591.2", "rs12902421.1", "rs12902421.2", "rs5742915.1", "rs5742915.2", "rs11259936.1", "rs11259936.2", "rs16942341.1", "rs16942341.2", "rs2871865.1", "rs2871865.2", "rs4965598.1", "rs4965598.2", "rs11648796.1", "rs11648796.2", "rs26868.1", "rs26868.2", "rs1659127.1", "rs1659127.2", "rs8052560.1", "rs8052560.2", "rs4640244.1", "rs4640244.2", "rs3110496.1", "rs3110496.2", "rs3764419.1", "rs3764419.2", "rs17780086.1", "rs17780086.2", "rs1043515.1", "rs1043515.2", "rs4986172.1", "rs4986172.2", "rs2072153.1", "rs2072153.2", "rs4605213.1", "rs4605213.2", "rs227724.1", "rs227724.2", "rs2079795.1", "rs2079795.2", "rs2665838.1", "rs2665838.2", "rs11867479.1", "rs11867479.2", "rs4800452.1", "rs4800452.2", "rs9967417.1", "rs9967417.2", "rs17782313.1", "rs17782313.2", "rs12982744.1", "rs12982744.2", "rs7507204.1", "rs7507204.2", "rs891088.1", "rs891088.2", "rs4072910.1", "rs4072910.2", "rs2279008.1", "rs2279008.2", "rs17318596.1", "rs17318596.2", "rs1741344.1", "rs1741344.2", "rs2145272.1", "rs2145272.2", "rs7274811.1", "rs7274811.2", "rs143384.1", "rs143384.2", "rs237743.1", "rs237743.2", "rs2834442.1", "rs2834442.2", "rs4821083.1", "rs4821083.2" ], "rows": 1000, "table": true, "tojson": true }, { "name": "exampleBetas", "title": "Example data for the Mangrove vignette", "object": "exampleBetas", "file": "exampleBetas.rda", "class": [ "MangroveBetas", "data.frame" ], "fields": [ "rsID", "RiskAllele", "beta", "Freq", "betaBar" ], "rows": 179, "table": true, "tojson": true }, { "name": "exampleORs", "title": "Example data for the Mangrove vignette", "object": "exampleORs", "file": "exampleORs.rda", "class": [ "MangroveORs", "data.frame" ], "fields": [ "rsID", "RiskAllele", "ORhet", "ORhom", "Freq", "meanOR" ], "rows": 4, "table": true, "tojson": true }, { "name": "famped", "title": "Example data for the Mangrove vignette", "object": "famped", "file": "famped.rda", "class": [ "MangrovePed", "data.frame" ], "fields": [ "Family", "ID", "Mother", "Father", "Sex", "Phenotype", "SNP1.1", "SNP1.2", "SNP2.1", "SNP2.2", "SNP3.1", "SNP3.2", "SNP4.1", "SNP4.2" ], "rows": 19, "table": true, "tojson": true }, { "name": "mendT", "title": "Internal Mangrove objects", "object": "mendT", "file": "mendT.rda", "class": [ "array" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "Mangrove-package", "title": "Mangrove: Risk prediction on trees", "topics": [ "Mangrove-package", "Mangrove" ] }, { "page": "getVarExp", "title": "Calculating liability-scale variance explained by genetic risk variants", "topics": [ "getVarExp", "getVarExpSim" ] }, { "page": "MangroveBetas", "title": "The MangroveBetas class", "topics": [ "MangroveBetas", "plot.MangroveBetas", "print.MangroveBetas", "readBetas", "summary.MangroveBetas" ] }, { "page": "MangroveContPreds", "title": "The MangroveContPreds class", "topics": [ "applyBetas", "calcBetas", "MangroveContPreds", "plot.MangroveContPreds", "print.MangroveContPreds", "summary.MangroveContPreds" ] }, { "page": "MangroveExamples", "title": "Example data for the Mangrove vignette", "topics": [ "ccped", "contped", "exampleBetas", "exampleORs", "famped", "MangroveExamples" ] }, { "page": "MangroveORs", "title": "The MangroveORs class", "topics": [ "MangroveORs", "plot.MangroveORs", "print.MangroveORs", "readORs", "summary.MangroveORs" ] }, { "page": "MangrovePed", "title": "The MangrovePed class", "topics": [ "MangrovePed", "plot.MangrovePed", "print.MangrovePed", "readPed", "summary.MangrovePed" ] }, { "page": "MangroveRiskPreds", "title": "The