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no longer refs to older installer and robustify one test

ramon diaz-uriarte (at Phelsuma) authored on 16/07/2018 20:27:32
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@@ -2,7 +2,7 @@ Package: OncoSimulR
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 Type: Package
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 Title: Forward Genetic Simulation of Cancer Progression with Epistasis 
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 Version: 2.11.0
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-Date: 2018-04-19
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+Date: 2018-07-16
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 Authors@R: c(person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
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 		     email = "rdiaz02@gmail.com"),
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 	      person("Mark", "Taylor", role = "ctb", email = "ningkiling@gmail.com"))
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@@ -1616,6 +1616,7 @@ plotClonePhylog <- function(x, N = 1, t = "last",
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 closest_time <- function(x, size) {
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     ## Find the first time when a given size is reached
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+    ## But these are not times, but the position in pops.by.time. Bad naming.
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     sizes <- rowSums(x$pops.by.time[, -1, drop = FALSE])
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     candidates <- which(sizes >= size)
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     if(length(candidates) == 0) {
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@@ -1630,6 +1631,7 @@ closest_time <- function(x, size) {
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 get.the.time.for.sample <- function(tmp, timeSample, popSizeSample) {
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     if( !is.null(popSizeSample) && (popSizeSample >= 0) )  {
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+        ## should be "closest_index" and "the.index"
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         the.time <- closest_time(tmp, popSizeSample)
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     } else if(timeSample == "last") {
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         if(tmp$TotalPopSize == 0) {
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@@ -17,7 +17,8 @@
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 ##     plot.genotype_fitness_matrix <- plotFitnessLandscape 
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 ## FIXME: show only accessible paths? 
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-
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+## FIXME: when show_labels = FALSE we still show the boxes
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+##        and some of the labels.!!!
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 ## FIXME: if using only_accessible, maybe we
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 ## can try to use fast_peaks, and use the slower
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 ## approach as fallback (if identical fitness)
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@@ -1,3 +1,6 @@
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+Changes in version 2.11.1:
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+	- robustify test.fixation.R, Local max, tolerance
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+	
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 Changes in version 2.10.0 (for BioC 3.7):
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 	- probDetect mechanism changed. This could be a BREAKING CHANGE.
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 	  The expression divides by the baseline. For fixed initSize, this
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@@ -864,6 +864,14 @@ void addToPhylog(PhylogName& phylog,
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 // Use a map for LOD, and overwrite the parent:
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 // we only add when the size of the child is 0
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 // The key of the map is the child.
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+
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+// FIXME: we might want to store the time? Not really clear even if that
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+// makes sense. We would be storing the last time the child (which had 0
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+// size at that time) arose from the parent.
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+// A simple kludge is to have two maps, the second with child and time.
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+// Or do it properly as map<int, genot_time_struct>
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+// genot_time_struct {string parent; double time}
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+
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 void addToLOD(std::map<std::string, std::string>& lod,
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 	      const Genotype& parent,
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 	      const Genotype& child,
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@@ -441,7 +441,7 @@ date()
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 test_that("Local max: not stopping, stopping, and tolerance", {
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-        initS <- 2000
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+    initS <- 2000
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     rl1 <- matrix(0, ncol = 6, nrow = 9)
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     colnames(rl1) <- c(LETTERS[1:5], "Fitness")
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     rl1[1, 6] <- 1
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@@ -512,7 +512,10 @@ test_that("Local max: not stopping, stopping, and tolerance", {
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     sgsp2 <- sampledGenotypes(sp2)
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     expect_true(all(sgsp2$Genotype %in% local_max_g))
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     ## tolerance
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-    r3 <- oncoSimulPop(100,
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+    ## yes, this can occasionally fail, because all are in
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+    ## the list of local_max_g
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+        
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+    r3 <- oncoSimulPop(200,
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                        fp = fr1,
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                        model = "McFL",
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                        initSize = initS,
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@@ -521,7 +524,7 @@ test_that("Local max: not stopping, stopping, and tolerance", {
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                        sampleEvery = .03,
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                        keepEvery = 1, 
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                        finalTime = 50000,
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-                       fixation = c(local_max, fixation_tolerance = 0.1),
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+                       fixation = c(local_max, fixation_tolerance = 0.5),
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                        detectionDrivers = NA,
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                        detectionProb = NA,
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                        onlyCancer = TRUE,
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@@ -535,6 +538,8 @@ test_that("Local max: not stopping, stopping, and tolerance", {
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     sp3 <- samplePop(r3, "last", "singleCell")
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     sgsp3 <- sampledGenotypes(sp3)
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     expect_true(!all(sgsp3$Genotype %in% local_max_g))
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+    ## sum(sgsp3$Genotype %in% local_max_g)
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+    ## sum(!(sgsp3$Genotype %in% local_max_g))
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 })
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