Rd check links

R/add_forests.R

@@ -31,14 +31,14 @@
 #' \item{"Z50": Depth (in mm) corresponding to 50 percent of fine roots.}
 #' \item{"Z95": Depth (in mm) corresponding to 95 percent of fine roots.}
 #' }
-#' @param SpParams A data frame with species parameters (see \code{\link{SpParamsMED}}) from which valid species names are drawn.
-#' @param merge_trees A logical flag to simplify tree cohorts by merging tree records in DBH classes (see \code{\link{forest_mergeTrees}}).
-#' @param merge_shrubs A logical flag to simplify shrub cohorts by merging shrub records in height classes (see \code{\link{forest_mergeShrubs}}).
+#' @param SpParams A data frame with species parameters (see \code{\link[medfate]{SpParamsMED}}) from which valid species names are drawn.
+#' @param merge_trees A logical flag to simplify tree cohorts by merging tree records in DBH classes (see \code{\link[medfate]{forest_mergeTrees}}).
+#' @param merge_shrubs A logical flag to simplify shrub cohorts by merging shrub records in height classes (see \code{\link[medfate]{forest_mergeShrubs}}).
 #' @param progress A logical flag to include a progress bar while processing the data.
 #'
 #' @details The current implementation will replace existing forests of the indicated 'id' values.
 #'
-#' @return A modified object of class \code{\link{sf}} with column 'forest'.
+#' @return A modified object of class \code{\link[sf]{sf}} with column 'forest'.
 #' @seealso [impute_forests()], \code{\link[medfate]{forest_mapWoodyTables}}, \code{\link[medfate]{forest_mergeTrees}}
 #' 
 #' @author Miquel De \enc{Cáceres}{Caceres} Ainsa, CREAF

R/add_soilgrids.R

@@ -4,7 +4,7 @@
 #' Function \code{modify_soils} modifies soil definition according to soil depth and depth to bedrock information.
 #' Function \code{check_soils} verifies that soil data does not contain missing values for key variables and, if so, assigns default values. 
 #'
-#' @param x An object of class \code{\link{sf}} with a valid CRS definition. If it contains a column called 'land_cover_type', soils will be retrieved for "agriculture" and "wildland" 
+#' @param x An object of class \code{\link[sf]{sf}} with a valid CRS definition. If it contains a column called 'land_cover_type', soils will be retrieved for "agriculture" and "wildland" 
 #'          cover types only. Otherwise, soils are retrieved for all locations. For functions \code{modify_soils} or \code{check_soils}, \code{x} should already contain a column named "soil".
 #' @param soilgrids_path Path to SoilGrids rasters (see details). If missing, the SoilGrids REST API (https://rest.isric.org) will be queried.
 #' @param widths A numeric vector indicating the desired layer widths, in \emph{mm}. If \code{NULL} the default soil grids layer definition is returned.
@@ -31,7 +31,7 @@
 #' When \code{depth_to_bedrock_map} is provided, the function truncates the total depth of the soil definition to the depth to bedrock.
 #' If regional maps of soil depth are not available, users are recommended to resort on Shangguan et al (2017).
 #' 
-#' @return A modified object of class \code{\link{sf}} with column 'soil'.
+#' @return A modified object of class \code{\link[sf]{sf}} with column 'soil'.
 #'
 #' @author \enc{Víctor}{Victor} Granda, EMF-CREAF
 #' @author Miquel De \enc{Cáceres}{Caceres} Ainsa, EMF-CREAF
@@ -217,8 +217,8 @@ add_soilgrids <- function(x, soilgrids_path = NULL,
   return(soildf)
 }
 
-#' @param soil_depth_map An object of class \code{\link{rast}} or \code{\link{vect}} with the soil depth (in \emph{mm}) values.
-#' @param depth_to_bedrock_map An object of class \code{\link{rast}} or \code{\link{vect}} with depth to bedrock (in \emph{mm}) values.
+#' @param soil_depth_map An object of class \code{\link[terra]{SpatRaster}} or \code{\link[terra]{SpatVector}} with the soil depth (in \emph{mm}) values.
+#' @param depth_to_bedrock_map An object of class \code{\link[terra]{SpatRaster}} or \code{\link[terra]{SpatVector}} with depth to bedrock (in \emph{mm}) values.
 #' @param regolith_rfc Rock fragment content, in percent volume, between soil depth and 200cm depth (or lower depths, if modified via \code{widths}).
 #' @param full_rock_filling Logical flag to modify rock fragment content in all soil layers with according to distance to soil depth.
 #'

