# ranger

##### Ranger

Ranger is a fast implementation of random forests (Breiman 2001) or recursive partitioning, particularly suited for high dimensional data. Classification, regression, and survival forests are supported. Classification and regression forests are implemented as in the original Random Forest (Breiman 2001), survival forests as in Random Survival Forests (Ishwaran et al. 2008). Includes implementations of extremely randomized trees (Geurts et al. 2006) and quantile regression forests (Meinshausen 2006).

##### Usage

```
ranger(formula = NULL, data = NULL, num.trees = 500, mtry = NULL,
importance = "none", write.forest = TRUE, probability = FALSE,
min.node.size = NULL, replace = TRUE, sample.fraction = ifelse(replace,
1, 0.632), case.weights = NULL, class.weights = NULL, splitrule = NULL,
num.random.splits = 1, alpha = 0.5, minprop = 0.1,
split.select.weights = NULL, always.split.variables = NULL,
respect.unordered.factors = NULL, scale.permutation.importance = FALSE,
keep.inbag = FALSE, holdout = FALSE, quantreg = FALSE,
num.threads = NULL, save.memory = FALSE, verbose = TRUE, seed = NULL,
dependent.variable.name = NULL, status.variable.name = NULL,
classification = NULL)
```

##### Arguments

- formula
Object of class

`formula`

or`character`

describing the model to fit. Interaction terms supported only for numerical variables.- data
Training data of class

`data.frame`

,`matrix`

,`dgCMatrix`

(Matrix) or`gwaa.data`

(GenABEL).- num.trees
Number of trees.

- mtry
Number of variables to possibly split at in each node. Default is the (rounded down) square root of the number variables.

- importance
Variable importance mode, one of 'none', 'impurity', 'impurity_corrected', 'permutation'. The 'impurity' measure is the Gini index for classification, the variance of the responses for regression and the sum of test statistics (see

`splitrule`

) for survival.- write.forest
Save

`ranger.forest`

object, required for prediction. Set to`FALSE`

to reduce memory usage if no prediction intended.- probability
Grow a probability forest as in Malley et al. (2012).

- min.node.size
Minimal node size. Default 1 for classification, 5 for regression, 3 for survival, and 10 for probability.

- replace
Sample with replacement.

- sample.fraction
Fraction of observations to sample. Default is 1 for sampling with replacement and 0.632 for sampling without replacement. For classification, this can be a vector of class-specific values.

- case.weights
Weights for sampling of training observations. Observations with larger weights will be selected with higher probability in the bootstrap (or subsampled) samples for the trees.

- class.weights
Weights for the outcome classes (in order of the factor levels) in the splitting rule (cost sensitive learning). Classification and probability prediction only. For classification the weights are also applied in the majority vote in terminal nodes.

- splitrule
Splitting rule. For classification and probability estimation "gini" or "extratrees" with default "gini". For regression "variance", "extratrees" or "maxstat" with default "variance". For survival "logrank", "extratrees", "C" or "maxstat" with default "logrank".

- num.random.splits
For "extratrees" splitrule.: Number of random splits to consider for each candidate splitting variable.

- alpha
For "maxstat" splitrule: Significance threshold to allow splitting.

- minprop
For "maxstat" splitrule: Lower quantile of covariate distribution to be considered for splitting.

- split.select.weights
Numeric vector with weights between 0 and 1, representing the probability to select variables for splitting. Alternatively, a list of size num.trees, containing split select weight vectors for each tree can be used.

- always.split.variables
Character vector with variable names to be always selected in addition to the

`mtry`

variables tried for splitting.- respect.unordered.factors
Handling of unordered factor covariates. One of 'ignore', 'order' and 'partition'. For the "extratrees" splitrule the default is "partition" for all other splitrules 'ignore'. Alternatively TRUE (='order') or FALSE (='ignore') can be used. See below for details.

- scale.permutation.importance
Scale permutation importance by standard error as in (Breiman 2001). Only applicable if permutation variable importance mode selected.

- keep.inbag
Save how often observations are in-bag in each tree.

- holdout
Hold-out mode. Hold-out all samples with case weight 0 and use these for variable importance and prediction error.

- quantreg
Prepare quantile prediction as in quantile regression forests (Meinshausen 2006). Regression only. Set

`keep.inbag = TRUE`

to prepare out-of-bag quantile prediction.- num.threads
Number of threads. Default is number of CPUs available.

- save.memory
Use memory saving (but slower) splitting mode. No effect for survival and GWAS data. Warning: This option slows down the tree growing, use only if you encounter memory problems.

- verbose
Show computation status and estimated runtime.

