[Mattice-commits] r131 - in pkg: DATA inst/doc man misc
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jan 2 03:14:33 CET 2009
Author: andrew_hipp
Date: 2009-01-02 03:14:32 +0100 (Fri, 02 Jan 2009)
New Revision: 131
Added:
pkg/DATA/carex.R
pkg/misc/carex.rda
pkg/misc/chromo.txt
pkg/misc/nodes.R
pkg/misc/taxonSets.R
Removed:
pkg/DATA/carex.rda
pkg/DATA/carexdata.R
pkg/DATA/chromo.txt
pkg/DATA/nodes.R
pkg/DATA/taxonSets.R
Modified:
pkg/inst/doc/maticce.Rnw
pkg/man/informationCriterion.Rd
Log:
numerous miscellaneous fixes to documentation and data files
Copied: pkg/DATA/carex.R (from rev 115, pkg/DATA/carexdata.R)
===================================================================
--- pkg/DATA/carex.R (rev 0)
+++ pkg/DATA/carex.R 2009-01-02 02:14:32 UTC (rev 131)
@@ -0,0 +1,108 @@
+carex <- structure(list(tree = structure(list(edge = structure(c(54L,
+55L, 55L, 56L, 56L, 54L, 57L, 58L, 58L, 59L, 59L, 57L, 60L, 61L,
+62L, 63L, 63L, 64L, 64L, 62L, 61L, 65L, 65L, 60L, 66L, 67L, 67L,
+66L, 68L, 68L, 69L, 70L, 71L, 72L, 73L, 73L, 74L, 75L, 75L, 74L,
+76L, 76L, 77L, 77L, 72L, 78L, 79L, 79L, 80L, 80L, 81L, 81L, 82L,
+82L, 83L, 83L, 78L, 84L, 85L, 86L, 86L, 85L, 87L, 88L, 88L, 89L,
+90L, 90L, 89L, 91L, 91L, 87L, 92L, 92L, 93L, 93L, 84L, 94L, 94L,
+71L, 95L, 95L, 70L, 96L, 97L, 98L, 98L, 97L, 99L, 99L, 100L,
+101L, 101L, 100L, 102L, 102L, 96L, 103L, 103L, 104L, 104L, 69L,
+105L, 105L, 55L, 1L, 56L, 2L, 3L, 57L, 58L, 4L, 59L, 5L, 6L,
+60L, 61L, 62L, 63L, 7L, 64L, 8L, 9L, 10L, 65L, 11L, 12L, 66L,
+67L, 13L, 14L, 68L, 15L, 69L, 70L, 71L, 72L, 73L, 16L, 74L, 75L,
+17L, 18L, 76L, 19L, 77L, 20L, 21L, 78L, 79L, 22L, 80L, 23L, 81L,
+24L, 82L, 25L, 83L, 26L, 27L, 84L, 85L, 86L, 28L, 29L, 87L, 88L,
+30L, 89L, 90L, 31L, 32L, 91L, 33L, 34L, 92L, 35L, 93L, 36L, 37L,
+94L, 38L, 39L, 95L, 40L, 41L, 96L, 97L, 98L, 42L, 43L, 99L, 44L,
+100L, 101L, 45L, 46L, 102L, 47L, 48L, 103L, 49L, 104L, 50L, 51L,
+105L, 52L, 53L), .Dim = c(104L, 2L)), edge.length = c(0.131608041,
+0.868391959, 0.4774298606, 0.3909620984, 0.3909620984, 0.0376523746,
+0.0915148608, 0.8708327646, 0.228673604, 0.6421591606, 0.6421591606,
+0.03047094, 0.197188661, 0.3667080933, 0.1187924864, 0.2491874447,
+0.0680851795, 0.1811022651, 0.1811022651, 0.3679799311, 0.2879776585,
+0.4467103659, 0.4467103659, 0.0760667065, 0.2546030817, 0.6012068973,
+0.6012068973, 0.0734898564, 0.7823201225, 0.0354531643, 0.0805067273,
+0.1044180282, 0.1470105274, 0.0657037966, 0.3492278788, 0.119097461,
+0.0354160188, 0.194714399, 0.194714399, 0.0351340264, 0.1949963914,
+0.0734473345, 0.1215490569, 0.1215490569, 0.0370307146, 0.0478702765,
+0.3300306842, 0.1023596238, 0.2276710604, 0.0531080597, 0.1745630008,
+0.0755096136, 0.0990533872, 0.0744081089, 0.0246452783, 0.0246452783,
+0.0339921757, 0.0610205014, 0.1472200431, 0.1356682405, 0.1356682405,
+0.055626089, 0.053885115, 0.1733770795, 0.0401682819, 0.0513531937,
+0.0818556039, 0.0818556039, 0.0352913046, 0.0979174931, 0.0979174931,
+0.0400989858, 0.1871632087, 0.0547825691, 0.1323806396, 0.1323806396,
+0.0591487349, 0.2847600501, 0.2847600501, 0.0421214255, 0.5198207772,
+0.5198207772, 0.0696998161, 0.2044319398, 0.1668478906, 0.2253805845,
+0.2253805845, 0.0732033467, 0.3190251283, 0.1229909423, 0.1015139286,
+0.0945202574, 0.0945202574, 0.034953098, 0.161081088, 0.161081088,
+0.1165220723, 0.4801383425, 0.3700801096, 0.1100582329, 0.1100582329,
+0.0946612554, 0.6522057028, 0.6522057028), Nnode = 52L, tip.label = c("argyrantha",
+"preslii", "phaeocephala", "bohemica", "foenea", "praticola",
+"ebenea", "haydeniana", "microptera", "peucophila", "integra",
