1. OncoSimulR
  2. NAMESPACE
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
Showing 1 changed files
NAMESPACE
History View file @ 19885ad
... ... 
@@ -48,7 +48,7 @@ import(ggplot2)
48 48 
 importFrom("ggrepel", geom_text_repel, geom_label_repel)
49 49 
 importFrom("utils", "read.table", "write.table")
50 50 
 importFrom("stats", "rnorm")
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-importFrom("data.table", rbindlist, .rbind.data.table)
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+importFrom("data.table", rbindlist)
52 52 
 importFrom(Rcpp, evalCpp)
53 53 
 importFrom("igraph", igraph.to.graphNEL, graph.data.frame, V, E,
54 54 
            "V<-", "E<-", plot.igraph, layout.reingold.tilford,
Browse code

3.99.1: interventions, death with fdf, user variables

ramon diaz-uriarte (at Phelsuma) authored on 25/06/2022 14:24:13
Showing 1 changed files
NAMESPACE
History View file @ 79ffadf
... ... 
@@ -13,7 +13,10 @@ export("oncoSimulPop", "oncoSimulIndiv", "samplePop",
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        "Magellan_stats",
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        "sampledGenotypes"
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      , "POM", "LOD"
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-     , "diversityPOM", "diversityLOD"
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+     , "diversityPOM", "diversityLOD",
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+     "createInterventions",
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+     "createUserVars",
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+     "createRules"
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 ##     , "meanCompositionPop", "compositionPop2"
18 21 
        )
19 22
Browse code

version 2.99.1: frequency-dependent fitness functionality

ramon diaz-uriarte (at Phelsuma) authored on 10/12/2020 11:41:53
Showing 1 changed files
NAMESPACE
History View file @ 4068375
... ... 
@@ -12,8 +12,9 @@ export("oncoSimulPop", "oncoSimulIndiv", "samplePop",
12 12 
        "to_Magellan",
13 13 
        "Magellan_stats",
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        "sampledGenotypes"
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-       , "POM", "LOD"
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-       , "diversityPOM", "diversityLOD"
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+     , "POM", "LOD"
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+     , "diversityPOM", "diversityLOD"
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+##     , "meanCompositionPop", "compositionPop2"
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        )
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19 20 
 S3method(plot, oncosimul)
... ... 
@@ -56,8 +57,8 @@ importFrom("gtools", combinations, permutations, mixedorder)
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 ## importFrom("compare", compare)
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 importFrom("graphics", "axis", "box", "legend", "matplot", "par", "polygon")
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 importFrom("methods", "as")
59 
-importFrom("stats", "na.omit", "runif", "smooth.spline")
60 
-importFrom("utils", "type.convert")
60 
+importFrom("stats", "na.omit", "runif", "smooth.spline", "setNames")
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+importFrom("utils", "type.convert", "combn")
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 importFrom("RColorBrewer", "brewer.pal")
62 63 
 importFrom("grDevices", "colorRampPalette", "hsv", "rainbow")
63 64 
 importFrom("dplyr", "full_join", "left_join", "right_join", "%>%", "mutate",
... ... 
@@ -65,8 +66,7 @@ importFrom("dplyr", "full_join", "left_join", "right_join", "%>%", "mutate",
65 66 
 importFrom("smatr", "ma") ## for major axis regression in some tests
66 67 
 importFrom("car", "linearHypothesis")
67 68 
 ## importFrom("nem", "transitive.reduction") ## now in file nem_transitive_reduction.R
69 
+importFrom("stringr", "regex", "str_extract_all", "str_replace_all")
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 ## importFrom("slam", "simple_triplet_zero_matrix", ## "colapply_simple_triplet_matrix",
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 ##            "col_sums")
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-
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-
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-
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+## importFrom("graphics", "segments", "stripchart")
Browse code

