edit documentation

R/class-distance.R

@@ -6,12 +6,20 @@
 #' @rdname distance-class
 #' @exportClass distance
 #' 
-#' @field distance object of class \code{matrix}.
-#' @field datID object of class \code{character}.
-#' @field components object of class \code{list}.
+#' @field distance two-dimensional \code{matrix} of mode \code{numeric} 
+#' with rows as types, columns as types, and elements containing the pairwise
+#' distance of types
+#' @field datID object of class \code{character} describing the class of 
+#' distance / similarity being used, e.g. "naive", "taxonomic", and so on
+#' @field components list containining the components necessary to calculate
+#' similarity. This list is empty when \code{precompute_dist = TRUE} when
+#' calculating distance. When a pairwise distance matrix is too large and  
+#' \code{precompute_dist = FALSE}, this list contains all the information 
+#' required to calculate pairwise distance between types
 #' 
-setClass("distance", slots = c(distance = "matrix",
-                               datID = "character",
-                               components = "list"))
+setClass("distance", 
+         slots = c(distance = "matrix",
+                   datID = "character",
+                   components = "list"))
 
 

R/class-metacommunity.R

@@ -9,27 +9,37 @@ setOldClass("phylo")
 #' 
 #' @field type_abundance two-dimensional \code{matrix} of mode \code{numeric}  
 #' with rows as types, columns as subcommunities, and elements containing  
-#' relative abundances of types in subcommunities.  In the phylogenetic case, 
+#' relative abundances of types in subcommunities. In the phylogenetic case, 
 #' this corresponds to the proportional abundance of historic species, which
-#' is calculated from the proportional abundance of present day species.
-#' @field similarity object
-#' @field similarity_components object
-#' @field similarity_parameters object
+#' is calculated from the proportional abundance of present day species
+#' @field similarity two-dimensional \code{matrix} of mode \code{numeric} 
+#' with rows as types, columns as types, and elements containing the pairwise
+#' similarity of types
+#' @field similarity_components list containining the components necessary to 
+#' calculate similarity. This list is empty when \code{precompute_dist = TRUE} 
+#' when calculating distance. When a pairwise distance matrix is too large and  
+#' \code{precompute_dist = FALSE}, this list contains all the information 
+#' required to calculate pairwise distance between types
+#' @field similarity_parameters list containining parameters associated with
+#' converting pairwise distances to similarities (the \code{dist2sim()} 
+#' arguments)
 #' @field ordinariness two-dimensional \code{matrix} of mode \code{numeric} 
 #' with rows as types, columns as subcommunities, and elements containing the
 #' ordinariness of types within subcommunities 
-#' @field subcommunity_weights \code{vector} of mode \code{numeric}; contains
+#' @field subcommunity_weights \code{vector} of mode \code{numeric} containing
 #' subcommunity weights
 #' @field type_weights two-dimensional \code{matrix} of mode \code{numeric}, 
 #' with rows as types, columns as subcommunities, and elements containing 
 #' weights of types within a subcommunity
+#' @field datID object of class \code{character} describing the class of 
+#' distance / similarity being used, e.g. "naive", "taxonomic", and so on
 #' @field raw_abundance [Phylogenetic] two-dimensional \code{matrix} of mode 
 #' \code{numeric} with rows as types, columns as subcommunities, and elements 
 #' containing the relative abundance of present day species
 #' @field raw_structure [Phylogenetic] two-dimensional \code{matrix} of mode 
 #' \code{numeric} with rows as historical species, columns as present day 
 #' species, and elements containing historical species lengths within lineages
-#' @field parameters [Phylogenetic] \code{tibble} containing parameters 
+#' @field parameters [Phylogenetic] \code{data.frame} containing parameters 
 #' associated with each historic species in the phylogeny
 #' 
 setClass("metacommunity", 
@@ -40,8 +50,8 @@ setClass("metacommunity",
                    ordinariness = "matrix",
                    subcommunity_weights = "numeric", 
                    type_weights = "matrix",
+                   datID = "character",
                    raw_abundance = "matrix",
                    raw_structure = "matrix",
-                   parameters = "data.frame",
-                   datID = "character"))
+                   parameters = "data.frame"))
 

