[docs] R docs cleanup (#2375)

* R docs cleanup

* regenerated R documentation files

R-package/man/lgb.plot.interpretation.Rd

@@ -42,8 +42,7 @@ test <- agaricus.test
 params <- list(objective = "binary",
                learning_rate = 0.01, num_leaves = 63, max_depth = -1,
                min_data_in_leaf = 1, min_sum_hessian_in_leaf = 1)
-              model <- lgb.train(params, dtrain, 20)
-model <- lgb.train(params, dtrain, 20)
+model <- lgb.train(params, dtrain, 10)
 
 tree_interpretation <- lgb.interprete(model, test$data, 1:5)
 lgb.plot.interpretation(tree_interpretation[[1]], top_n = 10)

R-package/man/lgb.prepare.Rd

@@ -10,31 +10,20 @@ lgb.prepare(data)
 \item{data}{A data.frame or data.table to prepare.}
 }
 \value{
-The cleaned dataset. It must be converted to a matrix format (\code{as.matrix}) for input in lgb.Dataset.
+The cleaned dataset. It must be converted to a matrix format (\code{as.matrix}) for input in \code{lgb.Dataset}.
 }
 \description{
-Attempts to prepare a clean dataset to prepare to put in a lgb.Dataset. Factors and characters are converted to numeric without integers. Please use \code{lgb.prepare_rules} if you want to apply this transformation to other datasets.
+Attempts to prepare a clean dataset to prepare to put in a \code{lgb.Dataset}. Factors and characters are converted to numeric without integers. Please use \code{lgb.prepare_rules} if you want to apply this transformation to other datasets.
 }
 \examples{
 library(lightgbm)
 data(iris)
 
 str(iris)
-# 'data.frame':	150 obs. of  5 variables:
-# $ Sepal.Length: num  5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
-# $ Sepal.Width : num  3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
-# $ Petal.Length: num  1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
-# $ Petal.Width : num  0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
-# $ Species     : Factor w/ 3 levels "setosa","versicolor",..: 1 1 1 1 ...
 
 str(lgb.prepare(data = iris)) # Convert all factors/chars to numeric
-# 'data.frame':	150 obs. of  5 variables:
-# $ Sepal.Length: num  5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
-# $ Sepal.Width : num  3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
-# $ Petal.Length: num  1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
-# $ Petal.Width : num  0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
-# $ Species     : num  1 1 1 1 1 1 1 1 1 1 ...
 
+\dontrun{
 # When lightgbm package is installed, and you do not want to load it
 # You can still use the function!
 lgb.unloader()
@@ -45,5 +34,6 @@ str(lightgbm::lgb.prepare(data = iris))
 # $ Petal.Length: num  1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
 # $ Petal.Width : num  0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
 # $ Species     : num  1 1 1 1 1 1 1 1 1 1 ...
+}
 
 }

R-package/man/lgb.prepare2.Rd

@@ -10,32 +10,21 @@ lgb.prepare2(data)
 \item{data}{A data.frame or data.table to prepare.}
 }
 \value{
-The cleaned dataset. It must be converted to a matrix format (\code{as.matrix}) for input in lgb.Dataset.
+The cleaned dataset. It must be converted to a matrix format (\code{as.matrix}) for input in \code{lgb.Dataset}.
 }
 \description{
-Attempts to prepare a clean dataset to prepare to put in a lgb.Dataset. Factors and characters are converted to numeric (specifically: integer). Please use \code{lgb.prepare_rules2} if you want to apply this transformation to other datasets. This is useful if you have a specific need for integer dataset instead of numeric dataset. Note that there are programs which do not support integer-only input. Consider this as a half memory technique which is dangerous, especially for LightGBM.
+Attempts to prepare a clean dataset to prepare to put in a \code{lgb.Dataset}. Factors and characters are converted to numeric (specifically: integer). Please use \code{lgb.prepare_rules2} if you want to apply this transformation to other datasets. This is useful if you have a specific need for integer dataset instead of numeric dataset. Note that there are programs which do not support integer-only input. Consider this as a half memory technique which is dangerous, especially for LightGBM.
 }
 \examples{
 library(lightgbm)
 data(iris)
 
 str(iris)
-# 'data.frame':	150 obs. of  5 variables:
-# $ Sepal.Length: num  5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
-# $ Sepal.Width : num  3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
-# $ Petal.Length: num  1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
-# $ Petal.Width : num  0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
-# $ Species     : Factor w/ 3 levels "setosa","versicolor",..: 1 1 1 1 ...
 
