1. OncoSimulR
  2. DESCRIPTION
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_17 branch

J Wokaty authored on 25/04/2023 14:33:19
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DESCRIPTION
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1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 4.2.0
4 
+Version: 4.3.0
5 5 
 Date: 2023-03-08
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_17 branch

J Wokaty authored on 25/04/2023 14:33:19
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DESCRIPTION
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1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 4.1.4
4 
+Version: 4.2.0
5 5 
 Date: 2023-03-08
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
Browse code

4.1.4 --- updated exprTk and removed CXX_STD

ramon diaz-uriarte (at Phelsuma) authored on 08/03/2023 19:30:52
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1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 4.1.3
5 
-Date: 2023-02-20
4 
+Version: 4.1.4
5 
+Date: 2023-03-08
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

version bump in devel

ramon diaz-uriarte (at Phelsuma) authored on 20/02/2023 19:04:27
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1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 4.1.2
4 
+Version: 4.1.3
5 5 
 Date: 2023-02-20
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
Browse code

v.4.1.1: do not import .rbind.data.table

ramon diaz-uriarte (at Phelsuma) authored on 20/02/2023 18:01:31
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DESCRIPTION
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1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 4.1.1
5 
-Date: 2022-11-24
4 
+Version: 4.1.2
5 
+Date: 2023-02-20
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

4.1.1: improved and faster intervention tests

ramon diaz-uriarte (at Phelsuma) authored on 24/11/2022 13:24:15
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DESCRIPTION
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@@ -1,8 +1,8 @@
1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 4.1.0
5 
-Date: 2022-10-19
4 
+Version: 4.1.1
5 
+Date: 2022-11-24
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:10:00
Showing 1 changed files
DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 4.0.0
4 
+Version: 4.1.0
5 5 
 Date: 2022-10-19
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:10:00
Showing 1 changed files
DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 3.99.12
4 
+Version: 4.0.0
5 5 
 Date: 2022-10-19
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
Browse code

3.99.12

ramon diaz-uriarte (at Phelsuma) authored on 19/10/2022 19:10:17
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DESCRIPTION
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@@ -1,8 +1,8 @@
1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 3.99.11
5 
-Date: 2022-10-13
4 
+Version: 3.99.12
5 
+Date: 2022-10-19
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

3.99.11: increase max.wall.time in two tests that can take very long in Windoze

ramon diaz-uriarte (at Phelsuma) authored on 13/10/2022 21:54:17
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 3.99.10
4 
+Version: 3.99.11
5 5 
 Date: 2022-10-13
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
... ... 
@@ -154,7 +154,7 @@ Author: Ramon Diaz-Uriarte [aut, cre],
154 154 
 	Rafael Barrero Rodriguez [ctb],
155 155 
 	Silvia Talavera Marcos [ctb]
156 156 
 Maintainer: Ramon Diaz-Uriarte <rdiaz02@gmail.com>
157 
-Description: Functions for forward population genetic simulation in asexual populations, with special focus on cancer progression. Fitness can be an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, order restrictions in mutation accumulation, and order effects. Fitness (including just birth, just death, or both and death) can also be a function of the relative and absolute frequencies of other genotypes (i.e., frequency-dependent fitness). Mutation rates can differ between genes, and we can include mutator/antimutator genes (to model mutator phenotypes). Simulating multi-species scenarios and therapeutic interventions, including adaptive therapy, is also possible. Simulations use continuous-time models and can include driver and passenger genes and modules. Also included are functions for: simulating random DAGs of the type found in Oncogenetic Trees, Conjunctive Bayesian Networks, and other cancer progression models; plotting and sampling from single or multiple realizations of the simulations, including single-cell sampling; plotting the parent-child relationships of the clones; generating random fitness landscapes (Rough Mount Fuji, House of Cards, additive, NK, Ising, and Eggbox models) and plotting them.
157 
+Description: Functions for forward population genetic simulation in asexual populations, with special focus on cancer progression. Fitness can be an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, order restrictions in mutation accumulation, and order effects. Fitness (including just birth, just death, or both birth and death) can also be a function of the relative and absolute frequencies of other genotypes (i.e., frequency-dependent fitness). Mutation rates can differ between genes, and we can include mutator/antimutator genes (to model mutator phenotypes). Simulating multi-species scenarios and therapeutic interventions, including adaptive therapy, is also possible. Simulations use continuous-time models and can include driver and passenger genes and modules. Also included are functions for: simulating random DAGs of the type found in Oncogenetic Trees, Conjunctive Bayesian Networks, and other cancer progression models; plotting and sampling from single or multiple realizations of the simulations, including single-cell sampling; plotting the parent-child relationships of the clones; generating random fitness landscapes (Rough Mount Fuji, House of Cards, additive, NK, Ising, and Eggbox models) and plotting them.
158 158 
 biocViews: BiologicalQuestion, SomaticMutation
159 159 
 License: GPL (>= 3)
160 160 
 URL: https://github.com/rdiaz02/OncoSimul, https://popmodels.cancercontrol.cancer.gov/gsr/packages/oncosimulr/
Browse code

