[Phylobase-commits] r925 - in pkg: inst/unitTests tests/testthat
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Apr 9 21:59:12 CEST 2014
Author: francois
Date: 2014-04-09 21:59:11 +0200 (Wed, 09 Apr 2014)
New Revision: 925
Added:
pkg/tests/testthat/test.readNCL.R
Removed:
pkg/inst/unitTests/runit.readNCL.R
Log:
converted readNCL unit tests to testthat
Deleted: pkg/inst/unitTests/runit.readNCL.R
===================================================================
--- pkg/inst/unitTests/runit.readNCL.R 2014-04-09 19:57:40 UTC (rev 924)
+++ pkg/inst/unitTests/runit.readNCL.R 2014-04-09 19:59:11 UTC (rev 925)
@@ -1,466 +0,0 @@
-#
-# --- Test readNCL.R ---
-#
-
-### Get all the test files
-if (Sys.getenv("RCMDCHECK") == FALSE) {
- pth <- file.path(getwd(), "..", "inst", "nexusfiles")
-} else {
- pth <- system.file(package="phylobase", "nexusfiles")
-}
-## co1.nex -- typical output from MrBayes. Contains 2 identical trees, the first
-## one having posterior probabilities as node labels
-co1File <- file.path(pth, "co1.nex")
-
-## MultiLineTrees.nex -- 2 identical trees stored on several lines
-multiLinesFile <- file.path(pth, "MultiLineTrees.nex")
-
-## treeWithDiscreteData.nex -- Mesquite file with discrete data
-treeDiscDt <- file.path(pth, "treeWithDiscreteData.nex")
-
-## treeWithPolyExcludedData.nex -- Mesquite file with polymorphic and excluded
-## characters
-treePolyDt <- file.path(pth, "treeWithPolyExcludedData.nex")
-
-## treeWithContinuousData.nex -- Mesquite file with continuous characters
-treeContDt <- file.path(pth, "treeWithContinuousData.nex")
-
-## treeWithDiscAndContData.nex -- Mesquite file with both discrete and
-## continuous data
-treeDiscCont <- file.path(pth, "treeWithDiscAndContData.nex")
-
-## noStateLabels.nex -- Discrete characters with missing state labels
-noStateLabels <- file.path(pth, "noStateLabels.nex")
-
-## Newick trees
-newick <- file.path(pth, "newick.tre")
-
-## Contains correct (as of 2010-03-08) phylo4 representation of one of the tree
-## stored in the nexus file
-mlFile <- file.path(pth, "multiLines.Rdata")
-
-## Contains representation of data associated with continuous data
-ExContDataFile <- file.path(pth, "ExContData.Rdata")
-
-
-stopifnot(file.exists(co1File))
-stopifnot(file.exists(treeDiscDt))
-stopifnot(file.exists(multiLinesFile))
-stopifnot(file.exists(mlFile))
-stopifnot(file.exists(treePolyDt))
-stopifnot(file.exists(treeContDt))
-stopifnot(file.exists(treeDiscCont))
-stopifnot(file.exists(ExContDataFile))
-stopifnot(file.exists(noStateLabels))
-
-op <- phylobase.options()
-
-test.readNCL <- function() {
- ## function (file, simplify=TRUE, type=c("all", "tree", "data"),
- ## char.all=FALSE, polymorphic.convert=TRUE, levels.uniform=TRUE,
- ## check.node.labels=c("keep", "drop", "asdata"))
-
- ## ########### CO1 -- MrBayes file -- tree only
- ## Tree properties
- ## Labels
- labCo1 <- c("Cow", "Seal", "Carp", "Loach", "Frog", "Chicken", "Human",
- "Mouse", "Rat", "Whale", NA, NA, NA, NA, NA, NA, NA, NA)
- names(labCo1) <- 1:18
- ## Edge lengths
- eLco1 <- c(0.143336, 0.225087, 0.047441, 0.055934, 0.124549, 0.204809, 0.073060, 0.194575,
- 0.171296, 0.222039, 0.237101, 0.546258, 0.533183, 0.154442, 0.134574, 0.113163,
- 0.145592)
- names(eLco1) <- c("11-1", "11-2", "11-12", "12-13", "13-14", "14-15", "15-16", "16-17", "17-3",
- "17-4", "16-5", "15-6", "14-7", "13-18", "18-8", "18-9", "12-10")
- ## Node types
- nTco1 <- c("tip", "tip", "tip", "tip", "tip", "tip", "tip", "tip", "tip",
- "tip", "internal", "internal", "internal", "internal", "internal",
- "internal", "internal", "internal")
- names(nTco1) <- 1:18
- ## Label values
- lVco1 <- c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.93, 0.88, 0.99, 1.00,
- 0.76, 1.00, 1.00)
- ## Read trees
