{ "_id": "6a227cbbcd65a98ecbd4f0a3", "Package": "aIc", "Type": "Package", "Title": "Testing for Compositional Pathologies in Datasets", "Version": "1.0", "Date": "2022-09-27", "Author": "Greg Gloor", "Maintainer": "Greg Gloor ", "Description": "A set of tests for compositional pathologies. Tests for\ncoherence of correlations with aIc.coherent() as suggested by\n(Erb et al. (2020) ),\ncompositional dominance of distance with aIc.dominant(),\ncompositional perturbation invariance with aIc.perturb() as\nsuggested by (Aitchison (1992) ) and\nsingularity of the covariation matrix with aIc.singular().\nCurrently tests five data transformations: prop, clr, TMM,\nTMMwsp, and RLE from the R packages 'ALDEx2', 'edgeR' and\n'DESeq2' (Fernandes et al (2014) ,\nAnders et al. (2013)).", "License": "GPL (>= 3)", "Encoding": "UTF-8", "URL": "https://github.com/ggloor/aIc", "BugReports": "https://github.com/ggloor/aIc/issues", "RoxygenNote": "7.2.1", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake make libjpeg-dev libpng-dev libuv1-dev\nzlib1g-dev", "Repository": "https://ggloor.r-universe.dev", "Date/Publication": "2024-01-18 19:41:42 UTC", "RemoteUrl": "https://github.com/ggloor/aic", "RemoteRef": "HEAD", "RemoteSha": "ada8f7e396ebb275dcd22b2af6123681dd1c8b4e", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-05 07:21:20 UTC", "User": "root" }, "MD5sum": "003fe9bf01e23d7d585d07612c8045b2", "_user": "ggloor", "_type": "src", "_file": "aIc_1.0.tar.gz", "_fileid": "ee78241e4fc07895a9978b361d031fc20e859630424ec475e42c7288322d7dbc", "_filesize": 3250139, "_sha256": "ee78241e4fc07895a9978b361d031fc20e859630424ec475e42c7288322d7dbc", "_created": "2026-06-05T07:21:20.000Z", "_published": "2026-06-05T07:37:31.378Z", "_distro": "noble", "_jobs": [ { "job": 79682589901, "time": 265, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7431084609" }, { "job": 79682589882, "time": 272, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7431086673" }, { "job": 79682589907, "time": 207, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7431262769" }, { "job": 79682589879, "time": 263, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7431263611" }, { "job": 79682066727, "time": 242, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7431012157" }, { "job": 79682589880, "time": 142, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7431050383" }, { "job": 79682589898, "time": 237, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7431076938" }, { "job": 79682589928, "time": 229, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7431074674" }, { "job": 79682590069, "time": 236, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7431076631" } ], "_buildurl": "https://github.com/r-universe/ggloor/actions/runs/27001260325", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/ggloor/aic", "_commit": { "id": "ada8f7e396ebb275dcd22b2af6123681dd1c8b4e", "author": "ggloor ", "committer": "ggloor ", "message": "added entropy normalization\n", "time": 1705606902 }, "_maintainer": { "name": "Greg Gloor", "email": "ggloor@uwo.ca", "login": "ggloor", "description": "", "uuid": 6034128 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "matrixcalc", "role": "Imports" }, { "package": "zCompositions", "role": "Imports" }, { "package": "shiny", "role": "Imports" }, { "package": "edgeR", "role": "Imports" }, { "package": "ALDEx2", "role": "Imports" }, { "package": "vegan", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "ggloor", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 2, "_contributors": [ { "user": "ggloor", "count": 28, "uuid": 6034128 } ], "_userbio": { "uuid": 6034128, "type": "user", "name": "Greg Gloor" }, "_downloads": { "count": 268, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/aIc" }, "_devurl": "https://github.com/ggloor/aic", "_searchresults": 11, "_rbuild": "4.6.0", "_assets": [ "extra/aIc.