- seed
Random seed. Default is

`NULL`

, which generates the seed from`R`

. Set to`0`

to ignore the`R`

seed.- dependent.variable.name
Name of dependent variable, needed if no formula given. For survival forests this is the time variable.

- status.variable.name
Name of status variable, only applicable to survival data and needed if no formula given. Use 1 for event and 0 for censoring.

- classification
Only needed if data is a matrix. Set to

`TRUE`

to grow a classification forest.

##### Details

The tree type is determined by the type of the dependent variable. For factors classification trees are grown, for numeric values regression trees and for survival objects survival trees. The Gini index is used as default splitting rule for classification. For regression, the estimated response variances or maximally selected rank statistics (Wright et al. 2016) can be used. For Survival the log-rank test, a C-index based splitting rule (Schmid et al. 2015) and maximally selected rank statistics (Wright et al. 2016) are available. For all tree types, forests of extremely randomized trees (Geurts et al. 2006) can be grown.

With the `probability`

option and factor dependent variable a probability forest is grown.
Here, the node impurity is used for splitting, as in classification forests.
Predictions are class probabilities for each sample.
In contrast to other implementations, each tree returns a probability estimate and these estimates are averaged for the forest probability estimate.
For details see Malley et al. (2012).

Note that for classification and regression nodes with size smaller than `min.node.size`

can occur, as in original Random Forests.
For survival all nodes contain at `min.node.size`

samples.
Variables selected with `always.split.variables`

are tried additionally to the mtry variables randomly selected.
In `split.select.weights`

variables weighted with 0 are never selected and variables with 1 are always selected.
Weights do not need to sum up to 1, they will be normalized later.
The weights are assigned to the variables in the order they appear in the formula or in the data if no formula is used.
Names of the `split.select.weights`

vector are ignored.
The usage of `split.select.weights`

can increase the computation times for large forests.

Unordered factor covariates can be handled in 3 different ways by using `respect.unordered.factors`

:
For 'ignore' all factors are regarded ordered, for 'partition' all possible 2-partitions are considered for splitting.
For 'order' and 2-class classification the factor levels are ordered by their proportion falling in the second class, for regression by their mean response, as described in Hastie et al. (2009), chapter 9.2.4.
For multiclass classification the factor levels are ordered by the first principal component of the weighted covariance matrix of the contingency table (Coppersmith et al. 1999), for survival by the median survival (or the largest available quantile if the median is not available).
The use of 'order' is recommended, as it computationally fast and can handle an unlimited number of factor levels.
Note that the factors are only reordered once and not again in each split.

The 'impurity_corrected' importance measure is unbiased in terms of the number of categories and category frequencies and is almost as fast as the standard impurity importance.
It is a modified version of the method by Sandri & Zuccolotto (2008), which is faster and more memory efficient.
See Nembrini et al. (2018) for details.
This importance measure can be combined with the methods to estimate p-values in `importance_pvalues`

.

For a large number of variables and data frames as input data the formula interface can be slow or impossible to use.
Alternatively `dependent.variable.name`

(and `status.variable.name`

for survival) can be used.
Consider setting `save.memory = TRUE`

if you encounter memory problems for very large datasets, but be aware that this option slows down the tree growing.

For GWAS data consider combining `ranger`

with the `GenABEL`

package.
See the Examples section below for a demonstration using `Plink`

data.
All SNPs in the `GenABEL`

object will be used for splitting.
To use only the SNPs without sex or other covariates from the phenotype file, use `0`

on the right hand side of the formula.
Note that missing values are treated as an extra category while splitting.

See https://github.com/imbs-hl/ranger for the development version.

With recent R versions, multithreading on Windows platforms should just work. If you compile yourself, the new RTools toolchain is required.

##### Value

Object of class `ranger`

with elements

`forest`

Saved forest (If write.forest set to TRUE). Note that the variable IDs in the `split.varIDs`

object do not necessarily represent the column number in R.

`predictions`

Predicted classes/values, based on out of bag samples (classification and regression only).

`variable.importance`

Variable importance for each independent variable.

`prediction.error`

Overall out of bag prediction error. For classification this is the fraction of missclassified samples, for probability estimation the Brier score, for regression the mean squared error and for survival one minus Harrell's C-index.

`r.squared`

R squared. Also called explained variance or coefficient of determination (regression only). Computed on out of bag data.

`confusion.matrix`

Contingency table for classes and predictions based on out of bag samples (classification only).

`unique.death.times`

Unique death times (survival only).

`chf`

Estimated cumulative hazard function for each sample (survival only).

`survival`

Estimated survival function for each sample (survival only).

