Merge branch 'master' of github.com:0xdata/h2o

R/H2O_Load.R

@@ -1,5 +1,5 @@
 # Change this global variable to match your own system's path
-ROOT.PATH <- "/Users/spencer/master/h2o/R/h2o-package/R/"
+ROOT.PATH <- "/Users/anqi_fu/Documents/workspace/h2o/R/h2o-package/R/"
 src <-
 function() {
   warning("MAY NOT WORK ON YOUR SYSTEM -- **TRY TO CHANGE `ROOT.PATH`!**")

R/h2o-package/R/Algorithms.R

@@ -205,38 +205,6 @@ h2o.glm <- function(x, y, data, key = "", family, nfolds = 0, alpha = 0.5, nlamb
                            variable_importances = variable_importances, use_all_factor_levels = use_all_factor_levels)
 }
 
-.get.glm.model <- function(data, model_key, return_all_lambda = TRUE) {
-  res <- .h2o.__remoteSend(data@h2o, .h2o.__PAGE_GLMModelView, '_modelKey'=model_key)
-  params <- res$glm_model$parameters
-  params$h2o <- data@h2o
-  resModel <- res$glm_model
-  destKey <- resModel$'_key'
-
-  model.make<-
-  function(x, data, raw_model, model_key, return_all_lambda) {
-    m <- .h2o.__getGLM2Results(raw_model, .get.glm.params(data@h2o, model_key), x)
-    res_xval <- list()
-    if(!is.null(resModel$submodels[[x]]$xvalidation)) {
-      xvalKeys <- resModel$submodels[[x]]$xvalidation$xval_models
-      if(!is.null(xvalKeys) && length(xvalKeys) >= 2) {
-        for (i in 1:length(xvalKeys)) {
-          res_xval[[i]] <- .get.glm.model(data, xvalKeys[[i]], return_all_lambda)
-        }
-      }
-    }
-    new("H2OGLMModel", key = model_key, data = data, model = m, xval = res_xval)
-  }
-
-  if (return_all_lambda) {
-    return_all_lambda <<- FALSE
-    models <- lapply(1:length(resModel$submodels), model.make, data, resModel, model_key, return_all_lambda)
-    best_model <- resModel$best_lambda_idx+1
-    return(new("H2OGLMModelList", models = models, best_model = best_model))
-  } else {
-    return(model.make(resModel$best_lambda_idx+1, data, resModel, model_key, return_all_lambda))
-  }
-}
-
 .h2o.glm2grid.internal <- function(x_ignore, y, data, key, family, nfolds, alpha, nlambda, lambda.min.ratio, lambda, epsilon, standardize, prior, tweedie.p, iter.max, higher_accuracy, lambda_search, return_all_lambda,
                                    variable_importances, use_all_factor_levels) {
   if(family == "tweedie")

R/h2o-package/R/Internal.R

@@ -866,6 +866,13 @@ h2o.getModel <- function(h2o, key) {
   json <- .fetchJSON(h2o, key)
   algo <- model.type <- names(json)[3]
   response   <- json[[model.type]]
+
+  # Special cases: glm_model, grid, pca_model, modelw
+
+  if(algo == "glm_model") {
+      model <- .h2o.get.glm(h2o, as.character(key), TRUE)
+      return(model)
+  }
   if (algo == "grid") return(.h2o.get.glm.grid(h2o, key, TRUE, h2o.getFrame(h2o, response$"_dataKey")))
   if(algo == "deeplearning_model")
     params <- json[[model.type]]$model_info$job
@@ -875,7 +882,7 @@ h2o.getModel <- function(h2o, key) {
   model_obj  <- switch(algo, gbm_model = "H2OGBMModel", drf_model = "H2ODRFModel", deeplearning_model = "H2ODeepLearningModel", speedrf_model = "H2OSpeeDRFModel", model= "H2OKMeansModel", glm_model = "H2OGLMModel", nb_model = "H2ONBModel", pca_model = "H2OPCAModel")
   results_fun <- switch(algo, gbm_model = .h2o.__getGBMResults,
                               drf_model = .h2o.__getDRFResults,
-                              glm_model = .get.glm.model, #.h2o.glm.get_model, #.h2o.__getGLM2Results,
+                              #glm_model = .get.glm.model, #.h2o.glm.get_model, #.h2o.__getGLM2Results,
                               deeplearning_model = .h2o.__getDeepLearningResults,
                               speedrf_model = .h2o.__getSpeeDRFResults,
                               model = .h2o.__getKM2Results,
@@ -895,10 +902,6 @@ h2o.getModel <- function(h2o, key) {
       if(!is.null(json[[model.type]]$validAUC)) params$distribution <- "bernoulli"
     }
   }
-  if(algo == "glm_model") {
-    model <- .h2o.get.glm(h2o, as.character(key), TRUE)
-    return(model)
-  }
   if(algo == "model") {
     newModel <- new(model_obj, key = dest_key, data = train_fr, model = results_fun(json[[model.type]], train_fr, params))
     return(newModel)