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
Showing 1 changed files
NAMESPACE
History View file @ eb53711
... ... 
@@ -64,7 +64,7 @@ importFrom("dplyr", "full_join", "left_join", "right_join", "%>%", "mutate",
64 64 
            "filter")
65 65 
 importFrom("smatr", "ma") ## for major axis regression in some tests
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 importFrom("car", "linearHypothesis")
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-importFrom("nem", "transitive.reduction")
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+## importFrom("nem", "transitive.reduction") ## now in file nem_transitive_reduction.R
68 68 
 ## importFrom("slam", "simple_triplet_zero_matrix", ## "colapply_simple_triplet_matrix",
69 69 
 ##            "col_sums")
70 70
Browse code

2.15.1: Added MAGELLANs sources and functionality from MAGELLAN

ramon diaz-uriarte (at Phelsuma) authored on 02/07/2019 14:55:40
Showing 1 changed files
NAMESPACE
History View file @ fd073de
... ... 
@@ -10,6 +10,7 @@ export("oncoSimulPop", "oncoSimulIndiv", "samplePop",
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        "rfitness",
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        "plotFitnessLandscape",
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        "to_Magellan",
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+       "Magellan_stats",
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        "sampledGenotypes"
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        , "POM", "LOD"
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        , "diversityPOM", "diversityLOD"
Browse code

v. 2.9.2 - LOD: using only the strict Szendro et al. meaning. - POM: computed in C++. - Using fitness landscape directly when given as input (no conversion to epistasis)

ramon diaz-uriarte (at Phelsuma) authored on 24/11/2017 12:41:48
Showing 1 changed files
NAMESPACE
History View file @ ab43994
... ... 
@@ -51,8 +51,8 @@ importFrom("igraph", igraph.to.graphNEL, graph.data.frame, V, E,
51 51 
 import(graph)
52 52 
 import(Rgraphviz)
53 53 
 importFrom("parallel", mclapply, detectCores, mcMap)
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-importFrom("gtools", combinations, permutations)
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-
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+importFrom("gtools", combinations, permutations, mixedorder)
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+## importFrom("compare", compare)
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 importFrom("graphics", "axis", "box", "legend", "matplot", "par", "polygon")
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 importFrom("methods", "as")
58 58 
 importFrom("stats", "na.omit", "runif", "smooth.spline")
Browse code

v.2.5.12

- Several improvements to rfitness.
- simOGraph using transitive reduction properly.
- Miscell documentation improvements.
- Updated citation to Bioinformatics paper.



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OncoSimulR@126818 bc3139a8-67e5-0310-9ffc-ced21a209358

Ramon Diaz-Uriarte authored on 18/02/2017 20:20:42
Showing 1 changed files
NAMESPACE
History View file @ b137a4a
... ... 
@@ -63,6 +63,7 @@ importFrom("dplyr", "full_join", "left_join", "right_join", "%>%", "mutate",
63 63 
            "filter")
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 importFrom("smatr", "ma") ## for major axis regression in some tests
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 importFrom("car", "linearHypothesis")
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+importFrom("nem", "transitive.reduction")
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 ## importFrom("slam", "simple_triplet_zero_matrix", ## "colapply_simple_triplet_matrix",
67 68 
 ##            "col_sums")
68 69
Browse code

v.2.5.2 - Lots and lots of addition to vignette including benchmarks. - Diversity of sampled genotypes. - Genotyping error can be added in samplePop. - LOD and POM (lines of descent, path of maximum, sensu Szendro et al.). - simOGraph can also out rT data frames. - Better (and better explained) estimates of simulation error for McFL.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OncoSimulR@124982 bc3139a8-67e5-0310-9ffc-ced21a209358