 # Convert all factors/chars to integer
 str(lgb.prepare2(data = iris))
-# 'data.frame':	150 obs. of  5 variables:
-# $ Sepal.Length: num  5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
-# $ Sepal.Width : num  3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
-# $ Petal.Length: num  1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
-# $ Petal.Width : num  0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
-# $ Species     : int  1 1 1 1 1 1 1 1 1 1 ...
 
+\dontrun{
 # When lightgbm package is installed, and you do not want to load it
 # You can still use the function!
 lgb.unloader()
@@ -46,5 +35,6 @@ str(lightgbm::lgb.prepare2(data = iris))
 # $ Petal.Length: num  1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
 # $ Petal.Width : num  0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
 # $ Species     : int  1 1 1 1 1 1 1 1 1 1 ...
+}
 
 }

R-package/man/lgb.prepare_rules.Rd

@@ -12,37 +12,22 @@ lgb.prepare_rules(data, rules = NULL)
 \item{rules}{A set of rules from the data preparator, if already used.}
 }
 \value{
-A list with the cleaned dataset (\code{data}) and the rules (\code{rules}). The data must be converted to a matrix format (\code{as.matrix}) for input in lgb.Dataset.
+A list with the cleaned dataset (\code{data}) and the rules (\code{rules}). The data must be converted to a matrix format (\code{as.matrix}) for input in \code{lgb.Dataset}.
 }
 \description{
-Attempts to prepare a clean dataset to prepare to put in a lgb.Dataset. Factors and characters are converted to numeric. In addition, keeps rules created so you can convert other datasets using this converter.
+Attempts to prepare a clean dataset to prepare to put in a \code{lgb.Dataset}. Factors and characters are converted to numeric. In addition, keeps rules created so you can convert other datasets using this converter.
 }
 \examples{
 library(lightgbm)
 data(iris)
 
 str(iris)
-# 'data.frame':	150 obs. of  5 variables:
-# $ Sepal.Length: num  5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
-# $ Sepal.Width : num  3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
-# $ Petal.Length: num  1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
-# $ Petal.Width : num  0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
-# $ Species     : Factor w/ 3 levels "setosa","versicolor",..: 1 1 1 1 ...
 
 new_iris <- lgb.prepare_rules(data = iris) # Autoconverter
 str(new_iris$data)
-# 'data.frame':	150 obs. of  5 variables:
-# $ Sepal.Length: num  5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
-# $ Sepal.Width : num  3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
-# $ Petal.Length: num  1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
-# $ Petal.Width : num  0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
-# $ Species     : num  1 1 1 1 1 1 1 1 1 1 ...
 
 data(iris) # Erase iris dataset
 iris$Species[1] <- "NEW FACTOR" # Introduce junk factor (NA)
-# Warning message:
-# In `[<-.factor`(`*tmp*`, 1, value = c(NA, 1L, 1L, 1L, 1L, 1L, 1L,  :
-#  invalid factor level, NA generated
 
 # Use conversion using known rules
 # Unknown factors become 0, excellent for sparse datasets
@@ -50,14 +35,11 @@ newer_iris <- lgb.prepare_rules(data = iris, rules = new_iris$rules)
 
 # Unknown factor is now zero, perfect for sparse datasets
 newer_iris$data[1, ] # Species became 0 as it is an unknown factor
-#   Sepal.Length Sepal.Width Petal.Length Petal.Width Species
-# 1          5.1         3.5          1.4         0.2       0
 
 newer_iris$data[1, 5] <- 1 # Put back real initial value
 
 # Is the newly created dataset equal? YES!
 all.equal(new_iris$data, newer_iris$data)
-# [1] TRUE
 
 # Can we test our own rules?
 data(iris) # Erase iris dataset
@@ -68,11 +50,5 @@ personal_rules <- list(Species = c("setosa" = 3,
                                    "virginica" = 1))
 newest_iris <- lgb.prepare_rules(data = iris, rules = personal_rules)
 str(newest_iris$data) # SUCCESS!
-# 'data.frame':	150 obs. of  5 variables:
-# $ Sepal.Length: num  5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
-# $ Sepal.Width : num  3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
-# $ Petal.Length: num  1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
-# $ Petal.Width : num  0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
-# $ Species     : num  3 3 3 3 3 3 3 3 3 3 ...
 
