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andrewherrenandrewherren
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Merge pull request #141 from StochasticTree/cran-submission-updates
Attempting to reduce runtime of several code examples
2 parents 7734d4a + 87f2776 commit c030f93

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‎DESCRIPTION

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Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
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Package: stochtree
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Title: Stochastic tree Ensembles (XBART and BART) for Supervised Learning and Causal Inference
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Title: Stochastic Tree Ensembles (XBART and BART) for Supervised Learning and Causal Inference
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Version: 0.1.0
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Authors@R:
55
c(

‎R/bart.R

Lines changed: 21 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -97,7 +97,8 @@
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#' X_train <- X[train_inds,]
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#' y_test <- y[test_inds]
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#' y_train <- y[train_inds]
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#' bart_model <- bart(X_train = X_train, y_train = y_train, X_test = X_test)
100+
#' bart_model <- bart(X_train = X_train, y_train = y_train, X_test = X_test,
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#' num_gfr = 10, num_burnin = 0, num_mcmc = 10)
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#' plot(rowMeans(bart_model$y_hat_test), y_test, xlab = "predicted", ylab = "actual")
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#' abline(0,1,col="red",lty=3,lwd=3)
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bart <- function(X_train, y_train, leaf_basis_train = NULL, rfx_group_ids_train = NULL,
@@ -990,7 +991,8 @@ bart <- function(X_train, y_train, leaf_basis_train = NULL, rfx_group_ids_train
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#' X_train <- X[train_inds,]
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#' y_test <- y[test_inds]
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#' y_train <- y[train_inds]
993-
#' bart_model <- bart(X_train = X_train, y_train = y_train)
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#' bart_model <- bart(X_train = X_train, y_train = y_train,
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#' num_gfr = 10, num_burnin = 0, num_mcmc = 10)
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#' y_hat_test <- predict(bart_model, X_test)$y_hat
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#' plot(rowMeans(y_hat_test), y_test, xlab = "predicted", ylab = "actual")
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#' abline(0,1,col="red",lty=3,lwd=3)
@@ -1150,7 +1152,7 @@ predict.bartmodel <- function(object, X, leaf_basis = NULL, rfx_group_ids = NULL
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#' rfx_group_ids_test = rfx_group_ids_test,
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#' rfx_basis_train = rfx_basis_train,
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#' rfx_basis_test = rfx_basis_test,
1153-
#' num_gfr = 100, num_burnin = 0, num_mcmc = 100)
1155+
#' num_gfr = 10, num_burnin = 0, num_mcmc = 10)
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#' rfx_samples <- getRandomEffectSamples(bart_model)
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getRandomEffectSamples.bartmodel <- function(object, ...){
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result = list()
@@ -1200,7 +1202,8 @@ getRandomEffectSamples.bartmodel <- function(object, ...){
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#' X_train <- X[train_inds,]
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#' y_test <- y[test_inds]
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#' y_train <- y[train_inds]
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#' bart_model <- bart(X_train = X_train, y_train = y_train)
1205+
#' bart_model <- bart(X_train = X_train, y_train = y_train,
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#' num_gfr = 10, num_burnin = 0, num_mcmc = 10)
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#' bart_json <- saveBARTModelToJson(bart_model)
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saveBARTModelToJson <- function(object){
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jsonobj <- createCppJson()
@@ -1309,7 +1312,8 @@ saveBARTModelToJson <- function(object){
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#' X_train <- X[train_inds,]
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#' y_test <- y[test_inds]
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#' y_train <- y[train_inds]
1312-
#' bart_model <- bart(X_train = X_train, y_train = y_train)
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#' bart_model <- bart(X_train = X_train, y_train = y_train,
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#' num_gfr = 10, num_burnin = 0, num_mcmc = 10)
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#' tmpjson <- tempfile(fileext = ".json")
