docs & cleanup

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rtemis
 Version: 0.98.0
 Title: Machine Learning and Visualization
-Date: 2024-09-30
+Date: 2024-10-08
 Authors@R: person(given = "E.D.", family = "Gennatas", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0001-9280-3609"))
 Description: Advanced Machine Learning and Visualization. Unsupervised Learning (Clustering, Decomposition), Supervised Learning (Classification, Regression), Cross-Decomposition, Bagging, Boosting, Meta-models. Static and interactive graphics.
 License: GPL (>= 3)

NAMESPACE

@@ -77,7 +77,6 @@ export(as.data.tree.rpart)
 export(auc)
 export(auc_pairs)
 export(bacc)
-export(bag)
 export(betas.lihad)
 export(bias_variance)
 export(binmat2vec)
@@ -306,6 +305,7 @@ export(prune.addtree)
 export(psd)
 export(qstat)
 export(read)
+export(read_config)
 export(recycle)
 export(relu)
 export(resample)

R/msg.R

@@ -248,7 +248,7 @@ msg2 <- function(...,
   }
   cat(paste(txt, collapse = sep))
   if (!is.null(caller) && !is.na(caller)) {
-    cat(gray(" [", caller, "]\n", sep = ""), sep = "")
+    cat(gray(" :", caller, "\n", sep = ""), sep = "")
   } else if (newline) {
     cat("\n")
   }
@@ -287,14 +287,12 @@ msg20 <- function(...,
   }
 
   txt <- Filter(Negate(is.null), list(...))
-  # .dt <- if (date) paste0(as.character(Sys.time())) else NULL
   .dt <- format(Sys.time(), "%m-%d-%y %H:%M:%S")
   if (newline.pre) cat("\n")
   cat(gray(paste0(.dt, gray(" "))))
   cat(paste(txt, collapse = sep))
-  # cat(gray(" [", caller, "]\n", sep = ""), sep = "")
   if (!is.null(caller) && !is.na(caller)) {
-    cat(gray(" [", caller, "]\n", sep = ""), sep = "")
+    cat(gray(" :", caller, "\n", sep = ""), sep = "")
   } else if (newline) {
     cat("\n")
   }

R/resample.R

@@ -52,7 +52,7 @@
 #' res <- resample(y, 25, "strat.sub")
 #' # 100 stratified bootstraps
 #' res <- resample(y, 100, "strat.boot")
-#'
+
 resample <- function(y,
                      n.resamples = 10,
                      resampler = c("strat.sub", "strat.boot", "kfold", 

R/s_LightGBM.R

@@ -443,7 +443,7 @@ s_LightGBM <- function(x, y = NULL,
   rt
 } # rtemis::s_LightGBM
 
-#' Random Forest with LightGBM
+#' Random Forest using LightGBM
 #'
 #' @inheritParams s_LightGBM
 #' @param nrounds Integer: Number of trees to grow

R/setup.R

@@ -14,12 +14,11 @@ NULL
 
 #' Set [resample] settings
 #'
-#'
 #' @inheritParams resample
 #' @export
 
 setup.resample <- function(
-    resampler = "strat.sub",
+    resampler = c("strat.sub", "strat.boot", "kfold", "bootstrap", "loocv"),
     n.resamples = 10,
     stratify.var = NULL,
     train.p = .8,
@@ -28,7 +27,7 @@ setup.resample <- function(
     id.strat = NULL,
     seed = NULL) {
   list(
-    resampler = resampler,
+    resampler = match.arg(resampler),
     n.resamples = n.resamples,
     stratify.var = stratify.var,
     train.p = train.p,

R/type_check.R

@@ -89,11 +89,11 @@ inherits_check <- function(x, cl) {
 
 
 #' Function that returns object if it is of a certain class
-#' 
+#'
 #' @param object Object to check and return
 #' @param class Character vector: class(es) to check against
 #' @param allow_null Logical: if TRUE, allows NULL objects
-#' 
+#'
 #' @return Object
 #' @author EDG
 #' @keywords internal
@@ -102,6 +102,7 @@ inherits_check <- function(x, cl) {
 #' strict("papaya", "character") # "papaya"
 #' strict(c(1, 2.5, 3.2), "integer") # Error
 #' strict(iris, "list") # Error
+#' }
 strict <- function(object, class, allow_null = TRUE) {
   if (allow_null && is.null(object)) {
     return(NULL)