3.99.10; faster vignette, onlyCancer=FALSE, plot fails with sensible error if simulation had exception

ramon diaz-uriarte (at Phelsuma) authored on 13/10/2022 13:32:19
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@@ -1,8 +1,8 @@
1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 3.99.9
5 
-Date: 2022-09-30
4 
+Version: 3.99.10
5 
+Date: 2022-10-13
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

3.99.9: vignette problem ARM64 Mac build?

ramon diaz-uriarte (at Phelsuma) authored on 01/10/2022 11:40:27
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@@ -1,8 +1,8 @@
1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 3.99.8
5 
-Date: 2022-09-15
4 
+Version: 3.99.9
5 
+Date: 2022-09-30
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

3.99.8: unity build

ramon diaz-uriarte (at Phelsuma) authored on 15/09/2022 19:29:51
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DESCRIPTION
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@@ -1,8 +1,8 @@
1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 3.99.7
5 
-Date: 2022-09-13
4 
+Version: 3.99.8
5 
+Date: 2022-09-15
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

3.99.7: c++14 and no o3 in win to try faster build

ramon diaz-uriarte (at Phelsuma) authored on 13/09/2022 15:28:36
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1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 3.99.6
5 
-Date: 2022-09-12
4 
+Version: 3.99.7
5 
+Date: 2022-09-13
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

ooops, wrong date

ramon diaz-uriarte (at Phelsuma) authored on 12/09/2022 18:23:45
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DESCRIPTION
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@@ -2,7 +2,7 @@ Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 4 
 Version: 3.99.6
5 
-Date: 2022-09-13
5 
+Date: 2022-09-12
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

3.99.6: exprtk updated

ramon diaz-uriarte (at Phelsuma) authored on 12/09/2022 18:21:57
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@@ -1,8 +1,8 @@
1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 3.99.5
5 
-Date: 2022-07-19
4 
+Version: 3.99.6
5 
+Date: 2022-09-13
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

3.99.5; logo funding

ramon diaz-uriarte (at Phelsuma) authored on 19/07/2022 14:19:56
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DESCRIPTION
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@@ -1,8 +1,8 @@
1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 3.99.4
5 
-Date: 2022-07-04
4 
+Version: 3.99.5
5 
+Date: 2022-07-19
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

3.99.4: fixing failing test.Z-interventions on Mac

ramon diaz-uriarte (at Phelsuma) authored on 04/07/2022 21:06:23
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@@ -1,8 +1,8 @@
1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 3.99.3
5 
-Date: 2022-06-30
4 
+Version: 3.99.4
5 
+Date: 2022-07-04
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

3.99.3: failing a test in Mac OS

ramon diaz-uriarte (at Phelsuma) authored on 30/06/2022 12:59:27
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@@ -1,8 +1,8 @@
1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 3.99.2
5 
-Date: 2022-06-29
4 
+Version: 3.99.3
5 
+Date: 2022-06-30
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

3.99.2

ramon diaz-uriarte (at Phelsuma) authored on 29/06/2022 12:44:37
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DESCRIPTION
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@@ -1,8 +1,8 @@
1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 3.99.1
5 
-Date: 2022-06-25
4 
+Version: 3.99.2
5 
+Date: 2022-06-29
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

