@@ -1,8 +1,8 @@

 Package: OncoSimulR

 Type: Package

 Title: Forward Genetic Simulation of Cancer Progression with Epistasis 

-Version: 2.9.9

-Date: 2018-04-10

+Version: 2.9.10

+Date: 2018-04-19

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

 		     email = "rdiaz02@gmail.com"),

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

@@ -1,3 +1,19 @@

+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

+	  is simply a matter of changing the cPDetect.

+	- fixation allows exact genotypes, includes tolerance,

+ 	  and checks for a successive number of specified periods

+	- LOD: using only the strict Szendro et al. meaning.

+	- POM: computed in C++.

+	- Using fitness landscape directly when given as input (no

+          conversion to epistasis) and several improvements in speed when

+	  using fitness landscapes as input.

+

+Changes in version 2.9.10 (2018-04-19):

+	- test.Z-fixation: some tests only on Linux because rng is done in

+	C++.

+	

 Changes in version 2.9.9 (2018-04-10):

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

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

@@ -32,8 +32,7 @@ test_that("exercising plotClonePhylog", {

               plotClonePhylog(tmp, N = 10, keepEvents = TRUE)

               ## Reaching the fixOverlap code

               plotClonePhylog(tmp, N = 0, timeEvents = TRUE)

-              expect_true(TRUE) ## dummy, to prevent the

-              ## attempt to apply non-function

+              expect_true(TRUE) 

               ## If plotting failed, this would fail

               expect_error(plotClonePhylog(c(1, 2)))

           })

@@ -68,10 +67,8 @@ test_that("exercising the fitnessEffects plotting code", {

               plot(fp4m, "igraph", layout = igraph::layout.reingold.tilford, 

                    expandModules = TRUE, autofit = TRUE)

               plot(fp4m, expandModules = TRUE, autofit = TRUE)

-              expect_true(TRUE) ## dummy, to prevent the

-              ## attempt to apply non-function

-              ## If plotting failed, this would fail

-          })

+              expect_true(TRUE)

+})

 date()

 test_that("xlab, ylab, ylim, xlim can be passed", {

@@ -181,9 +178,7 @@ test_that("xlab, ylab, ylim, xlim can be passed", {

          ylab = "ylab", ylim = c(-100, 1000),

          xlim = c(20, 70),

          plotDrivers = TRUE)

-    expect_true(TRUE) ## dummy, to prevent the

-    ## attempt to apply non-function

-    ## If plotting failed, this would fail

+    expect_true(TRUE) 

     expect_error(plot(e1, type = "stremaitoooihoh"))

 })

@@ -224,9 +219,7 @@ test_that("oncosimul v.1 objects and genotype plotting", {

     plot(p1, type = "stacked", show = "genotypes", thinData = TRUE)

     plot(p1, type = "stream", show = "genotypes", thinData = TRUE)

     plot(p1, type = "line", show = "genotypes", thinData = TRUE)

-    expect_true(TRUE) ## dummy, to prevent the

-    ## attempt to apply non-function

-    ## If plotting failed, this would fail

+    expect_true(TRUE) 

     expect_error(plot(tmp, type = "linito"))

 })

 date()

@@ -238,94 +231,90 @@ date()

-## test_that("passing colors", {

-##     data(examplePosets)

-##     ## An object of class oncosimul

-##     p705 <- examplePosets[["p705"]]

-##     max.tries <- 4

-##     for(i in 1:max.tries) {

-##     p1 <- oncoSimulIndiv(p705)

-##     if(nrow(p1$pops.by.time) >= 11) {

-##             break

-##     } else {

-##         cat("\n hummm.. had to run again in the plot")

-##         if(i >= max.tries) {

-##             print(p1)

-##             stop("stream will break")

-##         }

-##     }

-##     }

-##     ## class(p1)

-##     plot(p1, type = "stacked", show = "genotypes", thinData = TRUE)

-##     ## with newest testthat, the next make if fail with test_dir, but

-##     ## not if run from REPL. Go figure

-##     plot(p1, type = "stacked", show = "genotypes", col = rainbow(8))

-##     plot(p1, type = "stream", show = "genotypes", col = rainbow(18))

-##     plot(p1, type = "line", show = "genotypes", col = rainbow(3))

-##     expect_true(TRUE) ## dummy, to prevent the

-##     ## attempt to apply non-function

-##     ## If plotting failed, this would fail

-##     expect_error(plot(p1, type = "linito"))

-## })

+test_that("passing colors", {

+    data(examplePosets)

+    ## An object of class oncosimul

+    p705 <- examplePosets[["p705"]]

+    max.tries <- 4

+    for(i in 1:max.tries) {

+    p1 <- oncoSimulIndiv(p705)