Ramon Diaz-Uriarte authored on 10/12/2016 16:05:05
Showing 1 changed files
NAMESPACE
History View file @ fc38a87
... ... 
@@ -11,6 +11,8 @@ export("oncoSimulPop", "oncoSimulIndiv", "samplePop",
11 11 
        "plotFitnessLandscape",
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        "to_Magellan",
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        "sampledGenotypes"
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+       , "POM", "LOD"
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+       , "diversityPOM", "diversityLOD"
14 16 
        )
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16 18 
 S3method(plot, oncosimul)
... ... 
@@ -23,6 +25,19 @@ S3method(plot, fitnessEffects)
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 S3method(plot, genotype_fitness_matrix)
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 S3method(plot, evalAllGenotypes)
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 S3method(plot, evalAllGenotypesMut)
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+S3method(print, sampledGenotypes)
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+
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+S3method(POM, oncosimul2)
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+S3method(POM, oncosimulpop)
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+S3method(LOD, oncosimul2)
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+S3method(LOD, oncosimulpop)
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+
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+
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+## S3method(summary, oncosimul_lod_list)
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+## S3method(summary, oncosimul_pom_list)
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+
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+
40 
+
26 41
27 42 
 import(ggplot2)
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 importFrom("ggrepel", geom_text_repel, geom_label_repel)
Browse code

v.2.5.1. \n - much faster accessible genots \n - AND of drivers and size \n - fixation \n - doc. improvements

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OncoSimulR@123922 bc3139a8-67e5-0310-9ffc-ced21a209358

Ramon Diaz-Uriarte authored on 13/11/2016 09:46:27
Showing 1 changed files
NAMESPACE
History View file @ c95df82
... ... 
@@ -9,7 +9,8 @@ export("oncoSimulPop", "oncoSimulIndiv", "samplePop",
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        "evalAllGenotypesFitAndMut",
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        "rfitness",
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        "plotFitnessLandscape",
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-       "to_Magellan"
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+       "to_Magellan",
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+       "sampledGenotypes"
13 14 
        )
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15 16 
 S3method(plot, oncosimul)
... ... 
@@ -47,7 +48,8 @@ importFrom("dplyr", "full_join", "left_join", "right_join", "%>%", "mutate",
47 48 
            "filter")
48 49 
 importFrom("smatr", "ma") ## for major axis regression in some tests
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 importFrom("car", "linearHypothesis")
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-
51 
+## importFrom("slam", "simple_triplet_zero_matrix", ## "colapply_simple_triplet_matrix",
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+##            "col_sums")
51 53
52 54
53 55
Browse code

v.2.3.5; to_Magellan

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OncoSimulR@118942 bc3139a8-67e5-0310-9ffc-ced21a209358

Ramon Diaz-Uriarte authored on 25/06/2016 00:53:22
Showing 1 changed files
NAMESPACE
History View file @ 65cb86f
... ... 
@@ -8,7 +8,8 @@ export("oncoSimulPop", "oncoSimulIndiv", "samplePop",
8 8 
        "evalGenotypeMut", "evalGenotypeFitAndMut",
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        "evalAllGenotypesFitAndMut",
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        "rfitness",
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-       "plotFitnessLandscape"
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+       "plotFitnessLandscape",
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+       "to_Magellan"
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        )
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14 15 
 S3method(plot, oncosimul)
... ... 
@@ -24,7 +25,7 @@ S3method(plot, evalAllGenotypesMut)
24 25
25 26 
 import(ggplot2)
26 27 
 importFrom("ggrepel", geom_text_repel, geom_label_repel)
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-
28 
+importFrom("utils", "read.table", "write.table")
28 29 
 importFrom("stats", "rnorm")
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 importFrom("data.table", rbindlist, .rbind.data.table)
30 31 
 importFrom(Rcpp, evalCpp)
Browse code

v. 2.3.3.\n mutator, fitness landscapes, rfitness, and many other changes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OncoSimulR@118909 bc3139a8-67e5-0310-9ffc-ced21a209358