3.99.1: interventions, death with fdf, user variables

ramon diaz-uriarte (at Phelsuma) authored on 25/06/2022 14:24:13
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DESCRIPTION
History View file @ 79ffadf
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@@ -1,8 +1,8 @@
1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 3.5.0
5 
-Date: 2021-10-06
4 
+Version: 3.99.1
5 
+Date: 2022-06-25
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
... ... 
@@ -13,6 +13,14 @@ Authors@R: c(
13 13 
               person("Mark", "Taylor", role = "ctb",
14 14 
 	        email = "ningkiling@gmail.com",
15 15 
 		comment = "plot.stream, plot.stacked"),
16 
+	      person("Niklas", "Endres", role = "ctb",
17 
+	             comment = "vignette examples, freq-dep-fitness time"),
18 
+              person("Javier", "Mu~noz Haro", role = "aut",
19 
+		comment = "interventions"),
20 
+	      person("Alberto", "Gonzalez Klein", role = "aut",
21 
+	        comment = "user-specified death rates"),
22 
+	      person("Javier", "Lopez Cano", role = "aut",
23 
+	        comment = "user-defined variables"),
16 24 
 	      person("Arash", "Partow", role = "ctb", comment = "ExprTk"),
17 25 
 	      person("Sophie", "Brouillet", role = "ctb", comment = "MAGELLAN"),
18 26 
 	      person("Sebastian", "Matuszewski", role = "ctb",
... ... 
@@ -20,6 +28,7 @@ Authors@R: c(
20 28 
 	      person("Harry", "Annoni", role = "ctb", comment = "MAGELLAN"),
21 29 
 	      person("Luca", "Ferretti", role = "ctb", comment = "MAGELLAN"),
22 30 
 	      person("Guillaume", "Achaz", role = "ctb", comment = "MAGELLAN"),
31 
+	      person("Wolodzko", "Tymoteusz", role = "ctb", comment = "multivariate hypergeometric"),
23 32 
 	      person("Guillermo", "Gorines Cordero", role = "ctb",
24 33 
 	             comment = "rfitness"),
25 34 
 	      person("Ivan", "Lorca Alonso", role = "ctb",
... ... 
@@ -90,13 +99,15 @@ Authors@R: c(
90 99 
 	      person("Rafael", "Barrero Rodriguez", role = "ctb",
91 100 
 	             comment = "vignette examples"),
92 101 
 	      person("Silvia", "Talavera Marcos", role = "ctb",
93 
-	             comment = "vignette examples"),
94 
-	      person("Niklas", "Endres", role = "ctb",
95 
-	             comment = "vignette examples, freq-dep-fitness time")
102 
+	             comment = "vignette examples")
96 103 
 	      )
97 104 
 Author: Ramon Diaz-Uriarte [aut, cre],
98 105 
 	Sergio Sanchez-Carrillo [aut],
99 106 
 	Juan Antonio Miguel Gonzalez [aut],
107 
+	Alberto Gonzalez Klein [aut],
108 
+	Javier Mu\~noz Haro [aut],
109 
+	Javier Lopez Cano [aut],
110 
+	Niklas Endres [ctb],
100 111 
 	Mark Taylor [ctb],
101 112 
 	Arash Partow [ctb],
102 113 
 	Sophie Brouillet [ctb],
... ... 
@@ -104,6 +115,7 @@ Author: Ramon Diaz-Uriarte [aut, cre],
104 115 
 	Harry Annoni [ctb],
105 116 
 	Luca Ferretti [ctb],
106 117 
 	Guillaume Achaz [ctb],
118 
+	Tymoteusz Wolodzko [ctb],
107 119 
 	Guillermo Gorines Cordero [ctb],
108 120 
 	Ivan Lorca Alonso [ctb],
109 121 
 	Francisco Mu\~noz Lopez [ctb],
... ... 
@@ -140,27 +152,9 @@ Author: Ramon Diaz-Uriarte [aut, cre],
140 152 
 	Guillermo Garcia Hoyos [ctb],
141 153 
 	Rosalia Palomino Cabrera [ctb],
142 154 
 	Rafael Barrero Rodriguez [ctb],
143 
-	Silvia Talavera Marcos [ctb],
144 
-	Niklas Endres [ctb]
155 
+	Silvia Talavera Marcos [ctb]
145 156 
 Maintainer: Ramon Diaz-Uriarte <rdiaz02@gmail.com>
146 
-Description: Functions for forward population genetic simulation in
147 
-    asexual populations, with special focus on cancer progression.
148 
-    Fitness can be an arbitrary function of genetic interactions between
149 
-    multiple genes or modules of genes, including epistasis, order
150 
-    restrictions in mutation accumulation, and order effects.  Fitness can
151 
-    also be a function of the relative and absolute frequencies of other
152 
-    genotypes (i.e., frequency-dependent fitness). Mutation rates can
153 
-    differ between genes, and we can include mutator/antimutator genes (to
154 
-    model mutator phenotypes). Simulating multi-species scenarios and
155 
-    therapeutic interventions is also possible. Simulations use
156 
-    continuous-time models and can include driver and passenger genes and
157 
-    modules.  Also included are functions for: simulating random DAGs of
158 
-    the type found in Oncogenetic Trees, Conjunctive Bayesian Networks,
159 
-    and other cancer progression models; plotting and sampling from single
160 
-    or multiple realizations of the simulations, including single-cell
161 
-    sampling; plotting the parent-child relationships of the clones;
162 
-    generating random fitness landscapes (Rough Mount Fuji, House of
163 
-    Cards, additive, NK, Ising, and Eggbox models) and plotting them.
157 
+Description: Functions for forward population genetic simulation in asexual populations, with special focus on cancer progression. Fitness can be an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, order restrictions in mutation accumulation, and order effects. Fitness (including just birth, just death, or both and death) can also be a function of the relative and absolute frequencies of other genotypes (i.e., frequency-dependent fitness). Mutation rates can differ between genes, and we can include mutator/antimutator genes (to model mutator phenotypes). Simulating multi-species scenarios and therapeutic interventions, including adaptive therapy, is also possible. Simulations use continuous-time models and can include driver and passenger genes and modules. Also included are functions for: simulating random DAGs of the type found in Oncogenetic Trees, Conjunctive Bayesian Networks, and other cancer progression models; plotting and sampling from single or multiple realizations of the simulations, including single-cell sampling; plotting the parent-child relationships of the clones; generating random fitness landscapes (Rough Mount Fuji, House of Cards, additive, NK, Ising, and Eggbox models) and plotting them.
164 158 
 biocViews: BiologicalQuestion, SomaticMutation
165 159 
 License: GPL (>= 3)
166 160 
 URL: https://github.com/rdiaz02/OncoSimul, https://popmodels.cancercontrol.cancer.gov/gsr/packages/oncosimulr/
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:20:38
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 3.4.0
4 
+Version: 3.5.0
5 5 
 Date: 2021-10-06
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:20:38
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@@ -1,7 +1,7 @@
1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 3.3.0
4 
+Version: 3.4.0
5 5 
 Date: 2021-10-06
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 16:14:49
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DESCRIPTION
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@@ -1,7 +1,7 @@
1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 3.2.0
4 
+Version: 3.3.0
5 5 
 Date: 2021-10-06
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 16:14:49
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1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 3.1.2
4 
+Version: 3.2.0
5 5 
 Date: 2021-10-06
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
Browse code

