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2.19.2: Updated ctb: added Magellan and exprTk and clarified contributions

ramon diaz-uriarte (at Phelsuma) authored on 03/06/2020 13:57:39
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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: 2.19.1
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-Date: 2020-05-05
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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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-	      person("Guillermo", "Gorines Cordero", role = "ctb"),
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-	      person("Ivan", "Lorca Alonso", role = "ctb"),
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-	      person("Francisco", "Mu~noz Lopez", role = "ctb"),
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-	      person("David", "Roncero Moro~no", role = "ctb"),
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-	      person("Alvaro" , "Quevedo" , role = "ctb"),
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-	      person("Pablo" ,"Perez" , role = "ctb"),
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-	      person("Cristina" ,"Devesa" , role = "ctb"),
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-	      person("Alejandro", "Herrador" , role = "ctb"),
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-	      person("Holger", "Froehlich", role = "ctb"),
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-	      person("Florian", "Markowetz", role = "ctb"),
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-	      person("Achim", "Tresch", role = "ctb"),
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-	      person("Theresa", "Niederberger", role = "ctb"),
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-	      person("Christian", "Bender", role = "ctb"),
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-	      person("Matthias", "Maneck", role = "ctb"),
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-	      person("Claudio", "Lottaz", role = "ctb"),
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-	      person("Tim", "Beissbarth", role = "ctb"))
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+Version: 2.19.2
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+Date: 2020-06-03
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+Authors@R: c(
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+	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),	
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+ 	   		     email = "rdiaz02@gmail.com"),
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+              person("Sergio", "Sanchez-Carrillo", role = "aut", 
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+	        email = "sergiosanchezcarrillo@gmail.com"),
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+              person("Juan Antonio", "Miguel Gonzalez", role = "aut", 
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+	        email = "juanantonio.miguel792@gmail.com"),
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+              person("Mark", "Taylor", role = "ctb",
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+	        email = "ningkiling@gmail.com",
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+		comment = "plot.stream, plot.stacked"),
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+	      person("Arash", "Partow", role = "ctb", comment = "ExprTk"),
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+	      person("Sophie", "Brouillet", role = "ctb", comment = "MAGELLAN"),
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+	      person("Sebastian", "Matuszewski", role = "ctb",
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+	             comment = "MAGELLAN"),  
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+	      person("Harry", "Annoni", role = "ctb", comment = "MAGELLAN"),
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+	      person("Luca", "Ferretti", role = "ctb", comment = "MAGELLAN"),	      
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+	      person("Guillaume", "Achaz", role = "ctb", comment = "MAGELLAN"),
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+	      person("Guillermo", "Gorines Cordero", role = "ctb",
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+	             comment = "rfitness"),
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+	      person("Ivan", "Lorca Alonso", role = "ctb",
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+	             comment = "rfitness"),
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+	      person("Francisco", "Mu~noz Lopez", role = "ctb",
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+	             comment = "rfitness"),
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+	      person("David", "Roncero Moro~no", role = "ctb",
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+	             comment = "rfitness"),
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+	      person("Alvaro" , "Quevedo" , role = "ctb", comment = "rfitness"),
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+	      person("Pablo" ,"Perez" , role = "ctb", comment = "rfitness"),
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+	      person("Cristina" ,"Devesa" , role = "ctb", comment = "rfitness"),
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+	      person("Alejandro", "Herrador" , role = "ctb",
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+	             comment = "rfitness"),
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+	      person("Holger", "Froehlich", role = "ctb",
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+	             comment = "simOGraph (transitive closure)"),
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+	      person("Florian", "Markowetz", role = "ctb",
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+	             comment = "simOGraph (transitive closure)"),
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+	      person("Achim", "Tresch", role = "ctb",
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+	             comment = "simOGraph (transitive closure)"),
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+	      person("Theresa", "Niederberger", role = "ctb",
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+	             comment = "simOGraph (transitive closure)"),
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+	      person("Christian", "Bender", role = "ctb",
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+	             comment = "simOGraph (transitive closure)"),
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+	      person("Matthias", "Maneck", role = "ctb",
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+	             comment = "simOGraph (transitive closure)"),
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+	      person("Claudio", "Lottaz", role = "ctb",
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+	             comment = "simOGraph (transitive closure)"),
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+	      person("Tim", "Beissbarth", role = "ctb",
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+	             comment = "simOGraph (transitive closure)"),
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+	      person("Sara", "Dorado Alfaro", role = "ctb",
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+	             comment = "vignette examples"),
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+	      person("Miguel", "Hernandez del Valle", role = "ctb",
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+	             comment = "vignette examples"),
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+	      person("Alvaro", "Huertas Garcia", role = "ctb",
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+	             comment = "vignette examples"),