- co1 <- readNCL(file=co1File, check.node.labels="asdata")
- ## Tree 1
- co1Tree1 <- co1[[1]]
- checkIdentical(labels(co1Tree1), labCo1) # check labels
- checkIdentical(edgeLength(co1Tree1), eLco1) # check edge lengths
- checkIdentical(nodeType(co1Tree1), nTco1) # check node types
- checkIdentical(as(co1Tree1, "data.frame")$labelValues, lVco1) # check label values
- ## Tree 2
- co1Tree2 <- co1[[2]]
- checkIdentical(labels(co1Tree2), labCo1) # check labels
- checkIdentical(edgeLength(co1Tree2), eLco1) # check edge lengths
- checkIdentical(nodeType(co1Tree2), nTco1) # check node types
-
- ## Check option simplify
- co1 <- readNCL(file=co1File, check.node.labels="asdata", simplify=TRUE)
- checkIdentical(length(co1), as.integer(1)) # make sure there is only one tree
- checkIdentical(labels(co1), labCo1) # check labels
- checkIdentical(edgeLength(co1), eLco1) # check edge lengths
- checkIdentical(nodeType(co1), nTco1) # check node type
- checkIdentical(as(co1, "data.frame")$labelValues, lVco1) # check label values
-
- ## Check option check.node.labels
- phylobase.options(allow.duplicated.labels="fail")
- checkException(readNCL(file=co1File, check.node.labels="keep")) # fail because labels aren't unique
- phylobase.options(op)
- phylobase.options(allow.duplicated.labels="ok")
- co1 <- readNCL(file=co1File, check.node.labels="keep", simplify=TRUE)
- checkIdentical(nodeLabels(co1), setNames(c(NA, "0.93", "0.88", "0.99", "1.00", "0.76", "1.00", "1.00"),
- 11:18))
- phylobase.options(op)
- co1 <- readNCL(file=co1File, check.node.labels="drop", simplify=TRUE)
- checkIdentical(labels(co1), labCo1) # check labels
- checkIdentical(edgeLength(co1), eLco1) # check edge lengths
- checkIdentical(nodeType(co1), nTco1) # check node type
- checkIdentical(as(co1, "data.frame")$labelValues, NULL) # check label values don't exist
-
- ## ########### Mutli Lines -- tree only
- multiLines <- readNCL(file=multiLinesFile)
- ## load correct representation and make sure that the trees read
- ## match it
- load(mlFile)
- checkIdentical(multiLines[[1]], ml1)
- checkIdentical(multiLines[[2]], ml2)
- rm(ml1, ml2)
-
- ## ########### Tree + data -- file from Mesquite
- ## tree properties
- labTr <- c("Myrmecocystussemirufus", "Myrmecocystusplacodops",
- "Myrmecocystusmendax", "Myrmecocystuskathjuli",
- "Myrmecocystuswheeleri", "Myrmecocystusmimicus",
- "Myrmecocystusdepilis", "Myrmecocystusromainei",
- "Myrmecocystusnequazcatl", "Myrmecocystusyuma",
- "Myrmecocystuskennedyi", "Myrmecocystuscreightoni",
- "Myrmecocystussnellingi", "Myrmecocystustenuinodis",
- "Myrmecocystustestaceus", "Myrmecocystusmexicanus",
- "Myrmecocystuscfnavajo", "Myrmecocystusnavajo",
- NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA)
- names(labTr) <- 1:35
- eTr <- c(NA, 1.699299, 12.300701, 0.894820, 0.836689, 10.569191, 4.524387, 6.044804,
- 0.506099, 0.198842, 0.689044, 4.650818, 2.926053, 1.724765, 1.724765, 4.255993,
- 1.083870, 1.083870, 0.802512, 2.027251, 2.708942, 2.708942, 0.284767, 4.451425,
- 2.257581, 2.193845, 2.193845, 8.635503, 2.770378, 2.770378, 8.275077, 5.724923,
- 2.855375, 2.869547, 2.869547)
- names(eTr) <- c("0-19", "19-20", "20-15", "20-21", "21-22", "22-12", "22-23", "23-11", "23-24",
- "24-25", "25-26", "26-3", "26-27", "27-1", "27-2", "25-28", "28-4", "28-5",
- "24-29", "29-30", "30-6", "30-7", "29-31", "31-10", "31-32", "32-8", "32-9",
- "21-33", "33-13", "33-14", "19-34", "34-16", "34-35", "35-17", "35-18")
- nTtr <- c("tip", "tip", "tip", "tip", "tip", "tip", "tip", "tip", "tip",
- "tip", "tip", "tip", "tip", "tip", "tip", "tip", "tip", "tip",
- "root", "internal", "internal", "internal", "internal", "internal",
- "internal", "internal", "internal", "internal", "internal",
- "internal", "internal", "internal", "internal", "internal",
- "internal")