R/class-powermean.R

@@ -6,31 +6,32 @@
 #' @rdname powermean-class
 #' @exportClass powermean
 #' 
-#' @field results \code{matrix} of mode \code{numeric}; contains values 
-#' calculated from diversity-term values output from \code{raw_alpha()}, 
-#' \code{norm_alpha()}, \code{raw_rho()}, \code{norm_rho()}, or 
-#' \code{raw_gamma()}. An object of class \code{tibble}, with columns:
-#' \code{measure}, (raw alpha, norm alpha, raw rho, etc.),
-#' \code{q} (parameter of conservatism), 
-#' \code{type_level} (), 
-#' \code{type_name} (label attributed to type), 
-#' \code{partition_level} (level of diversity, \emph{i.e.} subcommunity), 
-#' \code{partition_name} (label attributed to partition), and 
-#' \code{diversity}
+#' @field results \code{data.frame} containing rdiversity output
+#' @field measure object of class \code{character} naming the diversity
+#' measure being calculated
 #' @field type_abundance two-dimensional \code{matrix} of mode \code{numeric}; 
 #' contains proportional abundance of \emph{types} in the subcommunity 
 #' as a fraction of the metacommunity as a whole (in the phylogenetic case, 
 #' this corresponds to the proportional abundance of historic species, which
 #' is calculated from the proportional abundance of present day species)
-#' @field ordinariness two-dimensional \code{matrix} of mode \code{numeric}; 
-#' contains ordinariness of types 
-#' @field subcommunity_weights \code{vector} of mode \code{numeric}; contains
+#' @field ordinariness two-dimensional \code{matrix} of mode \code{numeric} 
+#' with rows as types, columns as subcommunities, and elements containing the
+#' ordinariness of types within subcommunities 
+#' @field subcommunity_weights \code{vector} of mode \code{numeric} containing
 #' subcommunity weights
-#' @field type_weights two-dimensional \code{matrix} of mode \code{numeric}; 
-#' contains weight of types within a subcommunity
-#' @field datID class of similarity, which can be taxonomic, phylogenetic, or 
-#' naive
-#' @field parameters parameters associated with calculating similarity
+#' @field type_weights two-dimensional \code{matrix} of mode \code{numeric}, 
+#' with rows as types, columns as subcommunities, and elements containing 
+#' weights of types within a subcommunity
+#' @field datID object of class \code{character} describing the class of 
+#' distance / similarity being used, e.g. "naive", "taxonomic", and so on
+#' @field similarity_components list containining the components necessary to 
+#' calculate similarity. This list is empty when \code{precompute_dist = TRUE} 
+#' when calculating distance. When a pairwise distance matrix is too large and  
+#' \code{precompute_dist = FALSE}, this list contains all the information 
+#' required to calculate pairwise distance between types
+#' @field similarity_parameters list containining parameters associated with
+#' converting pairwise distances to similarities (the \code{dist2sim()} 
+#' arguments)
 #' 
 #' @references Reeve, R., T. Leinster, C. Cobbold, J. Thompson, N. Brummitt, 
 #' S. Mitchell, and L. Matthews. 2014. How to partition diversity. 
@@ -43,7 +44,6 @@ setClass("powermean", slots = c(results = "matrix",
                                 subcommunity_weights = "vector",
                                 type_weights = "matrix",
                                 datID = "character",
-                                parameters = "list",
                                 similarity_components = "list",
                                 similarity_parameters = "list"))
 

