further Rd cleaning

R/add_forests.R

@@ -1,9 +1,9 @@
 
 #' Add forests
 #'
-#' Creates and adds forest data to an \code{\link{sf}} object by reading from tree and shrub data tables
+#' Creates and adds forest data to an \code{\link[sf]{sf}} object by reading from tree and shrub data tables
 #' 
-#' @param x An object of class \code{\link{sf}} with a valid CRS definition, and a column called 'id'. 
+#' @param x An object of class \code{\link[sf]{sf}} with a valid CRS definition, and a column called 'id'. 
 #' @param tree_table A data frame with tree records in rows and attributes in columns. Tree records can correspond to individual trees or groups of trees with an associated density.
 #' @param tree_mapping  A named character vector to specify mappings of columns in \code{tree_table} into attributes of \code{treeData}. Accepted names (and the corresponding specifications for the columns in \code{tree_table}) are:
 #' \itemize{

R/dataset_documentation.R

@@ -2,7 +2,7 @@
 #'
 #' Default management prescriptions by species, defined according current practices in Catalonia (NE Spain)
 #'
-#' A data frame with 27 species (or species groups) in rows and management parameters in columns (defined in \code{\link{defaultManagementArguments}})
+#' A data frame with 27 species (or species groups) in rows and management parameters in columns (defined in \code{\link[medfate]{defaultManagementArguments}})
 #' 
 #' @name defaultPrescriptionsBySpecies
 #' @aliases defaultPrescriptionsBySpecies

R/impute_forests.R

@@ -47,10 +47,10 @@
 #' for correction of basal area. In that case, if there are no trees larger than \code{minDBH} but structural map indicates positive values of basal area, 
 #' DBH values will be set to minDBH, and correction of basal area will be performed.
 #' 
-#' Function \code{check_forest()} checks first that \code{\link{forest}} objects are defined in "wildland" locations. Then, it looks for missing
+#' Function \code{check_forest()} checks first that \code{\link[medfate]{forest}} objects are defined in "wildland" locations. Then, it looks for missing
 #' data in tree or shrub attributes required for simulations. The function does not modify the data.
 #' 
-#' @return Functions \code{impute_forests()} and \code{modify_forest_structure()} return a modified object of class \code{\link{sf}}.
+#' @return Functions \code{impute_forests()} and \code{modify_forest_structure()} return a modified object of class \code{\link[sf]{sf}}.
 #'  Function \code{check_forests()} returns an invisible data frame with columns indicating missing forest data and missing values in tree or shrub parameters.
 #' 
 #' @author Miquel De \enc{Cáceres}{Caceres} Ainsa, CREAF
@@ -222,7 +222,7 @@ impute_forests <-function(x, sf_fi, dem,
 
 
 #' @rdname forest_parametrization
-#' @param structure_map An object of class \code{\link{rast}} or \code{\link{vect}} with a forest structural variable map
+#' @param structure_map An object of class \code{\link[terra]{SpatRaster}} or \code{\link[terra]{SpatVector}} with a forest structural variable map
 #' @param variable Structural variable to correct. See options in details.
 #' @param map_var Variable name or index containing structural variable in 'structure_map'. If missing the first column is taken.
 #' @param minDBH Minimum diameter for stand metric calculation. If \code{minDBH > 0} then those stands with smaller trees will not be corrected

R/update_landscape.R

@@ -6,7 +6,7 @@
 #' @param y The object resulting of a simulation previously carried on \code{x} 
 #'    using \code{\link{spwb_spatial}}, \code{\link{growth_spatial}}, \code{\link{spwb_land}}, etc.
 #' 
-#' @return An object of class \code{\link{sf}} with modified state variables.
+#' @return An object of class \code{\link[sf]{sf}} with modified state variables.
 #' 
 #' @author Miquel De \enc{Cáceres}{Caceres} Ainsa, CREAF.
 #'