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/ggloor/aic", "_realowner": "ggloor", "_cranurl": true, "_releases": [ { "version": "1.0", "date": "2022-10-05" } ], "_exports": [ "aIc.coherent", "aIc.dominant", "aIc.perturb", "aIc.plot", "aIc.runExample", "aIc.scale", "aIc.singular" ], "_datasets": [ { "name": "meta16S", "title": "16S rRNA tag-sequencing data", "object": "meta16S", "file": "meta16S.rda", "class": [ "data.frame" ], "fields": [ "pup.1", "pup.2", "pup.3", "pup.4", "pup.5", "pup.6", "pup.7", "pup.8", "pup.9", "pup.10", "pup.11", "pup.12", "pup.13", "pup.14", "pup.15", "pup.16", "pup.17", "pup.18", "pup.19", "pup.20", "pup.21", "pup.22", "pup.23", "pup.24", "pup.25", "pup.26", "pup.27", "pup.28", "pup.29", "pup.30", "pup.31", "pup.32", "pup.33", "pup.34", "pup.35", "pup.36", "pup.37", "pup.38", "pup.39", "pup.40", "pup.41", "pup.42", "pup.43", "pup.44", "pup.45", "pup.46", "pup.47", "pup.48", "pup.49", "pup.50", "pup.51", "pup.52", "pup.53", "pup.54", "pup.55", "pup.56", "pup.57", "pup.58", "pup.59", "pup.60", "pup.61", "pup.62", "pup.63", "pup.64", "pup.65", "pup.66", "pup.67", "pup.68", "pup.69", "pup.70", "pup.71", "pup.72", "pup.73", "pup.74", "pup.75", "pup.76", "pup.77", "pup.78", "pup.79", "pup.80", "pup.81", "pup.82", "pup.83", "pup.84", "pup.85", "pup.86", "pup.87", "pup.88", "pup.89", "pup.90", "pup.91", "pup.92", "pup.93", "pup.94", "pup.95", "pup.96", "pup.97", "pup.98", "pup.99", "pup.100", "pup.101", "pup.102", "pup.103", "pup.104", "pup.105", "pup.106", "pup.107", "pup.108", "pup.109", "pup.110", "pup.111", "pup.112", "pup.113", "pup.114", "pup.115", "pup.116", "pup.117", "pup.118", "pup.119", "pup.120", "pup.121", "pup.122", "pup.123", "pup.124", "pup.125", "pup.126", "pup.127", "pup.128", "pup.129", "pup.130", "pup.131", "pup.132", "pup.133", "pup.134", "pup.135", "pup.136", "pup.137", "pup.138", "pup.139", "pup.140", "pup.141", "pup.142", "pup.143", "pup.144", "pup.145", "pup.146", "pup.147", "pup.148", "pup.149", "pup.150", "pup.151", "pup.152", "pup.153", "pup.154", "pup.155", "pup.156", "pup.157", "pup.158", "pup.159", "pup.160", "pup.161", "pup.162", "pup.163", "pup.164", "pup.165", "pup.166", "pup.167", "pup.168", "pup.169", "pup.170", "pup.171", "pup.172", "pup.173", "pup.174", "pup.175", "pup.176", "pup.177", "pup.178", "pup.179", "pup.180", "pup.181", "pup.182", "pup.183", "pup.184", "pup.185", "pup.186", "pup.187", "pup.188", "pup.189", "pup.190", "pup.191", "pup.192", "pup.193", "pup.194", "pup.195", "pup.196", "pup.197", "pup.198", "cent.1", "cent.2", "cent.3", "cent.4", "cent.5", "cent.6", "cent.7", "cent.8", "cent.9", "cent.10", "cent.11", "cent.12", "cent.13", "cent.14", "cent.15", "cent.16", "cent.17", "cent.18", "cent.19", "cent.20", "cent.21", "cent.22", "cent.23", "cent.24", "cent.25", "cent.26", "cent.27", "cent.28", "cent.29", "cent.30", "cent.31", "cent.32", "cent.33", "cent.34", "cent.35", "cent.36", "cent.37", "cent.38", "cent.39", "cent.40", "cent.41", "cent.42", "cent.43", "cent.44", "cent.45", "cent.46", "cent.47", "cent.48", "cent.49", "cent.50", "cent.51", "cent.52", "cent.53", "cent.54", "cent.55", "cent.56", "cent.57", "cent.58", "cent.59", "cent.60", "cent.61", "cent.62", "cent.63", "cent.64", "cent.65", "cent.66", "cent.67", "cent.68", "cent.69", "cent.70", "cent.71", "cent.72", "cent.73", "cent.74", "cent.75", "cent.76", "cent.77", "cent.78", "cent.79", "cent.80", "cent.81", "cent.82", "cent.83", "cent.84", "cent.85", "cent.86", "cent.87", "cent.88", "cent.89", "cent.90", "cent.91", "cent.92", "cent.93", "cent.94", "cent.95", "cent.96", "cent.97", "cent.98", "cent.99", "cent.100", "cent.101", "cent.102", "cent.103", "cent.104", "cent.105", "cent.106", "cent.107", "cent.108", "cent.109", "cent.110", "cent.111", "cent.112", "cent.113", "cent.114", "cent.115", "cent.116", "cent.117", "cent.118", "cent.119", "cent.120", "cent.121", "cent.122", "cent.123", "cent.124", "cent.125", "cent.126", "cent.127", "cent.128", "cent.129", "cent.130", "cent.131", "cent.132", "cent.133", "cent.134", "cent.135", "cent.136", "cent.137", "cent.138", "cent.139", "cent.140", "cent.141", "cent.142", "cent.143", "cent.144", "cent.145", "cent.146", "cent.147", "cent.148", "cent.149", "cent.150", "cent.151", "cent.152", "cent.153", "cent.154", "cent.155", "cent.156", "cent.157", "cent.158", "cent.159", "cent.160", "cent.161" ], "rows": 860, "table": true, "tojson": true }, { "name": "metaTscome", "title": "meta-transcriptome data", "object": "metaTscome", "file": "metaTscome.rda", "class": [ "data.frame" ], "fields": [ "h.001B", "h.002B", "h.004B", "h.006B", "h.009B", "h.010B", "h.020B", "v.006A", "v.008A", "v.009A", "v.010A", "v.012B", "v.014B", "v.018B", "v.017B", "v.012A", "v.013A" ], "rows": 3647, "table": true, "tojson": true }, { "name": "selex", "title": "Selection-based differential sequence variant abundance dataset", "object": "selex", "file": "selex.rda", "class": [ "data.frame" ], "fields": [ "X1_ANS", "X1_BNS", "X1_CNS", "X1_DNS", "X2_ANS", "X2_CNS", "X2_DNS", "X1_AS", "X1_BS", "X1_CS", "X1_DS", "X2_AS", "X2_CS", "X2_DS" ], "rows": 1600, "table": true, "tojson": true }, { "name": "singleCell", "title": "single cell transcriptome data", "object": "singleCell", "file": "singleCell.rda", "class": [ "data.frame" ], "fields": [ "R2", "R5", "R12", "R15", "R16", "R19", "R32", "R37", "R39", "R40", "R43", "R48", "R49", "R56", "R60", "R64", "R65", "R67", "R70", "R71", "R84", "R85", "R86", "R87", "R90", "R91", "R99", "R116", "R119", "R122", "R129", "R133", "R136", "R139", "R149", "R152", "R157", "R158", "R165", "R167", "R171", "R176", "R177", "R183", "R187", "R188", "R189", "R193", "R194", "R200", "R206", "R211", "R213", "R214", "R220", "R222", "R224", "R226", "R227", "R237", "R238", "R239", "R265", "R267", "R271", "R277", "R278", "R285", "R286", "R289", "R291", "R292", "R297", "R301", "R302", "R305", "R309", "R310", "R316", "R317", "R319", "R320", "R325", "R335", "R340", "R344", "R350", "R354", "R366", "R370", "R372", "R383", "R384", "R385", "R387", "R389", "R400", "R402", "R406", "R407", "R411", "R413", "R414", "R423", "R428", "R433", "R444", "R448", "R452", "R460", "R468", "R473", "R476", "R478", "R482", "R492", "R496", "R497", "R501", "R502", "R503", "R506", "R515", "R516", "R538", "R543", "R556", "R559", "R561", "R566", "R571", "R572", "R575", "R580", "R585", "R590", "R592", "R593", "R594", "R595", "R602", "R603", "R617", "R620", "R621", "R622", "R625", "R633", "R638", "R641", "R645", "R646", "R653", "R662", "R665", "R667", "R676", "R677", "R681", "R685", "R689", "R692", "R696", "R701", "R703", "R712", "R716", "R717", "R718", "R722", "R723", "R724", "R726", "R730", "R732", "R733", "R735", "R736", "R738", "R740", "R741", "R744", "R745", "R751", "R754", "R760", "R767", "R775", "R777", "R778", "R792", "R798", "R802", "R804", "R810", "R811", "R815", "R817", "R821", "R823", "R825", "R830", "R837", "R838", "R847", "R853", "R858", "R861", "R864", "R867", "R868", "R871", "R881", "R883", "R888", "R890", "R895", "R897", "R898", "R901", "R906", "R911", "R916", "R920", "R921", "R925", "R926", "R932", "R943", "R944", "R951", "R953", "R954", "R957", "R961", "R974", "R979", "R990", "R991", "R994", "R995", "R998", "R1003", "R1008", "R1016", "R1033", "R1034", "R1041", "R1043", "R1049", "R1054", "R1057", "R1062", "R1074", "R1079", "R1086", "R1088", "R1095", "R1100", "R1105", "R1118", "R1121", "R1123", "R1124", "R1127", "R1140", "R1147", "R1149", "R1153", "R1157", "R1158", "R1165", "R1171", "R1173", "R1174", "R1179", "R1181", "R1185", "R1186", "R1191", "R1192", "R1193", "R1194", "R1197", "R1198", "R1202", "R1206", "R1207", "R1212", "R1215", "R1222", "R1227", "R1234", "R1240", "R1245", "R1249", "R1250", "R1255", "R1260", "R1264", "R1266", "R1272", "R1273", "R1274", "R1275", "R1276", "R1289", "R1290", "R1305", "R1311", "R1312", "R1318", "R1322", "R1326", "R1335", "R1337", "R1346", "R1360", "R1366", "R1369", "R1370", "R1374", "R1388", "R1390", "R1397", "R1405", "R1411", "R1413", "R1420", "R1421", "R1422", "R1428", "R1429", "R1433", "R1436", "R1437", "R1448", "R1449", "R1450", "R1458", "R1460", "R1464", "R1467", "R1468", "R1471", "R1478", "R1483", "R1485", "R1489", "R1491", "R1493", "R1495", "R1497", "R1498", "R1502", "R1504", "R1508", "R1511", "R1514", "R1518", "R1520", "R1524", "R1535", "R1537", "R1538", "R1541", "R1542", "R1543", "R1547", "R1549", "R1551", "R1562", "R1570", "R1576", "R1578", "R1587", "R1592", "R1594", "R1595", "R1604", "R1605", "R1608", "R1614", "R1620", "R1622", "R1623", "R1627", "R1628", "R1630", "R1632", "R1635", "R1636", "R1640", "R1646", "R1648", "R1657", "R1658", "R1662", "R1671", "R1672", "R1676", "R1678", "R1679", "R1683", "R1687", "R1688", "R1691", "R1692", "R1699", "R1705", "R1706", "R1708", "R1714", "R1715", "R1733", "R1735", "R1745", "R1748", "R1750", "R1752", "R1756", "R1759", "R1760", "R1763", "R1772", "R1788", "R1790", "R1792", "R1796", "R1799", "R1804", "R1808", "R1812", "R1813", "R1820", "R1829", "R1831", "R1845", "R1847", "R1848", "R1849", "R1860", "R1866", "R1867", "R1873", "R1876", "R1881", "R1886", "R1893", "R1894", "R1907", "R1908", "R1910", "R1912", "R1913", "R1914", "R1915", "R1918", "R1920", "R1934", "R1944", "R1947", "R1948", "R1954", "R1956", "R1964", "R1967", "R1971", "R1972", "R1977", "R1988", "R1990", "R1991