R/h2o-package/man/Extremes.Rd

@@ -31,7 +31,3 @@ ausPath = system.file("extdata", "australia.csv", package = "h2o")
 australia.hex = h2o.importFile(localH2O, path = ausPath, key = "australia.hex")
 min(australia.hex)
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/H2OParsedData-class.Rd

@@ -166,7 +166,7 @@ Objects can be created by calls of the form \code{new("H2OParsedData", ...)}.
     \item{>=}{\code{signature(e1 = "H2OParsedData", e2 = "H2OParsedData")}: ... }
     \item{>=}{\code{signature(e1 = "H2OParsedData", e2 = "numeric")}: ... }
     \item{>=}{\code{signature(e1 = "numeric", e2 = "H2OParsedData")}: ... }
-    \item{|}{\code{signature(e1 = "H2OParsedData", e2 = "H2OParsedData")}: ... }'
+    \item{|}{\code{signature(e1 = "H2OParsedData", e2 = "H2OParsedData")}: ... }
     \item{^}{\code{signature(e1 = "numeric", e2 = "H2OParsedData")}: ... }
     \item{^}{\code{signature(e1 = "H2OParsedData", e2 = "numeric")}: ... }    
     \item{|}{\code{signature(e1 = "H2OParsedData", e2 = "logical")}: ... }

R/h2o-package/man/h2o.SpeeDRF.Rd

@@ -100,7 +100,3 @@ iris.hex = h2o.importFile(localH2O, path = irisPath, key = "iris.hex")
 h2o.SpeeDRF(x = c(2,3,4), y = 5, data = iris.hex, ntree = 50, depth = 100)
 }
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.addFunction.Rd

@@ -35,7 +35,3 @@ library(h2o)
 localH2O = h2o.init(ip = "localhost", port = 54321, startH2O = TRUE)
 h2o.addFunction(localH2O, function(x) { 2*x + 5 }, "simpleFun")
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.anomaly.Rd

@@ -33,7 +33,3 @@ prostate.dl = h2o.deeplearning(x = 3:9, y = 2, data = prostate.hex, autoencoder
 prostate.anon = h2o.anomaly(prostate.hex, prostate.dl)
 head(prostate.anon)
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.clearLogs.Rd

@@ -22,7 +22,3 @@ australia.hex = h2o.importFile(localH2O, path = ausPath)
 h2o.stopLogging()
 h2o.clearLogs()
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.clusterInfo.Rd

@@ -23,7 +23,3 @@ library(h2o)
 localH2O = h2o.init(ip = "localhost", port = 54321, startH2O = TRUE)
 h2o.clusterInfo(localH2O)
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.clusterStatus.Rd

@@ -50,7 +50,3 @@ library(h2o)
 localH2O = h2o.init(ip = "localhost", port = 54321, startH2O = TRUE)
 h2o.clusterStatus(localH2O)
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ cluster }
-\keyword{ cloud }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.confusionMatrix.Rd

@@ -30,7 +30,3 @@ prostate.gbm = h2o.gbm(x = 3:9, y = 2, data = prostate.hex)
 prostate.pred = h2o.predict(prostate.gbm)
 h2o.confusionMatrix(prostate.pred[,1], prostate.hex[,2])
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.createFrame.Rd