R/add_topography.R

@@ -2,25 +2,25 @@
 #'
 #' Initializes topography and land cover type for a set of target locations
 #'
-#' @param x An object of class \code{\link{sf}}
-#' @param dem A digital elevation model (class \code{\link{SpatRaster}}) with meters as units
-#' @param land_cover_map An object of class \code{\link{SpatRaster}} of land cover type. If missing, all locations are considered 'wildland'.
+#' @param x An object of class \code{\link[sf]{sf}}
+#' @param dem A digital elevation model (class \code{\link[terra]{SpatRaster}}) with meters as units
+#' @param land_cover_map An object of class \code{\link[terra]{SpatRaster}} of land cover type. If missing, all locations are considered 'wildland'.
 #' @param wildland,agriculture,rock,artificial,water Strings indicating the mapping from the legend of land_cover_map. 
 #' @param progress A logical flag to print console output
 #'
 #' @details
 #' The user should manually define the mapping of land cover classes in \code{land_cover_map} to the land cover types 
 #' used in medfateland.
 #' 
-#' @return Function \code{add_topography()} returns a modified object of class \code{\link{sf}} with columns:
+#' @return Function \code{add_topography()} returns a modified object of class \code{\link[sf]{sf}} with columns:
 #'        \itemize{
 #'           \item{\code{id}: Numeric location identifiers (if not existing).}
 #'           \item{\code{elevation}: Elevation above sea level (in m).}
 #'           \item{\code{slope}: Slope (in degrees).}
 #'           \item{\code{aspect}: Aspect (in degrees).}
 #'           \item{\code{land_cover_type}: Land cover type.}
 #'        }
-#'        Function \code{add_land_cover()} returns a modified object of class \code{\link{sf}} with new column:
+#'        Function \code{add_land_cover()} returns a modified object of class \code{\link[sf]{sf}} with new column:
 #'        \itemize{
 #'           \item{\code{id}: Numeric location identifiers (if not existing).}
 #'           \item{\code{land_cover_type}: Land cover type.}

R/create_management_scenario.R

@@ -11,7 +11,7 @@
 #'                   years according to the growth observed and the desired extraction rates.
 #' @param default_management_arguments A list of arguments to be passed to the managementFunction. These arguments will be taken as defaults 
 #'                            copied for all management units and can later be modified. If NULL, the result of calling function 
-#'                            \code{\link{defaultManagementArguments}} will be taken.
+#'                            \code{\link[medfate]{defaultManagementArguments}} will be taken.
 #'
 #' @details 
 #' Three kinds of management scenarios are allowed:
@@ -48,7 +48,7 @@
 #' 
 #' Aitor \enc{Améztegui}{Ameztegui}, UdL
 #' 
-#' @seealso \code{\link{fordyn_scenario}}, \code{\link{defaultManagementFunction}}, \code{\link{defaultPrescriptionsBySpecies}}, \code{\link{create_fire_regime}}
+#' @seealso \code{\link{fordyn_scenario}}, \code{\link[medfate]{defaultManagementFunction}}, \code{\link{defaultPrescriptionsBySpecies}}, \code{\link{create_fire_regime}}
 #' 
 #' @examples 
 #' 

R/dataset_documentation.R

@@ -11,21 +11,21 @@
 #'   Mario Beltrán & Míriam Piqué. Forest Science and Technology Centre of Catalonia (CTFC)
 #' @keywords data
 #' 
-#' @seealso \code{\link{create_management_scenario}}, \code{\link{defaultManagementArguments}},
+#' @seealso \code{\link{create_management_scenario}}, \code{\link[medfate]{defaultManagementArguments}},
 #' \code{\link{fordyn_scenario}}
 NULL
 
 
 #' Example of watershed
 #' 
-#' An example of an object of \code{\link{sf}} with data for a small catchment of 66 ha (0.66 km2) in Catalonia. 
+#' An example of an object of \code{\link[sf]{sf}} with data for a small catchment of 66 ha (0.66 km2) in Catalonia. 
 #' Object \code{example_watershed_burnin} is the result of three years of burn-in period.
 #' 
 #' @name example_watershed
 #' @aliases example_watershed example_watershed_burnin
 #' @docType data
 #' @format 
-#' The data format is that of an object \code{\link{sf}} 
+#' The data format is that of an object \code{\link[sf]{sf}} 
 #' 
 #' @source
 #'   \itemize{
@@ -55,7 +55,7 @@ NULL
 #'  
 #' @name example_ifn
 #' @docType data
-#' @format The data format is that of an object \code{\link{sf}} 
+#' @format The data format is that of an object \code{\link[sf]{sf}} 
 #' 
 #' @source
 #'  \itemize{