", "R1994", "R1995", "R1998", "R2008", "R2011", "R2012", "R2014", "R2015", "R2018", "R2019", "R2021", "R2027", "R2030", "R2035", "R2037", "R2044", "R2047", "R2050", "R2051", "R2055", "R2056", "R2059", "R2064", "R2080", "R2086", "R2089", "R2094", "R2100", "R2111", "R2113", "R2117", "R2119", "R2120", "R2124", "R2128", "R2133", "R2137", "R2140", "R2141", "R2142", "R2150", "R2166", "R2168", "R2171", "R2174", "R2177", "R2178", "R2185", "R2192", "R2193", "R2196", "R2197", "R2199", "R2202", "R2203", "R2213", "R2215", "R2218", "R2220", "R2235", "R2239", "R2242", "R2251", "R2253", "R2255", "R2256", "R2263", "R2264", "R2266", "R2270", "R2273", "R2281", "R2284", "R2291", "R2298", "R2303", "R2309", "R2310", "R2313", "R2314", "R2315", "R2318", "R2319", "R2325", "R2331", "R2332", "R2336", "R2337", "R2344", "R2346", "R2352", "R2358", "R2363", "R2367", "R2368", "R2369", "R2370", "R2375", "R2382", "R2383", "R2393", "R2395", "R2396", "R2399", "R2400", "R2411", "R2428", "R2437", "R2443", "R2444", "R2445", "R2450", "R2456", "R2462", "R2464", "R2469", "R2476", "R2478", "R2479", "R2499", "R2500", "R2504", "R2513", "R2516", "R2524", "R2525", "R2533", "R2537", "R2543", "R2544", "R2547", "R2551", "R2558", "R2559", "R2576", "R2579", "R2583", "R2586", "R2590", "R2591", "R2596", "R2599", "R2601", "R2616", "R2618", "R2620", "R2621", "R2622", "R2623", "R2634", "R2635", "R2637", "R2638", "R2647", "R2654", "R2657", "R2662", "R2676", "R2679", "R2680", "R2689", "R2690", "R2705", "R2706", "R2709", "R2716", "R2733", "R2736", "R2750", "R2759", "R2760", "R2772", "R2776", "R2779", "R2780", "R2781", "R2782", "R2787", "R2791", "R2795", "R2800", "R2814", "R2818", "R2821", "R2826", "R2851", "R2853", "R2861", "R2862", "R2864", "R2865", "R2868", "R2871", "R2874", "R2877", "R2887", "R2889", "R2895", "R2898", "R2901", "R2903", "R2910", "R2912", "R2913", "R2916", "R2919", "R2929", "R2933", "R2935", "R2939", "R2941", "R2943", "R2948", "R2952", "R2954", "R2958", "R2961", "R2962", "R2971", "R2977", "R2978", "R2985", "R2988", "R2990", "R2994", "R3007", "R3008", "R3009", "R3014", "R3017", "R3020", "R3021", "R3028", "R3030", "R3034", "R3037", "R3039", "R3044", "R3046", "R3048", "R3053", "R3057", "R3061", "R3064", "R3069", "R3078", "R3079", "R3084", "R3086", "R3090", "R3091", "R3099", "R3102", "R3105", "R3110", "R3114", "R3115", "R3120", "R3121", "R3122", "R3124", "R3127", "R3128", "R3138", "R3139", "R3140", "R3151", "R3156", "R3157", "R3170", "R3173", "R3175", "R3179", "R3183", "R3185", "R3190", "R3197", "R3199", "R3201", "R3203", "R3204", "R3210", "R3212", "R3213", "R3215", "R3216", "R3221", "R3222", "R3226", "R3237", "R3262", "R3269", "R3282", "R3284", "R3285", "R3286", "R3287", "R3288", "R3294", "R3302", "R3303", "R3307", "R3310", "R3316", "R3320", "R3325", "R3329", "R3333", "R3338", "R3356", "R3359", "R3369", "R3370", "R3373", "R3375", "R3388", "R3394", "R3399", "R3401", "R3404", "R3418", "R3422", "R3424", "R3426", "R3427", "R3429", "R3430", "R3431", "R3434", "R3435", "R3436", "R3437", "R3449", "R3452", "R3454", "R3459", "R3461", "R3472", "R3473", "R3474", "R3479", "R3484", "R3485", "R3488", "R3489", "R3493", "R3494", "R3498", "R3505", "R3510", "R3516", "R3518", "R3519", "R3523", "R3528", "R3531", "R3533", "R3534", "R3537", "R3539", "R3540", "R3541", "R3542", "R3543", "R3544", "R3545", "R3555", "R3559", "R3571", "R3579", "R3589", "R3593", "R3605", "R3611", "R3621", "R3623", "R3632", "R3639", "R3647", "R3648", "R3653", "R3657", "R3669", "R3670", "R3671", "R3672", "R3678", "R3679", "R3680", "R3682", "R3686", "R3687", "R3697", "R3703", "R3704", "R3733", "R3735", "R3737", "R3739", "R3741", "R3744", "R3745", "R3746", "R3749", "R3753", "R3758", "R3773", "R3774", "R3779", "R3782", "R3783", "R3786", "R3790", "R3792", "R3794", "R3805", "R3808", "R3816", "R3820", "R3823", "R3827", "R3831", "R3833", "R3841", "R3842", "R3851", "R3853", "R3856", "R3857", "R3862", "R3865", "R3867", "R3870", "R3878", "R3885", "R3890", "R3897", "R3909", "R3914", "R3924", "R3931", "R3934", "R3938", "R3939", "R3952", "R3953", "R3961", "R3966", "R3968", "R3970", "R3972", "R3977", "R3979", "R3980", "R3981", "R3984", "R3985", "R3992", "R4004", "R4009", "R4016", "R4022", "R4023", "R4025", "R4026", "R4029", "R4040", "R4045", "R4051", "R4052", "R4054", "R4058", "R4059", "R4068", "R4069", "R4076", "R4077", "R4078", "R4084", "R4086", "R4093", "R4094", "R4097", "R4111", "R4113", "R4116", "R4121", "R4122", "R4124", "R4125", "R4126", "R4129", "R4131", "R4133", "R4134", "R4135", "R4136", "R4137", "R4139", "R4147", "R4152", "R4153", "R4160", "R4163", "R4166", "R4170", "R4171", "R4174", "R4175", "R4178", "R4187", "R4188", "R4190", "R4201", "R4202", "R4203", "R4206", "R4227", "R4234", "R4238", "R4241", "R4244", "R4245", "R4249", "R4258", "R4259", "R4278", "B2319", "B2321", "B2329", "B2333", "B2337", "B2345", "B2353", "B2356", "B2358", "B2364", "B2367", "B2375", "B2379", "B2383", "B2386", "B2391", "B2394", "B2395", "B2396", "B2409", "B2411", "B2412", "B2430", "B2431", "B2437", "B2438", "B2442", "B2444", "B2447", "B2448", "B2461", "B2462", "B2464", "B2468", "B2470", "B2471", "B2494", "B2499", "B2511", "B2522", "B2525", "B2531", "B2532", "B2535", "B2536", "B2537", "B2538", "B2548", "B2557", "B2558", "B2559", "B2576", "B2586", "B2587", "B2590", "B2597", "B2598", "B2603", "B2605", "B2613", "B2626", "B2627", "B2631", "B2639", "B2647", "B2649", "B2653", "B2655", "B2656", "B2657", "B2662", "B2667", "B2674", "B2676", "B2677", "B2678", "B2679", "B2681", "B2682", "B2690", "B2695", "B2716", "B2725", "B2729", "B2732", "B2738", "B2740", "B2741", "B2752", "B2755", "B2760", "B2766", "B2774", "B2782", "B2784", "B2786", "B2788", "B2798", "B2809", "B2813", "B2814", "B2817", "B2821", "B2826", "B2828", "B2829", "B2830", "B2831", "B2841", "B2844", "B2850", "B2851", "B2853", "B2855", "B2863", "B2864", "B2872", "B2877", "B2878", "B2879", "B2880", "B2885", "B2886", "B2892", "B2908", "B2912", "B2916", "B2917", "B2925", "B2941", "B2943", "B2947", "B2960", "B2961", "B2970", "B2972", "B2981", "B2982", "B2987", "B2990", "B2995", "B2997", "B3001", "B3003", "B3005", "B3014", "B3025", "B3026", "B3032", "B3037", "B3039", "B3044", "B3048", "B3062", "B3063", "B3064", "B3070", "B3071", "B3076", "B3080", "B3081", "B3083", "B3084", "B3085", "B3088", "B3094", "B3098", "B3106", "B3107", "B3111", "B3113", "B3120", "B3128", "B3136", "B3140", "B3157", "B3158", "B3160", "B3161", "B3164", "B3167", "B3178", "B3179", "B3181", "B3183", "B3193", "B3198", "B3205", "B3206", "B3207", "B3211", "B3213", "B3214", "B3221", "B3223", "B3225", "B3226", "B3229", "B3236", "B3240", "B3242", "B3246", "B3247", "B3252", "B3258", "B3264", "B3266", "B3273", "B3274", "B3284", "B3295", "B3297", "B3303", "B3306", "B3311", "B3312", "B3313", "B3325", "B3328", "B3329", "B3336", "B3340", "B3345", "B3349", "B3350", "B3351", "B3364", "B3368", "B3375", "B3376", "B3378", "B3379", "B3380", "B3382", "B3390", "B3391", "B3394", "B3396", "B3407", "B3421", "B3424", "B3429", "B3433", "B3437", "B3443", "B3445", "B3448", "B3450", "B3451", "B3453", "B3459", "B3468", "B3480", "B3481", "B3486", "B3488", "B3493", "B3496", "B3497", "B3499", "B3501", "B3511", "B3514", "B3516", "B3517", "B3518", "B3519", "B3520", "B3521", "B3522", "B3526", "B3530", "B3531", "B3532", "B3534", "B3542", "B3543", "B3550", "B3563", "B3564", "B3568", "B3571", "B3574", "B3575", "B3578", "B3583", "B3594", "B3599", "B3601", "B3602", "B3604", "B3611", "B3613", "B3614", "B3617", "B3618", "B3619", "B3622", "B3628", "B3629", "B3634", "B3635", "B3637", "B3641", "B3646", "B3655", "B3658", "B3666", "B3673", "B3674", "B3683", "B3690", "B3694", "B3695", "B3699", "B3700", "B3704", "B3706", "B3712", "B3716", "B3721", "B3733", "B3736", "B3737", "B3738", "B3740", "B3741", "B3746", "B3768", "B3780", "B3781", "B3784", "B3786", "B3787", "B3792", "B3808", "B3812", "B3814", "B3826", "B3827", "B3828", "B3833", "B3839", "B3840", "B3843", "B3865", "B3870", "B3877", "B3879", "B3880", "B3883", "B3885", "B3902", "B3906", "B3918", "B3930", "B3933", "B3934", "B3939", "B3942", "B3948", "B3950", "B3967", "B3971", "B3976", "B3977", "B3979", "B3980", "B3981", "B3985", "B3988", "B3991", "B4002", "B4004", "B4006", "B4007", "B4011", "B4019", "B4021", "B4023", "B4025", "B4027", "B4032", "B4043", "B4045", "B4046", "B4047", "B4048", "B4049", "B4055", "B4061", "B4062", "B4071", "B4074", "B4076", "B4084", "B4095", "B4098", "B4099", "B4101", "B4102", "B4109", "B4115", "B4117", "B4125", "B4126", "B4131", "B4132", "B4133", "B4135", "B4146", "B4152", "B4157", "B4166", "B4169", "B4173", "B4176", "B4179", "B4180", "B4183", "B4186", "B4189", "B4190", "B4192", "B4196", "B4197", "B4200", "B4201", "B4203", "B4209", "B4210", "B4211", "B4213", "B4214", "B4225", "B4230", "B4237", "B4239", "B4241", "B4242", "B4245", "B4248", "B4253", "B4258", "B4266", "B