@@ -1,21 +1,20 @@

 Package: OncoSimulR

 Type: Package

 Title: Simulation of cancer progresion with order restrictions

-Version: 1.3.0

-Date: 2014-07-14

-Author: Ramon Diaz-Uriarte.

+Version: 1.3.1

+Date: 2015-04-30

+Author: Ramon Diaz-Uriarte. 

 Maintainer: Ramon Diaz-Uriarte <rdiaz02@gmail.com>

 Description: Functions for simulating and plotting cancer progression

-        data, including drivers and passengers, and allowing for order

-        restrictions. Simulations use continuous-time models (based on

-        Bozic et al., 2010 and McFarland et al., 2013) and fitness

-        functions account for possible restrictions in the order of

-        accumulation of mutations.

+    data, including drivers and passengers, and allowing for order

+    restrictions. Simulations use continuous-time models (based on Bozic

+    et al., 2010 and McFarland et al., 2013) and fitness functions account

+    for possible restrictions in the order of accumulation of mutations.

 biocViews: BiologicalQuestion, SomaticMutation

 License: GPL (>= 3)

 Depends: R (>= 3.1.0)

 Imports: Rcpp (>= 0.11.1), parallel, data.table, graph, Rgraphviz

-Suggests: BiocStyle, knitr, Oncotree

+Suggests: BiocStyle, knitr, Oncotree, testthat

 LinkingTo: Rcpp

 VignetteBuilder: knitr

 SystemRequirements: C++11

@@ -45,12 +45,15 @@ oncoSimulPop <- function(Nindiv,

                          mu = 1e-6,

                          detectionSize = 1e8,

                          detectionDrivers = 4,

-                         sampleEvery = 1,

+                         sampleEvery = ifelse(model %in% c("Bozic", "Exp"), 1,

+                             0.025),

                          initSize = 500,

                          s = 0.1,

                          sh = -1,

                          K = initSize/(exp(1) - 1),

                          keepEvery = sampleEvery,

+                         endTimeEvery = ifelse(model %in% c("Bozic", "Exp"), -9,

+                                               5 * sampleEvery),

                          finalTime = 0.25 * 25 * 365,

                          onlyCancer = TRUE,

                          max.memory = 2000,

@@ -78,6 +81,7 @@ oncoSimulPop <- function(Nindiv,

                         sh = sh,

                         K = K,

                         keepEvery = keepEvery,

+                        endTimeEvery = endTimeEvery,

                         finalTime = finalTime,

                         onlyCancer = onlyCancer,

                         max.memory = max.memory,

@@ -99,12 +103,15 @@ oncoSimulIndiv <- function(poset,

                            mu = 1e-6,

                            detectionSize = 1e8,

                            detectionDrivers = 4,

-                           sampleEvery = 1,

+                           sampleEvery = ifelse(model %in% c("Bozic", "Exp"), 1,

+                               0.025),

                            initSize = 500,

                            s = 0.1,

                            sh = -1,

                            K = initSize/(exp(1) - 1),

                            keepEvery = sampleEvery,

+                           endTimeEvery = ifelse(model %in% c("Bozic", "Exp"), -9,

+                               5 * sampleEvery),

                            finalTime = 0.25 * 25 * 365,

                            onlyCancer = TRUE,

                            max.memory = 2000,

@@ -112,7 +119,11 @@ oncoSimulIndiv <- function(poset,

                            verbosity = 0

                            ) {

     call <- match.call()

-    rt <- poset.to.restrictTable(poset)

+    ## a backdoor to allow passing restrictionTables directly

+    if(inherits(poset, "restrictionTable"))

+        rt <- poset

+    else

+        rt <- poset.to.restrictTable(poset)

     numDrivers <- nrow(rt)

@@ -148,11 +159,11 @@ oncoSimulIndiv <- function(poset,

         warning("With the McFarland model you often want smaller sampleEvery")