+"subfusca", "macloviana", "pachystachya", "adusta", "cumulata",
+"hyalina", "brevior", "reniformis", "molestiformis", "shinnersii",
+"opaca", "crawfordii", "bebbii", "cristatella", "projecta", "tribuloidesVtribuloides",
+"buffaloriver", "teneraVechinodes", "missouriensis", "teneraVtenera",
+"tincta", "festucacea", "oronensis", "muskingumensis", "bicknellii",
+"merrittfernaldii", "molesta", "normalis", "ovalis3098", "feta",
+"longii", "vexans", "alata", "scopariaVscoparia", "scopariaVtessellata",
+"albolutescens", "suberecta", "ozarkana", "hormathodes", "straminea",
+"xerantica", "athrostachya")), .Names = c("edge", "edge.length",
+"Nnode", "tip.label"), class = "phylo", origin = "bayes.tre"),
+ dat = structure(c(4.382026635, 4.369447852, 4.430816799,
+ 4.382026635, 4.414856779, 4.336767728, 4.430816799, 4.406719247,
+ 4.384274107, 4.304065093, 4.406719247, 4.430816799, 4.454347296,
+ 4.363862664, 4.356708827, 4.048824047, 4.304065093, 4.085976313,
+ 4.382026635, 4.272630208, 4.099829492, 4.201703081, 4.222151267,
+ 4.229312423, 4.248495242, 4.158883083, 4.25561271, 4.248495242,
+ 4.335982696, 3.947003974, 3.999117712, 4.317488114, 4.243769809,
+ 4.304065093, 4.382026635, 4.33073334, 4.276666119, 4.227855121,
+ 4.236133434, 4.175770928, 4.189654742, 4.107589789, 4.237723145,
+ 4.304065093, 4.159976236, 4.219507705, 4.189654742, 4.276666119,
+ 4.077537444, 4.304065093, 4.304065093, 4.219507705, 4.219507705
+ ), .Names = c("argyrantha", "preslii", "phaeocephala", "bohemica",
+ "foenea", "praticola", "ebenea", "haydeniana", "microptera",
+ "peucophila", "integra", "subfusca", "macloviana", "pachystachya",
+ "adusta", "cumulata", "hyalina", "brevior", "reniformis",
+ "molestiformis", "shinnersii", "opaca", "crawfordii", "bebbii",
+ "cristatella", "projecta", "tribuloidesVtribuloides", "buffaloriver",
+ "teneraVechinodes", "missouriensis", "teneraVtenera", "tincta",
+ "festucacea", "oronensis", "muskingumensis", "bicknellii",
+ "merrittfernaldii", "molesta", "normalis", "ovalis3098",
+ "feta", "longii", "vexans", "alata", "scopariaVscoparia",
+ "scopariaVtessellata", "albolutescens", "suberecta", "ozarkana",
+ "hormathodes", "straminea", "xerantica", "athrostachya")),
+ nodes = list(c("alata", "albolutescens", "bebbii", "bicknellii",
+ "brevior", "buffaloriver", "crawfordii", "cristatella", "cumulata",
+ "festucacea", "feta", "hormathodes", "hyalina", "longii",
+ "merrittfernaldii", "missouriensis", "molesta", "molestiformis",
+ "muskingumensis", "normalis", "opaca", "oronensis", "ovalis3098",
+ "ozarkana", "projecta", "reniformis", "scopariaVscoparia",
+ "scopariaVtessellata", "shinnersii", "straminea", "suberecta",
+ "teneraVechinodes", "teneraVtenera", "tincta", "tribuloidesVtribuloides",
+ "vexans", "adusta", "athrostachya", "pachystachya", "xerantica",
+ "macloviana"), c("alata", "albolutescens", "bebbii", "bicknellii",
+ "brevior", "buffaloriver", "crawfordii", "cristatella", "cumulata",
+ "festucacea", "feta", "hormathodes", "hyalina", "longii",
+ "merrittfernaldii", "missouriensis", "molesta", "molestiformis",
+ "muskingumensis", "normalis", "opaca", "oronensis", "ovalis3098",
+ "ozarkana", "projecta", "reniformis", "scopariaVscoparia",
+ "scopariaVtessellata", "shinnersii", "straminea", "suberecta",
+ "teneraVechinodes", "teneraVtenera", "tincta", "tribuloidesVtribuloides",
+ "vexans"), c("bebbii", "bicknellii", "brevior", "buffaloriver",
+ "crawfordii", "cristatella", "cumulata", "festucacea", "hyalina",
+ "merrittfernaldii", "missouriensis", "molesta", "molestiformis",