MangroveRiskPreds class", "topics": [ "applyORs", "calcORs", "MangroveRiskPreds", "plot.MangroveRiskPreds", "print.MangroveRiskPreds", "summary.MangroveRiskPreds" ] }, { "page": "MangroveSample", "title": "The MangroveSample class", "topics": [ "MangroveSample", "plot.MangroveSample", "print.MangroveSample", "summary.MangroveSample" ] }, { "page": "MangroveTree", "title": "The MangroveTree class", "topics": [ "addPed", "getPrevs", "initialiseTree", "MangroveTree", "plot.MangroveTree", "print.MangroveTree", "summary.MangroveTree" ] }, { "page": "plotSampledPrev", "title": "Plotting expected", "topics": [ "plotNaivePrev", "plotSampledPrev" ] } ], "_rundeps": [], "_vignettes": [ { "source": "Mangrove.Rnw", "filename": "Mangrove.pdf", "title": "Mangrove", "engine": "utils::Sweave", "headings": [], "created": "2017-02-22 16:15:37", "modified": "2017-02-22 16:15:37", "commits": 1 } ], "_score": 2.653212513775344, "_indexed": true, "_nocasepkg": "mangrove", "_universes": [ "lowk" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21", "date": "2026-05-19T06:55:46.000Z", "distro": "noble", "commit": "a302411add434c6056126a3fd3eded27339d47aa", "fileid": "a8b612c365b90c3cfdb20ccf5820e69c81c4cd6223e1f703dc76fd3308a3ae11", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/lowk/actions/runs/26081245172" }, { "r": "4.6.0", "os": "linux", "version": "1.21", "date": "2026-05-19T06:55:44.000Z", "distro": "noble", "commit": "a302411add434c6056126a3fd3eded27339d47aa", "fileid": "842af32ff41fd77071974d32c2f09cdec0a39f0bdecbc7b5202b5d5723506d29", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/lowk/actions/runs/26081245172" }, { "r": "4.5.3", "os": "mac", "version": "1.21", "date": "2026-05-19T06:56:24.000Z", "commit": "a302411add434c6056126a3fd3eded27339d47aa", "fileid": "8959be917cc82585808985665c58e38a81e5c707497f363f1b719d4286da2e8e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/lowk/actions/runs/26081245172" }, { "r": "4.6.0", "os": "mac", "version": "1.21", "date": "2026-05-19T06:56:23.000Z", "commit": "a302411add434c6056126a3fd3eded27339d47aa", "fileid": "5997a67e8f80c6a5781803ed4efecc1a76e6646a5bbf13bb6605e35f44c185d8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/lowk/actions/runs/26081245172" }, { "r": "4.7.0", "os": "win", "version": "1.21", "date": "2026-05-19T06:55:07.000Z", "commit": "a302411add434c6056126a3fd3eded27339d47aa", "fileid": "4b7ae36384c5d7aa64a2a0ef3a508e1e670338686a060132e3244697a719b727", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/lowk/actions/runs/26081245172" }, { "r": "4.5.3", "os": "win", "version": "1.21", "date": "2026-05-19T06:55:16.000Z", "commit": "a302411add434c6056126a3fd3eded27339d47aa", "fileid": "5f4f00db4349084e4dce9bb06751073b8484e13b9eca3df398b5c03685f943f1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/lowk/actions/runs/26081245172" }, { "r": "4.6.0", "os": "win", "version": "1.21", "date": "2026-05-19T06:55:23.000Z", "commit": "a302411add434c6056126a3fd3eded27339d47aa", "fileid": "3e209dc60c7a8248ca0a637aee9b7a40b2d9de8f0aee3887bcb297fe5e85fd2d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/lowk/actions/runs/26081245172" }, { "r": "4.6.0", "os": "wasm", "version": "1.21", "date": "2026-06-02T15:22:08.000Z", "commit": "a302411add434c6056126a3fd3eded27339d47aa", "fileid": "b2056b6be5872310155e2f7422bb691946b73387e8cd4106c764b826dd46161c", "status": "success", "buildurl": "https://github.com/r-universe/lowk/actions/runs/26081245172" } ] }