Apply a model stack to create different types of predictions.
A model stack with fitted members outputted from
A rectangular data object, such as a data frame.
Format of returned predicted values—one of "numeric", "class",
or "prob". When NULL,
Logical. Whether or not to additionally return the predictions for each of the ensemble members.
A list of optional arguments to the underlying predict function passed on to parsnip::predict.model_fit for each member.
Additional arguments. Currently ignored.
This package provides some resampling objects and datasets for use in examples and vignettes derived from a study on 1212 red-eyed tree frog embryos!
Red-eyed tree frog (RETF) embryos can hatch earlier than their normal 7ish days if they detect potential predator threat. Researchers wanted to determine how, and when, these tree frog embryos were able to detect stimulus from their environment. To do so, they subjected the embryos at varying developmental stages to "predator stimulus" by jiggling the embryos with a blunt probe. Beforehand, though some of the embryos were treated with gentamicin, a compound that knocks out their lateral line (a sensory organ.) Researcher Julie Jung and her crew found that these factors inform whether an embryo hatches prematurely or not!
Note that the data included with the stacks package is not necessarily a representative or unbiased subset of the complete dataset, and is only for demonstrative purposes.
rset cross-fold validation objects
rsample, splitting the training data into for the regression
and classification model objects, respectively.
tree_frogs_class_test are the analogous testing sets.
reg_res_sp contain regression tuning results
for a linear regression, support vector machine, and spline model, respectively,
latency (i.e. how long the embryos took to hatch in response
to the jiggle) in the
tree_frogs data, using most all of the other
variables as predictors. Note that the data underlying these models is
filtered to include data only from embryos that hatched in response to
class_res_nn contain multiclass classification tuning
results for a random forest and neural network classification model,
reflex (a measure of ear function) in the
data using most all of the other variables as predictors.
log_res_nn, contain binary classification tuning results
for a random forest and neural network classification model, respectively,
hatched (whether or not the embryos hatched in response
to the stimulus) using most all of the other variables as predictors.
?example_data to learn more about these objects, as well as browse
the source code that generated them.
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# see the "Example Data" section above for # clarification on the data and tuning results # objects used in these examples! data(tree_frogs_reg_test) data(tree_frogs_class_test) # build and fit a regression model stack reg_st <- stacks() %>% add_candidates(reg_res_lr) %>% add_candidates(reg_res_sp) %>% blend_predictions() %>% fit_members() reg_st # predict on the tree frogs testing data predict(reg_st, tree_frogs_reg_test) # include the predictions from the members predict(reg_st, tree_frogs_reg_test, members = TRUE) # build and fit a classification model stack class_st <- stacks() %>% add_candidates(class_res_nn) %>% add_candidates(class_res_rf) %>% blend_predictions() %>% fit_members() class_st # predict reflex, first as a class, then as # class probabilities predict(class_st, tree_frogs_class_test) predict(class_st, tree_frogs_class_test, type = "prob") # returning the member predictions as well predict( class_st, tree_frogs_class_test, type = "prob", members = TRUE )
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