+ "muskingumensis", "normalis", "opaca", "oronensis", "projecta",
+ "reniformis", "shinnersii", "teneraVechinodes", "teneraVtenera",
+ "tincta", "tribuloidesVtribuloides", "feta", "ovalis3098"
+ ), c("bebbii", "bicknellii", "brevior", "buffaloriver", "crawfordii",
+ "cristatella", "cumulata", "festucacea", "hyalina", "merrittfernaldii",
+ "missouriensis", "molesta", "molestiformis", "muskingumensis",
+ "normalis", "opaca", "oronensis", "projecta", "reniformis",
+ "shinnersii", "teneraVechinodes", "teneraVtenera", "tincta",
+ "tribuloidesVtribuloides"), c("brevior", "hyalina", "molestiformis",
+ "reniformis", "shinnersii"), c("suberecta", "albolutescens",
+ "scopariaVscoparia", "scopariaVtessellata", "alata", "vexans",
+ "longii"), c("subfusca", "integra", "peucophila", "microptera",
+ "haydeniana", "ebenea"), c("phaeocephala", "preslii", "argyrantha"
+ ))), .Names = c("ovales.tree", "ovales.data", "ovales.nodes"))
\ No newline at end of file
Deleted: pkg/DATA/carex.rda
===================================================================
(Binary files differ)
Deleted: pkg/DATA/carexdata.R
===================================================================
--- pkg/DATA/carexdata.R 2008-12-31 20:21:05 UTC (rev 130)
+++ pkg/DATA/carexdata.R 2009-01-02 02:14:32 UTC (rev 131)
@@ -1,108 +0,0 @@
-carex <- structure(list(tree = structure(list(edge = structure(c(54L,
-55L, 55L, 56L, 56L, 54L, 57L, 58L, 58L, 59L, 59L, 57L, 60L, 61L,
-62L, 63L, 63L, 64L, 64L, 62L, 61L, 65L, 65L, 60L, 66L, 67L, 67L,
-66L, 68L, 68L, 69L, 70L, 71L, 72L, 73L, 73L, 74L, 75L, 75L, 74L,
-76L, 76L, 77L, 77L, 72L, 78L, 79L, 79L, 80L, 80L, 81L, 81L, 82L,
-82L, 83L, 83L, 78L, 84L, 85L, 86L, 86L, 85L, 87L, 88L, 88L, 89L,
-90L, 90L, 89L, 91L, 91L, 87L, 92L, 92L, 93L, 93L, 84L, 94L, 94L,
-71L, 95L, 95L, 70L, 96L, 97L, 98L, 98L, 97L, 99L, 99L, 100L,
-101L, 101L, 100L, 102L, 102L, 96L, 103L, 103L, 104L, 104L, 69L,
-105L, 105L, 55L, 1L, 56L, 2L, 3L, 57L, 58L, 4L, 59L, 5L, 6L,
-60L, 61L, 62L, 63L, 7L, 64L, 8L, 9L, 10L, 65L, 11L, 12L, 66L,
-67L, 13L, 14L, 68L, 15L, 69L, 70L, 71L, 72L, 73L, 16L, 74L, 75L,
-17L, 18L, 76L, 19L, 77L, 20L, 21L, 78L, 79L, 22L, 80L, 23L, 81L,
-24L, 82L, 25L, 83L, 26L, 27L, 84L, 85L, 86L, 28L, 29L, 87L, 88L,
-30L, 89L, 90L, 31L, 32L, 91L, 33L, 34L, 92L, 35L, 93L, 36L, 37L,
-94L, 38L, 39L, 95L, 40L, 41L, 96L, 97L, 98L, 42L, 43L, 99L, 44L,
-100L, 101L, 45L, 46L, 102L, 47L, 48L, 103L, 49L, 104L, 50L, 51L,
-105L, 52L, 53L), .Dim = c(104L, 2L)), edge.length = c(0.131608041,
-0.868391959, 0.4774298606, 0.3909620984, 0.3909620984, 0.0376523746,
-0.0915148608, 0.8708327646, 0.228673604, 0.6421591606, 0.6421591606,
-0.03047094, 0.197188661, 0.3667080933, 0.1187924864, 0.2491874447,
-0.0680851795, 0.1811022651, 0.1811022651, 0.3679799311, 0.2879776585,
-0.4467103659, 0.4467103659, 0.0760667065, 0.2546030817, 0.6012068973,
-0.6012068973, 0.0734898564, 0.7823201225, 0.0354531643, 0.0805067273,
-0.1044180282, 0.1470105274, 0.0657037966, 0.3492278788, 0.119097461,
-0.0354160188, 0.194714399, 0.194714399, 0.0351340264, 0.1949963914,
-0.0734473345, 0.1215490569, 0.1215490569, 0.0370307146, 0.0478702765,
-0.3300306842, 0.1023596238, 0.2276710604, 0.0531080597, 0.1745630008,
-0.0755096136, 0.0990533872, 0.0744081089, 0.0246452783, 0.0246452783,
-0.0339921757, 0.0610205014, 0.1472200431, 0.1356682405, 0.1356682405,
-0.055626089, 0.053885115, 0.1733770795, 0.0401682819, 0.0513531937,
-0.0818556039, 0.0818556039, 0.0352913046, 0.0979174931, 0.0979174931,
-0.0400989858, 0.1871632087, 0.0547825691, 0.1323806396, 0.1323806396,
-0.0591487349, 0.2847600501, 0.2847600501, 0.0421214255, 0.5198207772,