+    if(nrow(p1$pops.by.time) >= 11) {

+            break

+    } else {

+        cat("\n hummm.. had to run again in the plot")

+        if(i >= max.tries) {

+            print(p1)

+            stop("stream will break")

+        }

+    }

+    }

+    ## class(p1)

+    plot(p1, type = "stacked", show = "genotypes", thinData = TRUE)

+    ## with newest testthat, the next make if fail with test_dir, but

+    ## not if run from REPL. Go figure

+    plot(p1, type = "stacked", show = "genotypes", col = rainbow(8))

+    plot(p1, type = "stream", show = "genotypes", col = rainbow(18))

+    plot(p1, type = "line", show = "genotypes", col = rainbow(3))

+    expect_true(TRUE) 

+    expect_error(plot(p1, type = "linito"))

+})

-## date()

-## test_that("stacked, stream, genotypes and some colors", {

-##     data(examplesFitnessEffects)

-##     max.tries <- 4

-##     for(i in 1:max.tries) {

-##         tmp <-  oncoSimulIndiv(examplesFitnessEffects[["o3"]],

-##                                model = "McFL", 

-##                                mu = 5e-5,

-##                                detectionSize = 1e8, 

-##                                detectionDrivers = 3,

-##                                sampleEvery = 0.025,

-##                                max.num.tries = 10,

-##                                keepEvery = 5,

-##                                initSize = 2000,

-##                                finalTime = 3000,

-##                                onlyCancer = FALSE, detectionProb = NA,

-##                                keepPhylog = TRUE)

-##         if(nrow(tmp$pops.by.time) >= 5) {

-##             break

-##         } else {

-##             cat("\n hummm.. had to run again in the plot")

-##             if(i >= max.tries) {

-##                 print(tmp)

-##                 stop("stream will break")

-##             }

-##         }

-##     }

-##     plot(tmp, type = "stacked", show = "genotypes")

-##     plot(tmp, type = "stream", show = "genotypes")

-##     plot(tmp, type = "line", show = "genotypes")

-##     plot(tmp, type = "stacked", show = "drivers")

-##     plot(tmp, type = "stream", show = "drivers")

-##     plot(tmp, type = "line", show = "drivers")

-##     plot(tmp, type = "stacked", order.method = "max")

-##     plot(tmp, type = "stacked", order.method = "first")

-##     plot(tmp, type = "stream", order.method = "max")

-##     plot(tmp, type = "stream", order.method = "first")

-##     plot(tmp, type = "stream", stream.center = TRUE)

-##     plot(tmp, type = "stream", stream.center = FALSE)

-##     plot(tmp, type = "stream", stream.center = TRUE, log = "x")

-##     plot(tmp, type = "stacked", stream.center = TRUE, log = "x")

-##     plot(tmp, type = "stacked", show = "genotypes",

-##          breakSortColors = "random")

-##     plot(tmp, type = "stream", show = "genotypes",

-##          breakSortColors = "distave")

-##     plot(tmp, type = "stacked", show = "genotypes", col = rainbow(9))

-##     plot(tmp, type = "stream", show = "genotypes", col = rainbow(3))

-##     plot(tmp, type = "line", show = "genotypes", col = rainbow(20))

-##     expect_true(TRUE) ## dummy, to prevent the

-##     ## attempt to apply non-function

-##     ## If plotting failed, this would fail

-##     expect_error(plot(tmp, type = "linito"))

-## })

-## date()

+date()

+test_that("stacked, stream, genotypes and some colors", {

+    data(examplesFitnessEffects)

+    max.tries <- 4

+    for(i in 1:max.tries) {

+        tmp <-  oncoSimulIndiv(examplesFitnessEffects[["o3"]],

+                               model = "McFL", 

+                               mu = 5e-5,

+                               detectionSize = 1e8, 

+                               detectionDrivers = 3,

+                               sampleEvery = 0.025,

+                               max.num.tries = 10,

+                               keepEvery = 5,

+                               initSize = 2000,

+                               finalTime = 3000,

+                               onlyCancer = FALSE, detectionProb = NA,

+                               keepPhylog = TRUE)

+        if(nrow(tmp$pops.by.time) >= 5) {

+            break

+        } else {

+            cat("\n hummm.. had to run again in the plot")

+            if(i >= max.tries) {

+                print(tmp)

+                stop("stream will break")

+            }

+        }

+    }

+    plot(tmp, type = "stacked", show = "genotypes")

+    plot(tmp, type = "stream", show = "genotypes")

+    plot(tmp, type = "line", show = "genotypes")

+    plot(tmp, type = "stacked", show = "drivers")

+    plot(tmp, type = "stream", show = "drivers")

+    plot(tmp, type = "line", show = "drivers")