- names(nTtr) <- 1:35
- ## data to test against
- dtTest1 <- data.frame(time = factor(c(2,1,0,0,0,0,2,0,2,0,0,0,0,1,1,1,0,1)),
- subgenus = factor(c(2,1,0,0,0,0,2,0,2,0,0,0,0,1,1,2,0,1)))
- row.names(dtTest1) <- c("Myrmecocystuscfnavajo","Myrmecocystuscreightoni",
- "Myrmecocystusdepilis","Myrmecocystuskathjuli",
- "Myrmecocystuskennedyi","Myrmecocystusmendax",
- "Myrmecocystusmexicanus","Myrmecocystusmimicus",
- "Myrmecocystusnavajo","Myrmecocystusnequazcatl",
- "Myrmecocystusplacodops","Myrmecocystusromainei",
- "Myrmecocystussemirufus","Myrmecocystussnellingi",
- "Myrmecocystustenuinodis","Myrmecocystustestaceus",
- "Myrmecocystuswheeleri","Myrmecocystusyuma")
- dtTest2 <- dtTest1
- levels(dtTest2$time) <- c("diurnal", "crepuscular", "nocturnal")
- levels(dtTest2$subgenus) <- c("Endiodioctes", "Eremnocystus", "Myrmecocystus")
- p4 <- "phylo4"
- p4d <- "phylo4d"
- attributes(p4) <- attributes(p4d) <- list(package="phylobase")
- ## Tree only
- tr <- readNCL(file=treeDiscDt, type="tree")
- checkIdentical(labels(tr), labTr) # check labels
- checkIdentical(edgeLength(tr), eTr) # check edge lengths
- checkIdentical(nodeType(tr), nTtr) # check node types
- checkIdentical(class(tr), p4) # check class
- ## Data only
- dt1 <- readNCL(file=treeDiscDt, type="data", return.labels=FALSE,
- levels.uniform=FALSE)
- checkIdentical(dt1, dtTest1)
- dt2 <- readNCL(file=treeDiscDt, type="data", return.labels=TRUE,
- levels.uniform=FALSE)
- checkIdentical(dt2, dtTest2)
- ## Tree + Data
- trDt1 <- readNCL(file=treeDiscDt, type="all", return.labels=FALSE,
- levels.uniform=FALSE)
- checkIdentical(labels(trDt1), labTr) # check labels
- checkIdentical(edgeLength(trDt1), eTr) # check edge lengths
- checkIdentical(nodeType(trDt1), nTtr) # check node types
- checkIdentical(class(trDt1), p4d) # check class
- checkIdentical(tdata(trDt1, type="tip")[rownames(dtTest1), ], dtTest1)
- trDt2 <- readNCL(file=treeDiscDt, type="all", return.labels=TRUE,
- levels.uniform=FALSE)
- checkIdentical(labels(trDt2), labTr) # check labels
- checkIdentical(edgeLength(trDt2), eTr) # check edge lengths
- checkIdentical(nodeType(trDt2), nTtr) # check node types
- checkIdentical(class(trDt2), p4d) # check class
- checkIdentical(tdata(trDt2, type="tip")[rownames(dtTest2), ], dtTest2)
-
- ## ########## Tree + Data -- Test for polymorphic.convert, levels.uniform and char.all
- ## data to test against
- ## dtTest 3 -- levels.uniform=FALSE, return.labels=FALSE, polymorphic.convert=FALSE
- dtPoly1 <- data.frame(Test1=factor(c(0,0,1,1,0,NA,1,1,1,0,0,NA,1,1,NA,0,1,
- NA)),
- Test2=factor(c(0,0,0,0,0,NA,0,1,0,1,1,
- "{0,1}",NA,0,NA,0,"{0,1}",1)),
- Test3=factor(c(1,1,1,0,0,0,2,
- "{0,1,2}",0,NA,0,"{0,1}",0,1,0,0,"{0,1,2}",1)),
- row.names=c("Myrmecocystussemirufus","Myrmecocystusplacodops",
- "Myrmecocystusmendax","Myrmecocystuskathjuli",
- "Myrmecocystuswheeleri","Myrmecocystusmimicus",
- "Myrmecocystusdepilis","Myrmecocystusromainei",
- "Myrmecocystusnequazcatl","Myrmecocystusyuma",
- "Myrmecocystuskennedyi","Myrmecocystuscreightoni",
- "Myrmecocystussnellingi","Myrmecocystustenuinodis",
- "Myrmecocystustestaceus","Myrmecocystusmexicanus",
- "Myrmecocystuscfnavajo","Myrmecocystusnavajo"))
- ## dtPoly2 -- levels.uniform=FALSE, return.labels=FALSE, polymorphic.convert=TRUE
- dtPoly2 <- dtPoly1
- dtPoly2[c(12,17),2] <- NA
- dtPoly2[c(8,12,17),3] <- NA
- dtPoly2$Test1 <- factor(dtPoly2$Test1)
- dtPoly2$Test2 <- factor(dtPoly2$Test2)
- dtPoly2$Test3 <- factor(dtPoly2$Test3)
- ## dtPoly3 -- levels.uniform=FALSE, return.labels=TRUE, polymorphic.convert=TRUE
- dtPoly3 <- dtPoly2
- levels(dtPoly3$Test1) <- c("test1A", "test1B")
- levels(dtPoly3$Test2) <- c("test2A", "test2B")
- levels(dtPoly3$Test3) <- c("test3A", "test3B", "test3C")
- ## dtPoly4 -- levels.uniform=FALSE, return.labels=TRUE, polymorphic.convert=FALSE