-0.5198207772, 0.0696998161, 0.2044319398, 0.1668478906, 0.2253805845,
-0.2253805845, 0.0732033467, 0.3190251283, 0.1229909423, 0.1015139286,
-0.0945202574, 0.0945202574, 0.034953098, 0.161081088, 0.161081088,
-0.1165220723, 0.4801383425, 0.3700801096, 0.1100582329, 0.1100582329,
-0.0946612554, 0.6522057028, 0.6522057028), Nnode = 52L, tip.label = c("argyrantha",
-"preslii", "phaeocephala", "bohemica", "foenea", "praticola",
-"ebenea", "haydeniana", "microptera", "peucophila", "integra",
-"subfusca", "macloviana", "pachystachya", "adusta", "cumulata",
-"hyalina", "brevior", "reniformis", "molestiformis", "shinnersii",
-"opaca", "crawfordii", "bebbii", "cristatella", "projecta", "tribuloidesVtribuloides",
-"buffaloriver", "teneraVechinodes", "missouriensis", "teneraVtenera",
-"tincta", "festucacea", "oronensis", "muskingumensis", "bicknellii",
-"merrittfernaldii", "molesta", "normalis", "ovalis3098", "feta",
-"longii", "vexans", "alata", "scopariaVscoparia", "scopariaVtessellata",
-"albolutescens", "suberecta", "ozarkana", "hormathodes", "straminea",
-"xerantica", "athrostachya")), .Names = c("edge", "edge.length",
-"Nnode", "tip.label"), class = "phylo", origin = "bayes.tre"),
- dat = structure(c(4.382026635, 4.369447852, 4.430816799,
- 4.382026635, 4.414856779, 4.336767728, 4.430816799, 4.406719247,
- 4.384274107, 4.304065093, 4.406719247, 4.430816799, 4.454347296,
- 4.363862664, 4.356708827, 4.048824047, 4.304065093, 4.085976313,
- 4.382026635, 4.272630208, 4.099829492, 4.201703081, 4.222151267,
- 4.229312423, 4.248495242, 4.158883083, 4.25561271, 4.248495242,
- 4.335982696, 3.947003974, 3.999117712, 4.317488114, 4.243769809,
- 4.304065093, 4.382026635, 4.33073334, 4.276666119, 4.227855121,
- 4.236133434, 4.175770928, 4.189654742, 4.107589789, 4.237723145,
- 4.304065093, 4.159976236, 4.219507705, 4.189654742, 4.276666119,
- 4.077537444, 4.304065093, 4.304065093, 4.219507705, 4.219507705
- ), .Names = c("argyrantha", "preslii", "phaeocephala", "bohemica",
- "foenea", "praticola", "ebenea", "haydeniana", "microptera",
- "peucophila", "integra", "subfusca", "macloviana", "pachystachya",
- "adusta", "cumulata", "hyalina", "brevior", "reniformis",
- "molestiformis", "shinnersii", "opaca", "crawfordii", "bebbii",
- "cristatella", "projecta", "tribuloidesVtribuloides", "buffaloriver",
- "teneraVechinodes", "missouriensis", "teneraVtenera", "tincta",
- "festucacea", "oronensis", "muskingumensis", "bicknellii",
- "merrittfernaldii", "molesta", "normalis", "ovalis3098",
- "feta", "longii", "vexans", "alata", "scopariaVscoparia",
- "scopariaVtessellata", "albolutescens", "suberecta", "ozarkana",
- "hormathodes", "straminea", "xerantica", "athrostachya")),
- nodes = list(c("alata", "albolutescens", "bebbii", "bicknellii",
- "brevior", "buffaloriver", "crawfordii", "cristatella", "cumulata",
- "festucacea", "feta", "hormathodes", "hyalina", "longii",
- "merrittfernaldii", "missouriensis", "molesta", "molestiformis",
- "muskingumensis", "normalis", "opaca", "oronensis", "ovalis3098",
- "ozarkana", "projecta", "reniformis", "scopariaVscoparia",
- "scopariaVtessellata", "shinnersii", "straminea", "suberecta",
- "teneraVechinodes", "teneraVtenera", "tincta", "tribuloidesVtribuloides",
- "vexans", "adusta", "athrostachya", "pachystachya", "xerantica",
- "macloviana"), c("alata", "albolutescens", "bebbii", "bicknellii",
- "brevior", "buffaloriver", "crawfordii", "cristatella", "cumulata",
- "festucacea", "feta", "hormathodes", "hyalina", "longii",
- "merrittfernaldii", "missouriensis", "molesta", "molestiformis",
