stacks provides some resampling objects and datasets for use in examples and vignettes derived from a study on 1212 red-eyed tree frog embryos!
Usage
reg_res_svm
reg_res_sp
reg_res_lr
reg_folds
class_res_nn
class_res_rf
class_folds
log_res_nn
log_res_rfFormat
An object of class tune_results (inherits from tbl_df, tbl, data.frame) with 5 rows and 5 columns.
An object of class tune_results (inherits from tbl_df, tbl, data.frame) with 5 rows and 5 columns.
An object of class resample_results (inherits from tune_results, tbl_df, tbl, data.frame) with 5 rows and 5 columns.
An object of class vfold_cv (inherits from rset, tbl_df, tbl, data.frame) with 5 rows and 2 columns.
An object of class resample_results (inherits from tune_results, tbl_df, tbl, data.frame) with 5 rows and 5 columns.
An object of class tune_results (inherits from tbl_df, tbl, data.frame) with 5 rows and 5 columns.
An object of class vfold_cv (inherits from rset, tbl_df, tbl, data.frame) with 5 rows and 2 columns.
An object of class resample_results (inherits from tune_results, tbl_df, tbl, data.frame) with 5 rows and 5 columns.
An object of class tune_results (inherits from tbl_df, tbl, data.frame) with 5 rows and 5 columns.
Source
Julie Jung et al. (2020) Multimodal mechanosensing enables treefrog embryos to escape egg-predators. doi:10.1242/jeb.236141
Details
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.
reg_folds and class_folds are rset cross-fold validation objects
from rsample, splitting the training data into for the regression
and classification model objects, respectively. tree_frogs_reg_test and
tree_frogs_class_test are the analogous testing sets.
reg_res_lr, reg_res_svm, and reg_res_sp contain regression tuning results
for a linear regression, support vector machine, and spline model, respectively,
fitting 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
the stimulus.
class_res_rf and class_res_nn contain multiclass classification tuning
results for a random forest and neural network classification model,
respectively, fitting reflex (a measure of ear function) in the
data using most all of the other variables as predictors.
log_res_rf and log_res_nn, contain binary classification tuning results
for a random forest and neural network classification model, respectively,
fitting hatched (whether or not the embryos hatched in response
to the stimulus) using most all of the other variables as predictors.
The source code for generating these objects is given below.
# setup: packages, data, resample, basic recipe ------------------------
library(stacks)
library(tune)
library(rsample)
library(parsnip)
library(workflows)
library(recipes)
library(yardstick)
library(workflowsets)
set.seed(1)
ctrl_grid <-
tune::control_grid(
save_pred = TRUE,
save_workflow = TRUE
)
ctrl_res <-
tune::control_resamples(
save_pred = TRUE,
save_workflow = TRUE
)
# for regression, predict latency to hatch (excluding NAs)
tree_frogs_reg <-
tree_frogs %>%
filter(!is.na(latency)) %>%
select(-clutch, -hatched)
set.seed(1)
tree_frogs_reg_split <- rsample::initial_split(tree_frogs_reg)
set.seed(1)
tree_frogs_reg_train <- rsample::training(tree_frogs_reg_split)
set.seed(1)
tree_frogs_reg_test <- rsample::testing(tree_frogs_reg_split)
set.seed(1)
reg_folds <- rsample::vfold_cv(tree_frogs_reg_train, v = 5)
tree_frogs_reg_rec <-
recipes::recipe(latency ~ ., data = tree_frogs_reg_train) %>%
recipes::step_dummy(recipes::all_nominal()) %>%
recipes::step_zv(recipes::all_predictors())
metric <- yardstick::metric_set(yardstick::rmse)
# linear regression ---------------------------------------
lin_reg_spec <-
parsnip::linear_reg() %>%
parsnip::set_engine("lm")
reg_wf_lr <-
workflows::workflow() %>%
workflows::add_model(lin_reg_spec) %>%