- ## not yet implemented
-
- ## dtPoly5 -- levels.uniform=TRUE, return.labels=FALSE, polymorphic.convert=FALSE
- dtPoly5 <- dtPoly1
- levels(dtPoly5$Test1) <- levels(dtPoly5$Test2) <- levels(dtPoly5$Test3) <-
- union(levels(dtPoly1$Test1), c(levels(dtPoly1$Test2), levels(dtPoly1$Test3)))
- ## dtPoly6 -- levels.uniform=TRUE, return.labels=FALSE, polymorphic.convert=TRUE
- dtPoly6 <- dtPoly2
- levels(dtPoly6$Test1) <- levels(dtPoly6$Test2) <- levels(dtPoly6$Test3) <-
- union(levels(dtPoly2$Test1), c(levels(dtPoly2$Test2), levels(dtPoly2$Test3)))
- ## dtPoly7 -- levels.uniform=TRUE, return.labels=TRUE, polymorphic.convert=FALSE
- ## not yet implemented
-
- ## dtPoly8 -- levels.uniform=TRUE, return.labels=TRUE, polymorphic.convert=TRUE
- dtPoly8 <- dtPoly3
- levels(dtPoly8$Test1) <- levels(dtPoly8$Test2) <- levels(dtPoly8$Test3) <-
- union(levels(dtPoly3$Test1), c(levels(dtPoly3$Test2), levels(dtPoly3$Test3)))
- ## dtPoly5F -- char.all=FALSE, levels.uniform=TRUE, return.labels=FALSE, polymorphic.convert=FALSE
- dtPoly5F <- dtPoly1[, 1:2]
- levels(dtPoly5F$Test1) <- levels(dtPoly5F$Test2) <-
- union(levels(dtPoly1$Test1), levels(dtPoly1$Test2))
- ## dtPoly6F -- char.all=FALSE, levels.uniform=TRUE, return.labels=FALSE, polymorphic.convert=TRUE
- dtPoly6F <- dtPoly2[, 1:2]
- levels(dtPoly6F$Test1) <- levels(dtPoly6F$Test2) <-
- union(levels(dtPoly2$Test1), levels(dtPoly2$Test2))
- ## dtPoly8F -- char.all=FALSE, levels.uniform=TRUE, return.labels=TRUE, polymorphic.convert=TRUE
- dtPoly8F <- dtPoly3[, 1:2]
- levels(dtPoly8F$Test1) <- levels(dtPoly8F$Test2) <-
- union(levels(dtPoly3$Test1), levels(dtPoly3$Test2))
-
- ## char.all=TRUE, levels.uniform=FALSE, return.labels=FALSE, polymorphic.convert=FALSE
- trChr1 <- readNCL(file=treePolyDt, type="all", polymorphic.convert=FALSE,
- levels.uniform=FALSE, char.all=TRUE, return.labels=FALSE)
- checkIdentical(labels(trChr1), labTr) # check labels
- checkIdentical(edgeLength(trChr1), eTr) # check edge lengths
- checkIdentical(nodeType(trChr1), nTtr) # check node types
- checkIdentical(class(trChr1), p4d) # check class
- checkIdentical(tdata(trChr1, "tip"), dtPoly1)
- ## char.all=TRUE, levels.uniform=FALSE, return.labels=FALSE, polymorphic.convert=TRUE
- trChr2 <- readNCL(file=treePolyDt, type="all", polymorphic.convert=TRUE,
- levels.uniform=FALSE, return.labels=FALSE, char.all=TRUE)
- checkIdentical(labels(trChr2), labTr) # check labels
- checkIdentical(edgeLength(trChr2), eTr) # check edge lengths
- checkIdentical(nodeType(trChr2), nTtr) # check node types
- checkIdentical(class(trChr2), p4d) # check class
- checkIdentical(tdata(trChr2, "tip"), dtPoly2)
- ## char.all=TRUE, levels.uniform=FALSE, return.labels=TRUE, polymorphic.convert=TRUE
- trChr3 <- readNCL(file=treePolyDt, type="all", polymorphic.convert=TRUE,
- levels.uniform=FALSE, char.all=TRUE, return.labels=TRUE)
- checkIdentical(labels(trChr3), labTr) # check labels
- checkIdentical(edgeLength(trChr3), eTr) # check edge lengths
- checkIdentical(nodeType(trChr3), nTtr) # check node types
- checkIdentical(class(trChr3), p4d) # check class
- checkIdentical(tdata(trChr3, "tip"), dtPoly3)
- ## char.all=TRUE, levels.uniform=FALSE, return.labels=TRUE, polymorphic.convert=FALSE
- ## not yet implemented
- ## trChr4 <-
- checkException(readNCL(file=treePolyDt, type="all",
- levels.uniform=FALSE,
- return.labels=TRUE,
- polymorphic.convert=FALSE))
- ## char.all=TRUE, levels.uniform=TRUE, return.labels=FALSE, polymorphic.convert=FALSE
- trChr5 <- readNCL(file=treePolyDt, type="all", polymorphic.convert=FALSE,
- levels.uniform=TRUE, char.all=TRUE, return.labels=FALSE)
- checkIdentical(labels(trChr5), labTr) # check labels
- checkIdentical(edgeLength(trChr5), eTr) # check edge lengths