3.1.2, better test of poset transformation

ramon diaz-uriarte (at Phelsuma) authored on 06/10/2021 20:18:41
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1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 3.1.1
4 
+Version: 3.1.2
5 5 
 Date: 2021-10-06
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
Browse code

3.1.1: XOR, AND, OR: plots of DAGs honor all possible values

ramon diaz-uriarte (at Phelsuma) authored on 06/10/2021 18:38:06
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1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 3.1.0
5 
-Date: 2021-05-04
4 
+Version: 3.1.1
5 
+Date: 2021-10-06
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 16:06:18
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1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 3.0.0
4 
+Version: 3.1.0
5 5 
 Date: 2021-05-04
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 16:06:18
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1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 2.99.94
4 
+Version: 3.0.0
5 5 
 Date: 2021-05-04
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
Browse code

increased version to force rebuild with new NEWS file

ramon diaz-uriarte (at Phelsuma) authored on 04/05/2021 13:12:02
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@@ -1,8 +1,8 @@
1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 2.99.93
5 
-Date: 2021-04-30
4 
+Version: 2.99.94
5 
+Date: 2021-05-04
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

2.99.93; fixed bugs and test errors for three-element vector

ramon diaz-uriarte (at Phelsuma) authored on 29/04/2021 23:22:43
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1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 2.99.92
5 
-Date: 2021-04-27
4 
+Version: 2.99.93
5 
+Date: 2021-04-30
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

2.99.92: rfitness with a three-element vector for scale and SSWM examples

ramon diaz-uriarte (at Phelsuma) authored on 27/04/2021 13:58:19
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1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 2.99.9
5 
-Date: 2021-04-22
4 
+Version: 2.99.92
5 
+Date: 2021-04-27
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

v. 2.99.9: fixed one-gene cases, nem in Readme, typos; removin unused code and v.1 from long tests

ramon diaz-uriarte (at Phelsuma) authored on 22/04/2021 10:27:49
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1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 2.99.7
5 
-Date: 2020-12-30
4 
+Version: 2.99.9
5 
+Date: 2021-04-22
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

v.2.99.7

ramon diaz-uriarte (at Phelsuma) authored on 30/12/2020 15:01:49
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1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 2.99.6
4 
+Version: 2.99.7
5 5 
 Date: 2020-12-30
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
Browse code

correct date

ramon diaz-uriarte (at Phelsuma) authored on 30/12/2020 00:43:01
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@@ -2,7 +2,7 @@ Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 4 
 Version: 2.99.6
5 
-Date: 2020-12-13
5 
+Date: 2020-12-30
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

v. 2.99.6: no v.1

ramon diaz-uriarte (at Phelsuma) authored on 30/12/2020 00:29:19
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1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 2.99.5
5 
-Date: 2020-12-18
4 
+Version: 2.99.6
5 
+Date: 2020-12-13
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
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2.99.5

ramon diaz-uriarte (at Phelsuma) authored on 18/12/2020 22:20:58
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History View file @ 04c0640
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1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 2.99.4
5 
-Date: 2020-12-17
4 
+Version: 2.99.5
5 
+Date: 2020-12-18
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
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2.99.4

ramon diaz-uriarte (at Phelsuma) authored on 17/12/2020 15:07:07
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1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 2.99.3
5 
-Date: 2020-12-13
4 
+Version: 2.99.4
5 
+Date: 2020-12-17
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

v. 2.99.3

ramon diaz-uriarte (at Phelsuma) authored on 13/12/2020 14:35:47
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1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 2.99.2
5 
-Date: 2020-12-11
4 
+Version: 2.99.3
5 
+Date: 2020-12-13
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

2.99.2

ramon diaz-uriarte (at Phelsuma) authored on 11/12/2020 20:53:48
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@@ -1,8 +1,8 @@
1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 2.99.1
5 
-Date: 2020-12-10
4 
+Version: 2.99.2
5 
+Date: 2020-12-11
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
Browse code

