Change code to look like a function
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El Potaeto
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@ -1,60 +1,109 @@
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require(DiagrammeR)
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require(stringr)
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require(data.table)
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require(magrittr)
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text <- readLines('xgb.model.dump') %>% str_trim(side = "both")
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position <- str_match(text, "booster") %>% is.na %>% not %>% which %>% c(length(text)+1)
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#' Plot a boosted tree model
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#'
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#' Read a xgboost model text dump.
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#' Only works for boosted tree model (not linear model).
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#'
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#' @importFrom data.table data.table
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#' @importFrom data.table set
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#' @importFrom data.table rbindlist
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#' @importFrom magrittr %>%
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#' @importFrom data.table :=
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#' @importFrom stringr str_extract
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#' @importFrom stringr str_split
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#' @importFrom stringr str_extract
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#' @importFrom stringr str_trim
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#' @importFrom DiagrammeR DiagrammeR
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#' @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}.
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#' @param filename_dump the path to the text file storing the model. Model dump must include the gain per feature and per tree (\code{with.stats = T} in function \code{xgb.dump}).
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#'
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#' @return A \code{data.table} of the features used in the model with their average gain (and their weight for boosted tree model) in the model.
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#'
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#' @details
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#' This is the function to plot the trees growned.
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#' It uses Mermaid JS library for that purpose.
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#' Performance can be low for huge models.
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#'
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#'
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#' @examples
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#' data(agaricus.train, package='xgboost')
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#'
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#' #Both dataset are list with two items, a sparse matrix and labels (labels = outcome column which will be learned).
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#' #Each column of the sparse Matrix is a feature in one hot encoding format.
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#' train <- agaricus.train
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#'
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#' bst <- xgboost(data = train$data, label = train$label, max.depth = 2,
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#' eta = 1, nround = 2,objective = "binary:logistic")
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#' xgb.dump(bst, 'xgb.model.dump', with.stats = T)
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#'
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#' #agaricus.test$data@@Dimnames[[2]] represents the column names of the sparse matrix.
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#' xgb.plot.tree(agaricus.train$data@@Dimnames[[2]], 'xgb.model.dump')
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#'
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#' @export
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xgb.plot.tree <- function(feature_names = NULL, filename_dump = NULL){
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extract <- function(x, pattern) str_extract(x, pattern) %>% str_split("=") %>% lapply(function(x) x[2] %>% as.numeric) %>% unlist
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if (!class(feature_names) %in% c("character", "NULL")) {
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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.")
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}
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if (class(filename_dump) != "character" & file.exists(filename_dump)) {
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stop("filename_dump: Has to be a path to the model dump file.")
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}
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addTreeId <- function(x, i) paste(i,x,sep = "-")
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text <- readLines(filename_dump) %>% str_trim(side = "both")
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position <- str_match(text, "booster") %>% is.na %>% not %>% which %>% c(length(text)+1)
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allTrees <- data.table()
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extract <- function(x, pattern) str_extract(x, pattern) %>% str_split("=") %>% lapply(function(x) x[2] %>% as.numeric) %>% unlist
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for(i in 1:(length(position)-1)){
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addTreeId <- function(x, i) paste(i,x,sep = "-")
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tree <- text[(position[i]+1):(position[i+1]-1)]
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allTrees <- data.table()
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notLeaf <- str_match(tree, "leaf") %>% is.na
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leaf <- notLeaf %>% not %>% tree[.]
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branch <- notLeaf %>% tree[.]
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idBranch <- str_extract(branch, "\\d*:") %>% str_replace(":", "") %>% addTreeId(i)
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idLeaf <- str_extract(leaf, "\\d*:") %>% str_replace(":", "") %>% addTreeId(i)
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featureBranch <- str_extract(branch, "f\\d*<") %>% str_replace("<", "") %>% str_replace("f", "") %>% as.numeric
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featureLeaf <- rep("Leaf", length(leaf))
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splitBranch <- str_extract(branch, "<\\d*\\.*\\d*\\]") %>% str_replace("<", "") %>% str_replace("\\]", "")
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splitLeaf <- rep(NA, length(leaf))
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yesBranch <- extract(branch, "yes=\\d*") %>% addTreeId(i)
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yesLeaf <- rep(NA, length(leaf))
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noBranch <- extract(branch, "no=\\d*") %>% addTreeId(i)
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noLeaf <- rep(NA, length(leaf))
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missingBranch <- extract(branch, "missing=\\d+") %>% addTreeId(i)
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missingLeaf <- rep(NA, length(leaf))
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qualityBranch <- extract(branch, "gain=\\d*\\.*\\d*")
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qualityLeaf <- extract(leaf, "leaf=\\-*\\d*\\.*\\d*")
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coverBranch <- extract(branch, "cover=\\d*\\.*\\d*")
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coverLeaf <- extract(leaf, "cover=\\d*\\.*\\d*")
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dt <- data.table(ID = c(idBranch, idLeaf), Feature = c(featureBranch, featureLeaf), Split = c(splitBranch, splitLeaf), Yes = c(yesBranch, yesLeaf), No = c(noBranch, noLeaf), Missing = c(missingBranch, missingLeaf), Quality = c(qualityBranch, qualityLeaf), Cover = c(coverBranch, coverLeaf))[order(ID)][,Tree:=i]
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for(i in 1:(length(position)-1)){
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set(dt, i = which(dt[,Feature]!= "Leaf"), j = "YesFeature", value = dt[ID == dt[,Yes], Feature])
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set(dt, i = which(dt[,Feature]!= "Leaf"), j = "NoFeature", value = dt[ID == dt[,No], Feature])
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tree <- text[(position[i]+1):(position[i+1]-1)]
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dt[Feature!="Leaf" ,yesPath:= paste(ID,"[", Feature, "]-->|< ", Split, "|", Yes, "[", YesFeature, "]", sep = "")]
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notLeaf <- str_match(tree, "leaf") %>% is.na
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leaf <- notLeaf %>% not %>% tree[.]