     }

-    if(typeFitness == "mcfarlandlog") {

-        endTimeEvery <- keepEvery

-    } else {

-        endTimeEvery <- -9

-    }

+    ## if(typeFitness == "mcfarlandlog") {

+    ##     endTimeEvery <- keepEvery

+    ## } else {

+    ##     endTimeEvery <- -9

+    ## }

@@ -472,7 +483,7 @@ oncoSimul.internal <- function(restrict.table,

                                keepEvery = 20,

                                alpha = 0.0015,

                                K = 1000,

-                               endTimeEvery = NULL,

+                               endTimeEvery = 5 * sampleEvery,

                                finalDrivers = 1000) {

     if(initSize_species < 10) {

@@ -514,18 +525,18 @@ oncoSimul.internal <- function(restrict.table,

         warning("Using fitness exp with death != 1")

-    if( (is.null(endTimeEvery) || (endTimeEvery > 0)) &&

-       (typeFitness %in% c("bozic1", "exp") )) {

-        warning(paste("endTimeEvery will take a positive value. ",

-                      "This will make simulations not stop until the next ",

-                      "endTimeEvery has been reached. Thus, in simulations ",

-                      "with very fast growth, simulations can take a long ",

-                      "time to finish, or can hit the wall time limit. "))

-    }

-    if(is.null(endTimeEvery))

-        endTimeEvery <- keepEvery

-    if( (endTimeEvery > 0) && (endTimeEvery %% keepEvery) )

-        warning("!(endTimeEvery %% keepEvery)")

+    ## if( (is.null(endTimeEvery) || (endTimeEvery > 0)) &&

+    ##    (typeFitness %in% c("bozic1", "exp") )) {

+    ##     warning(paste("endTimeEvery will take a positive value. ",

+    ##                   "This will make simulations not stop until the next ",

+    ##                   "endTimeEvery has been reached. Thus, in simulations ",

+    ##                   "with very fast growth, simulations can take a long ",

+    ##                   "time to finish, or can hit the wall time limit. "))

+    ## }

+    ## if(is.null(endTimeEvery))

+    ##     endTimeEvery <- keepEvery

+    ## if( (endTimeEvery > 0) && (endTimeEvery %% keepEvery) )

+    ##     warning("!(endTimeEvery %% keepEvery)")

     ## a sanity check in restricTable, so no neg. indices for the positive deps

     neg.deps <- function(x) {

         ## checks a row of restrict.table

@@ -743,9 +754,27 @@ convertRestrictTable <- function(x) {

-adjmat.to.restrictTable <- function(x) {

+adjmat.to.restrictTable <- function(x, root = FALSE,

+                                    rootNames = c("0", "root", "Root")) {

     ## we have the zero

-    ## x <- x[-1, -1]

+    if( any(colnames(x) %in% c("0", "root", "Root")) & !root)

+        warning("Looks like the matrix has a root but you specified root = FALSE")

+

+    if(!identical(colnames(x), rownames(x)))

+        stop("colnames and rownames not identical")

+    if(root) {

+        posRoot <- which(colnames(x) %in% rootNames)

+        if(!length(posRoot))

+            stop("No column with the root name")

+        if(length(posRoot) > 1)

+            stop("Ambiguous location of root")

+        x <- x[-posRoot, -posRoot]

+    }

+

+    if(typeof(x) != "integer")

+        warning("This is not an _integer_ adjacency matrix")

+    if( !all(x %in% c(0, 1) ))

+        stop("Values not in [0, 1]")

     if(!is.null(colnames(x))) {

         ## FIXME: this makes sense with numeric labels for columns, but

         ## not ow.

@@ -758,15 +787,16 @@ adjmat.to.restrictTable <- function(x) {

     num.deps <- colSums(x)

     max.n.deps <- max(num.deps)

-    rt <- matrix(-9, nrow = nrow(x),

+    rt <- matrix(-9L, nrow = nrow(x),

                  ncol = max.n.deps + 2)

     for(i in 1:ncol(x)) {

         if( num.deps[ i ])

             rt[i , 1:(2 + num.deps[ i ])] <- c(i, num.deps[i ],

                                                which(x[, i ] != 0))

         else

-            rt[i , 1:2] <- c(i , 0)

+            rt[i , 1:2] <- c(i , 0L)

     }

+    class(rt) <- "restrictionTable"

     return(rt)

 }

@@ -800,7 +830,7 @@ posetToGraph <- function(x, names,

     ## But we do not for now. Note we show lonely nodes, which oncotrees

     ## do not.  wait: when using root, we do not have "lonely nodes"

     ## anymore.  But that is irrelevant for metrics based on transitive

-    ## closure. Note for Diff, etc.