version 2.99.1: frequency-dependent fitness functionality

ramon diaz-uriarte (at Phelsuma) authored on 10/12/2020 11:41:53
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History View file @ 4068375
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@@ -1,8 +1,8 @@
1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 2.21.0
5 
-Date: 2020-06-03
4 
+Version: 2.99.1
5 
+Date: 2020-12-10
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 8 
  	   		     email = "rdiaz02@gmail.com"),
... ... 
@@ -141,29 +141,32 @@ Author: Ramon Diaz-Uriarte [aut, cre],
141 141 
 	Rosalia Palomino Cabrera [ctb],
142 142 
 	Rafael Barrero Rodriguez [ctb],
143 143 
 	Silvia Talavera Marcos [ctb],
144 
-	Niklas Endres [ctb]
144 
+	Niklas Endres [ctb]
145 145 
 Maintainer: Ramon Diaz-Uriarte <rdiaz02@gmail.com>
146 146 
 Description: Functions for forward population genetic simulation in
147 147 
     asexual populations, with special focus on cancer progression.
148 148 
     Fitness can be an arbitrary function of genetic interactions between
149 149 
     multiple genes or modules of genes, including epistasis, order
150 
-    restrictions in mutation accumulation, and order effects.  Mutation
151 
-    rates can differ between genes, and we can include mutator/antimutator
152 
-    genes (to model mutator phenotypes). Simulations use continuous-time
153 
-    models and can include driver and passenger genes and modules.  Also
154 
-    included are functions for: simulating random DAGs of the type found
155 
-    in Oncogenetic Trees, Conjunctive Bayesian Networks, and other cancer
156 
-    progression models; plotting and sampling from single or multiple
157 
-    realizations of the simulations, including single-cell sampling;
158 
-    plotting the parent-child relationships of the clones; generating
159 
-    random fitness landscapes (from Rough Mount Fuji, House of Cards,
160 
-    additive, NK, Ising, and Eggbox models) and plotting them.
150 
+    restrictions in mutation accumulation, and order effects.  Fitness can
151 
+    also be a function of the relative and absolute frequencies of other
152 
+    genotypes (i.e., frequency-dependent fitness). Mutation rates can
153 
+    differ between genes, and we can include mutator/antimutator genes (to
154 
+    model mutator phenotypes). Simulating multi-species scenarios and
155 
+    therapeutic interventions is also possible. Simulations use
156 
+    continuous-time models and can include driver and passenger genes and
157 
+    modules.  Also included are functions for: simulating random DAGs of
158 
+    the type found in Oncogenetic Trees, Conjunctive Bayesian Networks,
159 
+    and other cancer progression models; plotting and sampling from single
160 
+    or multiple realizations of the simulations, including single-cell
161 
+    sampling; plotting the parent-child relationships of the clones;
162 
+    generating random fitness landscapes (Rough Mount Fuji, House of
163 
+    Cards, additive, NK, Ising, and Eggbox models) and plotting them.
161 164 
 biocViews: BiologicalQuestion, SomaticMutation
162 165 
 License: GPL (>= 3)
163 166 
 URL: https://github.com/rdiaz02/OncoSimul, https://popmodels.cancercontrol.cancer.gov/gsr/packages/oncosimulr/
164 167 
 BugReports: https://github.com/rdiaz02/OncoSimul/issues
165 
-Depends: R (>= 3.3.0)
166 
-Imports: Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz, gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr, smatr, ggplot2, ggrepel
168 
+Depends: R (>= 3.5.0)
169 
+Imports: Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz, gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr, smatr, ggplot2, ggrepel, stringr
167 170 
 Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander
168 171 
 LinkingTo: Rcpp
169 172 
 VignetteBuilder: knitr
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 14:57:45
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1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 2.20.0
4 
+Version: 2.21.0
5 5 
 Date: 2020-06-03
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 14:57:45
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1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 2.19.2
4 
+Version: 2.20.0
5 5 
 Date: 2020-06-03
6 6 
 Authors@R: c(
7 7 
 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
Browse code

