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

 Package: OncoSimulR

 Type: Package

 Title: Forward Genetic Simulation of Cancer Progresion with Epistasis 

-Version: 2.3.7

-Date: 2016-07-05

+Version: 2.3.8

+Date: 2016-07-08

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

 		     email = "rdiaz02@gmail.com"),

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

@@ -1563,7 +1563,7 @@ nr_oncoSimul.internal <- function(rFE,

         ## muEF <- emptyFitnessEffects()

     }

-    dpr <- detectionProbCheckParse(detectionProb, initSize)

+    dpr <- detectionProbCheckParse(detectionProb, initSize, verbosity)

     ## if( !is.null(cPDetect) && (sum(!is.null(p2), !is.null(n2)) >= 1 ))

     ##     stop("Specify only cPDetect xor both of p2 and n2")

     ## if( (is.null(p2) + is.null(n2)) == 1 )

@@ -1747,10 +1747,10 @@ matchGeneIDs <- function(x, refFE) {

 }

-detectionProbCheckParse <- function(x, initSize) {

+detectionProbCheckParse <- function(x, initSize, verbosity) {

     default_p2 <- 0.1

     default_n2 <- 2 * initSize

-    default_PDBaseline <- 1.1 * initSize

+    default_PDBaseline <- 1.2 * initSize

     default_checkSizePEvery <- 20

     ## No default cPDetect. That is done from p2 and n2 in C++.

@@ -1787,12 +1787,14 @@ detectionProbCheckParse <- function(x, initSize) {

     if(is.na(x["PDBaseline"])) {

         x["PDBaseline"] <- default_PDBaseline

-        cat("\n  PDBaseline set to default value of ", default_PDBaseline, "\n")

+        if(verbosity > -1)

+            message("\n  PDBaseline set to default value of ", default_PDBaseline, "\n")

         }

     if(is.na(x["checkSizePEvery"])) {

         x["checkSizePEvery"] <- default_checkSizePEvery

-        cat("\n  checkSizePEvery set to default value of ",

-            default_checkSizePEvery, "\n")

+        if(verbosity > -1)

+            message("\n  checkSizePEvery set to default value of ",

+                default_checkSizePEvery, "\n")

         }

     ## If we get here, we checked consistency of whether cPDetect or p2/n2.

@@ -1803,8 +1805,9 @@ detectionProbCheckParse <- function(x, initSize) {

             if(!is.na(x["n2"])) stop("Eh? no p2 but n2? Bug")

             x["n2"] <- default_n2

             x["p2"] <- default_p2

-            cat("\n  n2, p2 set to default values of ",

-                default_n2, ", ", default_p2, "\n")

+            if(verbosity > -1)

+                message("\n  n2, p2 set to default values of ",

+                    default_n2, ", ", default_p2, "\n")

         }

     }

@@ -1823,7 +1826,8 @@ detectionProbCheckParse <- function(x, initSize) {

         if(is.na(x["cPDetect"])) stop("eh? you found a bug")## paranoia

         x["n2"] <- -9

         x["p2"] <- -9

-        cat("\n Using user-specified cPDetect as n2, p2 not given.\n")

+        if(verbosity > -1)

+            message("\n Using user-specified cPDetect as n2, p2 not given.\n")

     }

     return(x)

 }

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

+Changes in version 2.3.8 (2017-07-08):

+	- PDBasline default is now 1.2.

+	

 Changes in version 2.3.7 (2016-07-05):

 	- Unused C++ code reorganiz.

 	- Added tests

@@ -224,7 +224,7 @@ simulations.

     \item{PDBaseline}{Baseline size subtracted to total population size

     to compute the probability of detection. If not given explicitly,

-    the default is \code{1.1*initSize}.

+    the default is \code{1.2 * initSize}.

     }

     \item{p2}{The probability of detection at population size

@@ -501,10 +501,10 @@ of \code{sampleEvery} that is larger than or equal to \code{keepEvery}.

-\item{verbosity}{

-  If 0, run as silently as possible. Otherwise, increasing values of

-  verbosity provide progressively more information about intermediate

-  steps, possible numerical notes/warnings from the C++ code, etc.