`call`

Function call.

`num.trees`

Number of trees.

`num.independent.variables`

Number of independent variables.

`mtry`

Value of mtry used.

`min.node.size`

Value of minimal node size used.

`treetype`

Type of forest/tree. classification, regression or survival.

`importance.mode`

Importance mode used.

`num.samples`

Number of samples.

`inbag.counts`

Number of times the observations are in-bag in the trees.

##### References

Wright, M. N. & Ziegler, A. (2017). ranger: A fast implementation of random forests for high dimensional data in C++ and R. J Stat Softw 77:1-17. http://dx.doi.org/10.18637/jss.v077.i01.

Schmid, M., Wright, M. N. & Ziegler, A. (2016). On the use of Harrell's C for clinical risk prediction via random survival forests. Expert Syst Appl 63:450-459. http://dx.doi.org/10.1016/j.eswa.2016.07.018.

Wright, M. N., Dankowski, T. & Ziegler, A. (2017). Unbiased split variable selection for random survival forests using maximally selected rank statistics. Stat Med 36:1272-1284. http://dx.doi.org/10.1002/sim.7212.

Nembrini, S., Koenig, I. R. & Wright, M. N. (2018). The revival of the Gini Importance? Bioinformatics. http://dx.doi.org/10.1093/bioinformatics/bty373.

Breiman, L. (2001). Random forests. Mach Learn, 45:5-32. http://dx.doi.org/10.1023/A:1010933404324.

Ishwaran, H., Kogalur, U. B., Blackstone, E. H., & Lauer, M. S. (2008). Random survival forests. Ann Appl Stat 2:841-860. http://dx.doi.org/10.1097/JTO.0b013e318233d835.

Malley, J. D., Kruppa, J., Dasgupta, A., Malley, K. G., & Ziegler, A. (2012). Probability machines: consistent probability estimation using nonparametric learning machines. Methods Inf Med 51:74-81. http://dx.doi.org/10.3414/ME00-01-0052.

Hastie, T., Tibshirani, R., Friedman, J. (2009). The Elements of Statistical Learning. Springer, New York. 2nd edition.

Geurts, P., Ernst, D., Wehenkel, L. (2006). Extremely randomized trees. Mach Learn 63:3-42. http://dx.doi.org/10.1007/s10994-006-6226-1.

Meinshausen (2006). Quantile Regression Forests. J Mach Learn Res 7:983-999. http://www.jmlr.org/papers/v7/meinshausen06a.html.

Sandri, M. & Zuccolotto, P. (2008). A bias correction algorithm for the Gini variable importance measure in classification trees. J Comput Graph Stat, 17:611-628. http://dx.doi.org/10.1198/106186008X344522.

Coppersmith D., Hong S. J., Hosking J. R. (1999). Partitioning nominal attributes in decision trees. Data Min Knowl Discov 3:197-217. http://dx.doi.org/10.1023/A:1009869804967.

##### See Also

##### Examples

```
# NOT RUN {
require(ranger)
## Classification forest with default settings
ranger(Species ~ ., data = iris)
## Prediction
train.idx <- sample(nrow(iris), 2/3 * nrow(iris))
iris.train <- iris[train.idx, ]
iris.test <- iris[-train.idx, ]
rg.iris <- ranger(Species ~ ., data = iris.train)
pred.iris <- predict(rg.iris, data = iris.test)
table(iris.test$Species, pred.iris$predictions)
## Quantile regression forest
rf <- ranger(mpg ~ ., mtcars[1:26, ], quantreg = TRUE)
pred <- predict(rf, mtcars[27:32, ], type = "quantiles")
pred$predictions
## Variable importance
rg.iris <- ranger(Species ~ ., data = iris, importance = "impurity")
rg.iris$variable.importance
## Survival forest
require(survival)
rg.veteran <- ranger(Surv(time, status) ~ ., data = veteran)
plot(rg.veteran$unique.death.times, rg.veteran$survival[1,])
## Alternative interface
ranger(dependent.variable.name = "Species", data = iris)
# }
# NOT RUN {
## Use GenABEL interface to read Plink data into R and grow a classification forest
## The ped and map files are not included
library(GenABEL)
convert.snp.ped("data.ped", "data.map", "data.raw")
dat.gwaa <- load.gwaa.data("data.pheno", "data.raw")
phdata(dat.gwaa)$trait <- factor(phdata(dat.gwaa)$trait)
ranger(trait ~ ., data = dat.gwaa)
# }
# NOT RUN {
# }
```

*Documentation reproduced from package ranger, version 0.10.1, License: GPL-3*