+    ## closure. Not for Diff, etc.

     ## In fact, this is all OK, but is confussing, because I can

     ## have two kinds of posets: ones that are full, with NAs, etc, if

@@ -808,9 +838,10 @@ posetToGraph <- function(x, names,

     ## using the later, the user needs to make sure that the last node is

     ## in the poset. This can be used as a shortcut trick, but in the docs

     ## I do not do it, as it is bad practice.

-    

+

+

     m <- length(names) 

-    m1 <- matrix(0, nrow = m, ncol = m)

+    m1 <- matrix(0L, nrow = m, ncol = m)

     colnames(m1) <- names

     rownames(m1) <- names

     if(is.null(dim(x)) ) {

@@ -829,16 +860,21 @@ posetToGraph <- function(x, names,

         }

         if(nrow(x) > 0) {

             if(addroot)

-                m1[x + 1] <- 1

+                m1[x + 1] <- 1L

             else

-                m1[x] <- 1

+                m1[x] <- 1L ## this will remove all entries with a 0

+                            ## index. So posets where explicit the dep. on

+                            ## 0.

         }

         if((length(names) > 1) & addroot) {

             no.ancestor <- which(apply(m1, 2, function(x) all(x == 0)))

             no.ancestor <- no.ancestor[-1]

-            m1[cbind(1, no.ancestor)] <- 1

+            m1[cbind(1, no.ancestor)] <- 1L

         } ## o.w. do nothing

     }

+    if(addroot)

+        m1[1, 1] <- 0L

+    

     if(type == "adjmat") return(m1)

     else if (type == "graphNEL") return(as(m1, "graphNEL"))

     ## does not show the labels

new file mode 100644

@@ -0,0 +1,33 @@

+citHeader("If you use OncoSimulR, please cite OncoSimulR itself. Note that a former version of OncoSimulR has been used in a large comparative study of methods to infer restrictions, published in BMC Bioinformatics; you might want to cite that too, if appropriate.")

+

+citEntry(entry="Manual",

+         author = "R Diaz-Uriarte",

+         title = "OncoSimulR: Simulation of cancer progresion with order restrictions.",

+         ## journal = "Bioinformatics",

+         year = "2015",

+         note = "R package version 1.3.1",

+         ## doi = "{10.1093/bioinformatics/btu099}",

+         ## volume = "30",

+         ## number = "12",

+         ## pages = "1759--1761",

+         textVersion = paste("R Diaz-Uriarte.",

+             "OncoSimulR: Simulation of cancer progression with order restrictions. 2015. R package version 1.3.1. ")

+)

+

+

+## citHeader("A former version of OncoSimulR has been used in this paper:")

+

+citEntry(entry="Article",

+         author = "R Diaz-Uriarte",

+         title = "Identifying restrictions in the order of accumulation of mutations during tumor progression: effects of passengers, evolutionary models, and sampling",

+         journal = "BMC Bioinformatics",

+         year = "2015",

+         doi = "{10.1186/s12859-015-0466-7}",

+         url = "{http://www.biomedcentral.com/1471-2105/16/41/abstract}",

+         volume = "16",

+         number = "41",

+         ## pages = "1759--1761",

+         textVersion = paste("R Diaz-Uriarte.",

+             "Identifying restrictions in the order of accumulation of mutations during tumor progression: effects of passengers, evolutionary models, and sampling",

+             "BMC Bioinformatics, 16(41), 2015.")

+)

@@ -1,3 +1,9 @@

+Changes in version 1.3.1 (2015-04-30)

+	- Added CITATION

+	- Changed defaults for sampleEvery and added endTimeEvery.

+	- Added some preliminary tests of poset transformations.

