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add new parameters model to avoid the use of dump file for functions plot, dt.tree, importance

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add new size parameter for plot function
This commit is contained in:
El Potaeto 2015-01-11 09:40:55 +01:00
parent c8c5789efd
commit 31a3b38ef8
5 changed files with 40 additions and 25 deletions
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4
R-package/R/xgb.importance.R
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@ -64,9 +64,9 @@ xgb.importance <- function(feature_names = NULL, filename_dump = NULL, model = N
} }
if(text[2] == "bias:"){ if(text[2] == "bias:"){
result <- linearDump(feature_names, text) result <- readLines(filename_dump) %>% linearDump(feature_names, .)
} else { } else {
result <- treeDump(feature_names, text) result <- treeDump(feature_names, text = text)
} }
result result
} }

28
R-package/R/xgb.model.dt.tree.R
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@ -16,6 +16,8 @@
#' @importFrom stringr str_trim #' @importFrom stringr str_trim
#' @param feature_names names of each feature as a character vector. Can be extracted from a sparse matrix (see example). If model dump already contains feature names, this argument should be \code{NULL}. #' @param feature_names names of each feature as a character vector. Can be extracted from a sparse matrix (see example). If model dump already contains feature names, this argument should be \code{NULL}.
#' @param filename_dump the path to the text file storing the model. Model dump must include the gain per feature and per tree (parameter \code{with.stats = T} in function \code{xgb.dump}). #' @param filename_dump the path to the text file storing the model. Model dump must include the gain per feature and per tree (parameter \code{with.stats = T} in function \code{xgb.dump}).
#' @param model dump generated by the \code{xgb.train} function. Avoid the creation of a dump file.
#' @param text dump generated by the \code{xgb.dump} function. Avoid the creation of a dump file. Model dump must include the gain per feature and per tree (parameter \code{with.stats = T} in function \code{xgb.dump}).
#' @param n_first_tree limit the plot to the n first trees. If \code{NULL}, all trees of the model are plotted. Performance can be low for huge models. #' @param n_first_tree limit the plot to the n first trees. If \code{NULL}, all trees of the model are plotted. Performance can be low for huge models.
#' #'
#' @return A \code{data.table} of the features used in the model with their gain, cover and few other thing. #' @return A \code{data.table} of the features used in the model with their gain, cover and few other thing.
@ -49,29 +51,37 @@
#' xgb.dump(bst, 'xgb.model.dump', with.stats = T) #' xgb.dump(bst, 'xgb.model.dump', with.stats = T)
#' #'
#' #agaricus.test$data@@Dimnames[[2]] represents the column names of the sparse matrix. #' #agaricus.test$data@@Dimnames[[2]] represents the column names of the sparse matrix.
#' xgb.model.dt.tree(agaricus.train$data@@Dimnames[[2]], 'xgb.model.dump') #' xgb.model.dt.tree(agaricus.train$data@@Dimnames[[2]], filename_dump = 'xgb.model.dump')
#' #'
#' @export #' @export
xgb.model.dt.tree <- function(feature_names = NULL, filename_dump = NULL, text = NULL, n_first_tree = NULL){ xgb.model.dt.tree <- function(feature_names = NULL, filename_dump = NULL, model = NULL, text = NULL, n_first_tree = NULL){
if (!class(feature_names) %in% c("character", "NULL")) { if (!class(feature_names) %in% c("character", "NULL")) {
stop("feature_names: Has to be a vector of character or NULL if the model dump already contains feature name. Look at this function documentation to see where to get feature names.") stop("feature_names: Has to be a vector of character or NULL if the model dump already contains feature name. Look at this function documentation to see where to get feature names.")
} }
if (!class(filename_dump) %in% c("character", "NULL")) { if (!(class(filename_dump) %in% c("character", "NULL") && length(filename_dump) <= 1)) {
stop("filename_dump: Has to be a character vector representing the path to the model dump file.") stop("filename_dump: Has to be a character vector of size 1 representing the path to the model dump file.")