- checkIdentical(nodeType(trChr5), nTtr) # check node types
- checkIdentical(class(trChr5), p4d) # check class
- checkIdentical(tdata(trChr5, "tip"), dtPoly5)
- ## char.all=TRUE, levels.uniform=TRUE, return.labels=FALSE, polymorphic.convert=TRUE
- trChr6 <- readNCL(file=treePolyDt, type="all", polymorphic.convert=TRUE,
- levels.uniform=TRUE, char.all=TRUE, return.labels=FALSE)
- checkIdentical(labels(trChr6), labTr) # check labels
- checkIdentical(edgeLength(trChr6), eTr) # check edge lengths
- checkIdentical(nodeType(trChr6), nTtr) # check node types
- checkIdentical(class(trChr6), p4d) # check class
- checkIdentical(tdata(trChr6, "tip"), dtPoly6)
- ## char.all=TRUE, levels.uniform=TRUE, return.labels=TRUE, polymorphic.convert=FALSE
- ## not yet implemented
- ## trChr7 <-
- checkException(readNCL(file=treePolyDt, type="all", char.all=TRUE,
- levels.uniform=TRUE,
- return.labels=TRUE,
- polymorphic.convert=FALSE))
- ## char.all=TRUE, levels.uniform=TRUE, return.labels=TRUE, polymorphic.convert=TRUE
- trChr8 <- readNCL(file=treePolyDt, type="all", char.all=TRUE,
- levels.uniform=TRUE,
- return.labels=TRUE,
- polymorphic.convert=TRUE)
- checkIdentical(labels(trChr8), labTr) # check labels
- checkIdentical(edgeLength(trChr8), eTr) # check edge lengths
- checkIdentical(nodeType(trChr8), nTtr) # check node types
- checkIdentical(class(trChr8), p4d) # check class
- checkIdentical(tdata(trChr8, "tip"), dtPoly8)
-
- ## -- with char.all=FALSE
- ## char.all=FALSE, levels.uniform=FALSE, return.labels=FALSE, polymorphic.convert=FALSE
- trChr1F <- readNCL(file=treePolyDt, type="all", polymorphic.convert=FALSE,
- levels.uniform=FALSE, char.all=FALSE, return.labels=FALSE)
- checkIdentical(labels(trChr1F), labTr) # check labels
- checkIdentical(edgeLength(trChr1F), eTr) # check edge lengths
- checkIdentical(nodeType(trChr1F), nTtr) # check node types
- checkIdentical(class(trChr1F), p4d) # check class
- checkIdentical(tdata(trChr1F, "tip"), dtPoly1[, 1:2])
- ## char.all=FALSE, levels.uniform=FALSE, return.labels=FALSE, polymorphic.convert=TRUE
- trChr2F <- readNCL(file=treePolyDt, type="all", polymorphic.convert=TRUE,
- levels.uniform=FALSE, return.labels=FALSE, char.all=FALSE)
- checkIdentical(labels(trChr2F), labTr) # check labels
- checkIdentical(edgeLength(trChr2F), eTr) # check edge lengths
- checkIdentical(nodeType(trChr2F), nTtr) # check node types
- checkIdentical(class(trChr2F), p4d) # check class
- checkIdentical(tdata(trChr2F, "tip"), dtPoly2[, 1:2])
- ## char.all=FALSE, levels.uniform=FALSE, return.labels=TRUE, polymorphic.convert=TRUE
- trChr3F <- readNCL(file=treePolyDt, type="all", polymorphic.convert=TRUE,
- levels.uniform=FALSE, char.all=FALSE, return.labels=TRUE)
- checkIdentical(labels(trChr3F), labTr) # check labels
- checkIdentical(edgeLength(trChr3F), eTr) # check edge lengths
- checkIdentical(nodeType(trChr3F), nTtr) # check node types
- checkIdentical(class(trChr3F), p4d) # check class
- checkIdentical(tdata(trChr3F, "tip"), dtPoly3[, 1:2])
- ## char.all=FALSE, levels.uniform=FALSE, return.labels=TRUE, polymorphic.convert=FALSE
- ## not yet implemented
- ## trChr4F <-
- checkException(readNCL(file=treePolyDt, type="all",
- levels.uniform=FALSE,
- return.labels=TRUE,
- polymorphic.convert=FALSE))
- ## char.all=FALSE, levels.uniform=TRUE, return.labels=FALSE, polymorphic.convert=FALSE
- trChr5F <- readNCL(file=treePolyDt, type="all", polymorphic.convert=FALSE,
- levels.uniform=TRUE, char.all=FALSE, return.labels=FALSE)
- checkIdentical(labels(trChr5F), labTr) # check labels
- checkIdentical(edgeLength(trChr5F), eTr) # check edge lengths
- checkIdentical(nodeType(trChr5F), nTtr) # check node types
- checkIdentical(class(trChr5F), p4d) # check class
- checkIdentical(tdata(trChr5F, "tip"), dtPoly5F)