+\item{verbosity}{ If 0, run silently. Iincreasing values of verbosity

+  provide progressively more information about intermediate steps,

+  possible numerical notes/warnings from the C++ code, etc. Values less

+  than 0 supress some default notes: use with care.

 }

@@ -1,4 +1,7 @@

-

+## 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.

 test_that("exercise no positions left for mutation, updating in null mut, old format", {

     ## Do not do the capture output from oncoSimulPop,

@@ -17,9 +20,11 @@ test_that("exercise no positions left for mutation, updating in null mut, old fo

                               extraTime = 3.17,

                               onlyCancer = FALSE,

                               seed = NULL)

-        })

-    expect_true(any(grepl("mutation = 0", st)))

-    expect_true(any(grepl("updating in null mutation", st)))

+    })

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

+        expect_true(any(grepl("mutation = 0", st)))

+        expect_true(any(grepl("updating in null mutation", st)))

+    }

     expect_output(print(pp1),

                    "Individual OncoSimul trajectory", fixed = TRUE)

 })

@@ -40,7 +45,9 @@ test_that("exercise mu > 1, old format", {

                           finalTime = 2000,

                           onlyCancer = FALSE,

                           seed = NULL))

+    

     expect_true(any(grepl("mutation > 1", st)))

+    

     expect_output(print(pp1),

                   "Individual OncoSimul trajectory", fixed = TRUE)

 })

@@ -122,8 +129,10 @@ test_that("exercise no positions left for mutation, updating in null mut, new fo

                           verbosity = 1))

     expect_output(print(pp1),

                   "Individual OncoSimul", fixed = TRUE)

-    expect_true(any(grepl("mutation = 0", st)))

-    expect_true(any(grepl("updating in null mutation", st)))

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

+        expect_true(any(grepl("mutation = 0", st)))

+        expect_true(any(grepl("updating in null mutation", st)))

+    }

 })

@@ -377,7 +377,7 @@ test_that("Increasing n2 increases time" , {

     gi <- rep(0.0,  10)

     names(gi) <- letters[1:10]

     oi <- allFitnessEffects(noIntGenes = gi)

-    n <- 20

+    n <- 30

     max.tries <- 4  

     for(tries in 1:max.tries) {

         sa <- oncoSimulPop(n,

@@ -385,7 +385,7 @@ test_that("Increasing n2 increases time" , {

                            model = "McFL",

                            initSize = 2000,

                            keepEvery = NA,

-                           detectionProb = c(p2 = .1, n2 = 5000, checkSizePEvery = 5,PDBaseline = 1100, cPDetect = NA),

+                           detectionProb = c(p2 = .15, n2 = 7000, checkSizePEvery = 5,PDBaseline = 1100, cPDetect = NA),

                            finalTime = NA, detectionSize = NA,

                            onlyCancer = FALSE,

                            detectionDrivers = NA, mc.cores = 2)

@@ -394,12 +394,13 @@ test_that("Increasing n2 increases time" , {

                            model = "McFL",

                            initSize = 2000,

                            keepEvery = NA,

-                           detectionProb = c(p2 = .1, n2 = 2001, checkSizePEvery = 5,PDBaseline = 1100, cPDetect = NA),

+                           detectionProb = c(p2 = .15, n2 = 2001, checkSizePEvery = 5,PDBaseline = 1100, cPDetect = NA),

                            finalTime = NA, detectionSize = NA,

                            onlyCancer = FALSE,

                            detectionDrivers = NA, mc.cores = 2)

         (ta <- unlist(lapply(sa, function(x) x$FinalTime)))

-        (tb <- unlist(lapply(sb, function(x) x$FinalTime)))         

+        (tb <- unlist(lapply(sb, function(x) x$FinalTime)))

+        print(suppressWarnings(wilcox.test(ta, tb, alternative = "greater")$p.value))

         T1 <- suppressWarnings(wilcox.test(ta, tb, alternative = "greater")$p.value < p.value.threshold)

         if(T1) break;