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#' saveBARTModelToJsonFile(bart_model, file.path(tmpjson))
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#' unlink(tmpjson)
@@ -1348,7 +1352,8 @@ saveBARTModelToJsonFile <- function(object, filename){
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#' X_train <- X[train_inds,]
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#' y_test <- y[test_inds]
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#' y_train <- y[train_inds]
1351-
#' bart_model <- bart(X_train = X_train, y_train = y_train)
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#' bart_model <- bart(X_train = X_train, y_train = y_train,
1356+
#' num_gfr = 10, num_burnin = 0, num_mcmc = 10)
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#' bart_json_string <- saveBARTModelToJsonString(bart_model)
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saveBARTModelToJsonString <- function(object){
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# Convert to Json
@@ -1387,7 +1392,8 @@ saveBARTModelToJsonString <- function(object){
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#' X_train <- X[train_inds,]
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#' y_test <- y[test_inds]
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#' y_train <- y[train_inds]
1390-
#' bart_model <- bart(X_train = X_train, y_train = y_train)
1395+
#' bart_model <- bart(X_train = X_train, y_train = y_train,
1396+
#' num_gfr = 10, num_burnin = 0, num_mcmc = 10)
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#' bart_json <- saveBARTModelToJson(bart_model)
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#' bart_model_roundtrip <- createBARTModelFromJson(bart_json)
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createBARTModelFromJson <- function(json_object){
@@ -1501,7 +1507,8 @@ createBARTModelFromJson <- function(json_object){
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#' X_train <- X[train_inds,]
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#' y_test <- y[test_inds]
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#' y_train <- y[train_inds]
1504-
#' bart_model <- bart(X_train = X_train, y_train = y_train)
1510+
#' bart_model <- bart(X_train = X_train, y_train = y_train,
1511+
#' num_gfr = 10, num_burnin = 0, num_mcmc = 10)
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#' tmpjson <- tempfile(fileext = ".json")
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#' saveBARTModelToJsonFile(bart_model, file.path(tmpjson))
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#' bart_model_roundtrip <- createBARTModelFromJsonFile(file.path(tmpjson))
@@ -1545,7 +1552,8 @@ createBARTModelFromJsonFile <- function(json_filename){
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#' X_train <- X[train_inds,]
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#' y_test <- y[test_inds]
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#' y_train <- y[train_inds]
1548-
#' bart_model <- bart(X_train = X_train, y_train = y_train)
1555+
#' bart_model <- bart(X_train = X_train, y_train = y_train,
1556+
#' num_gfr = 10, num_burnin = 0, num_mcmc = 10)
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#' bart_json <- saveBARTModelToJsonString(bart_model)
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#' bart_model_roundtrip <- createBARTModelFromJsonString(bart_json)
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#' y_hat_mean_roundtrip <- rowMeans(predict(bart_model_roundtrip, X_train)$y_hat)
@@ -1590,7 +1598,8 @@ createBARTModelFromJsonString <- function(json_string){
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#' X_train <- X[train_inds,]
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#' y_test <- y[test_inds]
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#' y_train <- y[train_inds]
1593-
#' bart_model <- bart(X_train = X_train, y_train = y_train)
1601+
#' bart_model <- bart(X_train = X_train, y_train = y_train,
1602+
#' num_gfr = 10, num_burnin = 0, num_mcmc = 10)
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#' bart_json <- list(saveBARTModelToJson(bart_model))
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#' bart_model_roundtrip <- createBARTModelFromCombinedJson(bart_json)
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createBARTModelFromCombinedJson <- function(json_object_list){
@@ -1735,7 +1744,8 @@ createBARTModelFromCombinedJson <- function(json_object_list){
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#' X_train <- X[train_inds,]
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#' y_test <- y[test_inds]
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#' y_train <- y[train_inds]
1738-
#' bart_model <- bart(X_train = X_train, y_train = y_train)
1747+
#' bart_model <- bart(X_train = X_train, y_train = y_train,
1748+
#' num_gfr = 10, num_burnin = 0, num_mcmc = 10)
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#' bart_json_string_list <- list(saveBARTModelToJsonString(bart_model))
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#' bart_model_roundtrip <- createBARTModelFromCombinedJsonString(bart_json_string_list)
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createBARTModelFromCombinedJsonString <- function(json_string_list){