- "muskingumensis", "normalis", "opaca", "oronensis", "ovalis3098",
- "ozarkana", "projecta", "reniformis", "scopariaVscoparia",
- "scopariaVtessellata", "shinnersii", "straminea", "suberecta",
- "teneraVechinodes", "teneraVtenera", "tincta", "tribuloidesVtribuloides",
- "vexans"), c("bebbii", "bicknellii", "brevior", "buffaloriver",
- "crawfordii", "cristatella", "cumulata", "festucacea", "hyalina",
- "merrittfernaldii", "missouriensis", "molesta", "molestiformis",
- "muskingumensis", "normalis", "opaca", "oronensis", "projecta",
- "reniformis", "shinnersii", "teneraVechinodes", "teneraVtenera",
- "tincta", "tribuloidesVtribuloides", "feta", "ovalis3098"
- ), c("bebbii", "bicknellii", "brevior", "buffaloriver", "crawfordii",
- "cristatella", "cumulata", "festucacea", "hyalina", "merrittfernaldii",
- "missouriensis", "molesta", "molestiformis", "muskingumensis",
- "normalis", "opaca", "oronensis", "projecta", "reniformis",
- "shinnersii", "teneraVechinodes", "teneraVtenera", "tincta",
- "tribuloidesVtribuloides"), c("brevior", "hyalina", "molestiformis",
- "reniformis", "shinnersii"), c("suberecta", "albolutescens",
- "scopariaVscoparia", "scopariaVtessellata", "alata", "vexans",
- "longii"), c("subfusca", "integra", "peucophila", "microptera",
- "haydeniana", "ebenea"), c("phaeocephala", "preslii", "argyrantha"
- ))), .Names = c("tree", "dat", "nodes"))
\ No newline at end of file
Deleted: pkg/DATA/chromo.txt
===================================================================
--- pkg/DATA/chromo.txt 2008-12-31 20:21:05 UTC (rev 130)
+++ pkg/DATA/chromo.txt 2009-01-02 02:14:32 UTC (rev 131)
@@ -1,53 +0,0 @@
-argyrantha 4.382026635
-preslii 4.369447852
-phaeocephala 4.430816799
-bohemica 4.382026635
-foenea 4.414856779
-praticola 4.336767728
-ebenea 4.430816799
-haydeniana 4.406719247
-microptera 4.384274107
-peucophila 4.304065093
-integra 4.406719247
-subfusca 4.430816799
-macloviana 4.454347296
-pachystachya 4.363862664
-adusta 4.356708827
-cumulata 4.048824047
-hyalina 4.304065093
-brevior 4.085976313
-reniformis 4.382026635
-molestiformis 4.272630208
-shinnersii 4.099829492
-opaca 4.201703081
-crawfordii 4.222151267
-bebbii 4.229312423
-cristatella 4.248495242
-projecta 4.158883083
-tribuloidesVtribuloides 4.25561271
-buffaloriver 4.248495242
-teneraVechinodes 4.335982696
-missouriensis 3.947003974
-teneraVtenera 3.999117712
-tincta 4.317488114
-festucacea 4.243769809
-oronensis 4.304065093
-muskingumensis 4.382026635
-bicknellii 4.33073334
-merrittfernaldii 4.276666119
-molesta 4.227855121
-normalis 4.236133434
-ovalis3098 4.175770928
-feta 4.189654742
-longii 4.107589789
-vexans 4.237723145
-alata 4.304065093
-scopariaVscoparia 4.159976236
-scopariaVtessellata 4.219507705
-albolutescens 4.189654742
-suberecta 4.276666119
-ozarkana 4.077537444
-hormathodes 4.304065093
-straminea 4.304065093
-xerantica 4.219507705
-athrostachya 4.219507705
Deleted: pkg/DATA/nodes.R
===================================================================
--- pkg/DATA/nodes.R 2008-12-31 20:21:05 UTC (rev 130)
+++ pkg/DATA/nodes.R 2009-01-02 02:14:32 UTC (rev 131)
@@ -1,32 +0,0 @@
-nodes <- list(c("alata", "albolutescens", "bebbii", "bicknellii", "brevior",
-"buffaloriver", "crawfordii", "cristatella", "cumulata", "festucacea",
-"feta", "hormathodes", "hyalina", "longii", "merrittfernaldii",
-"missouriensis", "molesta", "molestiformis", "muskingumensis",
-"normalis", "opaca", "oronensis", "ovalis3098", "ozarkana", "projecta",
-"reniformis", "scopariaVscoparia", "scopariaVtessellata", "shinnersii",
-"straminea", "suberecta", "teneraVechinodes", "teneraVtenera",