} else if (class(filename_dump) == "character" && !file.exists(filename_dump)) { } else if (!is.null(filename_dump) && !file.exists(filename_dump)) {
stop("filename_dump: path to the model doesn't exist.") stop("filename_dump: path to the model doesn't exist.")
} else if(is.null(filename_dump) & is.null(text)){ } else if(is.null(filename_dump) && is.null(model) && is.null(text)){
stop("filename_dump: no path and no string version of the model dump have been provided.") stop("filename_dump & model & text: no path to dump model, no model, no text dump, have been provided.")
} }
if (!class(text) %in% c("character", "NULL")) {
if (!class(model) %in% c("xgb.Booster", "NULL")) {
stop("model: Has to be an object of class xgb.Booster model generaged by the xgb.train function.")
}
if (!class(text) %in% c("character", "NULL")) {
stop("text: Has to be a vector of character or NULL if a path to the model dump has already been provided.") stop("text: Has to be a vector of character or NULL if a path to the model dump has already been provided.")
} }
if (!class(n_first_tree) %in% c("numeric", "NULL") | length(n_first_tree) > 1) { if (!class(n_first_tree) %in% c("numeric", "NULL") | length(n_first_tree) > 1) {
stop("n_first_tree: Has to be a numeric vector of size 1.") stop("n_first_tree: Has to be a numeric vector of size 1.")
} }
if(is.null(text)){ if(!is.null(model)){
text = xgb.dump(model = model, with.stats = T)
} else if(!is.null(filename_dump)){
text <- readLines(filename_dump) %>% str_trim(side = "both") text <- readLines(filename_dump) %>% str_trim(side = "both")
} }

19
R-package/R/xgb.plot.tree.R
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@ -20,7 +20,9 @@
#' @param filename_dump the path to the text file storing the model. Model dump must include the gain per feature and per tree (parameter \code{with.stats = T} in function \code{xgb.dump}). Possible to provide a model directly (see \code{model} argument). #' @param filename_dump the path to the text file storing the model. Model dump must include the gain per feature and per tree (parameter \code{with.stats = T} in function \code{xgb.dump}). Possible to provide a model directly (see \code{model} argument).
#' @param model generated by the \code{xgb.train} function. Avoid the creation of a dump file. #' @param model generated by the \code{xgb.train} function. Avoid the creation of a dump file.
#' @param n_first_tree limit the plot to the n first trees. If \code{NULL}, all trees of the model are plotted. Performance can be low for huge models. #' @param n_first_tree limit the plot to the n first trees. If \code{NULL}, all trees of the model are plotted. Performance can be low for huge models.
#' @param style a \code{character} vector storing a css style to customize the appearance of nodes. Look at the \href{https://github.com/knsv/mermaid/wiki}{Mermaid wiki} for more information. #' @param CSSstyle a \code{character} vector storing a css style to customize the appearance of nodes. Look at the \href{https://github.com/knsv/mermaid/wiki}{Mermaid wiki} for more information.
#' @param width the width of the diagram in pixels.
#' @param height the height of the diagram in pixels.
#' #'
#' @return A \code{DiagrammeR} of the model. #' @return A \code{DiagrammeR} of the model.
#' #'
@ -52,9 +54,9 @@
#' #'
#' @export #' @export
#' #'
xgb.plot.tree <- function(feature_names = NULL, filename_dump = NULL, model = NULL, n_first_tree = NULL, styles = NULL){ xgb.plot.tree <- function(feature_names = NULL, filename_dump = NULL, model = NULL, n_first_tree = NULL, CSSstyle = NULL, width = NULL, height = NULL){
if (!(class(styles) %in% c("character", "NULL") && length(styles) == 1)) { if (!(class(CSSstyle) %in% c("character", "NULL") && length(CSSstyle) <= 1)) {
stop("style: Has to be a character vector of size 1.") stop("style: Has to be a character vector of size 1.")