- ## char.all=FALSE, levels.uniform=TRUE, return.labels=FALSE, polymorphic.convert=TRUE
- trChr6F <- readNCL(file=treePolyDt, type="all", polymorphic.convert=TRUE,
- levels.uniform=TRUE, char.all=FALSE, return.labels=FALSE)
- checkIdentical(labels(trChr6F), labTr) # check labels
- checkIdentical(edgeLength(trChr6F), eTr) # check edge lengths
- checkIdentical(nodeType(trChr6F), nTtr) # check node types
- checkIdentical(class(trChr6F), p4d) # check class
- checkIdentical(tdata(trChr6F, "tip"), dtPoly6F)
- ## char.all=FALSE, levels.uniform=TRUE, return.labels=TRUE, polymorphic.convert=FALSE
- ## not yet implemented
- ## trChr7F <-
- checkException(readNCL(file=treePolyDt, type="all", char.all=FALSE,
- levels.uniform=TRUE,
- return.labels=TRUE,
- polymorphic.convert=FALSE))
- ## char.all=FALSE, levels.uniform=TRUE, return.labels=TRUE, polymorphic.convert=TRUE
- trChr8F <- readNCL(file=treePolyDt, type="all", char.all=FALSE,
- levels.uniform=TRUE,
- return.labels=TRUE,
- polymorphic.convert=TRUE)
- checkIdentical(labels(trChr8F), labTr) # check labels
- checkIdentical(edgeLength(trChr8F), eTr) # check edge lengths
- checkIdentical(nodeType(trChr8F), nTtr) # check node types
- checkIdentical(class(trChr8F), p4d) # check class
- checkIdentical(tdata(trChr8F, "tip"), dtPoly8F)
-
- ## ########## Tree + Data -- test with continuous Characters
- DtCont <- readNCL(file=treeContDt, type="data")
- trDtCont <- readNCL(file=treeContDt, type="all")
- load(ExContDataFile)
- checkIdentical(DtCont, ExContData[rownames(DtCont), ])
- checkIdentical(tdata(trDtCont, "tip"), ExContData)
- rm(ExContData)
- checkIdentical(labels(trDtCont), labTr) # check labels
- checkIdentical(edgeLength(trDtCont), eTr) # check edge lengths
- checkIdentical(nodeType(trDtCont), nTtr) # check node types
- checkIdentical(class(trDtCont), p4d) # check class
-
- ## ########## Tree + Data -- both types (Discrete & Continuous)
- dtDiscCont <- readNCL(file=treeDiscCont, type="data", levels.uniform=FALSE)
- trDtDiscCont <- readNCL(file=treeDiscCont, type="all", levels.uniform=FALSE)
- load(ExContDataFile)
- dtDiscContTest <- cbind(ExContData, dtTest2[rownames(ExContData), ])
- rm(ExContDataFile)
- checkIdentical(dtDiscCont, dtDiscContTest[rownames(dtDiscCont), ])
- checkIdentical(tdata(trDtDiscCont, "tip"), dtDiscContTest)
- checkIdentical(labels(trDtDiscCont), labTr) # check labels
- checkIdentical(edgeLength(trDtDiscCont), eTr) # check edge lengths
- checkIdentical(nodeType(trDtDiscCont), nTtr) # check node types
- checkIdentical(class(trDtDiscCont), p4d) # check class
-
- ## ########### Check for proper handling of missing files
- checkException(readNCL(file="foo.bar"))
-
- ## ########### Check behavior in case of missing state labels
- ow <- options("warn")
- options(warn=2)
- checkException(readNCL(file=noStateLabels, return.labels=TRUE))
- options(ow)
- dtNoSt <- readNCL(file=noStateLabels, type="data", return.labels=TRUE)
- checkIdentical(dtNoSt$char1, factor(c(1,2,0,1)))
-
- ## ########### Newick files
- ## Tree representation
- labNew <- c("a", "b", "c", NA, NA)
- names(labNew) <- 1:5
- eLnew <- c(NA, 1, 4, 2, 3)
- names(eLnew) <- c("0-4", "4-1", "4-5", "5-2", "5-3")
- nTnew <- c("tip", "tip", "tip", "root", "internal")
- names(nTnew) <- 1:5
- ## check.node.labels="drop" with readNCL
- newTr <- readNCL(file=newick, file.format="newick", check.node.labels="drop")
- checkIdentical(labels(newTr), labNew)
- checkIdentical(edgeLength(newTr), eLnew)
- checkIdentical(nodeType(newTr), nTnew)
- ## check.node.labels="drop" with readNewick
- newTr <- readNewick(file=newick, check.node.labels="drop")
- checkIdentical(labels(newTr), labNew)
- checkIdentical(edgeLength(newTr), eLnew)
- checkIdentical(nodeType(newTr), nTnew)
- ## check.node.labels="asdata" with readNCL