-"tincta", "tribuloidesVtribuloides", "vexans", "adusta", "athrostachya",
-"pachystachya", "xerantica", "macloviana"), c("alata", "albolutescens",
-"bebbii", "bicknellii", "brevior", "buffaloriver", "crawfordii",
-"cristatella", "cumulata", "festucacea", "feta", "hormathodes",
-"hyalina", "longii", "merrittfernaldii", "missouriensis", "molesta",
-"molestiformis", "muskingumensis", "normalis", "opaca", "oronensis",
-"ovalis3098", "ozarkana", "projecta", "reniformis", "scopariaVscoparia",
-"scopariaVtessellata", "shinnersii", "straminea", "suberecta",
-"teneraVechinodes", "teneraVtenera", "tincta", "tribuloidesVtribuloides",
-"vexans"), c("bebbii", "bicknellii", "brevior", "buffaloriver",
-"crawfordii", "cristatella", "cumulata", "festucacea", "hyalina",
-"merrittfernaldii", "missouriensis", "molesta", "molestiformis",
-"muskingumensis", "normalis", "opaca", "oronensis", "projecta",
-"reniformis", "shinnersii", "teneraVechinodes", "teneraVtenera",
-"tincta", "tribuloidesVtribuloides", "feta", "ovalis3098"), c("bebbii",
-"bicknellii", "brevior", "buffaloriver", "crawfordii", "cristatella",
-"cumulata", "festucacea", "hyalina", "merrittfernaldii", "missouriensis",
-"molesta", "molestiformis", "muskingumensis", "normalis", "opaca",
-"oronensis", "projecta", "reniformis", "shinnersii", "teneraVechinodes",
-"teneraVtenera", "tincta", "tribuloidesVtribuloides"), c("brevior",
-"hyalina", "molestiformis", "reniformis", "shinnersii"), c("suberecta",
-"albolutescens", "scopariaVscoparia", "scopariaVtessellata",
-"alata", "vexans", "longii"), c("subfusca", "integra", "peucophila",
-"microptera", "haydeniana", "ebenea"), c("phaeocephala", "preslii",
-"argyrantha"))
Deleted: pkg/DATA/taxonSets.R
===================================================================
--- pkg/DATA/taxonSets.R 2008-12-31 20:21:05 UTC (rev 130)
+++ pkg/DATA/taxonSets.R 2009-01-02 02:14:32 UTC (rev 131)
@@ -1,22 +0,0 @@
-taxonSets <- list(ENA = c("alata", "albolutescens", "bebbii", "bicknellii",
-"brevior", "buffaloriver", "crawfordii", "cristatella", "cumulata",
-"festucacea", "feta", "hormathodes", "hyalina", "longii", "merrittfernaldii",
-"missouriensis", "molesta", "molestiformis", "muskingumensis",
-"normalis", "opaca", "oronensis", "ovalis3098", "ozarkana", "projecta",
-"reniformis", "scopariaVscoparia", "scopariaVtessellata", "shinnersii",
-"straminea", "suberecta", "teneraVechinodes", "teneraVtenera",
-"tincta", "tribuloidesVtribuloides", "vexans"), ENAI = c("bebbii",
-"bicknellii", "brevior", "buffaloriver", "crawfordii", "cristatella",
-"cumulata", "festucacea", "hyalina", "merrittfernaldii", "missouriensis",
-"molesta", "molestiformis", "muskingumensis", "normalis", "opaca",
-"oronensis", "projecta", "reniformis", "shinnersii", "teneraVechinodes",
-"teneraVtenera", "tincta", "tribuloidesVtribuloides"), ENAII = c("alata",
-"albolutescens", "hormathodes", "longii", "ozarkana", "scopariaVscoparia",
-"scopariaVtessellata", "straminea", "suberecta", "vexans"), ENAIII = c("feta",
-"ovalis3098"), WNA = c("adusta", "argyrantha", "athrostachya",
-"bohemica", "ebenea", "foenea", "haydeniana", "integra", "macloviana",
-"microptera", "pachystachya", "peucophila", "phaeocephala", "praticola",
-"preslii", "subfusca", "xerantica"), WNAI = c("argyrantha", "bohemica",
-"ebenea", "foenea", "haydeniana", "integra", "microptera", "peucophila",
-"phaeocephala", "praticola", "preslii", "subfusca"), WNAII = c("adusta",
-"athrostachya", "pachystachya", "xerantica", "macloviana"))
\ No newline at end of file
Modified: pkg/inst/doc/maticce.Rnw