4274", "B4279", "B4280", "B4282", "B4289", "B4291", "B4306", "B4309", "B4310", "B4319", "B4321", "B4324", "B4325", "B4326", "B4329", "B4336", "B4337", "B4343", "B4351", "B4353", "B4354", "B4356", "B4358", "B4360", "B4364", "B4365", "B4369", "B4370", "B4375", "B4378", "B4381", "B4382", "B4385", "B4392", "B4400", "B4412", "B4413", "B4418", "B4419", "B4422", "B4423", "B4430", "B4437", "B4440", "B4442", "B4446", "B4457", "B4461", "B4466", "B4468", "B4472", "B4473", "B4474", "B4481", "B4485", "B4486", "B4490", "B4494", "B4497", "B4502", "B4504", "B4505", "B4506", "B4510", "B4515", "B4523", "B4524", "B4525", "B4533", "B4535", "B4536", "B4540", "B4547", "B4548", "B4551", "B4552", "B4553", "B4560", "B4564", "B4565", "B4571", "B4578", "B4584", "B4590", "B4592", "B4594", "B4598", "B4602", "B4604", "B4617", "B4619", "B4624", "B4629", "B4631", "B4632", "B4633", "B4653", "B4654", "B4658", "B4667", "B4670", "B4671", "B4674", "B4675", "B4678", "B4679", "B4687", "B4689", "B4698", "B4701", "B4702", "B4706", "B4707", "B4714", "B4715", "B4721", "B4722", "B4724", "B4733", "B4734", "B4735", "B4736", "B4740", "B4742", "B4744", "B4749", "B4750", "B4758", "B4768", "B4769", "B4775", "B4781", "B4789", "B4791", "B4793", "B4794", "B4795", "B4800", "B4801", "B4807", "B4810", "B4811", "B4813", "B4815", "B4817", "B4825", "B4827", "B4839", "B4841", "B4842", "B4843", "B4856", "B4866", "B4869", "B4877", "B4888", "B4893", "B4896", "B4897", "B4902", "B4904", "B4905", "B4906", "B4908", "B4910", "B4912", "B4914", "B4915", "B4916", "B4918", "B4925", "B4930", "B4935", "B4939", "B4941", "B4948", "B4951", "B4953", "B4954", "B4956", "B4957", "B4958", "B4962", "B4966", "B4967", "B4968", "B4975", "B4984", "B4989", "B4990", "B4991", "B4993", "B4995", "B4997", "B5005", "B5011", "B5013", "B5016", "B5021", "B5038", "B5039", "B5042", "B5049", "B5062", "B5064", "B5067", "B5069", "B5070", "B5072", "B5074", "B5075", "B5087", "B5088", "B5091", "B5098", "B5099", "B5100", "B5102", "B5103", "B5107", "B5108", "B5110", "B5114", "B5119", "B5141", "B5143", "B5149", "B5167", "B5169", "B5170", "B5173", "B5192", "B5199", "B5200", "B5201", "B5202", "B5203", "B5207", "B5220", "B5223", "B5224", "B5226", "B5229", "B5233", "B5235", "B5236", "B5240", "B5253", "B5254", "B5255", "B5256", "B5259", "B5267", "B5273", "B5275", "B5279", "B5282", "B5289", "B5295", "B5297", "B5303", "B5316", "B5317", "B5319", "B5323", "B5325", "B5326", "B5327", "B5330", "B5335", "B5336", "B5339", "B5346", "B5350", "B5359", "B5363", "B5366", "B5369", "B5370", "B5371", "B5374", "B5381", "B5386", "B5391", "B5396", "B5398", "B5399", "B5402", "B5403", "B5405", "B5407", "B5410", "B5411", "B5424", "B5426", "B5431", "B5439", "B5440", "B5447", "B5448", "B5458", "B5460", "B5461", "B5471", "B5473", "B5474", "B5476", "B5480", "B5485", "B5489", "B5494", "B5507", "B5510", "B5516", "B5520", "B5527", "B5528", "B5529", "B5534", "B5538", "B5541", "B5543", "B5546", "B5555", "B5563", "B5569", "B5574", "B5576", "B5577", "B5578", "B5579", "B5587", "B5592", "B5596", "B5598", "B5613", "B5614", "B5617", "B5618", "B5626", "B5643", "B5646", "B5654", "B5659", "B5665", "B5687", "B5694", "B5698", "B5708", "B5720", "B5727", "B5729", "B5731", "B5734", "B5736", "B5746", "B5748", "B5749", "B5757", "B5759", "B5763", "B5764", "B5772", "B5773", "B5777", "B5779", "B5792", "B5795", "B5801", "B5807", "B5815", "B5816", "B5820", "B5824", "B5828", "B5829", "B5834", "B5850", "B5854", "B5861", "B5862", "B5866", "B5869", "B5872", "B5876", "B5877", "B5879", "B5882", "B5884", "B5885", "B5903", "B5905", "B5907", "B5909", "B5916", "B5918", "B5921", "B5937", "B5938", "B5942", "B5946", "B5948", "B5953", "B5957", "B5958", "B5959", "B5963", "B5964", "B5975", "B5978", "B5981", "B5984", "B5985", "B5986", "B5988", "B5989", "B5990", "B5998", "B6000", "B6001", "B6003", "B6006", "B6007", "B6013", "B6015", "B6022", "B6027", "B6029", "B6030", "B6031", "B6036", "B6037", "B6043", "B6044", "B6046", "B6049", "B6053", "B6065", "B6066", "B6067", "B6073", "B6076", "B6078", "B6079", "B6083", "B6096", "B6098", "B6105", "B6106", "B6110", "B6122", "B6126", "B6131", "B6139", "B6140", "B6143", "B6146", "B6148", "B6152", "B6154", "B6157", "B6161", "B6168", "B6171", "B6180", "B6182", "B6184", "B6185", "B6204", "B6210", "B6211", "B6212", "B6213", "B6218", "B6226", "B6229", "B6235", "B6238", "B6251", "B6253", "B6254", "B6255", "B6256", "B6257", "B6261", "B6263", "B6276", "B6289", "B6293", "B6294", "B6295", "B6298", "B6304", "B6330", "B6336", "B6342", "B6344", "B6356", "B6367", "B6368", "B6371", "B6374", "B6386", "B6387", "B6394", "B6397", "B6399", "B6402", "B6407", "B6408", "B6417", "B6428", "B6429", "B6430", "B6439", "B6442", "B6454", "B6462", "B6464", "B6472", "B6475", "B6476", "B6487", "B6488", "B6491", "B6496", "B6502", "B6506", "B6520", "B6521", "B6524", "B6538", "B6540", "B6549", "B6550", "B6552", "B6553", "B6561", "B6567", "B6569", "B6573", "B6574", "B6582", "B6585", "B6588", "B6600", "B6601", "B6603", "B6606", "B6615", "B6617", "B6621", "B6624", "B6629", "B6632" ], "rows": 