 }

R-package/man/lgb.prepare_rules2.Rd

@@ -12,37 +12,22 @@ lgb.prepare_rules2(data, rules = NULL)
 \item{rules}{A set of rules from the data preparator, if already used.}
 }
 \value{
-A list with the cleaned dataset (\code{data}) and the rules (\code{rules}). The data must be converted to a matrix format (\code{as.matrix}) for input in lgb.Dataset.
+A list with the cleaned dataset (\code{data}) and the rules (\code{rules}). The data must be converted to a matrix format (\code{as.matrix}) for input in \code{lgb.Dataset}.
 }
 \description{
-Attempts to prepare a clean dataset to prepare to put in a lgb.Dataset. Factors and characters are converted to numeric (specifically: integer). In addition, keeps rules created so you can convert other datasets using this converter. This is useful if you have a specific need for integer dataset instead of numeric dataset. Note that there are programs which do not support integer-only input. Consider this as a half memory technique which is dangerous, especially for LightGBM.
+Attempts to prepare a clean dataset to prepare to put in a \code{lgb.Dataset}. Factors and characters are converted to numeric (specifically: integer). In addition, keeps rules created so you can convert other datasets using this converter. This is useful if you have a specific need for integer dataset instead of numeric dataset. Note that there are programs which do not support integer-only input. Consider this as a half memory technique which is dangerous, especially for LightGBM.
 }
 \examples{
 library(lightgbm)
 data(iris)
 
 str(iris)
-# 'data.frame':	150 obs. of  5 variables:
-# $ Sepal.Length: num  5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
-# $ Sepal.Width : num  3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
-# $ Petal.Length: num  1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
-# $ Petal.Width : num  0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
-# $ Species     : Factor w/ 3 levels "setosa","versicolor",..: 1 1 1 1 ...
 
 new_iris <- lgb.prepare_rules2(data = iris) # Autoconverter
 str(new_iris$data)
-# 'data.frame':	150 obs. of  5 variables:
-# $ Sepal.Length: num  5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
-# $ Sepal.Width : num  3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
-# $ Petal.Length: num  1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
-# $ Petal.Width : num  0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
-# $ Species     : int  1 1 1 1 1 1 1 1 1 1 ...
 
 data(iris) # Erase iris dataset
 iris$Species[1] <- "NEW FACTOR" # Introduce junk factor (NA)
-# Warning message:
-# In `[<-.factor`(`*tmp*`, 1, value = c(NA, 1L, 1L, 1L, 1L, 1L, 1L,  :
-#  invalid factor level, NA generated
 
 # Use conversion using known rules
 # Unknown factors become 0, excellent for sparse datasets
@@ -50,14 +35,11 @@ newer_iris <- lgb.prepare_rules2(data = iris, rules = new_iris$rules)
 
 # Unknown factor is now zero, perfect for sparse datasets
 newer_iris$data[1, ] # Species became 0 as it is an unknown factor
-#   Sepal.Length Sepal.Width Petal.Length Petal.Width Species
-# 1          5.1         3.5          1.4         0.2       0
 
 newer_iris$data[1, 5] <- 1 # Put back real initial value
 
 # Is the newly created dataset equal? YES!
 all.equal(new_iris$data, newer_iris$data)
-# [1] TRUE
 
 # Can we test our own rules?
 data(iris) # Erase iris dataset
@@ -68,11 +50,5 @@ personal_rules <- list(Species = c("setosa" = 3L,
                                    "virginica" = 1L))
 newest_iris <- lgb.prepare_rules2(data = iris, rules = personal_rules)
 str(newest_iris$data) # SUCCESS!
-# 'data.frame':	150 obs. of  5 variables:
-# $ Sepal.Length: num  5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
-# $ Sepal.Width : num  3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
-# $ Petal.Length: num  1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
-# $ Petal.Width : num  0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
-# $ Species     : int  3 3 3 3 3 3 3 3 3 3 ...
 
 }

R-package/man/lgb.save.Rd

@@ -31,11 +31,11 @@ params <- list(objective = "regression", metric = "l2")
 valids <- list(test = dtest)
 model <- lgb.train(params,
                    dtrain,
-                   100,
+                   10,
                    valids,
                    min_data = 1,
                    learning_rate = 1,
-                   early_stopping_rounds = 10)
+                   early_stopping_rounds = 5)
 lgb.save(model, "model.txt")
 
 }

R-package/man/lgb.train.Rd

@@ -80,10 +80,9 @@ params <- list(objective = "regression", metric = "l2")
 valids <- list(test = dtest)
 model <- lgb.train(params,
                    dtrain,
-                   100,
+                   10,
                    valids,
                    min_data = 1,
                    learning_rate = 1,
-                   early_stopping_rounds = 10)
-
+                   early_stopping_rounds = 5)
 }