} }
@ -65,8 +67,7 @@ xgb.plot.tree <- function(feature_names = NULL, filename_dump = NULL, model = NU
if(is.null(model)){ if(is.null(model)){
allTrees <- xgb.model.dt.tree(feature_names = feature_names, filename_dump = filename_dump, n_first_tree = n_first_tree) allTrees <- xgb.model.dt.tree(feature_names = feature_names, filename_dump = filename_dump, n_first_tree = n_first_tree)
} else { } else {
text = xgb.dump(model = model, with.stats = T) allTrees <- xgb.model.dt.tree(feature_names = feature_names, model = model, n_first_tree = n_first_tree)
allTrees <- xgb.model.dt.tree(feature_names = feature_names, text = text, n_first_tree = n_first_tree)
} }
allTrees[Feature!="Leaf" ,yesPath:= paste(ID,"(", Feature, "<br/>Cover: ", Cover, "<br/>Gain: ", Quality, ")-->|< ", Split, "|", Yes, ">", Yes.Feature, "]", sep = "")] allTrees[Feature!="Leaf" ,yesPath:= paste(ID,"(", Feature, "<br/>Cover: ", Cover, "<br/>Gain: ", Quality, ")-->|< ", Split, "|", Yes, ">", Yes.Feature, "]", sep = "")]
@ -74,14 +75,14 @@ xgb.plot.tree <- function(feature_names = NULL, filename_dump = NULL, model = NU
allTrees[Feature!="Leaf" ,noPath:= paste(ID,"(", Feature, ")-->|>= ", Split, "|", No, ">", No.Feature, "]", sep = "")] allTrees[Feature!="Leaf" ,noPath:= paste(ID,"(", Feature, ")-->|>= ", Split, "|", No, ">", No.Feature, "]", sep = "")]
if(is.null(styles)){ if(is.null(CSSstyle)){
styles <- "classDef greenNode fill:#A2EB86, stroke:#04C4AB, stroke-width:2px;classDef redNode fill:#FFA070, stroke:#FF5E5E, stroke-width:2px" CSSstyle <- "classDef greenNode fill:#A2EB86, stroke:#04C4AB, stroke-width:2px;classDef redNode fill:#FFA070, stroke:#FF5E5E, stroke-width:2px"
} }
yes <- allTrees[Feature!="Leaf", c(Yes)] %>% paste(collapse = ",") %>% paste("class ", ., " greenNode", sep = "") yes <- allTrees[Feature!="Leaf", c(Yes)] %>% paste(collapse = ",") %>% paste("class ", ., " greenNode", sep = "")
no <- allTrees[Feature!="Leaf", c(No)] %>% paste(collapse = ",") %>% paste("class ", ., " redNode", sep = "") no <- allTrees[Feature!="Leaf", c(No)] %>% paste(collapse = ",") %>% paste("class ", ., " redNode", sep = "")
path <- allTrees[Feature!="Leaf", c(yesPath, noPath)] %>% .[order(.)] %>% paste(sep = "", collapse = ";") %>% paste("graph LR", .,collapse = "", sep = ";") %>% paste(styles, yes, no, sep = ";") path <- allTrees[Feature!="Leaf", c(yesPath, noPath)] %>% .[order(.)] %>% paste(sep = "", collapse = ";") %>% paste("graph LR", .,collapse = "", sep = ";") %>% paste(CSSstyle, yes, no, sep = ";")
DiagrammeR(path) DiagrammeR(path, width, height)
} }

10
R-package/man/xgb.model.dt.tree.Rd
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@ -4,14 +4,18 @@
\alias{xgb.model.dt.tree} \alias{xgb.model.dt.tree}
\title{Convert tree model dump to data.table} \title{Convert tree model dump to data.table}
\usage{ \usage{
xgb.model.dt.tree(feature_names = NULL, filename_dump = NULL, text = NULL, xgb.model.dt.tree(feature_names = NULL, filename_dump = NULL,
n_first_tree = NULL) model = NULL, text = NULL, n_first_tree = NULL)
} }
\arguments{ \arguments{
\item{feature_names}{names of each feature as a character vector. Can be extracted from a sparse matrix (see example). If model dump already contains feature names, this argument should be \code{NULL}.} \item{feature_names}{names of each feature as a character vector. Can be extracted from a sparse matrix (see example). If model dump already contains feature names, this argument should be \code{NULL}.}