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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1 1 
 Package: OncoSimulR
2 2 
 Type: Package
3 3 
 Title: Forward Genetic Simulation of Cancer Progression with Epistasis
4 
-Version: 2.19.1
5 
-Date: 2020-05-05
6 
-Authors@R: c(person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
7 
-		     email = "rdiaz02@gmail.com"),
8 
-	      person("Mark", "Taylor", role = "ctb", email = "ningkiling@gmail.com"),
9 
-	      person("Guillermo", "Gorines Cordero", role = "ctb"),
10 
-	      person("Ivan", "Lorca Alonso", role = "ctb"),
11 
-	      person("Francisco", "Mu~noz Lopez", role = "ctb"),
12 
-	      person("David", "Roncero Moro~no", role = "ctb"),
13 
-	      person("Alvaro" , "Quevedo" , role = "ctb"),
14 
-	      person("Pablo" ,"Perez" , role = "ctb"),
15 
-	      person("Cristina" ,"Devesa" , role = "ctb"),
16 
-	      person("Alejandro", "Herrador" , role = "ctb"),
17 
-	      person("Holger", "Froehlich", role = "ctb"),
18 
-	      person("Florian", "Markowetz", role = "ctb"),
19 
-	      person("Achim", "Tresch", role = "ctb"),
20 
-	      person("Theresa", "Niederberger", role = "ctb"),
21 
-	      person("Christian", "Bender", role = "ctb"),
22 
-	      person("Matthias", "Maneck", role = "ctb"),
23 
-	      person("Claudio", "Lottaz", role = "ctb"),
24 
-	      person("Tim", "Beissbarth", role = "ctb"))
4 
+Version: 2.19.2
5 
+Date: 2020-06-03
6 
+Authors@R: c(
7 
+	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
8 
+ 	   		     email = "rdiaz02@gmail.com"),
9 
+              person("Sergio", "Sanchez-Carrillo", role = "aut",
10 
+	        email = "sergiosanchezcarrillo@gmail.com"),
11 
+              person("Juan Antonio", "Miguel Gonzalez", role = "aut",
12 
+	        email = "juanantonio.miguel792@gmail.com"),
13 
+              person("Mark", "Taylor", role = "ctb",
14 
+	        email = "ningkiling@gmail.com",
15 
+		comment = "plot.stream, plot.stacked"),
16 
+	      person("Arash", "Partow", role = "ctb", comment = "ExprTk"),
17 
+	      person("Sophie", "Brouillet", role = "ctb", comment = "MAGELLAN"),
18 
+	      person("Sebastian", "Matuszewski", role = "ctb",
19 
+	             comment = "MAGELLAN"),
20 
+	      person("Harry", "Annoni", role = "ctb", comment = "MAGELLAN"),
21 
+	      person("Luca", "Ferretti", role = "ctb", comment = "MAGELLAN"),
22 
+	      person("Guillaume", "Achaz", role = "ctb", comment = "MAGELLAN"),
23 
+	      person("Guillermo", "Gorines Cordero", role = "ctb",
24 
+	             comment = "rfitness"),
25 
+	      person("Ivan", "Lorca Alonso", role = "ctb",
26 
+	             comment = "rfitness"),
27 
+	      person("Francisco", "Mu~noz Lopez", role = "ctb",
28 
+	             comment = "rfitness"),
29 
+	      person("David", "Roncero Moro~no", role = "ctb",
30 
+	             comment = "rfitness"),
31 
+	      person("Alvaro" , "Quevedo" , role = "ctb", comment = "rfitness"),
32 
+	      person("Pablo" ,"Perez" , role = "ctb", comment = "rfitness"),
33 
+	      person("Cristina" ,"Devesa" , role = "ctb", comment = "rfitness"),
34 
+	      person("Alejandro", "Herrador" , role = "ctb",
35 
+	             comment = "rfitness"),
36 
+	      person("Holger", "Froehlich", role = "ctb",
37 
+	             comment = "simOGraph (transitive closure)"),
38 
+	      person("Florian", "Markowetz", role = "ctb",
39 
+	             comment = "simOGraph (transitive closure)"),
40 