Ramon Diaz-Uriarte authored on 23/06/2016 16:43:51
Showing 1 changed files
NAMESPACE
History View file @ 50a9420
... ... 
@@ -2,8 +2,13 @@ useDynLib(OncoSimulR, .registration=TRUE)
2 2
3 3 
 export("oncoSimulPop", "oncoSimulIndiv", "samplePop",
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        "plotPoset", "oncoSimulSample", "allFitnessEffects",
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-       "evalGenotype", "evalAllGenotypes", "simOGraph"
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-     , "plotClonePhylog", "OncoSimulWide2Long"
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+       "evalGenotype", "evalAllGenotypes", "simOGraph",
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+       "plotClonePhylog", "OncoSimulWide2Long",
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+       "allMutatorEffects", "evalAllGenotypesMut",
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+       "evalGenotypeMut", "evalGenotypeFitAndMut",
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+       "evalAllGenotypesFitAndMut",
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+       "rfitness",
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+       "plotFitnessLandscape"
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        )
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9 14 
 S3method(plot, oncosimul)
... ... 
@@ -13,8 +18,14 @@ S3method(plot, oncosimulpop)
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 S3method(summary, oncosimulpop)
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 S3method(print, oncosimulpop)
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 S3method(plot, fitnessEffects)
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+S3method(plot, genotype_fitness_matrix)
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+S3method(plot, evalAllGenotypes)
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+S3method(plot, evalAllGenotypesMut)
16 24
25 
+import(ggplot2)
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+importFrom("ggrepel", geom_text_repel, geom_label_repel)
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28 
+importFrom("stats", "rnorm")
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 importFrom("data.table", rbindlist, .rbind.data.table)
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 importFrom(Rcpp, evalCpp)
20 31 
 importFrom("igraph", igraph.to.graphNEL, graph.data.frame, V, E,
... ... 
@@ -31,3 +42,11 @@ importFrom("stats", "na.omit", "runif", "smooth.spline")
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 importFrom("utils", "type.convert")
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 importFrom("RColorBrewer", "brewer.pal")
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 importFrom("grDevices", "colorRampPalette", "hsv", "rainbow")
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+importFrom("dplyr", "full_join", "left_join", "right_join", "%>%", "mutate",
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+           "filter")
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+importFrom("smatr", "ma") ## for major axis regression in some tests
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+importFrom("car", "linearHypothesis")
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+
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+
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+
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+
Browse code

v-2.1.1: stacked and area plots, genotype plots, and mut.prop.growth

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OncoSimulR@114315 bc3139a8-67e5-0310-9ffc-ced21a209358

Ramon Diaz-Uriarte authored on 07/03/2016 13:48:31
Showing 1 changed files
NAMESPACE
History View file @ debcf5f
... ... 
@@ -3,7 +3,7 @@ useDynLib(OncoSimulR, .registration=TRUE)
3 3 
 export("oncoSimulPop", "oncoSimulIndiv", "samplePop",
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        "plotPoset", "oncoSimulSample", "allFitnessEffects",
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        "evalGenotype", "evalAllGenotypes", "simOGraph"
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-     , "plotClonePhylog"
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+     , "plotClonePhylog", "OncoSimulWide2Long"
7 7 
        )
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9 9 
 S3method(plot, oncosimul)
... ... 
@@ -24,3 +24,10 @@ import(graph)
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 import(Rgraphviz)
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 importFrom("parallel", mclapply, detectCores, mcMap)
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 importFrom("gtools", combinations, permutations)
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+
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+importFrom("graphics", "axis", "box", "legend", "matplot", "par", "polygon")
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+importFrom("methods", "as")
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+importFrom("stats", "na.omit", "runif", "smooth.spline")
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+importFrom("utils", "type.convert")
32 
+importFrom("RColorBrewer", "brewer.pal")
33 
+importFrom("grDevices", "colorRampPalette", "hsv", "rainbow")
Browse code

fixed Windows issues with bool; added phylogenies

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OncoSimulR@105324 bc3139a8-67e5-0310-9ffc-ced21a209358