\item{filename_dump}{the path to the text file storing the model. Model dump must include the gain per feature and per tree (parameter \code{with.stats = T} in function \code{xgb.dump}).} \item{filename_dump}{the path to the text file storing the model. Model dump must include the gain per feature and per tree (parameter \code{with.stats = T} in function \code{xgb.dump}).}
\item{model}{dump generated by the \code{xgb.train} function. Avoid the creation of a dump file.}
\item{text}{dump generated by the \code{xgb.dump} function. Avoid the creation of a dump file. Model dump must include the gain per feature and per tree (parameter \code{with.stats = T} in function \code{xgb.dump}).}
\item{n_first_tree}{limit the plot to the n first trees. If \code{NULL}, all trees of the model are plotted. Performance can be low for huge models.} \item{n_first_tree}{limit the plot to the n first trees. If \code{NULL}, all trees of the model are plotted. Performance can be low for huge models.}
} }
\value{ \value{
@ -49,6 +53,6 @@ bst <- xgboost(data = train$data, label = train$label, max.depth = 2,
xgb.dump(bst, 'xgb.model.dump', with.stats = T) xgb.dump(bst, 'xgb.model.dump', with.stats = T)
#agaricus.test$data@Dimnames[[2]] represents the column names of the sparse matrix. #agaricus.test$data@Dimnames[[2]] represents the column names of the sparse matrix.
xgb.model.dt.tree(agaricus.train$data@Dimnames[[2]], 'xgb.model.dump') xgb.model.dt.tree(agaricus.train$data@Dimnames[[2]], filename_dump = 'xgb.model.dump')
} }

4
R-package/man/xgb.plot.tree.Rd
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@ -5,7 +5,7 @@
\title{Plot a boosted tree model} \title{Plot a boosted tree model}
\usage{ \usage{
xgb.plot.tree(feature_names = NULL, filename_dump = NULL, model = NULL, xgb.plot.tree(feature_names = NULL, filename_dump = NULL, model = NULL,
n_first_tree = NULL, styles = NULL) n_first_tree = NULL, CSSstyle = NULL)
} }
\arguments{ \arguments{
\item{feature_names}{names of each feature as a character vector. Can be extracted from a sparse matrix (see example). If model dump already contains feature names, this argument should be \code{NULL}.} \item{feature_names}{names of each feature as a character vector. Can be extracted from a sparse matrix (see example). If model dump already contains feature names, this argument should be \code{NULL}.}
@ -16,7 +16,7 @@ xgb.plot.tree(feature_names = NULL, filename_dump = NULL, model = NULL,
\item{n_first_tree}{limit the plot to the n first trees. If \code{NULL}, all trees of the model are plotted. Performance can be low for huge models.} \item{n_first_tree}{limit the plot to the n first trees. If \code{NULL}, all trees of the model are plotted. Performance can be low for huge models.}
\item{style}{a \code{character} vector storing a css style to customize the appearance of nodes. Look at the \href{https://github.com/knsv/mermaid/wiki}{Mermaid wiki} for more information.} \item{CSSstyle}{a \code{character} vector storing a css style to customize the appearance of nodes. Look at the \href{https://github.com/knsv/mermaid/wiki}{Mermaid wiki} for more information.}
} }
\value{ \value{
A \code{DiagrammeR} of the model. A \code{DiagrammeR} of the model.