@@ -538,7 +538,7 @@ to be detected.  For \code{oncoSimulSample} this can be a vector.

   as labels for the genes, you will see numbers (however, as a character

   string).}

-

+%% Fixme: mention probCancer is not a binomial, but a negative binomial.

 }

@@ -777,6 +777,7 @@ test_that("long example OK", {

                  "H" = "h1, h2", "I" = "i1",

                  "J" = "j1, j2", "K" = "k1, k2", "M" = "m1")

     set.seed(1) ## for repeatability

+    ## These are seeds in R; no problems with different compilers, etc.

     noint <- rexp(5, 10)

     names(noint) <- paste0("n", 1:5)

     fea <- allFitnessEffects(rT = p4, epistasis = epist, orderEffects = oe,

@@ -2,11 +2,13 @@ data(examplePosets)

 p701 <- examplePosets[["p701"]]

-nindiv <- 4

-

 test_that("oncoSimulSample success with large num tries", {

-    p1 <- oncoSimulSample(nindiv, p701, max.num.tries = 5000 * nindiv,

+    ## If nindiv small, sometimes you reach cancer at first try in every

+    ## indiv.

+    nindiv <- 500

+    p1 <- oncoSimulSample(nindiv, p701,

+                          max.num.tries = 5000 * nindiv,

                           onlyCancer = TRUE)

     expect_true(p1$probCancer < 1)

     expect_true(p1$attemptsUsed > nindiv)

@@ -15,7 +17,9 @@ test_that("oncoSimulSample success with large num tries", {

+

 test_that("oncoSimulSample success when no onlyCancer", {

+    nindiv <- 4

     p4 <- oncoSimulSample(nindiv, p701,

                           max.num.tries = nindiv,

                           onlyCancer = FALSE)

@@ -27,6 +31,7 @@ test_that("oncoSimulSample success when no onlyCancer", {

 test_that("oncoSimulSample exits with minimal num tries", {

+    nindiv <- 50

     p5 <- oncoSimulSample(nindiv, p701,

                           initSize = 10,

                           finalTime = 50,

@@ -38,10 +43,11 @@ test_that("oncoSimulSample exits with minimal num tries", {

 test_that("oncoSimulSample exits with small num tries", {

+    nindiv <- 50

     p6 <- oncoSimulSample(nindiv, p701,

                           initSize = 10,

                           finalTime = 50,

-                          max.num.tries = nindiv + 1,

+                          max.num.tries = nindiv + 2,

                           onlyCancer = TRUE)

     expect_true(p6$HittedMaxTries)

     expect_true(is.na(p6$popSummary))

@@ -5,15 +5,25 @@ data(examplesFitnessEffects)

 ## sometimes cancer is not reached. No problem.

+## Very rarely, popSize > 1e15, and we get an exception. Decrease

+## sampleEvery. And e2 only has two genes.

+

 for(i in 1:length(examplesFitnessEffects)) {

     cat(paste("\n Doing i = ", i , " name = ",

               names(examplesFitnessEffects)[i], "\n"))

+    if (names(examplesFitnessEffects)[16] == "e2") {

+        detectionDrv <- 2

+        sE <- 0.05

+    } else {

+        detectionDrv <- 4

+        sE <- 2

+    }

     tmp <-  oncoSimulIndiv(examplesFitnessEffects[[i]],

                            model = "Bozic", 

                            mu = 1e-6,

                            detectionSize = 1e8, 

-                           detectionDrivers = 4,

-                           sampleEvery = 2,

+                           detectionDrivers = detectionDrv,

+                           sampleEvery = sE,

                            max.num.tries = 100,

                            initSize = 2000,

                            onlyCancer = FALSE)

@@ -23,12 +33,19 @@ for(i in 1:length(examplesFitnessEffects)) {

 for(i in 1:length(examplesFitnessEffects)) {

     cat(paste("\n Doing i = ", i , " name = ",

               names(examplesFitnessEffects)[i], "\n"))

+    if (names(examplesFitnessEffects)[16] == "e2") {

+        detectionDrv <- 2

+        sE <- 0.05

+    } else {

+        detectionDrv <- 4

+        sE <- 2

+    }

     tmp <-  oncoSimulIndiv(examplesFitnessEffects[[i]],

                            model = "Exp", 

                            mu = 1e-6,

                            detectionSize = 1e8, 

-                           detectionDrivers = 4,

-                           sampleEvery = 2,

+                           detectionDrivers = detectionDrv,

+                           sampleEvery = sE,

                            max.num.tries = 100,

                            initSize = 2000,

                            onlyCancer = FALSE)

@@ -37,8 +54,6 @@ for(i in 1:length(examplesFitnessEffects)) {

 for(i in 1:length(examplesFitnessEffects)) {

-    cat(paste("\n Doing i = ", i , " name = ",

-              names(examplesFitnessEffects)[i], "\n"))

     tmp <-  oncoSimulIndiv(examplesFitnessEffects[[i]],

                            model = "McFL", 

                            mu = 5e-6,

@@ -57,8 +72,16 @@ for(i in 1:length(examplesFitnessEffects)) {

 for(i in 1:length(examplesFitnessEffects)) {

     cat(paste("\n Doing i = ", i , " name = ",

               names(examplesFitnessEffects)[i], "\n"))

+        cat(paste("\n Doing i = ", i , " name = ",

+              names(examplesFitnessEffects)[i], "\n"))

+    if (names(examplesFitnessEffects)[16] == "e2") {

+        sE <- 0.05

+    } else {

+        sE <- 1

+    }

     tmp <-  oncoSimulSample(4, examplesFitnessEffects[[i]],

-                            onlyCancer = FALSE)

+                            onlyCancer = FALSE,

+                            sampleEvery = sE)

     expect_true(inherits(tmp, "list"))

 }

@@ -67,8 +90,17 @@ for(i in 1:length(examplesFitnessEffects)) {

 for(i in 1:length(examplesFitnessEffects)) {

     cat(paste("\n Doing i = ", i , " name = ",

               names(examplesFitnessEffects)[i], "\n"))

+    if (names(examplesFitnessEffects)[16] == "e2") {

+        detectionDrv <- 2

+        sE <- 0.05

+    } else {

+        detectionDrv <- 4

+        sE <- 2

+    }

     tmp <-  oncoSimulPop(4, examplesFitnessEffects[[i]],

                          onlyCancer = FALSE,

+                         detectionDrivers = detectionDrv,

+                         sampleEvery = sE,

                          mc.cores = 2)

     expect_true(inherits(tmp, "oncosimulpop"))

     tmp2 <- samplePop(tmp)

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

 \usepackage[%

-		shash={2119409},

-		lhash={2119409e5d31dac53d3c0b23928336e598abaef8},

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

+		shash={64e7888},

+		lhash={64e788807673dc53fae66cf103085fd0b76cbe0c},

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

 		authemail={rdiaz02@gmail.com},

-		authsdate={2015-10-01},

-		authidate={2015-10-01 17:30:24 +0200},

-		authudate={1443713424},

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

+		authsdate={2015-10-02},

+		authidate={2015-10-02 12:15:15 +0200},

+		authudate={1443780915},

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

 		commemail={rdiaz02@gmail.com},

-		commsdate={2015-10-01},

-		commidate={2015-10-01 17:30:24 +0200},

-		commudate={1443713424},

+		commsdate={2015-10-02},

+		commidate={2015-10-02 12:15:15 +0200},

+		commudate={1443780915},

 		refnames={ (HEAD -> master)}

 	]{gitsetinfo}

\ No newline at end of file