docs

Author: bbuchsbaum

NAMESPACE

@@ -1,5 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(balance_partitions,blocked_cross_validation)
+S3method(balance_partitions,bootstrap_blocked_cross_validation)
+S3method(balance_partitions,custom_cross_validation)
+S3method(balance_partitions,default)
+S3method(balance_partitions,kfold_cross_validation)
+S3method(balance_partitions,sequential_blocked_cross_validation)
+S3method(balance_partitions,twofold_blocked_cross_validation)
 S3method(crossval_samples,blocked_cross_validation)
 S3method(crossval_samples,bootstrap_blocked_cross_validation)
 S3method(crossval_samples,custom_cross_validation)
@@ -54,6 +61,7 @@ S3method(print,mvpa_dataset)
 S3method(print,mvpa_design)
 S3method(print,mvpa_model)
 S3method(print,mvpa_surface_dataset)
+S3method(print,mvpa_sysinfo)
 S3method(print,regression_result)
 S3method(print,rsa_design)
 S3method(print,rsa_model)
@@ -64,6 +72,7 @@ S3method(print,vector_rsa_design)
 S3method(print,vector_rsa_model)
 S3method(prob_observed,binary_classification_result)
 S3method(prob_observed,multiway_classification_result)
+S3method(process_roi,custom_internal_model_spec)
 S3method(run_regional,default)
 S3method(run_regional,feature_rsa_model)
 S3method(run_regional,mvpa_model)
@@ -89,6 +98,7 @@ S3method(y_train,feature_rsa_model)
 S3method(y_train,mvpa_design)
 S3method(y_train,mvpa_model)
 export(MVPAModels)
+export(balance_partitions)
 export(binary_classification_result)
 export(blocked_cross_validation)
 export(bootstrap_blocked_cross_validation)
@@ -130,6 +140,7 @@ export(mvpa_design)
 export(mvpa_iterate)
 export(mvpa_model)
 export(mvpa_surface_dataset)
+export(mvpa_sysinfo)
 export(nobs)
 export(nresponses)
 export(pcadist)
@@ -142,6 +153,8 @@ export(regional_mvpa_result)
 export(robustmahadist)
 export(rsa_design)
 export(rsa_model)
+export(run_custom_regional)
+export(run_custom_searchlight)
 export(run_regional)
 export(run_regional_base)
 export(run_searchlight)
@@ -160,19 +173,37 @@ export(y_train)
 import(dplyr)
 import(stringr)
 importFrom(MASS,huber)
+importFrom(Matrix,sparseMatrix)
 importFrom(Rfit,rfit)
 importFrom(assertthat,assert_that)
 importFrom(corpcor,invcov.shrink)
+importFrom(dplyr,all_of)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,filter)
+importFrom(dplyr,mutate)
+importFrom(dplyr,pull)
+importFrom(dplyr,rename)
+importFrom(dplyr,select)
 importFrom(ffmanova,ffmanova)
 importFrom(furrr,future_map)
 importFrom(furrr,future_pmap)
+importFrom(futile.logger,flog.debug)
 importFrom(futile.logger,flog.error)
 importFrom(futile.logger,flog.info)
+importFrom(futile.logger,flog.warn)
+importFrom(future,"%<-%")
+importFrom(future,"%globals%")
+importFrom(future,multisession)
+importFrom(future,plan)
+importFrom(future,sequential)
+importFrom(future.apply,future_lapply)
+importFrom(future.apply,future_mapply)
+importFrom(glmnet,cv.glmnet)
+importFrom(glmnet,glmnet)
 importFrom(io,qread)
 importFrom(memoise,memoise)
 importFrom(methods,as)
+importFrom(methods,is)
 importFrom(modelr,resample)
 importFrom(neuroim2,NeuroVol)
 importFrom(neuroim2,ROIVec)
@@ -194,19 +225,28 @@ importFrom(neurosurf,ROISurfaceVector)
 importFrom(neurosurf,geometry)
 importFrom(neurosurf,nodes)
 importFrom(purrr,is_formula)
+importFrom(purrr,list_assign)
 importFrom(purrr,map)
 importFrom(purrr,map_dbl)
 importFrom(purrr,map_df)
+importFrom(purrr,map_int)
+importFrom(purrr,map_lgl)
 importFrom(sda,sda.ranking)
 importFrom(stats,as.formula)
 importFrom(stats,coef)
 importFrom(stats,cor)
 importFrom(stats,dist)
+importFrom(stats,dnorm)
 importFrom(stats,lm)
 importFrom(stats,mahalanobis)
 importFrom(stats,median)
 importFrom(stats,pf)
 importFrom(stats,prcomp)
 importFrom(stats,rnorm)
 importFrom(stats,sd)
+importFrom(stats,setNames)
 importFrom(stats,terms)
+importFrom(stats,var)
+importFrom(tibble,is_tibble)
+importFrom(tibble,tibble)
+importFrom(tidyr,unnest_wider)

R/custom.R

@@ -417,8 +417,7 @@ process_roi.custom_internal_model_spec <- function(mod_spec, roi, rnum, ...) {
 #' @importFrom dplyr bind_rows select filter pull mutate
 #' @importFrom tidyr unnest_wider
 #' @importFrom tibble tibble is_tibble
-#' @importFrom neuroim2 values indices space mask NeuroVol NeuroSurface SparseNeuroVec geometry NeuroSurfaceVector get_searchlight NeuroSpace
-#' @importFrom Matrix sparseMatrix sweep
+#' @importFrom Matrix sparseMatrix 
 #' @importFrom purrr map map_int map_dbl map_lgl list_assign
 #' @importFrom stats setNames sd
 #' @importFrom futile.logger flog.info flog.warn flog.error flog.debug

R/feature_rsa_model.R

@@ -362,7 +362,7 @@ feature_rsa_model <- function(dataset,
 }
 
 
-#' @importFrom glmnet cv.glmnet glmnet coef.glmnet predict
+#' @importFrom glmnet cv.glmnet glmnet 
 #' @noRd
 .predict_glmnet <- function(model, F_new) {
   # F_new is test features (subset for that fold)