+	- (Subsumed all bumps in version in BioC)

+

 Changes in version 0.99.2 (2014-07-14)

 	- Consistently using indentation in .Rd files.

@@ -20,16 +20,24 @@

 \usage{

  oncoSimulIndiv(poset, model = "Bozic", numPassengers = 30, mu = 1e-6,

                 detectionSize = 1e8, detectionDrivers = 4,

-                sampleEvery = 1, initSize = 500, s = 0.1, sh = -1,

+                sampleEvery = ifelse(model \%in\% c("Bozic", "Exp"), 1,

+                             0.025),

+                initSize = 500, s = 0.1, sh = -1,

                 K = initSize/(exp(1) - 1), keepEvery = sampleEvery,

+                endTimeEvery = ifelse(model \%in\% c("Bozic", "Exp"), -9,

+                                               5 * sampleEvery),

                 finalTime = 0.25 * 25 * 365, onlyCancer = TRUE,

                 max.memory = 2000, max.wall.time = 200,

                 verbosity = 0)

  oncoSimulPop(Nindiv, poset, model = "Bozic", numPassengers = 30, mu = 1e-6,

                 detectionSize = 1e8, detectionDrivers = 4,

-                sampleEvery = 1, initSize = 500, s = 0.1, sh = -1,

+                sampleEvery = ifelse(model \%in\% c("Bozic", "Exp"), 1,

+                             0.025),

+                initSize = 500, s = 0.1, sh = -1,

                 K = initSize/(exp(1) - 1), keepEvery = sampleEvery,

+                endTimeEvery = ifelse(model \%in\% c("Bozic", "Exp"), -9,

+                                               5 * sampleEvery),

                 finalTime = 0.25 * 25 * 365, onlyCancer = TRUE,

                 max.memory = 2000, max.wall.time = 200,

                 verbosity = 0, mc.cores = detectCores())

@@ -121,6 +129,23 @@

   return objects are not huge.

 }

+

+\item{endTimeEvery}{

+  If endTimeEvery is > 0, even if conditions for finishing a simulation

+  (number of drivers or population size) are met at time \emph{t}, the

+  simulation will run at least until \emph{t + endTimeEvery} and

+  conditions will be checked again. Only if conditions for finishing a

+  simulation are still met, will the simulation end.

+

+  The reason for this parameter is to ensure that, say, a clone with a

+  certain number of drivers that would cause the simulation to end has

+  not just appeared but then gone extinct shortly after. Beware, though,

+  that in simulations with very fast growth, setting large endTimeEvery

+  can result in the simulations taking a long time to finish or hitting

+  the wall time limit.}

+

+

+

 \item{finalTime}{

   What is the maximum number of time units that the simulation can run.

@@ -256,7 +281,13 @@

   Academy of Sciences of the United States of America\/}, \bold{107},

   18545--18550.

-  Diaz-Uriarte, R. (2014). Inferring restrictions in the temporal order

+  Diaz-Uriarte, R. (2015). Identifying restrictions in the order of

+             accumulation of mutations during tumor progression: effects

+             of passengers, evolutionary models, and sampling, \emph{BMC

+             Bioinformatics\/},

+             \bold{16}(41). \url{http://www.biomedcentral.com/1471-2105/16/41/abstract}.

+

+  Inferring restrictions in the temporal order

   of mutations during tumor progression: effects of passenger mutations,

   evolutionary models, and

   sampling. \url{http://dx.doi.org/10.1101/005587}

@@ -295,7 +326,7 @@ summary(b1)

 plot(b1, addtot = TRUE)

-## McFarland; need to modify sampleEvery, but use a reasonable

+## McFarland; use a small sampleEvery, but also a reasonable

 ##   keepEvery.

 ## We also modify mutation rate to values similar to those in the

 ##   original paper.

@@ -63,9 +63,11 @@ samplePop(x, timeSample = "last", typeSample = "whole",

 }

 \references{

-  Diaz-Uriarte, R. (2014). Inferring restrictions in the temporal order

-  of mutations during tumor progression: effects of passenger mutations,

-  evolutionary models, and sampling. \url{http://dx.doi.org/10.1101/005587}

+  Diaz-Uriarte, R. (2015). Identifying restrictions in the order of

+             accumulation of mutations during tumor progression: effects

+             of passengers, evolutionary models, and sampling, \emph{BMC

+             Bioinformatics\/},

+             \bold{16}(41). \url{http://www.biomedcentral.com/1471-2105/16/41/abstract}.

