Merge pull request #50 from ahl27/master

feat: Random forests

.gitignore

@@ -4,6 +4,7 @@
 *.so
 */*.o
 */*.so
+*/*.mod
 .Rproj.user
 *.Rproj
 *.Rhistory

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SynExtend
 Type: Package
 Title: Tools for Working With Synteny Objects
-Version: 1.17.1
+Version: 1.17.2
 Authors@R: c(
 	person("Nicholas", "Cooley", email = "npc19@pitt.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6029-304X")),
 	person("Aidan", "Lakshman", email = "ahl27@pitt.edu", role = c("aut", "ctb"), comment = c(ORCID = "0000-0002-9465-6785")),

NAMESPACE

@@ -8,8 +8,12 @@ import(S4Vectors)
 import(DBI)
 import(RSQLite)
 
-importFrom("utils", "setTxtProgressBar", "txtProgressBar", "data", "object.size", "getS3method", "read.table")
-importFrom("stats", "predict", "runif", "setNames", "rnorm", "optim", "kmeans", "density", "nls", "ppois", "pt", "pnorm", "as.dist", "fisher.test", "is.leaf", "pchisq", "rbinom")
+importFrom("utils", "setTxtProgressBar", "txtProgressBar", "data", "object.size", 
+"getS3method", "read.table")
+importFrom("stats", "predict", "runif", "setNames", "rnorm", "optim", "kmeans", "density", "nls",
+"ppois", "pt", "pnorm", "as.dist", "fisher.test", "is.leaf", "pchisq", "rbinom", "as.dendrogram",
+".checkMFClasses", ".getXlevels", "delete.response", "is.empty.model", "model.frame", 
+"model.matrix", "model.response", "model.weights", "na.pass", "offset", "terms")
 importFrom("parallel", "mclapply", "detectCores")
 importFrom("graphics", "hist", "points", "abline", "axis", "layout", "lines", "par", "text")
 importFrom("grDevices", "topo.colors", "colorRampPalette")
@@ -109,3 +113,11 @@ S3method(names, 'simMat')
 S3method(`names<-`, 'simMat')
 S3method(as.data.frame, 'simMat')
 
+S3method(show, "DecisionTree")
+S3method(show, "RandForest")
+S3method(print, "RandForest")
+S3method(print, "DecisionTree")
+S3method(predict, "RandForest")
+S3method(as.dendrogram, "DecisionTree")
+S3method(plot, "DecisionTree")
+export(RandForest)

NEWS.md

@@ -1,3 +1,9 @@
+# SynExtend 1.17.2
+* `RandForest` function added to train random forest models
+* Associated man pages for `RandForest` and `DecisionTree` objects
+* New methods for `DecisionTree` objects to plot and coerce to `dendrogram`
+* Small bugfix to `subset.dendrogram`
+
 # SynExtend 1.17.1
 * Major updates to `EvoWeaver`:
   * `predict.EvoWeaver` now returns a `data.frame` by default