Ramon Diaz-Uriarte authored on 22/06/2015 17:55:14
Showing 1 changed files
NAMESPACE
History View file @ 5d9775a
... ... 
@@ -1,9 +1,9 @@
1 1 
 useDynLib(OncoSimulR, .registration=TRUE)
2 
-## useDynLib(OncoSimulR)
3 2
4 3 
 export("oncoSimulPop", "oncoSimulIndiv", "samplePop",
5 4 
        "plotPoset", "oncoSimulSample", "allFitnessEffects",
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        "evalGenotype", "evalAllGenotypes", "simOGraph"
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+     , "plotClonePhylog"
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        )
8 8
9 9 
 S3method(plot, oncosimul)
... ... 
@@ -17,9 +17,9 @@ S3method(plot, fitnessEffects)
17 17
18 18 
 importFrom("data.table", rbindlist, .rbind.data.table)
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 importFrom(Rcpp, evalCpp)
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-## import(igraph)
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 importFrom("igraph", igraph.to.graphNEL, graph.data.frame, V, E,
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-           "V<-", "E<-", plot.igraph)
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+           "V<-", "E<-", plot.igraph, layout.reingold.tilford,
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+           delete.vertices, neighborhood, get.adjacency)
23 23 
 import(graph)
24 24 
 import(Rgraphviz)
25 25 
 importFrom("parallel", mclapply, detectCores, mcMap)
Browse code

v. 1.99.0

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OncoSimulR@105089 bc3139a8-67e5-0310-9ffc-ced21a209358

Ramon Diaz-Uriarte authored on 17/06/2015 17:17:55
Showing 1 changed files
NAMESPACE
History View file @ e693f15
... ... 
@@ -1,7 +1,10 @@
1 1 
 useDynLib(OncoSimulR, .registration=TRUE)
2 2 
 ## useDynLib(OncoSimulR)
3 3
4 
-export("oncoSimulPop", "oncoSimulIndiv", "samplePop", "plotPoset")
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+export("oncoSimulPop", "oncoSimulIndiv", "samplePop",
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+       "plotPoset", "oncoSimulSample", "allFitnessEffects",
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+       "evalGenotype", "evalAllGenotypes", "simOGraph"
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+       )
5 8
6 9 
 S3method(plot, oncosimul)
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 S3method(print, oncosimul)
... ... 
@@ -9,13 +12,15 @@ S3method(summary, oncosimul)
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 S3method(plot, oncosimulpop)
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 S3method(summary, oncosimulpop)
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 S3method(print, oncosimulpop)
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+S3method(plot, fitnessEffects)
12 16
13 17
14 18 
 importFrom("data.table", rbindlist, .rbind.data.table)
15 19 
 importFrom(Rcpp, evalCpp)
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+## import(igraph)
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+importFrom("igraph", igraph.to.graphNEL, graph.data.frame, V, E,
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+           "V<-", "E<-", plot.igraph)
16 23 
 import(graph)
17 24 
 import(Rgraphviz)
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-importFrom("parallel", mclapply, detectCores)
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-
20 
-
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-
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+importFrom("parallel", mclapply, detectCores, mcMap)
26 
+importFrom("gtools", combinations, permutations)
Browse code

Adds OncoSimulR, missMethyl, ballgown and STAN to the repos.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OncoSimulR@92963 bc3139a8-67e5-0310-9ffc-ced21a209358

Marc Carlson authored on 28/07/2014 22:43:51
Showing 1 changed files
NAMESPACE
History View file @ 2f97de1
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,21 @@
1 
+useDynLib(OncoSimulR, .registration=TRUE)
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+## useDynLib(OncoSimulR)
3 
+
4 
+export("oncoSimulPop", "oncoSimulIndiv", "samplePop", "plotPoset")
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+
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+S3method(plot, oncosimul)
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+S3method(print, oncosimul)
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+S3method(summary, oncosimul)
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+S3method(plot, oncosimulpop)
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+S3method(summary, oncosimulpop)
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+S3method(print, oncosimulpop)
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+
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+
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+importFrom("data.table", rbindlist, .rbind.data.table)
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+importFrom(Rcpp, evalCpp)
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+import(graph)
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+import(Rgraphviz)
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+importFrom("parallel", mclapply, detectCores)
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+
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+
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+