+    plot(tmp, type = "stacked", order.method = "max")

+    plot(tmp, type = "stacked", order.method = "first")

+    plot(tmp, type = "stream", order.method = "max")

+    plot(tmp, type = "stream", order.method = "first")

+    plot(tmp, type = "stream", stream.center = TRUE)

+    plot(tmp, type = "stream", stream.center = FALSE)

+    plot(tmp, type = "stream", stream.center = TRUE, log = "x")

+    plot(tmp, type = "stacked", stream.center = TRUE, log = "x")

+    plot(tmp, type = "stacked", show = "genotypes",

+         breakSortColors = "random")

+    plot(tmp, type = "stream", show = "genotypes",

+         breakSortColors = "distave")

+    plot(tmp, type = "stacked", show = "genotypes", col = rainbow(9))

+    plot(tmp, type = "stream", show = "genotypes", col = rainbow(3))

+    plot(tmp, type = "line", show = "genotypes", col = rainbow(20))

+    expect_true(TRUE) 

+    expect_error(plot(tmp, type = "linito"))

+})

+date()

 cat(paste("\n Ending exercise-plotting-code long at", date()))

@@ -1,6 +1,11 @@

 inittime <- Sys.time()

 cat(paste("\n Starting test.Z-fixation at", date(), "\n"))

+## Some tests below might only work on Linux because of compiler

+## differences, because the rng is done in C++, etc.

+## Note that the difference is in whether a certain code

+## is exercised. The runs should work in all platforms, though.

+## This is the same as in test.Z-oncoSimulIndiv.R

 test_that("Three cases with fixation of genotypes" ,{

@@ -28,12 +33,13 @@ test_that("Three cases with fixation of genotypes" ,{

                          keepPhylog = FALSE)

     summary(r3)

+    if(Sys.info()["sysname"] == "Linux") {

     ## stopping at ABCG, which is not a maximum, not a labelled peak

-    expect_equal(

-        c(A = 1, B = 1, C = 1, D = 0, E = 0, F = 0, G = 1),

-        samplePop(r3, "last", "singleCell")[1, ])

+        expect_equal(

+            c(A = 1, B = 1, C = 1, D = 0, E = 0, F = 0, G = 1),

+            samplePop(r3, "last", "singleCell")[1, ])

+    }

     feex$labelled_peaks

-

     ## And not a single genotype unique

     expect_true(r3$TotalPopSize > r3$LargestClone)

@@ -57,9 +63,11 @@ test_that("Three cases with fixation of genotypes" ,{

                      keepPhylog = FALSE)

     summary(r4)

     ## now a local max is the single clone

-    expect_equal(

-        c(A = 1, B = 1, C = 1, D = 0, E = 0, F = 1, G = 1),

-        samplePop(r4, "last", "singleCell")[1, ])

+    if(Sys.info()["sysname"] == "Linux") {

+        expect_equal(

+            c(A = 1, B = 1, C = 1, D = 0, E = 0, F = 1, G = 1),

+            samplePop(r4, "last", "singleCell")[1, ])

+    }

     expect_true(r4$TotalPopSize == r4$LargestClone)

@@ -83,9 +91,11 @@ test_that("Three cases with fixation of genotypes" ,{

                          errorHitMaxTries = TRUE,

                          keepPhylog = FALSE)

     summary(r5)

+    if(Sys.info()["sysname"] == "Linux") {

     expect_equal(

         c(A = 1, B = 1, C = 1, D = 0, E = 0, F = 1, G = 1),

         samplePop(r5, "last", "singleCell")[1, ])

+    }

     ## but other clones present too

     expect_true(r5$TotalPopSize > r5$LargestClone)

 })

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

 \usepackage[%

-		shash={1bb7743},

-		lhash={1bb7743d2798aafc935d6e3fcdd9c78392564e9a},

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

+		shash={c58241c},

+		lhash={c58241c578e1e58ea975ab0283f4f9a9898be60a},

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

 		authemail={rdiaz02@gmail.com},

-		authsdate={2018-04-17},

-		authidate={2018-04-17 17:55:23 +0200},

-		authudate={1523980523},

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

+		authsdate={2018-04-18},

+		authidate={2018-04-18 02:15:18 +0200},

+		authudate={1524010518},

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

 		commemail={rdiaz02@gmail.com},

-		commsdate={2018-04-17},

-		commidate={2018-04-17 17:55:23 +0200},

-		commudate={1523980523},

+		commsdate={2018-04-18},

+		commidate={2018-04-18 02:15:18 +0200},

+		commudate={1524010518},

 		refnames={ (HEAD -> master, origin/master, origin/HEAD)}

 	]{gitsetinfo}

\ No newline at end of file