 }

 \author{

@@ -706,7 +706,7 @@ inline void reshape_to_outNS(Rcpp::NumericMatrix& outNS,

   std::vector<unsigned long long>::const_iterator fend = uniqueGenotV.end();

   int column;

-

+  // FIXME keepTheseMany: here, fill up only when index_out[i] takes certain values

   for(size_t i = 0; i < genot_out_ul.size(); ++i) {

     column = std::distance(fbeg, lower_bound(fbeg, fend, genot_out_ul[i]) );

     outNS(index_out[i], column + 1) =  popSizes_out[i];

@@ -1275,6 +1275,9 @@ SEXP Algorithm5(SEXP restrictTable_,

   IntegerMatrix returnGenotypes(numGenes, uniqueGenotypes_vector.size());

   create_returnGenotypes(returnGenotypes, numGenes, uniqueGenotypes_vector);

+  // FIXME: keepTheseMany: redo these calculations

+  // correctly. keepTheseMany, not outNS_i + 1;

+  

   int outNS_r, outNS_c, create_outNS;

   if( ( (uniqueGenotypes.size() + 1) *  (outNS_i + 1) ) > ( pow(2, 31) - 1 ) ) {

     Rcpp::Rcout << "\nWARNING: Return outNS object > 2^31 - 1. Not created.\n";

@@ -1289,7 +1292,7 @@ SEXP Algorithm5(SEXP restrictTable_,

     outNS_c = 1;

     create_outNS = 0;

   } else {

-    outNS_r = outNS_i + 1;

+    outNS_r = outNS_i + 1; //FIXME: here it is keepTheseMany

     outNS_c = uniqueGenotypes.size() + 1;

     create_outNS = 1;

   }

@@ -1298,6 +1301,8 @@ SEXP Algorithm5(SEXP restrictTable_,

     reshape_to_outNS(outNS, uniqueGenotypes_vector, genot_out_ullong, 

 		     popSizes_out, 

 		     index_out, time_out);

+

+    //FIXME: keepTheseMany need to prune the uniqueGenotypes

   } else {

     outNS(0, 0) = -99;

new file mode 100644

@@ -0,0 +1,4 @@

+library(testthat)

+# library(OncoSimulR)

+

+test_check("OncoSimulR")

new file mode 100644

@@ -0,0 +1,164 @@

+## A preliminary set of tests. More in the current unreleased code.

+## library(OncoSimulR); library(testthat)

+

+

+

+

+

+## This code is in devel

+## m0 <- matrix(0L, ncol = 4, nrow = 4)

+## colnames(m0) <- rownames(m0) <- c(0, 2, 3, 5)

+## m0[1, 4] <- 1L

+

+## test_that("adjmat illegal even in this conversion",

+##           expect_error(OncoSimulR:::OTtoPoset(m0)))

+

+

+## m0 <- matrix(0L, ncol = 4, nrow = 4)

+## colnames(m0) <- rownames(m0) <- c(0, 2, 3, 5)

+## m0[1,  ] <- 1L

+## test_that("does not conform to having root be called Root",

+##           expect_error(OncoSimulR:::OTtoPoset(m0)))

+

+## m0 <- matrix(0L, ncol = 4, nrow = 4)

+## colnames(m0) <- rownames(m0) <- c("Root", 2, 3, 5)

+## m0[1, ] <- 1L

+## test_that("but an edge to Root",

+##           expect_error(OncoSimulR:::OTtoPoset(m0)))

+

+## m0 <- matrix(0L, ncol = 4, nrow = 4)

+## colnames(m0) <- rownames(m0) <- c("Root", 2, 3, 5)