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+	      person("Diego", "Ma~nanes Cayero", role = "ctb",
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+	             comment = "vignette examples"),
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+	      person("Alejandro", "Martin Mu~noz", role = "ctb",
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+	             comment = "vignette examples"),
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+	      person("Marta", "Couce Iglesias", role = "ctb",
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+	             comment = "vignette examples"),
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+	      person("Silvia", "Garcia Cobos", role = "ctb",
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+	             comment = "vignette examples"),
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+	      person("Carlos", "Madariaga Aramendi", role = "ctb",
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+	             comment = "vignette examples"),
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+	      person("Ana", "Rodriguez Ronchel", role = "ctb",
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+	             comment = "vignette examples"),
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+	      person("Lucia", "Sanchez Garcia", role = "ctb",
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+	             comment = "vignette examples"),
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+	      person("Yolanda", "Benitez Quesada", role = "ctb",
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+	             comment = "vignette examples"),
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+	      person("Asier", "Fernandez Pato", role = "ctb",
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+	             comment = "vignette examples"),
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+	      person("Esperanza", "Lopez Lopez", role = "ctb",
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+	             comment = "vignette examples"),
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+	      person("Alberto Manuel", "Parra Perez", role = "ctb",
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+	             comment = "vignette examples"),
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+	      person("Jorge", "Garcia Calleja", role = "ctb",
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+	             comment = "vignette examples"),
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+	      person("Ana", "del Ramo Galian", role = "ctb",
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+	             comment = "vignette examples"),
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+	      person("Alejandro", "de los Reyes Benitez", role = "ctb",
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+	             comment = "vignette examples"), 
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+	      person("Guillermo", "Garcia Hoyos", role = "ctb",
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+	             comment = "vignette examples"),
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+	      person("Rosalia", "Palomino Cabrera", role = "ctb",
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+	             comment = "vignette examples"),
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+	      person("Rafael", "Barrero Rodriguez", role = "ctb",
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+	             comment = "vignette examples"),
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+	      person("Silvia", "Talavera Marcos", role = "ctb",
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+	             comment = "vignette examples"),
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+	      person("Niklas", "Endres", role = "ctb",
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+	             comment = "vignette examples, freq-dep-fitness time")
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+	      )  
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 Author: Ramon Diaz-Uriarte [aut, cre],
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+	Sergio Sanchez-Carrillo [aut],
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+	Juan Antonio Miguel Gonzalez [aut],
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 	Mark Taylor [ctb],
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+	Arash Partow [ctb],
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+	Sophie Brouillet [ctb],
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+	Sebastian Matuszewski [ctb],
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+	Harry Annoni [ctb],
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+	Luca Ferretti [ctb],
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+	Guillaume Achaz [ctb],
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 	Guillermo Gorines Cordero [ctb],
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 	Ivan Lorca Alonso [ctb],
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 	Francisco Mu\~noz Lopez [ctb],
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@@ -39,7 +119,29 @@ Author: Ramon Diaz-Uriarte [aut, cre],
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 	Christian Bender [ctb],
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 	Matthias Maneck [ctb],
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 	Claudio Lottaz [ctb],
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-	Tim Beissbarth [ctb]
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+	Tim Beissbarth [ctb],
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+ 	Sara Dorado Alfaro [ctb],
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+  	Miguel Hernandez del Valle [ctb],
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+  	Alvaro Huertas Garcia [ctb],
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+  	Diego Ma\~nanes Cayero [ctb],
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+  	Alejandro Martin Mu\~noz [ctb],
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+	Marta Couce Iglesias [ctb],
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+	Silvia Garcia Cobos [ctb],
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+	Carlos Madariaga Aramendi [ctb],
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+	Ana Rodriguez Ronchel [ctb],
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+	Lucia Sanchez Garcia [ctb],
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+	Yolanda Benitez Quesada [ctb],
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+	Asier Fernandez Pato [ctb],
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+	Esperanza Lopez Lopez [ctb],
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+	Alberto Manuel Parra Perez [ctb],
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+	Jorge Garcia Calleja [ctb],
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+	Ana del Ramo Galian [ctb],
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+	Alejandro de los Reyes Benitez [ctb], 
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+	Guillermo Garcia Hoyos [ctb],
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+	Rosalia Palomino Cabrera [ctb],
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+	Rafael Barrero Rodriguez [ctb],
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+	Silvia Talavera Marcos [ctb],
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+	Niklas Endres [ctb] 
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 Maintainer: Ramon Diaz-Uriarte <rdiaz02@gmail.com>
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 Description: Functions for forward population genetic simulation in
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     asexual populations, with special focus on cancer progression.