R-package/man/lgb.unloader.Rd

@@ -31,16 +31,19 @@ params <- list(objective = "regression", metric = "l2")
 valids <- list(test = dtest)
 model <- lgb.train(params,
                    dtrain,
-                   100,
+                   10,
                    valids,
                    min_data = 1,
                    learning_rate = 1,
-                   early_stopping_rounds = 10)
+                   early_stopping_rounds = 5)
+
+\dontrun{
 lgb.unloader(restore = FALSE, wipe = FALSE, envir = .GlobalEnv)
 rm(model, dtrain, dtest) # Not needed if wipe = TRUE
 gc() # Not needed if wipe = TRUE
 
 library(lightgbm)
 # Do whatever you want again with LightGBM without object clashing
+}
 
 }

R-package/man/predict.lgb.Booster.Rd

@@ -55,11 +55,11 @@ params <- list(objective = "regression", metric = "l2")
 valids <- list(test = dtest)
 model <- lgb.train(params,
                    dtrain,
-                   100,
+                   10,
                    valids,
                    min_data = 1,
                    learning_rate = 1,
-                   early_stopping_rounds = 10)
+                   early_stopping_rounds = 5)
 preds <- predict(model, test$data)
 
 }

R-package/man/readRDS.lgb.Booster.Rd

@@ -2,7 +2,7 @@
 % Please edit documentation in R/readRDS.lgb.Booster.R
 \name{readRDS.lgb.Booster}
 \alias{readRDS.lgb.Booster}
-\title{readRDS for lgb.Booster models}
+\title{readRDS for \code{lgb.Booster} models}
 \usage{
 readRDS.lgb.Booster(file = "", refhook = NULL)
 }
@@ -12,7 +12,7 @@ readRDS.lgb.Booster(file = "", refhook = NULL)
 \item{refhook}{a hook function for handling reference objects.}
 }
 \value{
-lgb.Booster.
+\code{lgb.Booster}.
 }
 \description{
 Attempts to load a model using RDS.
@@ -29,11 +29,11 @@ params <- list(objective = "regression", metric = "l2")
 valids <- list(test = dtest)
 model <- lgb.train(params,
                    dtrain,
-                   100,
+                   10,
                    valids,
                    min_data = 1,
                    learning_rate = 1,
-                   early_stopping_rounds = 10)
+                   early_stopping_rounds = 5)
 saveRDS.lgb.Booster(model, "model.rds")
 new_model <- readRDS.lgb.Booster("model.rds")
 

R-package/man/saveRDS.lgb.Booster.Rd

@@ -2,7 +2,7 @@
 % Please edit documentation in R/saveRDS.lgb.Booster.R
 \name{saveRDS.lgb.Booster}
 \alias{saveRDS.lgb.Booster}
-\title{saveRDS for lgb.Booster models}
+\title{saveRDS for \code{lgb.Booster} models}
 \usage{
 saveRDS.lgb.Booster(object, file = "", ascii = FALSE, version = NULL,
   compress = TRUE, refhook = NULL, raw = TRUE)
@@ -41,11 +41,11 @@ valids <- list(test = dtest)
 model <- lgb.train(
     params
     , dtrain
-    , 100
+    , 10
     , valids
     , min_data = 1
     , learning_rate = 1
-    , early_stopping_rounds = 10
+    , early_stopping_rounds = 5
 )
 saveRDS.lgb.Booster(model, "model.rds")
 }

R-package/man/setinfo.Rd

@@ -3,14 +3,14 @@
 \name{setinfo}
 \alias{setinfo}
 \alias{setinfo.lgb.Dataset}
-\title{Set information of an lgb.Dataset object}
+\title{Set information of an \code{lgb.Dataset} object}
 \usage{
 setinfo(dataset, ...)
 
 \method{setinfo}{lgb.Dataset}(dataset, name, info, ...)
 }
 \arguments{
-\item{dataset}{Object of class "lgb.Dataset"}
+\item{dataset}{Object of class \code{lgb.Dataset}}
 
 \item{...}{other parameters}
 
@@ -22,7 +22,7 @@ setinfo(dataset, ...)
 passed object
 }
 \description{
-Set information of an lgb.Dataset object
+Set information of an \code{lgb.Dataset} object
 }
 \details{
 The \code{name} field can be one of the following:

R-package/man/slice.Rd

@@ -10,7 +10,7 @@ slice(dataset, ...)
 \method{slice}{lgb.Dataset}(dataset, idxset, ...)
 }
 \arguments{
-\item{dataset}{Object of class "lgb.Dataset"}
+\item{dataset}{Object of class \code{lgb.Dataset}}
 
 \item{...}{other parameters (currently not used)}
 
@@ -21,7 +21,7 @@ constructed sub dataset
 }
 \description{
 Get a new \code{lgb.Dataset} containing the specified rows of
-original lgb.Dataset object
+original \code{lgb.Dataset} object
 }
 \examples{
 library(lightgbm)