===================================================================
--- pkg/inst/doc/maticce.Rnw 2008-12-31 20:21:05 UTC (rev 130)
+++ pkg/inst/doc/maticce.Rnw 2009-01-02 02:14:32 UTC (rev 131)
@@ -40,7 +40,6 @@
<<startAnalysis, fig=FALSE>>=
library(maticce) # load the maticce package into memory; also loads the required ouch package
-library(ouch)
data(carex)
#load('C:/Documents and Settings/Mortonarb/My Documents/mattice/pkg/DATA/carex.rda') # load demonstration data
attach(carex)
Modified: pkg/man/informationCriterion.Rd
===================================================================
--- pkg/man/informationCriterion.Rd 2008-12-31 20:21:05 UTC (rev 130)
+++ pkg/man/informationCriterion.Rd 2009-01-02 02:14:32 UTC (rev 131)
@@ -3,11 +3,9 @@
\alias{informationCriterion.hansenBatch}
\alias{print.informationCriterion}
\title{Information criterion and weights for a set of models}
-\description{
- Returns AIC, AICc, and BIC values and weights for a set of models.
-}
+\description{Returns AIC, AICc, and BIC values and weights for a set of models.}
\usage{
- informationCriterion(u = NULL, lnL = NULL, K, n = 0, names = NULL)
+ informationCriterion(u = NULL, lnL = NULL, K, n = 1, names = NULL)
informationCriterion.hansenBatch(hansenBatch)
print.informationCriterion(ic, ...)
}
Added: pkg/misc/carex.rda
===================================================================
(Binary files differ)
Property changes on: pkg/misc/carex.rda
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: pkg/misc/chromo.txt
===================================================================
--- pkg/misc/chromo.txt (rev 0)
+++ pkg/misc/chromo.txt 2009-01-02 02:14:32 UTC (rev 131)
@@ -0,0 +1,53 @@
+argyrantha 4.382026635
+preslii 4.369447852
+phaeocephala 4.430816799
+bohemica 4.382026635
+foenea 4.414856779
+praticola 4.336767728
+ebenea 4.430816799
+haydeniana 4.406719247
+microptera 4.384274107
+peucophila 4.304065093
+integra 4.406719247
+subfusca 4.430816799
+macloviana 4.454347296
+pachystachya 4.363862664
+adusta 4.356708827
+cumulata 4.048824047
+hyalina 4.304065093
+brevior 4.085976313
+reniformis 4.382026635
+molestiformis 4.272630208
+shinnersii 4.099829492
+opaca 4.201703081
+crawfordii 4.222151267
+bebbii 4.229312423
+cristatella 4.248495242
+projecta 4.158883083
+tribuloidesVtribuloides 4.25561271
+buffaloriver 4.248495242
+teneraVechinodes 4.335982696
+missouriensis 3.947003974
+teneraVtenera 3.999117712
+tincta 4.317488114
+festucacea 4.243769809
+oronensis 4.304065093
+muskingumensis 4.382026635
+bicknellii 4.33073334
+merrittfernaldii 4.276666119
+molesta 4.227855121
+normalis 4.236133434
+ovalis3098 4.175770928
+feta 4.189654742
+longii 4.107589789
+vexans 4.237723145
+alata 4.304065093
+scopariaVscoparia 4.159976236
+scopariaVtessellata 4.219507705
+albolutescens 4.189654742
+suberecta 4.276666119
+ozarkana 4.077537444
+hormathodes 4.304065093
+straminea 4.304065093
+xerantica 4.219507705
+athrostachya 4.219507705
Added: pkg/misc/nodes.R
===================================================================
--- pkg/misc/nodes.R (rev 0)
+++ pkg/misc/nodes.R 2009-01-02 02:14:32 UTC (rev 131)
@@ -0,0 +1,32 @@
+nodes <- list(c("alata", "albolutescens", "bebbii", "bicknellii", "brevior",
+"buffaloriver", "crawfordii", "cristatella", "cumulata", "festucacea",
+"feta", "hormathodes", "hyalina", "longii", "merrittfernaldii",
+"missouriensis", "molesta", "molestiformis", "muskingumensis",
+"normalis", "opaca", "oronensis", "ovalis3098", "ozarkana", "projecta",
+"reniformis", "scopariaVscoparia", "scopariaVtessellata", "shinnersii",