+## m0[1, 2:4] <- 1L

+## test_that("OT to the smallest Poset",

+##           expect_equal(matrix(nrow=0, ncol=2), OncoSimulR:::OTtoPoset(m0)))

+

+## new devel code

+## test_that("adjmat illegal because empty nodes",

+##           expect_error(OncoSimulR:::adjmat.to.restrictTable(m0, root = TRUE)))

+

+## test_that("adjmat illegal because empty nodes, 2",

+##           expect_error(OncoSimulR:::adjmat.to.restrictTable(m0, root = FALSE)))

+

+## m1 <- matrix(0L, ncol = 4, nrow = 4)

+## colnames(m1) <- rownames(m1) <- c(0, 2, 3, 5)

+## m1[, 4] <- 1L

+

+## test_that("adjmat illegal because lack of incoming",

+##           expect_error(OncoSimulR:::adjmat.to.restrictTable(m1, root = TRUE)))

+## test_that("adjmat illegal because lack of incoming, 2",

+##           expect_error(OncoSimulR:::adjmat.to.restrictTable(m1, root = FALSE)))

+## test_that("adjmat illegal because non-int column names",

+##           expect_error(OncoSimulR:::adjmat.to.restrictTable(m1[-1, -1], root = FALSE)))

+## test_that("adjmat illegal because of no root",

+##           expect_error(OncoSimulR:::adjmat.to.restrictTable(m1[-1, -1], root = TRUE)))

+

+## m2 <- matrix(0L, ncol = 4, nrow = 4)

+## colnames(m2) <- rownames(m2) <- c(0:3)

+## m2[, 4] <- 1L; m2[1, 3] <- 1L

+

+## test_that("adjmat illegal because lack of incoming",

+##           expect_error(OncoSimulR:::adjmat.to.restrictTable(m2, root = TRUE)))

+## test_that("adjmat illegal because lack of incoming, 2",

+##           expect_error(OncoSimulR:::adjmat.to.restrictTable(m2, root = FALSE)))

+

+

+m3 <- matrix(0L, ncol = 4, nrow = 4)

+colnames(m3) <- rownames(m3) <- c(0:3)

+m3[1, 2:4] <- 1L

+

+## test_that("inconsistency in root options",

+##           expect_error(OncoSimulR:::adjmat.to.restrictTable(m3, root = FALSE)))

+

+rt3 <- cbind(1:3, 0L); class(rt3) <- "restrictionTable"

+test_that("simple correct adjmat -> rT", {

+    expect_equal(rt3, OncoSimulR:::adjmat.to.restrictTable(m3, root = TRUE))})

+

+

+p3 <- cbind(0L, 3L)

+test_that("simple correct poset -> graph", {

+    expect_equal(m3,

+                 OncoSimulR:::posetToGraph(p3, names = 0:3, addroot = TRUE, type = "adjmat"))})

+

+

+

+m3 <- matrix(0L, ncol = 4, nrow = 4)

+colnames(m3) <- rownames(m3) <- c(0:3)

+m3[1, ] <- 1L

+## test_that("adjmat illegal because incoming to Root",

+##           expect_error(OncoSimulR:::adjmat.to.restrictTable(m3, root = TRUE)))

+## test_that("adjmat illegal because incoming to Root",

+##           expect_error(OncoSimulR:::adjmat.to.restrictTable(m3, root = FALSE)))

+

+

+

+

+p5 <- cbind(c(0L), c(5L))

+m5 <- matrix(0L, ncol = 6, nrow = 6); colnames(m5) <- rownames(m5) <- 0:5

+m5[1, 2:6] <- 1L

+test_that("simple correct poset -> graph, 5 nodes, root", {

+    expect_equal(m5,

+                 OncoSimulR:::posetToGraph(p5, names = 0:5,

+                                           addroot = TRUE, type = "adjmat"))})

+test_that("simple correct poset -> graph, 5 nodes, no root", {

+    expect_equal(m5[-1, -1],

+                 OncoSimulR:::posetToGraph(p5, names = 1:5,

+                                           addroot = FALSE, type = "adjmat"))})

+

+

+test_that("to rT from poset, through adjmat with and w.o. root",

+          {

+              expect_equal(

+                  OncoSimulR:::adjmat.to.restrictTable(

+                      OncoSimulR:::posetToGraph(p5, names = 1:5, addroot = FALSE, type = "adjmat"),

+                      root = FALSE),

+                  OncoSimulR:::adjmat.to.restrictTable(

+                      OncoSimulR:::posetToGraph(p5, names = 0:5, addroot = TRUE, type = "adjmat"),

+                      root = TRUE))

+          })

+

+

+

+

+## can convert if OT, not o.w.

