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2.5.9; code coverage comments in vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OncoSimulR@125769 bc3139a8-67e5-0310-9ffc-ced21a209358

Ramon Diaz-Uriarte authored on 08/01/2017 23:16:08
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 Package: OncoSimulR
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 Type: Package
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 Title: Forward Genetic Simulation of Cancer Progression with Epistasis 
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-Version: 2.5.8
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-Date: 2016-12-17
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+Version: 2.5.9
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+Date: 2017-01-09
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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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 	      person("Mark", "Taylor", role = "ctb", email = "ningkiling@gmail.com"))
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@@ -223,9 +223,6 @@ filter_inaccessible <- function(x, accessible_th) {
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     return(x)
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 }
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-f1 <- function() {}
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-
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-x <- 99
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 ## wrapper to the C++ code
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 wrap_accessibleGenotypes <- function(x, th) {
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+Changes in version 2.5.8 (2017-01-09):
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+	- Added code coverage comments to vignette.
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+
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 Changes in version 2.5.8 (2016-12-17):
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-	- Handle trivial cases in genotFitness
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+	- Handle trivial cases in genotFitness.
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 Changes in version 2.5.7 (2016-12-15):
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 	- Clarified McFarland parameterization.
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 ## Key features of OncoSimulR {#key}
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 As mentioned above, OncoSimulR is now a very general package for forward
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+## Testing, code coverage, and other examples {#codecover}
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+
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+OncoSimulR includes more than 2000 tests that are run at every check
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+cycle. These tests provide a code coverage of more than 90%
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+including both the C++ and R code. Another set of over 500
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+long-running (several hours) tests can be run on demand (see
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+directory '/tests/manual'). In addition to serving as test cases,
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+some of that code also provides further examples of usage.
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+
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 ## Versions {#versions}
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 In this vignette and the documentation I often refer to version 1 (v.1) and
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 Table: (\#tab:bench1) Benchmarks of Exp and McFL models using the default `detectionProb` with two settings of `keepEvery`. 
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 ```{r bench1, eval=TRUE, echo = FALSE}
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-## panderOptions("table.split.cells", 8) ## For PDF
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+panderOptions('table.split.table', 99999999)
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+panderOptions('table.split.cells', 900)  ## For HTML
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+## panderOptions('table.split.cells', 8) ## For PDF
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 set.alignment('right')
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 panderOptions('round', 2)
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 Table: (\#tab:bench1b) Benchmarks of Exp models modifying the default `detectionProb` with two settings of `keepEvery`.
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 ```{r bench1b, eval=TRUE, echo = FALSE}
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-panderOptions("table.split.cells", 900)  ## For HTML
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-## panderOptions("table.split.cells", 8) ## For PDF
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+panderOptions('table.split.table', 99999999)
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+panderOptions('table.split.cells', 900)  ## For HTML
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+## panderOptions('table.split.cells', 8) ## For PDF
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 set.alignment('right')
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 panderOptions('round', 2)
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 Table: (\#tab:bench1c) Number of attempts until cancer.
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 ```{r bench1c, eval=TRUE, echo = FALSE}
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-## panderOptions("table.split.cells", 12) ## For PDF
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+panderOptions('table.split.table', 99999999)
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+panderOptions('table.split.cells', 900)  ## For HTML
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+## panderOptions('table.split.cells', 12) ## For PDF
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 panderOptions('big.mark', ',')
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 Table: (\#tab:timing3) Benchmarks of models in Table \@ref(tab:bench1) and \@ref(tab:bench1b) when run with `onlyCancer = FALSE`
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 ```{r bench1d, eval=TRUE, echo = FALSE}
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-## panderOptions("table.split.cells", 8) ## For PDF
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-panderOptions("table.split.cells", 15) ## does not fit otherwise
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+panderOptions('table.split.table', 99999999)
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+panderOptions('table.split.cells', 900)  ## For HTML
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+## panderOptions('table.split.cells', 8) ## For PDF
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 set.alignment('right')
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 panderOptions('round', 3)
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 Table: (\#tab:allr1bck) Benchmarks of all models in Tables \@ref(tab:bench1), \@ref(tab:bench1b), and \@ref(tab:timing3).  
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 ```{r bench1dx0, eval=TRUE, echo = FALSE}
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 set.alignment('right') 
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 panderOptions('round', 3)
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 ## ##   \@ref(tab:bench1b) when run with `onlyCancer = FALSE`", 
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 ## 	align = "c")
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-## panderOptions("table.split.cells", 900)  ## For HTML
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-panderOptions("table.split.cells", 19)
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+panderOptions('table.split.table', 99999999)
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+## panderOptions('table.split.cells', 900)  ## For HTML
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 set.alignment('right') 
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 panderOptions('round', 3)
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 ## 				  ),
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 ## 	align = "c")
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-panderOptions("table.split.cells", 900)  ## For HTML
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-## panderOptions("table.split.cells", 8) ## For PDF
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+panderOptions('table.split.table', 99999999)
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+## panderOptions('table.split.cells', 8) ## For PDF
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 panderOptions('table.alignment.default', 'right')
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-panderOptions("table.split.cells", 900)  ## For HTML
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-## panderOptions("table.split.cells", 8) ## For PDF
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+panderOptions('table.split.table', 99999999)
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+panderOptions('table.split.cells', 900)  ## For HTML
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+## panderOptions('table.split.cells', 8) ## For PDF
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 panderOptions('round', 3)
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 \usepackage[%
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-		shash={4dc6adf},
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-		lhash={4dc6adf0f20920ff51825aa8ac8563837d4f1239},
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-		authname={Ramon Diaz-Uriarte (at Coleonyx)},
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+		shash={37dc184},
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+		lhash={37dc184ae1ccb70eaf93c8791c8f029a990d203a},
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+		authname={ramon diaz-uriarte (at Phelsuma)},
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 		authemail={rdiaz02@gmail.com},
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-		authsdate={2016-12-15},
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-		authidate={2016-12-15 17:47:46 +0100},
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-		authudate={1481820466},
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-		commname={Ramon Diaz-Uriarte (at Coleonyx)},
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+		authsdate={2017-01-08},
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+		authidate={2017-01-08 23:51:49 +0100},
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+		authudate={1483915909},
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+		commname={ramon diaz-uriarte (at Phelsuma)},
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 		commemail={rdiaz02@gmail.com},
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-		commsdate={2016-12-15},
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-		commidate={2016-12-15 17:47:46 +0100},
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-		commudate={1481820466},
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-		refnames={ (HEAD, origin/master, origin/HEAD)}
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+		commsdate={2017-01-08},
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+		commidate={2017-01-08 23:51:49 +0100},
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+		commudate={1483915909},
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+		refnames={ (HEAD -> master)}
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 	]{gitsetinfo}
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