+	      person("Achim", "Tresch", role = "ctb",
41 
+	             comment = "simOGraph (transitive closure)"),
42 
+	      person("Theresa", "Niederberger", role = "ctb",
43 
+	             comment = "simOGraph (transitive closure)"),
44 
+	      person("Christian", "Bender", role = "ctb",
45 
+	             comment = "simOGraph (transitive closure)"),
46 
+	      person("Matthias", "Maneck", role = "ctb",
47 
+	             comment = "simOGraph (transitive closure)"),
48 
+	      person("Claudio", "Lottaz", role = "ctb",
49 
+	             comment = "simOGraph (transitive closure)"),
50 
+	      person("Tim", "Beissbarth", role = "ctb",
51 
+	             comment = "simOGraph (transitive closure)"),
52 
+	      person("Sara", "Dorado Alfaro", role = "ctb",
53 
+	             comment = "vignette examples"),
54 
+	      person("Miguel", "Hernandez del Valle", role = "ctb",
55 
+	             comment = "vignette examples"),
56 
+	      person("Alvaro", "Huertas Garcia", role = "ctb",
57 
+	             comment = "vignette examples"),
58 
+	      person("Diego", "Ma~nanes Cayero", role = "ctb",
59 
+	             comment = "vignette examples"),
60 
+	      person("Alejandro", "Martin Mu~noz", role = "ctb",
61 
+	             comment = "vignette examples"),
62 
+	      person("Marta", "Couce Iglesias", role = "ctb",
63 
+	             comment = "vignette examples"),
64 
+	      person("Silvia", "Garcia Cobos", role = "ctb",
65 
+	             comment = "vignette examples"),
66 
+	      person("Carlos", "Madariaga Aramendi", role = "ctb",
67 
+	             comment = "vignette examples"),
68 
+	      person("Ana", "Rodriguez Ronchel", role = "ctb",
69 
+	             comment = "vignette examples"),
70 
+	      person("Lucia", "Sanchez Garcia", role = "ctb",
71 
+	             comment = "vignette examples"),
72 
+	      person("Yolanda", "Benitez Quesada", role = "ctb",
73 
+	             comment = "vignette examples"),
74 
+	      person("Asier", "Fernandez Pato", role = "ctb",
75 
+	             comment = "vignette examples"),
76 
+	      person("Esperanza", "Lopez Lopez", role = "ctb",
77 
+	             comment = "vignette examples"),
78 
+	      person("Alberto Manuel", "Parra Perez", role = "ctb",
79 
+	             comment = "vignette examples"),
80 
+	      person("Jorge", "Garcia Calleja", role = "ctb",
81 
+	             comment = "vignette examples"),
82 
+	      person("Ana", "del Ramo Galian", role = "ctb",
83 
+	             comment = "vignette examples"),
84 
+	      person("Alejandro", "de los Reyes Benitez", role = "ctb",
85 
+	             comment = "vignette examples"),
86 
+	      person("Guillermo", "Garcia Hoyos", role = "ctb",
87 
+	             comment = "vignette examples"),
88 
+	      person("Rosalia", "Palomino Cabrera", role = "ctb",
89 
+	             comment = "vignette examples"),
90 
+	      person("Rafael", "Barrero Rodriguez", role = "ctb",
91 
+	             comment = "vignette examples"),
92 
+	      person("Silvia", "Talavera Marcos", role = "ctb",
93 
+	             comment = "vignette examples"),
94 
+	      person("Niklas", "Endres", role = "ctb",
95 
+	             comment = "vignette examples, freq-dep-fitness time")
96 
+	      )
25 97 
 Author: Ramon Diaz-Uriarte [aut, cre],
98 
+	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],
... ... 
@@ -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.
... ... 
@@ -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/
Browse code