workflows::add_recipe(tree_frogs_reg_rec)
set.seed(1)
reg_res_lr <-
tune::fit_resamples(
object = reg_wf_lr,
resamples = reg_folds,
metrics = metric,
control = ctrl_res
)
# SVM regression ----------------------------------
svm_spec <-
parsnip::svm_rbf(
cost = tune::tune(),
rbf_sigma = tune::tune()
) %>%
parsnip::set_engine("kernlab") %>%
parsnip::set_mode("regression")
reg_wf_svm <-
workflows::workflow() %>%
workflows::add_model(svm_spec) %>%
workflows::add_recipe(tree_frogs_reg_rec)
set.seed(1)
reg_res_svm <-
tune::tune_grid(
object = reg_wf_svm,
resamples = reg_folds,
grid = 5,
control = ctrl_grid
)
# spline regression ---------------------------------------
spline_rec <-
tree_frogs_reg_rec %>%
recipes::step_ns(age, deg_free = tune::tune("age"))
reg_wf_sp <-
workflows::workflow() %>%
workflows::add_model(lin_reg_spec) %>%
workflows::add_recipe(spline_rec)
set.seed(1)
reg_res_sp <-
tune::tune_grid(
object = reg_wf_sp,
resamples = reg_folds,
metrics = metric,
control = ctrl_grid
)
# classification - preliminaries -----------------------------------
tree_frogs_class <-
tree_frogs %>%
dplyr::select(-c(clutch, latency))
set.seed(1)
tree_frogs_class_split <- rsample::initial_split(tree_frogs_class)
set.seed(1)
tree_frogs_class_train <- rsample::training(tree_frogs_class_split)
set.seed(1)
tree_frogs_class_test <- rsample::testing(tree_frogs_class_split)
set.seed(1)
class_folds <- rsample::vfold_cv(tree_frogs_class_train, v = 5)
tree_frogs_class_rec <-
recipes::recipe(reflex ~ ., data = tree_frogs_class_train) %>%
recipes::step_dummy(recipes::all_nominal(), -reflex) %>%
recipes::step_zv(recipes::all_predictors()) %>%
recipes::step_normalize(recipes::all_numeric())
# random forest classification --------------------------------------
rand_forest_spec <-
parsnip::rand_forest(
mtry = tune::tune(),
trees = 500,
min_n = tune::tune()
) %>%
parsnip::set_mode("classification") %>%
parsnip::set_engine("ranger")
class_wf_rf <-
workflows::workflow() %>%
workflows::add_recipe(tree_frogs_class_rec) %>%
workflows::add_model(rand_forest_spec)
set.seed(1)
class_res_rf <-
tune::tune_grid(
object = class_wf_rf,
resamples = class_folds,
grid = 10,
control = ctrl_grid
)
# neural network classification -------------------------------------
nnet_spec <-
mlp(hidden_units = 5, penalty = 0.01, epochs = 100) %>%
set_mode("classification") %>%
set_engine("nnet")
class_wf_nn <-
workflows::workflow() %>%
workflows::add_recipe(tree_frogs_class_rec) %>%
workflows::add_model(nnet_spec)
set.seed(1)
class_res_nn <-
tune::fit_resamples(
object = class_wf_nn,
resamples = class_folds,
control = ctrl_res
)
# binary classification --------------------------------
tree_frogs_2_class_rec <-
recipes::recipe(hatched ~ ., data = tree_frogs_class_train) %>%
recipes::step_dummy(recipes::all_nominal(), -hatched) %>%
recipes::step_zv(recipes::all_predictors()) %>%
recipes::step_normalize(recipes::all_numeric())
set.seed(1)
rand_forest_spec_2 <-
parsnip::rand_forest(
mtry = tune(),
trees = 500,
min_n = tune()
) %>%
parsnip::set_mode("classification") %>%
parsnip::set_engine("ranger")
log_wf_rf <-
workflows::workflow() %>%
workflows::add_recipe(tree_frogs_2_class_rec) %>%
workflows::add_model(rand_forest_spec_2)
set.seed(1)
log_res_rf <-
tune::tune_grid(
object = log_wf_rf,
resamples = class_folds,
grid = 10,
control = ctrl_grid
)
nnet_spec_2 <-
parsnip::mlp(epochs = 100, hidden_units = 5, penalty = 0.1) %>%
parsnip::set_mode("classification") %>%
parsnip::set_engine("nnet", verbose = 0)
log_wf_nn <-
workflows::workflow() %>%
workflows::add_recipe(tree_frogs_2_class_rec) %>%
workflows::add_model(nnet_spec_2)
set.seed(1)
log_res_nn <-
tune::fit_resamples(
object = log_wf_nn,
resamples = class_folds,
control = ctrl_res
)