1508, "table": true, "tojson": true }, { "name": "transcriptome", "title": "Saccharomyces cerevisiae transcriptome", "object": "transcriptome", "file": "transcriptome.rda", "class": [ "data.frame" ], "fields": [ "SNF2.1", "SNF2.10", "SNF2.11", "SNF2.12", "SNF2.13", "SNF2.14", "SNF2.15", "SNF2.16", "SNF2.17", "SNF2.18", "SNF2.19", "SNF2.2", "SNF2.20", "SNF2.21", "SNF2.22", "SNF2.23", "SNF2.24", "SNF2.25", "SNF2.26", "SNF2.27", "SNF2.28", "SNF2.29", "SNF2.3", "SNF2.30", "SNF2.31", "SNF2.32", "SNF2.33", "SNF2.34", "SNF2.35", "SNF2.36", "SNF2.37", "SNF2.38", "SNF2.39", "SNF2.4", "SNF2.40", "SNF2.41", "SNF2.42", "SNF2.43", "SNF2.44", "SNF2.45", "SNF2.46", "SNF2.47", "SNF2.48", "SNF2.5", "SNF2.6", "SNF2.7", "SNF2.8", "SNF2.9", "WT.1", "WT.10", "WT.11", "WT.12", "WT.13", "WT.14", "WT.15", "WT.16", "WT.17", "WT.18", "WT.19", "WT.2", "WT.20", "WT.21", "WT.22", "WT.23", "WT.24", "WT.25", "WT.26", "WT.27", "WT.28", "WT.29", "WT.3", "WT.30", "WT.31", "WT.32", "WT.33", "WT.34", "WT.35", "WT.36", "WT.37", "WT.38", "WT.39", "WT.4", "WT.40", "WT.41", "WT.42", "WT.43", "WT.44", "WT.45", "WT.46", "WT.47", "WT.48", "WT.5", "WT.6", "WT.7", "WT.8", "WT.9" ], "rows": 5892, "table": true, "tojson": true } ], "_help": [ { "page": "aIc.coherent", "title": "Calculate the subcompositional coherence of samples in a dataset for a given correction.", "topics": [ "aIc.coherent" ] }, { "page": "aIc.dominant", "title": "'aIc.dominant' calculates the subcompositional dominance of a sample in a dataset for a given correction. This compares the distances of samples of the full dataset and a subset of the dataset. This is expected to be true if the transform is behaving rationally in compositional datasets.", "topics": [ "aIc.dominant" ] }, { "page": "aIc.perturb", "title": "'aIc.perturb' calculates the perturbation invariance of distance for samples with a given correction. This compares the distances of samples of the full dataset and a the perturbed dataset. This is expected to be true if the transform is behaving rationally in compositional datasets.", "topics": [ "aIc.perturb" ] }, { "page": "aIc.plot", "title": "'aIc.plot' plots the result of the distance tests.", "topics": [ "aIc.plot" ] }, { "page": "aIc.runExample", "title": "'aIc.runExample' loads the associated shiny app This will load the selex example dataset with the default group sizes, the user can upload their own local dataset and adjust groups accordingly.", "topics": [ "aIc.runExample" ] }, { "page": "aIc.scale", "title": "'aIc.scale' calculates the scaling invariance of a sample in a dataset for a given correction. This compares the distances of samples of the full dataset and a scaled version of the dataset. This is expected to be true if the transform is behaving rationally in compositional datasets.", "topics": [ "aIc.scale" ] }, { "page": "aIc.singular", "title": "'aIc.singular' tests for singular data. This is expected to be true if the transform is behaving rationally in compositional datasets and also true in the case of datasets with more features than samples.", "topics": [ "aIc.singular" ] }, { "page": "meta16S", "title": "16S rRNA tag-sequencing data", "topics": [ "meta16S" ] }, { "page": "metaTscome", "title": "meta-transcriptome data", "topics": [ "metaTscome" ] }, { "page": "selex", "title": "Selection-based differential sequence variant abundance dataset", "topics": [ "selex" ] }, { "page": "singleCell", "title": "single cell transcriptome data", "topics": [ "singleCell" ] }, { "page": "transcriptome", "title": "Saccharomyces cerevisiae transcriptome", "topics": [ "transcriptome" ] } ], "_readme": "https://github.com/ggloor/aic/raw/HEAD/README.md", "_rundeps": [ "abind", "ALDEx2", "base64enc", "BH", "Biobase", "BiocGenerics", "BiocParallel", "bslib", "cachem", "cli", "cluster", "codetools", "commonmark", "cpp11", "DelayedArray", "deldir", "digest", "directlabels", "edgeR", "fastmap", "fontawesome", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomicRanges", "glue", "htmltools", "httpuv", "interp", "IRanges", "jpeg", "jquerylib", "jsonlite", "lambda.r", "later", "lattice", "latticeExtra", "lifecycle", "limma", "locfit", "magrittr", "MASS", "Matrix", "matrixcalc", "MatrixGenerics", "matrixStats", "memoise", "mgcv", "mime", "multtest", "nlme", "otel", "permute", "png", "promises", "quadprog", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RcppParallel", "Rfast", "rlang", "S4Arrays", "S4Vectors", "sass", "Seqinfo", "shiny", "snow", "sourcetools", "SparseArray", "statmod", "SummarizedExperiment", "survival", "truncnorm", "vegan", "withr", "xtable", "XVector", "zCompositions", "zigg" ], "_vignettes": [ { "source": "aIc_vignette.Rmd", "filename": "aIc_vignette.html", "title": "aIc: am I compositional?", "author": "Greg Gloor", "engine": "knitr::rmarkdown", "headings": [ "aIc and amIcomp implement simple test functions to determine if a particular dataset and transformation exhibit data pathologies that we can understand and control for. Since 'all models are wrong'[Box:1976] it is important to know at the outset what is wrong, why it is wrong, and how that wrongness would hinder general interpretability in some way.", "List of common data pathologies:", "Properties of datasets", "Example functions", "Sub-compositions and correlation (coherence)", "Sub-compositions and distance (dominance)", "Testing for scale invariance", "Testing for perturbation invariance", "Choosing parameters", "Conclusion", "SessionInfo" ], "created": "2022-06-24 20:25:51", "modified": "2024-01-18 18:21:22", "commits": 10 } ], "_score": 4.041392685158225, "_indexed": true, "_nocasepkg": "aic", "_universes": [ "ggloor" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0", "date": "2026-06-05T07:24:16.000Z", "distro": "noble", "commit": "ada8f7e396ebb275dcd22b2af6123681dd1c8b4e", "fileid": "abf71072e1fc2e7c48c104640ae4e42eb3cc7be092360a79be9ef3dcca41f41c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ggloor/actions/runs/27001260325" }, { "r": "4.6.0", "os": "linux", "version": "1.0", "date": "2026-06-05T07:24:15.000Z", "distro": "noble", "commit": "ada8f7e396ebb275dcd22b2af6123681dd1c8b4e", "fileid": "e8e77a01e43c756b3c3d692acb2de1dbd09788360ffa1ddb99f9b89a893a064e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ggloor/actions/runs/27001260325" }, { "r": "4.5.3", "os": "mac", "version": "1.0", "date": "2026-06-05T07:35:18.000Z", "commit": "ada8f7e396ebb275dcd22b2af6123681dd1c8b4e", "fileid": "b4e4e930bedf87394b3d8f3c6a1650778722c35f95650f04ce01c9a2facaa5c2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ggloor/actions/runs/27001260325" }, { "r": "4.6.0", "os": "mac", "version": "1.0", "date": "2026-06-05T07:34:47.000Z", "commit": "ada8f7e396ebb275dcd22b2af6123681dd1c8b4e", "fileid": "d01e0c081d4332b4579289ce64a01cac7a7384d7282eb52d1af19b99d1987b6a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ggloor/actions/runs/27001260325" }, { "r": "4.6.0", "os": "wasm", "version": "1.0", "date": "2026-06-05T07:24:16.000Z", "commit": "ada8f7e396ebb275dcd22b2af6123681dd1c8b4e", "fileid": "f2a3b63d5b17de3711d6594e2a9d08b6a8f7a1c68a923a9c6bd9bb1579cd1971", "status": "success", "buildurl": "https://github.com/r-universe/ggloor/actions/runs/27001260325" }, { "r": "4.7.0", "os": "win", "version": "1.0", "date": "2026-06-05T07:23:17.000Z", "commit": "ada8f7e396ebb275dcd22b2af6123681dd1c8b4e", "fileid": "892b9f03f4ed1904b33d92bb8d97de4660285e22467235fe04193efbb96d7399", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ggloor/actions/runs/27001260325" }, { "r": "4.5.3", "os": "win", "version": "1.0", "date": "2026-06-05T07:23:20.000Z", "commit": "ada8f7e396ebb275dcd22b2af6123681dd1c8b4e", "fileid": "0cf4c29f8e082c489a25050aee949124350d98f1c4a7abcd07e5331143b27fae", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ggloor/actions/runs/27001260325" }, { "r": "4.6.0", "os": "win", "version": "1.0", "date": "2026-06-05T07:23:18.000Z", "commit": "ada8f7e396ebb275dcd22b2af6123681dd1c8b4e", "fileid": "7bd778c9c180a7473c8a7602f0ac421a2d1a670c0d6038baa2e7b2f09a0e7fbe", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ggloor/actions/runs/27001260325" } ] }