- newTr <- readNCL(file=newick, file.format="newick", check.node.labels="asdata")
- checkIdentical(labels(newTr), labNew)
- checkIdentical(tdata(newTr)$labelValues, factor(c(NA, NA, NA, "yy", "xx")))
- ## check.node.labels="asdata" with readNewick
- newTr <- readNewick(file=newick, check.node.labels="asdata")
- checkIdentical(labels(newTr), labNew)
- checkIdentical(tdata(newTr)$labelValues, factor(c(NA, NA, NA, "yy", "xx")))
- ## check.node.labels="keep" with readNCL
- labNew[4:5] <- c("yy", "xx")
- newTr <- readNCL(file=newick, file.format="newick", check.node.labels="keep")
- checkIdentical(labels(newTr), labNew)
- ## check.node.labels="keep" with readNewick
- newTr <- readNewick(file=newick, check.node.labels="keep")
- checkIdentical(labels(newTr), labNew)
-}
Copied: pkg/tests/testthat/test.readNCL.R (from rev 880, pkg/inst/unitTests/runit.readNCL.R)
===================================================================
--- pkg/tests/testthat/test.readNCL.R (rev 0)
+++ pkg/tests/testthat/test.readNCL.R 2014-04-09 19:59:11 UTC (rev 925)
@@ -0,0 +1,537 @@
+#
+# --- Test readNCL.R ---
+#
+
+### Get all the test files
+if (Sys.getenv("RCMDCHECK") == FALSE) {
+ pth <- file.path(getwd(), "..", "inst", "nexusfiles")
+} else {
+ pth <- system.file(package="phylobase", "nexusfiles")
+}
+
+## co1.nex -- typical output from MrBayes. Contains 2 identical trees, the first
+## one having posterior probabilities as node labels
+co1File <- file.path(pth, "co1.nex")
+
+## MultiLineTrees.nex -- 2 identical trees stored on several lines
+multiLinesFile <- file.path(pth, "MultiLineTrees.nex")
+
+## treeWithDiscreteData.nex -- Mesquite file with discrete data
+treeDiscDt <- file.path(pth, "treeWithDiscreteData.nex")
+
+## treeWithPolyExcludedData.nex -- Mesquite file with polymorphic and excluded
+## characters
+treePolyDt <- file.path(pth, "treeWithPolyExcludedData.nex")
+
+## treeWithContinuousData.nex -- Mesquite file with continuous characters
+treeContDt <- file.path(pth, "treeWithContinuousData.nex")
+
+## treeWithDiscAndContData.nex -- Mesquite file with both discrete and
+## continuous data
+treeDiscCont <- file.path(pth, "treeWithDiscAndContData.nex")
+
+## noStateLabels.nex -- Discrete characters with missing state labels
+noStateLabels <- file.path(pth, "noStateLabels.nex")
+
+## Newick trees
+newick <- file.path(pth, "newick.tre")
+
+## Contains correct (as of 2010-03-08) phylo4 representation of one of the tree
+## stored in the nexus file
+mlFile <- file.path(pth, "multiLines.Rdata")
+
+## Contains representation of data associated with continuous data
+ExContDataFile <- file.path(pth, "ExContData.Rdata")
+
+
+stopifnot(file.exists(co1File))
+stopifnot(file.exists(treeDiscDt))
+stopifnot(file.exists(multiLinesFile))
+stopifnot(file.exists(mlFile))
+stopifnot(file.exists(treePolyDt))
+stopifnot(file.exists(treeContDt))
+stopifnot(file.exists(treeDiscCont))
+stopifnot(file.exists(ExContDataFile))
+stopifnot(file.exists(noStateLabels))
+
+op <- phylobase.options()
+
+
+## function (file, simplify=TRUE, type=c("all", "tree", "data"),
+## char.all=FALSE, polymorphic.convert=TRUE, levels.uniform=TRUE,
+## check.node.labels=c("keep", "drop", "asdata"))
+
+
+
+## ########### CO1 -- MrBayes file -- tree only
+
+## Tree properties
+## Labels
+labCo1 <- c("Cow", "Seal", "Carp", "Loach", "Frog", "Chicken", "Human",
+ "Mouse", "Rat", "Whale", NA, NA, NA, NA, NA, NA, NA, NA)
+names(labCo1) <- 1:18
+## Edge lengths
+eLco1 <- c(0.143336, 0.225087, 0.047441, 0.055934, 0.124549, 0.204809, 0.073060, 0.194575,
+ 0.171296, 0.222039, 0.237101, 0.546258, 0.533183, 0.154442, 0.134574, 0.113163,
+ 0.145592)
+names(eLco1) <- c("11-1", "11-2", "11-12", "12-13", "13-14", "14-15", "15-16", "16-17", "17-3",
+ "17-4", "16-5", "15-6", "14-7", "13-18", "18-8", "18-9", "12-10")