R/default_volume_function.R

@@ -2,7 +2,7 @@
 #' 
 #' Example function for estimating wood volume (in m3/ha) from a tree table or forest object. 
 #' 
-#' @param x A data frame with columns 'DBH', 'Height' and 'N' or a \code{\link{forest}} object
+#' @param x A data frame with columns 'DBH', 'Height' and 'N' or a \code{\link[medfate]{forest}} object
 #' @param SpParams A data frame with species parameters (not used in the default function but will be called)
 #' 
 #' @details Users should define their own functions taking into account that:

R/dispersal.R

@@ -49,17 +49,18 @@ kernel_int <- function(r, alpha, c) {
 #   }
 #   plot(dist_vec, kernel_fun(dist_vec, alpha,c), type = "l", log = log)
 # }
+
 #' Seed production, dispersal and seed bank dynamics
 #' 
 #' Simulates seed bank mortality, seed production and dispersal among stands
 #'
-#' @param sf An object of class \code{\link{sf}} using a UTM projection (to measure distances in m) and with the following columns:
+#' @param sf An object of class \code{\link[sf]{sf}} using a UTM projection (to measure distances in m) and with the following columns:
 #'   \itemize{
 #'     \item{\code{geometry}: Spatial geometry.}
-#'     \item{\code{forest}: Objects of class \code{\link{forest}}.}
+#'     \item{\code{forest}: Objects of class \code{\link[medfate]{forest}}.}
 #'   }
-#' @param SpParams A data frame with species parameters (see \code{\link{SpParamsMED}}).
-#' @param local_control A list of control parameters (see \code{\link{defaultControl}})
+#' @param SpParams A data frame with species parameters (see \code{\link[medfate]{SpParamsMED}}).
+#' @param local_control A list of control parameters (see \code{\link[medfate]{defaultControl}})
 #' @param distance_step Distance step in meters.
 #' @param maximum_dispersal_distance Maximum dispersal distance in meters.
 #' @param min_percent A minimum percent of seed bank to retain entry in \code{seedBank} element of \code{forest}.

R/extract_variables.R

@@ -313,11 +313,11 @@
 #' 
 #' Extract or estimate variables from landscape objects (class 'sf').
 #' 
-#' @param x An object of class \code{\link{sf}} with the appropriate columns.
+#' @param x An object of class \code{\link[sf]{sf}} with the appropriate columns.
 #' @param vars A string vector with the name of the variables to extract (see details).
 #' @param variable A string with the name of the variables to draw (see details).
-#' @param SpParams A data frame with species parameters (see \code{\link{SpParamsMED}}), required for most forest stand variables.
-#' @param r An object of class \code{\link{rast}}, defining the raster topology.
+#' @param SpParams A data frame with species parameters (see \code{\link[medfate]{SpParamsMED}}), required for most forest stand variables.
+#' @param r An object of class \code{\link[terra]{SpatRaster}}, defining the raster topology.
 #' @param ... Additional arguments (not used).
 #' 
 #' @details The following string values are available for \code{vars}. 
@@ -369,12 +369,12 @@
 #'      \item{\code{"shrub_volume"}: Shrub volume (m3/m2).}
 #'    }
 #'
-#' @returns Function \code{extract_variables()} returns an object of class \code{\link{sf}} with the desired variables.
+#' @returns Function \code{extract_variables()} returns an object of class \code{\link[sf]{sf}} with the desired variables.
 #' Function \code{plot_variables()} returns a ggplot object.
 #' 
 #' @author Miquel De \enc{Cáceres}{Caceres} Ainsa, CREAF.
 #' 
-#' @seealso \code{\link{forest}}, \code{\link{soil}}, \code{\link{summary.forest}}, \code{\link{shinyplot_land}}
+#' @seealso \code{\link[medfate]{forest}}, \code{\link[medfate]{soil}}, \code{\link[medfate]{summary.forest}}, \code{\link{shinyplot_land}}
 #' 
 #' @examples
 #' # Load data and species parameters from medfate

R/fire_regime_instance.R

@@ -2,7 +2,7 @@
 #' 
 #' Applies a fire regime object over a set of landscape units to determine a fire realization
 #'
-#' @param sf An object of class \code{\link{sf}} with the following columns:
+#' @param sf An object of class \code{\link[sf]{sf}} with the following columns:
 #'   \itemize{
 #'     \item{\code{geometry}: Spatial geometry.}
 #'     \item{\code{id}: Stand identifiers.}
@@ -14,7 +14,7 @@
 #' @details
 #' The function randomly determines the landscape units that will burn every year, depending on the specifications
 #' of the fire regime object. Users can define their own fire regime instances from other models (e.g. a fire landscape model)
-#' and then use those directly in functions \code{\link{fordyn_spatial}} or \code{\link{fordyn_scenario}}-
+#' and then use those directly in functions \code{\link{fordyn_spatial}} or \code{\link{fordyn_scenario}}.
 #' 
 #' @return An integer matrix specifying the day of the year of burning of each landscape unit for every year in the fire regime definition.
 #' Values are interpreted as follows:

R/fordyn_scenario.R

@@ -23,16 +23,16 @@
 #' 
 #' Evaluates forest dynamics over a landscape including climate and management scenarios
 #'
-#' @param sf An object of class \code{\link{sf}} with the following columns:
+#' @param sf An object of class \code{\link[sf]{sf}} with the following columns:
 #'   \itemize{
 #'     \item{\code{geometry}: Spatial geometry.}
 #'     \item{\code{id}: Stand identifiers.}
 #'     \item{\code{elevation}: Elevation above sea level (in m).}
 #'     \item{\code{slope}: Slope (in degrees).}
 #'     \item{\code{aspect}: Aspect (in degrees).}
-#'     \item{\code{forest}: Objects of class \code{\link{forest}}.}
-#'     \item{\code{soil}: Objects of class \code{\link{soil}}.}
-#'     \item{\code{state}: Objects of class \code{\link{spwbInput}} or \code{\link{growthInput}} (optional).}
+#'     \item{\code{forest}: Objects of class \code{\link[medfate]{forest}}.}
+#'     \item{\code{soil}: Objects of class \code{\link[medfate]{soil}}.}
+#'     \item{\code{state}: Objects of class \code{\link[medfate]{spwbInput}} or \code{\link[medfate]{growthInput}} (optional).}
 #'     \item{\code{meteo}: Data frames with weather data (required if parameter \code{meteo = NULL}).}
 #'     \item{\code{management_unit}: Management unit corresponding to each stand.}
 #'     \item{\code{represented_area_ha}: Area represented by each stand in hectares.}
@@ -42,9 +42,9 @@
 #'   }
 #'   Alternatively, the user may supply the result of a previous call to \code{fordyn_scenario}, where
 #'   to continue simulations.
-#' @param SpParams A data frame with species parameters (see \code{\link{SpParamsMED}}). 
+#' @param SpParams A data frame with species parameters (see \code{\link[medfate]{SpParamsMED}}). 
 #' @param meteo Meteorology data (see \code{\link{fordyn_spatial}}).
-#' @param local_control A list of local model control parameters (see \code{\link{defaultControl}}).
+#' @param local_control A list of local model control parameters (see \code{\link[medfate]{defaultControl}}).
 #' @param volume_function A function accepting a forest object or a tree data table, and a species parameter table, as input and 
 #' returning the wood volume (m3/ha) corresponding to each tree cohort. The function may accept additional arguments.
 #' If NULL, the default volume function is used (not recommended!).
@@ -56,7 +56,7 @@
 #' @param fire_regime A list of parameters defining the fire regime (see \code{\link{create_fire_regime}}) or 
 #'                    a matrix representing a fire regime instance (see \code{\link{fire_regime_instance}}). 
 #'                    If NULL, wildfires are not simulated. Details are given in \code{\link{fordyn_spatial}}.
-#' @param summary_function An appropriate function to calculate summaries from an object of class 'fordyn' (e.g., \code{\link{summary.fordyn}}).
+#' @param summary_function An appropriate function to calculate summaries from an object of class 'fordyn' (e.g., \code{\link[medfate]{summary.fordyn}}).
 #' @param summary_arguments List with additional arguments for the summary function.
 #' @param parallelize Boolean flag to try parallelization (will use all clusters minus one).
 #' @param num_cores Integer with the number of cores to be used for parallel computation.
@@ -76,8 +76,8 @@
 #' the previous state of the forest stand for the next year steps. Finally, the function evaluates how much of the specified demand
 #' has been fulfilled and stores the results, including demand offsets to be applied the year after.
 #' 
-#' Management is implemented using the \code{\link{defaultManagementFunction}} in medfate, 
-#' meaning that management parameters need to follow the structure of \code{\link{defaultManagementArguments}}
+#' Management is implemented using the \code{\link[medfate]{defaultManagementFunction}} in medfate, 
+#' meaning that management parameters need to follow the structure of \code{\link[medfate]{defaultManagementArguments}}
 #' 
 #' Details about the inclusion of fire regimes in simulations are explained in \code{\link{fordyn_spatial}}.
 #'