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v.2.1.5: \ - vignette improvement; - more verbosity in one test

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OncoSimulR@116051 bc3139a8-67e5-0310-9ffc-ced21a209358

Ramon Diaz-Uriarte authored on 09/04/2016 18:03:50
Showing 5 changed files

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@@ -1,7 +1,7 @@
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 Package: OncoSimulR
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 Type: Package
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 Title: Forward Genetic Simulation of Cancer Progresion with Epistasis 
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-Version: 2.1.4
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+Version: 2.1.5
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 Date: 2016-04-09
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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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@@ -8,6 +8,10 @@ Changes in version 2.2.0 (for BioC 3.3):
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 	- Added mutationPropGrowth as argument.
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 	- Some minor bug fixes and additional checks for user errors.
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+Changes in version 2.1.5 (2016-04-09):
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+	- Added a test of driverCounts, that does not depend on
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+          OS/compiler.
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+
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 Changes in version 2.1.4 (2016-04-09):
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 	- Moved to manual tests that depend on OS/compiler (for
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 	reproduction of random number stream in C++).
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@@ -68,6 +68,9 @@ date()
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 date()
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 test_that("Assertion is correct when nothing returned",{
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+    ## Fixing the seed here isn't really needed. These are just a few
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+    ## specific cases in Linux, but other compilers will give different
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+    ## runs. None should fail, though.
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     RNGkind("L'Ecuyer-CMRG") 
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     set.seed(13)
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     oi <- allFitnessEffects(orderEffects =
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@@ -114,4 +117,24 @@ test_that("Assertion is correct when nothing returned",{
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 date()
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+## Just to check no crashes and to show output
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+date()
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+test_that("driverCounts: a run that used to cause crashes", {
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+    set.seed(1)
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+    ni <- runif(10, min = -0.01, max = 0.1)
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+    names(ni) <- paste0("g", 2:11)
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+    fe31 <- allFitnessEffects(noIntGenes = ni,
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+                              drvNames = "g2") 
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+    set.seed(1)
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+    mue11 <- oncoSimulIndiv(fe31, 
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+                            mu = 1e-6,
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+                            initSize = 1e5,
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+                            model = "McFL",
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+                            detectionSize = 5e6,
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+                            finalTime = 5, 
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+                            onlyCancer = FALSE)
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+    cat("\n ... output from mue11\n")
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+    print(mue11)
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+})
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+
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 cat(paste("\n Ending driverCounts at", date(), "\n"))
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@@ -4264,6 +4264,9 @@ Note that in the McF model \texttt{detectionSize} really plays no
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 role. Note also how we pass the poset: it is the same as before, but now
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 we directly access the poset in the list of posets.
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+<<echo=FALSE,eval=TRUE>>=
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+set.seed(1) ## for repeatability. Once I saw it not reach cancer.
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+@ 
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 <<>>=
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 m2 <- oncoSimulIndiv(examplePosets[["p1101"]], model = "McFL", 
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@@ -4273,6 +4276,11 @@ m2 <- oncoSimulIndiv(examplePosets[["p1101"]], model = "McFL",
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                      finalTime = 25000, keepEvery = 5, 
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                      detectionSize = 1e6) 
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 @ 
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+
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+(Very rarely the above run will fail to reach cancer. If that
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+happens, execute it again.)
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+
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+
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 As usual, we will plot using both a line and a stacked plot:
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 <<m2x1,fig.width=6.5, fig.height=10>>=
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@@ -4283,7 +4291,6 @@ plot(m2, type = "stacked",
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      thinData = TRUE, thinData.keep = 0.5)
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 @ 
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-
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 The default is to simulate progression until a simulation reaches cancer
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 (i.e., only simulations that satisfy the detectionDrivers or the
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 detectionSize will be returned). If you use the McF model with large
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 \usepackage[%
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-		shash={72d08e2},
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-		lhash={72d08e233c63d9f3dbf9435388c3cd4c2a50f0d6},
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-		authname={ramon diaz-uriarte (at Bufo)},
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-		authemail={rdiaz02@gmail.com},
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+		shash={0df7857},
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+		lhash={0df78578e3ccebbb0e5e046b6445b47a0c343f7d},
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+		authname={Ramon Diaz-Uriarte},
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+		authemail={rdiaz02@users.noreply.github.com},
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 		authsdate={2016-04-09},
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-		authidate={2016-04-09 00:20:11 +0200},
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-		authudate={1460154011},
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-		commname={ramon diaz-uriarte (at Bufo)},
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-		commemail={rdiaz02@gmail.com},
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+		authidate={2016-04-09 18:50:52 +0200},
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+		authudate={1460220652},
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+		commname={Ramon Diaz-Uriarte},
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+		commemail={rdiaz02@users.noreply.github.com},
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 		commsdate={2016-04-09},
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-		commidate={2016-04-09 00:20:11 +0200},
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-		commudate={1460154011},
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-		refnames={ (HEAD -> master)}
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+		commidate={2016-04-09 18:50:52 +0200},
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+		commudate={1460220652},
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+		refnames={ (HEAD, origin/master, origin/HEAD)}
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 	]{gitsetinfo}
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