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

 Package: OncoSimulR

 Type: Package

 Title: Forward Genetic Simulation of Cancer Progression with Epistasis 

-Version: 3.1.0

-Date: 2021-05-04

+Version: 3.1.1

+Date: 2021-10-06

 Authors@R: c(

 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),	

  	   		     email = "rdiaz02@gmail.com"),

@@ -230,6 +230,9 @@ fast_peaks <- function(x, th) {

                           th)]))

 }

+## FIXME! Unclear if we need the complete fitness matrix or if it will work with

+## pieces (say, after removing those with fitness < WT, to try to make it faster

+## and for general use in other cases)

 ## wrapper to the C++ code

 wrap_accessibleGenotypes <- function(x, th) {

@@ -1511,8 +1511,15 @@ fitnessEffectsToIgraph <- function(rT, epistasis, orderEffects) {

     g1 <- graph.data.frame(df)

     E(g1)$color <- "black"

+

     E(g1)$color[E(g1)$typeDep == "SM"] <- "blue"

+    E(g1)$color[E(g1)$typeDep == "OR"] <- "blue"

+    E(g1)$color[E(g1)$typeDep == "semimonotone"] <- "blue"    

+    

     E(g1)$color[E(g1)$typeDep == "XMPN"] <- "red"

+    E(g1)$color[E(g1)$typeDep == "XOR"] <- "red"

+    E(g1)$color[E(g1)$typeDep == "xmpn"] <- "red"        

+    

     E(g1)$color[E(g1)$typeDep == "epistasis"] <- "orange"

     E(g1)$color[E(g1)$typeDep == "orderEffect"] <- "orange"

     E(g1)$lty <- 1

@@ -1,3 +1,7 @@

+Changes in version 3.1.1 (2021-10-06):

+	- XOR, AND, OR dependencies: plots of DAGs honor all possible values.

+	- Few miscell minor changes.

+

 Changes in version 3.0 (for BioC 3.13):

 	- MAJOR change: frequency dependent fitness available.

 	- Removed v.1 functionality.

@@ -151,13 +151,26 @@ test_that("simple correct poset -> graph, 5 nodes, no root", {

 test_that("to rT from poset, through adjmat with and w.o. root",

           {

-              expect_equal(

+              ## Now, this fails with

+              ## Error in `name %in% base || grepl("^%.*%$", name)`: 'length(x) = 3 > 1' in coercion to 'logical(1)'

+              ## But all.equal does not break. So me thinks this is a problem in expect_equal

+              ## and the new expect_waldo_equal.

+              ## So I'll use all.equal.

+              ## expect_equal(

+              ##     OncoSimulR:::adjmat.to.restrictTable(

+              ##         OncoSimulR:::posetToGraph(p5, names = 1:5, addroot = FALSE, type = "adjmat"),

+              ##         root = FALSE),

+              ##     OncoSimulR:::adjmat.to.restrictTable(

+              ##         OncoSimulR:::posetToGraph(p5, names = 0:5, addroot = TRUE, type = "adjmat"),

+              ##         root = TRUE))

+              expect_true(all.equal(

                   OncoSimulR:::adjmat.to.restrictTable(

                       OncoSimulR:::posetToGraph(p5, names = 1:5, addroot = FALSE, type = "adjmat"),

                       root = FALSE),

                   OncoSimulR:::adjmat.to.restrictTable(

                       OncoSimulR:::posetToGraph(p5, names = 0:5, addroot = TRUE, type = "adjmat"),

-                      root = TRUE))

+                      root = TRUE)

+              ))

           })

@@ -7695,7 +7695,7 @@ small number of children via mutation to non-viable

 "hybrids". Factor this into your equations for death rate, but this

 should be negligible if death rate $\gg$ mutation rate. (You can

 ameliorate this problem slightly by making mutation to the "species

-indicator" locus very small, say $10^{10}$ ---do not set it to 0, as

+indicator" locus very small, say $10^{-10}$ ---do not set it to 0, as

 you will get an error).

 Of course, you can extend the scheme above to arbitrary numbers of

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

 \usepackage[%

-		shash={bb4ad3b},

-		lhash={bb4ad3b194b97eba03a197a4e6d432f1a1e9167f},

+		shash={f4285fb},

+		lhash={f4285fb0479557c3f4d2b2f362703a464045bd2c},

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

 		authemail={rdiaz02@gmail.com},

-		authsdate={2021-04-27},

-		authidate={2021-04-27 15:43:25 +0200},

-		authudate={1619531005},

+		authsdate={2021-09-01},

+		authidate={2021-09-01 14:34:09 +0200},

+		authudate={1630499649},

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

 		commemail={rdiaz02@gmail.com},

-		commsdate={2021-04-27},

-		commidate={2021-04-27 15:43:25 +0200},

-		commudate={1619531005},

-		refnames={ (HEAD -> freq-dep-fitness, origin/rfitness_scale_3, rfitness_scale_3)}

+		commsdate={2021-09-01},

+		commidate={2021-09-01 14:34:09 +0200},

+		commudate={1630499649},

+		refnames={ (HEAD -> freq-dep-fitness, origin/freq-dep-fitness)}

 	]{gitsetinfo}

\ No newline at end of file