     }

@@ -534,7 +535,6 @@ test_that("Exercise the default option and other substitutions/defaults" , {

         detectionDrivers = NA)),

         "Individual OncoSimul trajectory",

         fixed = TRUE)

-    

     expect_output(print(oncoSimulIndiv(

         oi,

         model = "Exp",

@@ -547,7 +547,6 @@ test_that("Exercise the default option and other substitutions/defaults" , {

         detectionDrivers = NA)),

         "Individual OncoSimul trajectory",

         fixed = TRUE)

-

     expect_output(print(oncoSimulIndiv(

         oi,

         model = "Exp",

@@ -560,7 +559,6 @@ test_that("Exercise the default option and other substitutions/defaults" , {

         detectionDrivers = NA)),

         "Individual OncoSimul trajectory",

         fixed = TRUE)

-

     expect_output(print(oncoSimulIndiv(

         oi,

         model = "Exp",

@@ -573,7 +571,6 @@ test_that("Exercise the default option and other substitutions/defaults" , {

         detectionDrivers = NA)),

         "Individual OncoSimul trajectory",

         fixed = TRUE)

-

     expect_output(print(oncoSimulIndiv(

         oi,

         model = "Exp",

@@ -586,8 +583,50 @@ test_that("Exercise the default option and other substitutions/defaults" , {

         detectionDrivers = NA)),

         "Individual OncoSimul trajectory",

         fixed = TRUE)

-

-

+    expect_output(print(oncoSimulIndiv(

+        oi,

+        model = "Exp",

+        initSize = 2000, verbosity = -3,

+        keepEvery = NA,

+        detectionProb = c(cPDetect = 0.001),

+        finalTime = NA, detectionSize = NA,

+        onlyCancer = TRUE,

+        detectionDrivers = NA)),

+        "Individual OncoSimul trajectory",

+        fixed = TRUE)

+    expect_output(print(oncoSimulIndiv(

+        oi,

+        model = "Exp",

+        initSize = 2000, verbosity = -3,

+        keepEvery = NA,

+        detectionProb = c(p2 = .9, n2 = 3000),

+        finalTime = NA, detectionSize = NA,

+        onlyCancer = TRUE,

+        detectionDrivers = NA)),

+        "Individual OncoSimul trajectory",

+        fixed = TRUE)

+    expect_output(print(oncoSimulIndiv(

+        oi,

+        model = "Exp",

+        initSize = 2000, verbosity = -3,

+        keepEvery = NA,

+        detectionProb = c(PDBaseline = 2002),

+        finalTime = NA, detectionSize = NA,

+        onlyCancer = TRUE,

+        detectionDrivers = NA)),

+        "Individual OncoSimul trajectory",

+        fixed = TRUE)

+    expect_output(print(oncoSimulIndiv(

+        oi,

+        model = "Exp",

+        initSize = 2000, verbosity = -3,

+        keepEvery = NA,

+        detectionProb = c(checkSizePEvery = 31),

+        finalTime = NA, detectionSize = NA,

+        onlyCancer = TRUE,

+        detectionDrivers = NA)),

+        "Individual OncoSimul trajectory",

+        fixed = TRUE)

 })

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

 \usepackage[%

-		shash={2e4cc36},

-		lhash={2e4cc367294be5263e8e2fa2803e7700395684d9},

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

+		shash={23758f4},

+		lhash={23758f41c637253bd524665045d19c5b159d884c},

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

 		authemail={rdiaz02@gmail.com},

-		authsdate={2016-07-05},

-		authidate={2016-07-05 13:18:34 +0200},

-		authudate={1467717514},

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

+		authsdate={2016-07-07},

+		authidate={2016-07-07 01:50:25 +0200},

+		authudate={1467849025},

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

 		commemail={rdiaz02@gmail.com},

-		commsdate={2016-07-05},

-		commidate={2016-07-05 13:18:34 +0200},

-		commudate={1467717514},

+		commsdate={2016-07-07},

+		commidate={2016-07-07 01:50:25 +0200},

+		commudate={1467849025},

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

 	]{gitsetinfo}

\ No newline at end of file