‎R/bcf.R

Lines changed: 13 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -137,7 +137,8 @@
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#' tau_train <- tau_x[train_inds]
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#' bcf_model <- bcf(X_train = X_train, Z_train = Z_train, y_train = y_train,
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#' propensity_train = pi_train, X_test = X_test, Z_test = Z_test,
140-
#' propensity_test = pi_test)
140+
#' propensity_test = pi_test, num_gfr = 10,
141+
#' num_burnin = 0, num_mcmc = 10)
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#' plot(rowMeans(bcf_model$mu_hat_test), mu_test, xlab = "predicted",
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#' ylab = "actual", main = "Prognostic function")
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#' abline(0,1,col="red",lty=3,lwd=3)
@@ -1438,7 +1439,8 @@ bcf <- function(X_train, Z_train, y_train, propensity_train = NULL, rfx_group_id
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#' tau_test <- tau_x[test_inds]
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#' tau_train <- tau_x[train_inds]
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#' bcf_model <- bcf(X_train = X_train, Z_train = Z_train, y_train = y_train,
1441-
#' propensity_train = pi_train)
1442+
#' propensity_train = pi_train, num_gfr = 10,
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#' num_burnin = 0, num_mcmc = 10)
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#' preds <- predict(bcf_model, X_test, Z_test, pi_test)
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#' plot(rowMeans(preds$mu_hat), mu_test, xlab = "predicted",
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#' ylab = "actual", main = "Prognostic function")
@@ -1632,7 +1634,7 @@ predict.bcfmodel <- function(object, X, Z, propensity = NULL, rfx_group_ids = NU
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#' Z_test = Z_test, propensity_test = pi_test,
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#' rfx_group_ids_test = rfx_group_ids_test,
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#' rfx_basis_test = rfx_basis_test,
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#' num_gfr = 100, num_burnin = 0, num_mcmc = 100,
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#' num_gfr = 10, num_burnin = 0, num_mcmc = 10,
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#' mu_forest_params = mu_params,
16371639
#' tau_forest_params = tau_params)
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#' rfx_samples <- getRandomEffectSamples(bcf_model)
@@ -1723,7 +1725,7 @@ getRandomEffectSamples.bcfmodel <- function(object, ...){
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#' Z_test = Z_test, propensity_test = pi_test,
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#' rfx_group_ids_test = rfx_group_ids_test,
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#' rfx_basis_test = rfx_basis_test,
1726-
#' num_gfr = 100, num_burnin = 0, num_mcmc = 100,
1728+
#' num_gfr = 10, num_burnin = 0, num_mcmc = 10,
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#' mu_forest_params = mu_params,
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#' tau_forest_params = tau_params)
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#' # bcf_json <- saveBCFModelToJson(bcf_model)
@@ -1888,7 +1890,7 @@ saveBCFModelToJson <- function(object){
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#' Z_test = Z_test, propensity_test = pi_test,
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#' rfx_group_ids_test = rfx_group_ids_test,
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#' rfx_basis_test = rfx_basis_test,
1891-
#' num_gfr = 100, num_burnin = 0, num_mcmc = 100,
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#' num_gfr = 10, num_burnin = 0, num_mcmc = 10,
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#' mu_forest_params = mu_params,
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#' tau_forest_params = tau_params)
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#' # saveBCFModelToJsonFile(bcf_model, "test.json")
@@ -1966,7 +1968,7 @@ saveBCFModelToJsonFile <- function(object, filename){
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#' Z_test = Z_test, propensity_test = pi_test,
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#' rfx_group_ids_test = rfx_group_ids_test,