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branch <- notLeaf %>% tree[.]
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idBranch <- str_extract(branch, "\\d*:") %>% str_replace(":", "") %>% addTreeId(i)
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idLeaf <- str_extract(leaf, "\\d*:") %>% str_replace(":", "") %>% addTreeId(i)
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featureBranch <- str_extract(branch, "f\\d*<") %>% str_replace("<", "") %>% str_replace("f", "") %>% as.numeric
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if(!is.null(feature_names)){
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featureBranch <- feature_names[featureBranch + 1]
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}
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featureLeaf <- rep("Leaf", length(leaf))
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splitBranch <- str_extract(branch, "<\\d*\\.*\\d*\\]") %>% str_replace("<", "") %>% str_replace("\\]", "")
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splitLeaf <- rep(NA, length(leaf))
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yesBranch <- extract(branch, "yes=\\d*") %>% addTreeId(i)
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yesLeaf <- rep(NA, length(leaf))
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noBranch <- extract(branch, "no=\\d*") %>% addTreeId(i)
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noLeaf <- rep(NA, length(leaf))
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missingBranch <- extract(branch, "missing=\\d+") %>% addTreeId(i)
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missingLeaf <- rep(NA, length(leaf))
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qualityBranch <- extract(branch, "gain=\\d*\\.*\\d*")
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qualityLeaf <- extract(leaf, "leaf=\\-*\\d*\\.*\\d*")
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coverBranch <- extract(branch, "cover=\\d*\\.*\\d*")
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coverLeaf <- extract(leaf, "cover=\\d*\\.*\\d*")
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dt <- data.table(ID = c(idBranch, idLeaf), Feature = c(featureBranch, featureLeaf), Split = c(splitBranch, splitLeaf), Yes = c(yesBranch, yesLeaf), No = c(noBranch, noLeaf), Missing = c(missingBranch, missingLeaf), Quality = c(qualityBranch, qualityLeaf), Cover = c(coverBranch, coverLeaf))[order(ID)][,Tree:=i]
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dt[Feature!="Leaf" ,noPath:= paste(ID,"[", Feature, "]-->|> ", Split, "|", No, "[", NoFeature, "]", sep = "")]
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set(dt, i = which(dt[,Feature]!= "Leaf"), j = "YesFeature", value = dt[ID == dt[,Yes], Feature])
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set(dt, i = which(dt[,Feature]!= "Leaf"), j = "NoFeature", value = dt[ID == dt[,No], Feature])
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#missingPath <- paste(dtBranch[,ID], "-->|Missing|", dtBranch[,Missing], sep = "")
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dt[Feature!="Leaf" ,yesPath:= paste(ID,"[", Feature, "]-->|< ", Split, "|", Yes, "[", YesFeature, "]", sep = "")]
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allTrees <- rbindlist(list(allTrees, dt), use.names = T, fill = F)
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dt[Feature!="Leaf" ,noPath:= paste(ID,"[", Feature, "]-->|>= ", Split, "|", No, "[", NoFeature, "]", sep = "")]
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#missingPath <- paste(dtBranch[,ID], "-->|Missing|", dtBranch[,Missing], sep = "")
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allTrees <- rbindlist(list(allTrees, dt), use.names = T, fill = F)
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}
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styles <- "classDef greenNode fill:#A2EB86, stroke:#04C4AB, stroke-width:2px;classDef redNode fill:#FFA070, stroke:#FF5E5E, stroke-width:2px"
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yes <- allTrees[Feature!="Leaf", c(Yes)] %>% paste(collapse = ",") %>% paste("class ", ., " greenNode", sep = "")
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no <- allTrees[Feature!="Leaf", c(No)] %>% paste(collapse = ",") %>% paste("class ", ., " redNode", sep = "")
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path <- allTrees[Feature!="Leaf", c(yesPath, noPath)] %>% .[order(.)] %>% paste(sep = "", collapse = ";") %>% paste("graph LR", .,collapse = "", sep = ";") %>% paste(styles, yes, no, sep = ";")
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DiagrammeR(path)
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}
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styles <- "classDef greenNode fill:#A2EB86, stroke:#04C4AB, stroke-width:2px;classDef redNode fill:#FFA070, stroke:#FF5E5E, stroke-width:2px"
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yes <- allTrees[Feature!="Leaf", c(Yes)] %>% paste(collapse = ",") %>% paste("class ", ., " greenNode", sep = "")
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no <- allTrees[Feature!="Leaf", c(No)] %>% paste(collapse = ",") %>% paste("class ", ., " redNode", sep = "")
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path <- allTrees[Feature!="Leaf", c(yesPath, noPath)] %>% .[order(.)] %>% paste(sep = "", collapse = ";") %>% paste("graph LR", .,collapse = "", sep = ";") %>% paste(styles, yes, no, sep = ";")
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DiagrammeR(path, height =700)
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#}
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