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@@ -47,15 +149,15 @@ Description: Functions for forward population genetic simulation in
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     multiple genes or modules of genes, including epistasis, order
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     restrictions in mutation accumulation, and order effects.  Mutation
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     rates can differ between genes, and we can include mutator/antimutator
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-    genes (to model mutator phenotypes). Simulations
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-    use continuous-time models and can include driver and passenger genes
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-    and modules.  Also included are functions for: simulating random DAGs
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-    of the type found in Oncogenetic Trees, Conjunctive Bayesian Networks,
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-    and other cancer progression models; plotting and sampling from
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-    single or multiple realizations of the simulations, including
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-    single-cell sampling; plotting the parent-child relationships of the
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-    clones; generating random fitness landscapes (Rough Mount Fuji, House
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-    of Cards, and additive models) and plotting them.
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+    genes (to model mutator phenotypes). Simulations use continuous-time
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+    models and can include driver and passenger genes and modules.  Also
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+    included are functions for: simulating random DAGs of the type found
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+    in Oncogenetic Trees, Conjunctive Bayesian Networks, and other cancer
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+    progression models; plotting and sampling from single or multiple
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+    realizations of the simulations, including single-cell sampling;
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+    plotting the parent-child relationships of the clones; generating
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+    random fitness landscapes (from Rough Mount Fuji, House of Cards,
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+    additive, NK, Ising, and Eggbox models) and plotting them.
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 biocViews: BiologicalQuestion, SomaticMutation
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 License: GPL (>= 3)
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 URL: https://github.com/rdiaz02/OncoSimul, https://popmodels.cancercontrol.cancer.gov/gsr/packages/oncosimulr/
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+Changes in version 2.19.2 (2020-06-03):
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+	- Updated ctb: added Magellan and exprTk and clarified contributions.
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+
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 Changes in version 2.19.1 (2020-05-05):
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 	- Occasional failures of @test.sample-prob.R#42
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 	in Windows 386
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 \usepackage[%
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-		shash={e770649},
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-		lhash={e770649caae859dcb7db64eefbc62abeb3757406},
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+		shash={e979ff2},
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+		lhash={e979ff28d7cbfbdeaec8282920663097f9ebc81d},
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 		authname={ramon diaz-uriarte (at Phelsuma)},
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 		authemail={rdiaz02@gmail.com},
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-		authsdate={2020-05-05},
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-		authidate={2020-05-05 10:30:56 +0200},
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-		authudate={1588667456},
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+		authsdate={2020-06-03},
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+		authidate={2020-06-03 15:46:58 +0200},
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+		authudate={1591192018},
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 		commname={ramon diaz-uriarte (at Phelsuma)},
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 		commemail={rdiaz02@gmail.com},
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-		commsdate={2020-05-05},
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-		commidate={2020-05-05 10:30:56 +0200},
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-		commudate={1588667456},
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+		commsdate={2020-06-03},
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+		commidate={2020-06-03 15:46:58 +0200},
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+		commudate={1591192018},
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 		refnames={ (HEAD -> master, origin/master, origin/HEAD)}
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 	]{gitsetinfo}
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\ No newline at end of file