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#' rfx_basis_test = rfx_basis_test,
1969-
#' num_gfr = 100, num_burnin = 0, num_mcmc = 100,
1971+
#' num_gfr = 10, num_burnin = 0, num_mcmc = 10,
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#' mu_forest_params = mu_params,
19711973
#' tau_forest_params = tau_params)
19721974
#' # saveBCFModelToJsonString(bcf_model)
@@ -2046,7 +2048,7 @@ saveBCFModelToJsonString <- function(object){
20462048
#' Z_test = Z_test, propensity_test = pi_test,
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#' rfx_group_ids_test = rfx_group_ids_test,
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#' rfx_basis_test = rfx_basis_test,
2049-
#' num_gfr = 100, num_burnin = 0, num_mcmc = 100,
2051+
#' num_gfr = 10, num_burnin = 0, num_mcmc = 10,
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#' mu_forest_params = mu_params,
20512053
#' tau_forest_params = tau_params)
20522054
#' bcf_json <- saveBCFModelToJson(bcf_model)
@@ -2211,7 +2213,7 @@ createBCFModelFromJson <- function(json_object){
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#' Z_test = Z_test, propensity_test = pi_test,
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#' rfx_group_ids_test = rfx_group_ids_test,
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#' rfx_basis_test = rfx_basis_test,
2214-
#' num_gfr = 100, num_burnin = 0, num_mcmc = 100,
2216+
#' num_gfr = 10, num_burnin = 0, num_mcmc = 10,
22152217
#' mu_forest_params = mu_params,
22162218
#' tau_forest_params = tau_params)
22172219
#' # saveBCFModelToJsonFile(bcf_model, "test.json")
@@ -2292,7 +2294,7 @@ createBCFModelFromJsonFile <- function(json_filename){
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#' Z_test = Z_test, propensity_test = pi_test,
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#' rfx_group_ids_test = rfx_group_ids_test,
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#' rfx_basis_test = rfx_basis_test,
2295-
#' num_gfr = 100, num_burnin = 0, num_mcmc = 100)
2297+
#' num_gfr = 10, num_burnin = 0, num_mcmc = 10)
22962298
#' # bcf_json <- saveBCFModelToJsonString(bcf_model)
22972299
#' # bcf_model_roundtrip <- createBCFModelFromJsonString(bcf_json)
22982300
createBCFModelFromJsonString <- function(json_string){
@@ -2372,7 +2374,7 @@ createBCFModelFromJsonString <- function(json_string){
23722374
#' Z_test = Z_test, propensity_test = pi_test,
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#' rfx_group_ids_test = rfx_group_ids_test,
23742376
#' rfx_basis_test = rfx_basis_test,
2375-
#' num_gfr = 100, num_burnin = 0, num_mcmc = 100)
2377+
#' num_gfr = 10, num_burnin = 0, num_mcmc = 10)
23762378
#' # bcf_json_list <- list(saveBCFModelToJson(bcf_model))
23772379
#' # bcf_model_roundtrip <- createBCFModelFromCombinedJson(bcf_json_list)
23782380
createBCFModelFromCombinedJson <- function(json_object_list){
@@ -2584,7 +2586,7 @@ createBCFModelFromCombinedJson <- function(json_object_list){
25842586
#' Z_test = Z_test, propensity_test = pi_test,
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#' rfx_group_ids_test = rfx_group_ids_test,
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#' rfx_basis_test = rfx_basis_test,
2587-
#' num_gfr = 100, num_burnin = 0, num_mcmc = 100)
2589+
#' num_gfr = 10, num_burnin = 0, num_mcmc = 10)
25882590
#' # bcf_json_string_list <- list(saveBCFModelToJsonString(bcf_model))
25892591
#' # bcf_model_roundtrip <- createBCFModelFromCombinedJsonString(bcf_json_string_list)
25902592
createBCFModelFromCombinedJsonString <- function(json_string_list){

‎cran-comments.md

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@@ -1,6 +1,7 @@
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## R CMD check results
22

3-
0 errors | 0 warnings | 2 notes
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0 errors | 0 warnings | 3 notes
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* This is a new release.
6-
* checking installed package size ... NOTE installed size is 46.3Mb (linux-only)
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* Checking installed package size ... NOTE installed size is 46.3Mb (linux-only)
7+
* Possibly misspelled words in DESCRIPTION: All of the words are proper nouns or technical terms (BCF, Carvalho, Chipman, McCulloch, XBART)

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