explain {shapr}  R Documentation 
Explain the output of machine learning models with more accurately estimated Shapley values
Description
Explain the output of machine learning models with more accurately estimated Shapley values
Usage
explain(x, explainer, approach, prediction_zero, ...)
## S3 method for class 'empirical'
explain(
x,
explainer,
approach,
prediction_zero,
type = "fixed_sigma",
fixed_sigma_vec = 0.1,
n_samples_aicc = 1000,
eval_max_aicc = 20,
start_aicc = 0.1,
w_threshold = 0.95,
...
)
## S3 method for class 'gaussian'
explain(
x,
explainer,
approach,
prediction_zero,
mu = NULL,
cov_mat = NULL,
...
)
## S3 method for class 'copula'
explain(x, explainer, approach, prediction_zero, ...)
## S3 method for class 'ctree'
explain(
x,
explainer,
approach,
prediction_zero,
mincriterion = 0.95,
minsplit = 20,
minbucket = 7,
sample = TRUE,
...
)
## S3 method for class 'combined'
explain(
x,
explainer,
approach,
prediction_zero,
mu = NULL,
cov_mat = NULL,
...
)
## S3 method for class 'ctree_comb_mincrit'
explain(x, explainer, approach, prediction_zero, mincriterion, ...)
Arguments
x 
A matrix or data.frame. Contains the the features, whose predictions ought to be explained (test data). 
explainer 
An 
approach 
Character vector of length 
prediction_zero 
Numeric. The prediction value for unseen data, typically equal to the mean of the response. 
... 
Additional arguments passed to 
type 
Character. Should be equal to either 
fixed_sigma_vec 
Numeric. Represents the kernel bandwidth. Note that this argument is only
applicable when 
n_samples_aicc 
Positive integer. Number of samples to consider in AICc optimization.
Note that this argument is only applicable when 
eval_max_aicc 
Positive integer. Maximum number of iterations when
optimizing the AICc. Note that this argument is only applicable when

start_aicc 
Numeric. Start value of 
w_threshold 
Positive integer between 0 and 1. 
mu 
Numeric vector. (Optional) Containing the mean of the data generating distribution.
If 
cov_mat 
Numeric matrix. (Optional) Containing the covariance matrix of the data
generating distribution. 
mincriterion 
Numeric value or vector where length of vector is the number of features in model. Value is equal to 1  alpha where alpha is the nominal level of the conditional independence tests. If it is a vector, this indicates which mincriterion to use when conditioning on various numbers of features. 
minsplit 
Numeric value. Equal to the value that the sum of the left and right daughter nodes need to exceed. 
minbucket 
Numeric value. Equal to the minimum sum of weights in a terminal node. 
sample 
Boolean. If TRUE, then the method always samples 
Details
The most important thing to notice is that shapr
has implemented four different
approaches for estimating the conditional distributions of the data, namely "empirical"
,
"gaussian"
, "copula"
and "ctree"
.
In addition, the user also has the option of combining the four approaches.
E.g. if you're in a situation where you have trained a model the consists of 10 features,
and you'd like to use the "gaussian"
approach when you condition on a single feature,
the "empirical"
approach if you condition on 25 features, and "copula"
version
if you condition on more than 5 features this can be done by simply passing
approach = c("gaussian", rep("empirical", 4), rep("copula", 5))
. If
"approach[i]" = "gaussian"
it means that you'd like to use the "gaussian"
approach
when conditioning on i
features.
Value
Object of class c("shapr", "list")
. Contains the following items:
 dt
data.table
 model
Model object
 p
Numeric vector
 x_test
data.table
Note that the returned items model
, p
and x_test
are mostly added due
to the implementation of plot.shapr
. If you only want to look at the numerical results
it is sufficient to focus on dt
. dt
is a data.table where the number of rows equals
the number of observations you'd like to explain, and the number of columns equals m +1
,
where m
equals the total number of features in your model.
If dt[i, j + 1] > 0
it indicates that the jth feature increased the prediction for
the ith observation. Likewise, if dt[i, j + 1] < 0
it indicates that the jth feature
decreased the prediction for the ith observation. The magnitude of the value is also important
to notice. E.g. if dt[i, k + 1]
and dt[i, j + 1]
are greater than 0
,
where j != k
, and dt[i, k + 1]
> dt[i, j + 1]
this indicates that feature
j
and k
both increased the value of the prediction, but that the effect of the kth
feature was larger than the jth feature.
The first column in dt
, called 'none', is the prediction value not assigned to any of the features
(\phi
_{0}).
It's equal for all observations and set by the user through the argument prediction_zero
.
In theory this value should be the expected prediction without conditioning on any features.
Typically we set this value equal to the mean of the response variable in our training data, but other choices
such as the mean of the predictions in the training data are also reasonable.
Author(s)
Camilla Lingjaerde, Nikolai Sellereite, Martin Jullum, Annabelle Redelmeier
Examples
if (requireNamespace("MASS", quietly = TRUE)) {
# Load example data
data("Boston", package = "MASS")
# Split data into test and training data
x_train < head(Boston, 3)
x_test < tail(Boston, 3)
# Fit a linear model
model < lm(medv ~ lstat + rm + dis + indus, data = x_train)
# Create an explainer object
explainer < shapr(x_train, model)
# Explain predictions
p < mean(x_train$medv)
# Empirical approach
explain1 < explain(x_test, explainer,
approach = "empirical",
prediction_zero = p, n_samples = 1e2
)
# Gaussian approach
explain2 < explain(x_test, explainer,
approach = "gaussian",
prediction_zero = p, n_samples = 1e2
)
# Gaussian copula approach
explain3 < explain(x_test, explainer,
approach = "copula",
prediction_zero = p, n_samples = 1e2
)
# ctree approach
explain4 < explain(x_test, explainer,
approach = "ctree",
prediction_zero = p
)
# Combined approach
approach < c("gaussian", "gaussian", "empirical", "empirical")
explain5 < explain(x_test, explainer,
approach = approach,
prediction_zero = p, n_samples = 1e2
)
# Print the Shapley values
print(explain1$dt)
# Plot the results
if (requireNamespace("ggplot2", quietly = TRUE)) {
plot(explain1)
}
}