2.19.1

ramon diaz-uriarte (at Phelsuma) authored on 06/05/2020 10:10:54
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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: 2.19.0
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-Date: 2020-04-27
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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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bump x.y.z version to odd y following creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:41:48
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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: 2.18.0
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+Version: 2.19.0
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 Date: 2020-04-27
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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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bump x.y.z version to even y prior to creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:41:48
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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: 2.17.92
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+Version: 2.18.0
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 Date: 2020-04-27
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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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2.17.92

ramon diaz-uriarte (at Phelsuma) authored on 26/04/2020 23:20:51
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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: 2.17.91
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-Date: 2020-04-23
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+Version: 2.17.92
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+Date: 2020-04-27
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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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2.17.91: fixed warning with Wrestrict from Magellan sources

ramon diaz-uriarte (at Phelsuma) authored on 24/04/2020 01:29:59
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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: 2.17.9
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-Date: 2020-03-16
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+Version: 2.17.91
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+Date: 2020-04-23
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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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2.17.9: POM doc and adapt to stringsAsFactors = FALSE

ramon diaz-uriarte (at Phelsuma) authored on 17/03/2020 12:31:37
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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: 2.17.8
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-Date: 2020-02-02
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+Version: 2.17.9
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+Date: 2020-03-16
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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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2.17.8

ramon diaz-uriarte (at Phelsuma) authored on 01/02/2020 23:58:49
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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: 2.17.7
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-Date: 2020-01-30
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+Version: 2.17.8
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+Date: 2020-02-02
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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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2.17.7: no longer depends on nem; more models from MAGELLAN

ramon diaz-uriarte (at Phelsuma) authored on 30/01/2020 13:39:14
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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: 2.17.5
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-Date: 2019-12-19
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+Version: 2.17.7
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+Date: 2020-01-30
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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("Mark", "Taylor", role = "ctb", email = "ningkiling@gmail.com"),
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+	      pers