+"straminea", "suberecta", "teneraVechinodes", "teneraVtenera",
+"tincta", "tribuloidesVtribuloides", "vexans", "adusta", "athrostachya",
+"pachystachya", "xerantica", "macloviana"), c("alata", "albolutescens",
+"bebbii", "bicknellii", "brevior", "buffaloriver", "crawfordii",
+"cristatella", "cumulata", "festucacea", "feta", "hormathodes",
+"hyalina", "longii", "merrittfernaldii", "missouriensis", "molesta",
+"molestiformis", "muskingumensis", "normalis", "opaca", "oronensis",
+"ovalis3098", "ozarkana", "projecta", "reniformis", "scopariaVscoparia",
+"scopariaVtessellata", "shinnersii", "straminea", "suberecta",
+"teneraVechinodes", "teneraVtenera", "tincta", "tribuloidesVtribuloides",
+"vexans"), c("bebbii", "bicknellii", "brevior", "buffaloriver",
+"crawfordii", "cristatella", "cumulata", "festucacea", "hyalina",
+"merrittfernaldii", "missouriensis", "molesta", "molestiformis",
+"muskingumensis", "normalis", "opaca", "oronensis", "projecta",
+"reniformis", "shinnersii", "teneraVechinodes", "teneraVtenera",
+"tincta", "tribuloidesVtribuloides", "feta", "ovalis3098"), c("bebbii",
+"bicknellii", "brevior", "buffaloriver", "crawfordii", "cristatella",
+"cumulata", "festucacea", "hyalina", "merrittfernaldii", "missouriensis",
+"molesta", "molestiformis", "muskingumensis", "normalis", "opaca",
+"oronensis", "projecta", "reniformis", "shinnersii", "teneraVechinodes",
+"teneraVtenera", "tincta", "tribuloidesVtribuloides"), c("brevior",
+"hyalina", "molestiformis", "reniformis", "shinnersii"), c("suberecta",
+"albolutescens", "scopariaVscoparia", "scopariaVtessellata",
+"alata", "vexans", "longii"), c("subfusca", "integra", "peucophila",
+"microptera", "haydeniana", "ebenea"), c("phaeocephala", "preslii",
+"argyrantha"))
Added: pkg/misc/taxonSets.R
===================================================================
--- pkg/misc/taxonSets.R (rev 0)
+++ pkg/misc/taxonSets.R 2009-01-02 02:14:32 UTC (rev 131)
@@ -0,0 +1,22 @@
+taxonSets <- list(ENA = c("alata", "albolutescens", "bebbii", "bicknellii",
+"brevior", "buffaloriver", "crawfordii", "cristatella", "cumulata",
+"festucacea", "feta", "hormathodes", "hyalina", "longii", "merrittfernaldii",
+"missouriensis", "molesta", "molestiformis", "muskingumensis",
+"normalis", "opaca", "oronensis", "ovalis3098", "ozarkana", "projecta",
+"reniformis", "scopariaVscoparia", "scopariaVtessellata", "shinnersii",
+"straminea", "suberecta", "teneraVechinodes", "teneraVtenera",
+"tincta", "tribuloidesVtribuloides", "vexans"), ENAI = c("bebbii",
+"bicknellii", "brevior", "buffaloriver", "crawfordii", "cristatella",
+"cumulata", "festucacea", "hyalina", "merrittfernaldii", "missouriensis",
+"molesta", "molestiformis", "muskingumensis", "normalis", "opaca",
+"oronensis", "projecta", "reniformis", "shinnersii", "teneraVechinodes",
+"teneraVtenera", "tincta", "tribuloidesVtribuloides"), ENAII = c("alata",
+"albolutescens", "hormathodes", "longii", "ozarkana", "scopariaVscoparia",
+"scopariaVtessellata", "straminea", "suberecta", "vexans"), ENAIII = c("feta",
+"ovalis3098"), WNA = c("adusta", "argyrantha", "athrostachya",
+"bohemica", "ebenea", "foenea", "haydeniana", "integra", "macloviana",
+"microptera", "pachystachya", "peucophila", "phaeocephala", "praticola",
+"preslii", "subfusca", "xerantica"), WNAI = c("argyrantha", "bohemica",
+"ebenea", "foenea", "haydeniana", "integra", "microptera", "peucophila",
+"phaeocephala", "praticola", "preslii", "subfusca"), WNAII = c("adusta",
+"athrostachya", "pachystachya", "xerantica", "macloviana"))
\ No newline at end of file
More information about the Mattice-commits
mailing list