@@ -2,7 +2,7 @@ Package: OncoSimulR

 Type: Package

 Title: Forward Genetic Simulation of Cancer Progression with Epistasis 

 Version: 2.11.0

-Date: 2018-04-19

+Date: 2018-07-16

 Authors@R: c(person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),

 		     email = "rdiaz02@gmail.com"),

 	      person("Mark", "Taylor", role = "ctb", email = "ningkiling@gmail.com"))

@@ -1616,6 +1616,7 @@ plotClonePhylog <- function(x, N = 1, t = "last",

 closest_time <- function(x, size) {

     ## Find the first time when a given size is reached

+    ## But these are not times, but the position in pops.by.time. Bad naming.

     sizes <- rowSums(x$pops.by.time[, -1, drop = FALSE])

     candidates <- which(sizes >= size)

     if(length(candidates) == 0) {

@@ -1630,6 +1631,7 @@ closest_time <- function(x, size) {

 get.the.time.for.sample <- function(tmp, timeSample, popSizeSample) {

     if( !is.null(popSizeSample) && (popSizeSample >= 0) )  {

+        ## should be "closest_index" and "the.index"

         the.time <- closest_time(tmp, popSizeSample)

     } else if(timeSample == "last") {

         if(tmp$TotalPopSize == 0) {

@@ -17,7 +17,8 @@

 ##     plot.genotype_fitness_matrix <- plotFitnessLandscape 

 ## FIXME: show only accessible paths? 

-

+## FIXME: when show_labels = FALSE we still show the boxes

+##        and some of the labels.!!!

 ## FIXME: if using only_accessible, maybe we

 ## can try to use fast_peaks, and use the slower

 ## approach as fallback (if identical fitness)

@@ -1,3 +1,6 @@

+Changes in version 2.11.1:

+	- robustify test.fixation.R, Local max, tolerance

+	

 Changes in version 2.10.0 (for BioC 3.7):

 	- probDetect mechanism changed. This could be a BREAKING CHANGE.

 	  The expression divides by the baseline. For fixed initSize, this

@@ -864,6 +864,14 @@ void addToPhylog(PhylogName& phylog,

 // Use a map for LOD, and overwrite the parent:

 // we only add when the size of the child is 0

 // The key of the map is the child.

+

+// FIXME: we might want to store the time? Not really clear even if that

+// makes sense. We would be storing the last time the child (which had 0

+// size at that time) arose from the parent.

+// A simple kludge is to have two maps, the second with child and time.

+// Or do it properly as map<int, genot_time_struct>

+// genot_time_struct {string parent; double time}

+

 void addToLOD(std::map<std::string, std::string>& lod,

 	      const Genotype& parent,

 	      const Genotype& child,

@@ -441,7 +441,7 @@ date()

 test_that("Local max: not stopping, stopping, and tolerance", {

-        initS <- 2000

+    initS <- 2000

     rl1 <- matrix(0, ncol = 6, nrow = 9)

     colnames(rl1) <- c(LETTERS[1:5], "Fitness")

     rl1[1, 6] <- 1

@@ -512,7 +512,10 @@ test_that("Local max: not stopping, stopping, and tolerance", {

     sgsp2 <- sampledGenotypes(sp2)

     expect_true(all(sgsp2$Genotype %in% local_max_g))

     ## tolerance

-    r3 <- oncoSimulPop(100,

+    ## yes, this can occasionally fail, because all are in

+    ## the list of local_max_g

+        

+    r3 <- oncoSimulPop(200,

                        fp = fr1,

                        model = "McFL",

                        initSize = initS,

@@ -521,7 +524,7 @@ test_that("Local max: not stopping, stopping, and tolerance", {

                        sampleEvery = .03,

                        keepEvery = 1, 

                        finalTime = 50000,

-                       fixation = c(local_max, fixation_tolerance = 0.1),

+                       fixation = c(local_max, fixation_tolerance = 0.5),

                        detectionDrivers = NA,

                        detectionProb = NA,

                        onlyCancer = TRUE,

@@ -535,6 +538,8 @@ test_that("Local max: not stopping, stopping, and tolerance", {

     sp3 <- samplePop(r3, "last", "singleCell")

     sgsp3 <- sampledGenotypes(sp3)

     expect_true(!all(sgsp3$Genotype %in% local_max_g))

+    ## sum(sgsp3$Genotype %in% local_max_g)

+    ## sum(!(sgsp3$Genotype %in% local_max_g))

 })