+## Node types
+nTco1 <- c("tip", "tip", "tip", "tip", "tip", "tip", "tip", "tip", "tip",
+ "tip", "internal", "internal", "internal", "internal", "internal",
+ "internal", "internal", "internal")
+names(nTco1) <- 1:18
+## Label values
+lVco1 <- c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.93, 0.88, 0.99, 1.00,
+ 0.76, 1.00, 1.00)
+context("readNCL can deal with simple NEXUS files (tree only)")
+test_that("file with 2 trees (warning normal)", {
+ ## Read trees
+ co1 <- suppressWarnings(readNCL(file=co1File, check.node.labels="asdata"))
+ ## Tree 1
+ co1Tree1 <- co1[[1]]
+ expect_equal(labels(co1Tree1), labCo1) # check labels
+ expect_equal(edgeLength(co1Tree1), eLco1) # check edge lengths
+ expect_equal(nodeType(co1Tree1), nTco1) # check node types
+ expect_equal(as(co1Tree1, "data.frame")$labelValues, lVco1) # check label value
+ ## Tree 2
+ co1Tree2 <- co1[[2]]
+ expect_equal(labels(co1Tree2), labCo1) # check labels
+ expect_equal(edgeLength(co1Tree2), eLco1) # check edge lengths
+ expect_equal(nodeType(co1Tree2), nTco1) # check node types
+})
+
+test_that("test option simplify", {
+ ## Check option simplify
+ co1 <- readNCL(file=co1File, check.node.labels="asdata", simplify=TRUE)
+ expect_equal(length(co1), as.integer(1)) # make sure there is only one tree
+ expect_equal(labels(co1), labCo1) # check labels
+ expect_equal(edgeLength(co1), eLco1) # check edge lengths
+ expect_equal(nodeType(co1), nTco1) # check node type
+ expect_equal(as(co1, "data.frame")$labelValues, lVco1) # check label values
+})
+
+test_that("test option check.node.labels", {
+ ## Check option check.node.labels
+ phylobase.options(allow.duplicated.labels="fail")
+ expect_error(readNCL(file=co1File, check.node.labels="keep")) # fail because labels aren't unique
+ phylobase.options(op)
+ phylobase.options(allow.duplicated.labels="ok")
+ co1 <- readNCL(file=co1File, check.node.labels="keep", simplify=TRUE)
+ expect_equal(nodeLabels(co1),
+ setNames(c(NA, "0.93", "0.88", "0.99", "1.00", "0.76", "1.00", "1.00"),
+ 11:18))
+ phylobase.options(op)
+ co1 <- readNCL(file=co1File, check.node.labels="drop", simplify=TRUE)
+ expect_equal(labels(co1), labCo1) # check labels
+ expect_equal(edgeLength(co1), eLco1) # check edge lengths
+ expect_equal(nodeType(co1), nTco1) # check node type
+ expect_equal(as(co1, "data.frame")$labelValues, NULL) # check label values don't exist
+})
+
+test_that("readNCL can handle multi line files", {
+ ## ########### Mutli Lines -- tree only
+ multiLines <- readNCL(file=multiLinesFile)
+ ## load correct representation and make sure that the trees read
+ ## match it
+ load(mlFile)
+ expect_equal(multiLines[[1]], ml1)
+ expect_equal(multiLines[[2]], ml2)
+ rm(ml1, ml2)
+})
+
+## ########### Tree + data -- file from Mesquite
+context("readNCL can handle files with tree & data")
+## tree properties
+labTr <- c("Myrmecocystussemirufus", "Myrmecocystusplacodops",
+ "Myrmecocystusmendax", "Myrmecocystuskathjuli",
+ "Myrmecocystuswheeleri", "Myrmecocystusmimicus",
+ "Myrmecocystusdepilis", "Myrmecocystusromainei",
+ "Myrmecocystusnequazcatl", "Myrmecocystusyuma",
+ "Myrmecocystuskennedyi", "Myrmecocystuscreightoni",
+ "Myrmecocystussnellingi", "Myrmecocystustenuinodis",
+ "Myrmecocystustestaceus", "Myrmecocystusmexicanus",
+ "Myrmecocystuscfnavajo", "Myrmecocystusnavajo",
+ NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA)
+names(labTr) <- 1:35
+eTr <- c(NA, 1.699299, 12.300701, 0.894820, 0.836689, 10.569191, 4.524387, 6.044804,
+ 0.506099, 0.198842, 0.689044, 4.650818, 2.926053, 1.724765, 1.724765, 4.255993,
+ 1.083870, 1.083870, 0.802512, 2.027251, 2.708942, 2.708942, 0.284767, 4.451425,
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/phylobase -r 925
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