@@ -45,7 +45,3 @@ head(myframe)
 summary(myframe)
 h2o.shutdown(localH2O)
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.cut.Rd

@@ -30,7 +30,3 @@ sepal_len.cut = h2o.cut(iris.hex$sepal_len, c(4.2, 4.8, 5.8, 6, 8))
 head(sepal_len.cut)
 summary(sepal_len.cut)
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.ddply.Rd

@@ -63,7 +63,3 @@ h2o.addFunction(localH2O, fun)
 res = h2o.ddply(iris.hex, "class", fun)
 head(res)
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.downloadAllLogs.Rd

@@ -27,7 +27,3 @@ h2o.downloadAllLogs(localH2O, dirname = getwd(), filename = "h2o_logs.log")
 file.info(paste(getwd(), "h2o_logs.log", sep = .Platform$file.sep))
 file.remove(paste(getwd(), "h2o_logs.log", sep = .Platform$file.sep))
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.downloadCSV.Rd

@@ -33,7 +33,3 @@ h2o.downloadCSV(iris.hex, myFile)
 file.info(myFile)
 file.remove(myFile)
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.exec.Rd

@@ -31,7 +31,3 @@ res3<- h2o.exec(hex$nc<- ifelse(hex[,1]<5,log(hex[,3]+1),hex[,"Petal.Width"]/hex
 head(res3)
 head(hex)
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.gapStatistic.Rd

@@ -51,7 +51,3 @@ iris.hex = h2o.importFile(localH2O, path = irisPath)
 h2o.gapStatistic(iris.hex, K.max = 10, B = 100)
 }
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.getFrame.Rd

@@ -27,7 +27,3 @@ h2o.ls(localH2O)
 iris.hex = h2o.getFrame(localH2O, "iris.hex")
 h2o.shutdown(localH2O)
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.getGLMLambdaModel.Rd

@@ -27,7 +27,3 @@ prostate.srch = h2o.glm(x = 3:9, y = 2, data = prostate.hex, family = "binomial"
 random_lambda = sample(prostate.srch@model$params$lambda_all, 1)
 random_model = h2o.getGLMLambdaModel(prostate.srch, random_lambda)
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.getLogPath.Rd

@@ -22,7 +22,3 @@ library(h2o)
 h2o.getLogPath("Command")
 h2o.getLogPath("Error")
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.getModel.Rd

@@ -27,7 +27,3 @@ model <- h2o.randomForest(x = 1:4, y = 5, data = iris.hex)
 model.retrieved <- h2o.getModel(localH2O, model@key)
 h2o.shutdown(localH2O)
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.glm.Rd

@@ -114,7 +114,3 @@ h2o.glm(y = "CAPSULE", x = c("AGE","RACE","PSA","DCAPS"), data = prostate.hex, f
 myX = setdiff(colnames(prostate.hex), c("ID", "DPROS", "DCAPS", "VOL"))
 h2o.glm(y = "VOL", x = myX, data = prostate.hex, family = "gaussian", nfolds = 2, alpha = 0.1)
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.hitRatio.Rd

@@ -32,7 +32,3 @@ iris.gbm = h2o.gbm(x = 1:4, y = 5, data = iris.hex)
 iris.pred = h2o.predict(iris.gbm)
 h2o.hitRatio(iris.pred, iris.hex[,5], k = 3)
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.ignoreColumns.Rd

@@ -21,4 +21,3 @@ airlines.hex = h2o.importFile(localH2O, path = airlinesURL, key = "airlines.hex"
 h2o.ignoreColumns(airlines.hex)
 }
 }
-

R/h2o-package/man/h2o.importFolder.Rd

@@ -61,7 +61,3 @@ class(prostate_all.hex)
 summary(prostate_all.hex)
 }
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.importHDFS.Rd

@@ -71,7 +71,3 @@ iris_folder.hex = h2o.importHDFS(localH2O, path = paste("hdfs://192.168.1.161",
 summary(iris_folder.hex)
 }
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.importURL.Rd