+## m1 <- structure(c(0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L), .Dim = c(3L, 

+## 3L), .Dimnames = list(c("Root", "2", "4"), c("Root", "2", "4"

+##                                             )))

+## test_that("from adjmat to rT, if OT", {

+##           expect_identical(cbind(2L, 4L), OncoSimulR:::OTtoPoset(m1))})

+## test_that(".. but fails if not considered OT", {

+##           expect_error(OncoSimulR:::adjmat.to.restrictTable(m1, root = TRUE))})

+## test_that(".. but fails if not considered OT", {

+##           expect_error(OncoSimulR:::adjmat.to.restrictTable(m1, root = FALSE))})

+

+

+

+## m1b <- structure(c(0L, 0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L), .Dim = c(3L, 

+## 3L), .Dimnames = list(c("Root", "2", "4"), c("Root", "2", "4"

+## )))

+## test_that("Change pos of elements: from adjmat to rT, if OT", {

+##           expect_identical(cbind(4L, 2L), OncoSimulR:::OTtoPoset(m1b))})

+## test_that(".. but fails if not considered OT", {

+##           expect_error(OncoSimulR:::adjmat.to.restrictTable(m1b, root = TRUE))})

+## test_that(".. but fails if not considered OT", {

+##           expect_error(OncoSimulR:::adjmat.to.restrictTable(m1b, root = FALSE))})

+

+

+

+## posets with some nodes not explicit

+pm1 <- structure(c(0L, 2L, 2L, 4L), .Dim = c(2L, 2L))

+pm1.nr <- structure(c(2L, 4L), .Dim = 1:2)

+test_that("poset to rT, with some nodes missing",{

+          expect_identical(OncoSimulR:::poset.to.restrictTable(pm1.nr),

+                           OncoSimulR:::poset.to.restrictTable(pm1))})

+

+

+pm1b <- structure(c(4L, 0L, 2L, 4L), .Dim = c(2L, 2L))

+pm1b.nr <- structure(c(4L, 2L), .Dim = 1:2)

+test_that("poset to rT, with some nodes missing, nodes exchanged",{

+          expect_identical(OncoSimulR:::poset.to.restrictTable(pm1b.nr),

+                           OncoSimulR:::poset.to.restrictTable(pm1b))})

+

+

+

+

+

@@ -1,15 +1,15 @@

 \usepackage[%

-		shash={8c8c022},

-		lhash={8c8c02214b27f6421fc91523948e112019728983},

-		authname={ramon diaz-uriarte (at Bufo)},

+		shash={c523b93},

+		lhash={c523b93dcddd79d6547631d4ad7f6a4677187871},

+		authname={Ramon Diaz-Uriarte (at Coleonyx)},

 		authemail={rdiaz02@gmail.com},

-		authsdate={2014-07-14},

-		authidate={2014-07-14 19:05:47 +0200},

-		authudate={1405357547},

-		commname={ramon diaz-uriarte (at Bufo)},

+		authsdate={2015-04-30},

+		authidate={2015-04-30 14:13:55 +0200},

+		authudate={1430396035},

+		commname={Ramon Diaz-Uriarte (at Coleonyx)},

 		commemail={rdiaz02@gmail.com},

-		commsdate={2014-07-14},

-		commidate={2014-07-14 19:05:47 +0200},

-		commudate={1405357547},

+		commsdate={2015-04-30},

+		commidate={2015-04-30 14:13:55 +0200},

+		commudate={1430396035},

 		refnames={ (HEAD, master)}

 	]{gitsetinfo}

\ No newline at end of file