@@ -51,7 +51,3 @@ prostate.hex = h2o.importURL(localH2O, path = paste("https://raw.github.com",
 class(prostate.hex)
 summary(prostate.hex)
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.logAndEcho.Rd

@@ -24,7 +24,3 @@ library(h2o)
 localH2O = h2o.init(ip = "localhost", port = 54321, startH2O = TRUE)
 h2o.logAndEcho(localH2O, "Test log and echo method.")
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.month.Rd

@@ -29,7 +29,3 @@ A \code{\linkS4class{H2OParsedData}} object containing the entries of \code{x} c
 \seealso{
 \code{\link{h2o.year}}
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.mse.Rd

@@ -31,7 +31,3 @@ prostate.glm = prostate.glm = h2o.glm(x = c("RACE","PSA","DCAPS"), y = "AGE",
 prostate.pred = h2o.predict(prostate.glm)
 h2o.mse(prostate.pred[,1], prostate.hex[,2])
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.openLog.Rd

@@ -32,7 +32,3 @@ h2o.openLog("Command")
 h2o.openLog("Error")
 }
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.parseRaw.Rd

@@ -46,7 +46,3 @@ prostate.raw = h2o.importFile(localH2O, path = prosPath, parse = FALSE)
 prostate.hex = h2o.parseRaw(data = prostate.raw, key = "prostate.hex")
 # After parsing, it is okay to modify or delete prostate.csv
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.pcr.Rd

@@ -81,6 +81,6 @@ localH2O = h2o.init(ip = "localhost", port = 54321, startH2O = TRUE)
 prostate.hex = h2o.importURL(localH2O, path = paste("https://raw.github.com", 
   "0xdata/h2o/master/smalldata/logreg/prostate.csv", sep = "/"), key = "prostate.hex")
 h2o.pcr(x = c("AGE","RACE","PSA","DCAPS"), y = "CAPSULE", data = prostate.hex, family = "binomial", 
-  nfolds = 10, alpha = 0.5, ncomp = 3)
+  nfolds = 5, alpha = 0.5, ncomp = 3)
 }
 

R/h2o-package/man/h2o.prcomp.Rd

@@ -58,7 +58,3 @@ australia.hex = h2o.importFile(localH2O, path = ausPath)
 australia.pca = h2o.prcomp(data = australia.hex, standardize = TRUE)
 print(australia.pca)
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.predict.Rd

@@ -41,7 +41,3 @@ prostate.glm = h2o.glm(y = "CAPSULE", x = c("AGE","RACE","PSA","DCAPS"), data =
 prostate.fit = h2o.predict(object = prostate.glm, newdata = prostate.hex)
 summary(prostate.fit)
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.randomForest.Rd

@@ -79,7 +79,3 @@ irisPath = system.file("extdata", "iris.csv", package = "h2o")
 iris.hex = h2o.importFile(localH2O, path = irisPath, key = "iris.hex")
 h2o.randomForest(y = 5, x = c(2,3,4), data = iris.hex, ntree = 50, depth = 100)
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.setLogPath.Rd

@@ -24,7 +24,3 @@ h2o.getLogPath("Command")
 h2o.setLogPath(getwd(), "Command")
 h2o.getLogPath("Command")
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.shutdown.Rd

@@ -40,7 +40,3 @@ localH2O = h2o.init(ip = "localhost", port = 54321, startH2O = TRUE)
 h2o.shutdown(localH2O)
 }
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ shutdown }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.splitFrame.Rd

@@ -28,7 +28,3 @@ iris.split = h2o.splitFrame(iris.hex, ratios = c(0.2, 0.5))
 head(iris.split[[1]])
 summary(iris.split[[1]])
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.startLogging.Rd

@@ -21,7 +21,3 @@ ausPath = system.file("extdata", "australia.csv", package="h2o")
 australia.hex = h2o.importFile(localH2O, path = ausPath)
 h2o.stopLogging()
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line

R/h2o-package/man/h2o.stopLogging.Rd

@@ -21,7 +21,3 @@ ausPath = system.file("extdata", "australia.csv", package="h2o")
 australia.hex = h2o.importFile(localH2O, path = ausPath)
 h2o.stopLogging()
 }
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ ~kwd1 }
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line