R/class-relativeentropy.R

@@ -6,31 +6,32 @@
 #' @rdname relativeentropy-class
 #' @exportClass relativeentropy
 #' 
-#' @field results object of class \code{matrix} of mode \code{numeric}; contains
-#' diversity term values output from \code{raw_beta()} or \code{norm_beta()}
-#' @field measure measure
-#' An object of class \code{tibble}, with columns:
-#' \code{measure}, (raw alpha, norm alpha, raw rho, etc.),
-#' \code{q} (parameter of conservatism), 
-#' \code{type_level} (), 
-#' \code{type_name} (label attributed to type), 
-#' \code{partition_level} (level of diversity, \emph{i.e.} subcommunity), 
-#' \code{partition_name} (label attributed to partition), and 
-#' \code{diversity}
+#' @field results \code{data.frame} containing rdiversity output
+#' @field measure object of class \code{character} naming the diversity
+#' measure being calculated
 #' @field type_abundance two-dimensional \code{matrix} of mode \code{numeric}; 
 #' contains proportional abundance of \emph{types} in the subcommunity 
 #' as a fraction of the metacommunity as a whole (in the phylogenetic case, 
 #' this corresponds to the proportional abundance of historic species, which
 #' is calculated from the proportional abundance of present day species)
-#' @field ordinariness two-dimensional \code{matrix} of mode \code{numeric}; 
-#' contains ordinariness of types 
-#' @field subcommunity_weights \code{vector} of mode \code{numeric}; contains
+#' @field ordinariness two-dimensional \code{matrix} of mode \code{numeric} 
+#' with rows as types, columns as subcommunities, and elements containing the
+#' ordinariness of types within subcommunities 
+#' @field subcommunity_weights \code{vector} of mode \code{numeric} containing
 #' subcommunity weights
-#' @field type_weights two-dimensional \code{matrix} of mode \code{numeric}; 
-#' contains weight of types within a subcommunity
-#' @field datID class of similarity, which can be taxonomic, phylogenetic, or 
-#' naive
-#' @field parameters parameters associated with calculating similarity
+#' @field type_weights two-dimensional \code{matrix} of mode \code{numeric}, 
+#' with rows as types, columns as subcommunities, and elements containing 
+#' weights of types within a subcommunity
+#' @field datID object of class \code{character} describing the class of 
+#' distance / similarity being used, e.g. "naive", "taxonomic", and so on
+#' @field similarity_components list containining the components necessary to 
+#' calculate similarity. This list is empty when \code{precompute_dist = TRUE} 
+#' when calculating distance. When a pairwise distance matrix is too large and  
+#' \code{precompute_dist = FALSE}, this list contains all the information 
+#' required to calculate pairwise distance between types
+#' @field similarity_parameters list containining parameters associated with
+#' converting pairwise distances to similarities (the \code{dist2sim()} 
+#' arguments)
 #' 
 #' @references Reeve, R., T. Leinster, C. Cobbold, J. Thompson, N. Brummitt, 
 #' S. Mitchell, and L. Matthews. 2014. How to partition diversity. 
@@ -43,7 +44,6 @@ setClass("relativeentropy", slots = c(results = "matrix",
                                       subcommunity_weights = "vector",
                                       type_weights = "matrix",
                                       datID = "character",
-                                      parameters = "list",
                                       similarity_components = "list",
                                       similarity_parameters = "list"))
 

R/class-similarity.R

@@ -6,10 +6,19 @@
 #' @rdname similarity-class
 #' @exportClass similarity
 #' 
-#' @field similarity object of class \code{matrix}.
-#' @field datID object of class \code{character}.
-#' @field components object of class \code{list}.
-#' @field parameters object of class \code{list}.
+#' @field similarity two-dimensional \code{matrix} of mode \code{numeric} 
+#' with rows as types, columns as types, and elements containing the pairwise
+#' similarity of types
+#' @field datID object of class \code{character} describing the class of 
+#' distance / similarity being used, e.g. "naive", "taxonomic", and so on
+#' @field components list containining the components necessary to calculate
+#' similarity. This list is empty when \code{precompute_dist = TRUE} when
+#' calculating distance. When a pairwise distance matrix is too large and  
+#' \code{precompute_dist = FALSE}, this list contains all the information 
+#' required to calculate pairwise distance between types
+#' @field parameters list containining parameters associated with
+#' converting pairwise distances to similarities (the \code{dist2sim()} 
+#' arguments)
 #' 
 setClass("similarity", slots = c(similarity = "matrix",
                                  datID = "character",

R/metacommunity.R

@@ -1,17 +1,6 @@
 #' Metacommunity
 #'
 #' Functions to generate a \code{metacommunity} object.
-#'
-#' When calculating phylogenetic diversity either:
-#' \itemize{
-#' \item set \code{partition} as the relative abundance of terminal taxa,  
-#' in which case \code{similarity} (the pairwise similarity of historical species) is calculated from \code{phy2branch()} and 
-#' \code{dist2sim()}; or
-#' \item set \code{partition} as the relative abundance of historical species,
-#' with \code{similarity} (the pairwise similarity of historical species) is
-#' calculated from \code{phy2branch()} and 
-#' \code{dist2sim()}.
-#' }
 #' 
 #' @field type_abundance two-dimensional \code{matrix} of mode \code{numeric}  
 #' with rows as types, columns as subcommunities, and elements containing  
@@ -24,7 +13,7 @@
 #' @field ordinariness two-dimensional \code{matrix} of mode \code{numeric} 
 #' with rows as types, columns as subcommunities, and elements containing the
 #' ordinariness of types within subcommunities 
-#' @field subcommunity_weights \code{vector} of mode \code{numeric}; contains
+#' @field subcommunity_weights \code{vector} of mode \code{numeric} containing
 #' subcommunity weights
 #' @field type_weights two-dimensional \code{matrix} of mode \code{numeric}, 
 #' with rows as types, columns as subcommunities, and elements containing 
@@ -45,10 +34,10 @@
 #' @param partition two-dimensional \code{matrix} of mode \code{numeric}  
 #' with rows as types, columns as subcommunities, and elements containing  
 #' the relative abundances of types in subcommunities. For phylogenetic 
-#' diversity, see \emph{Details}.
+#' diversity, see \emph{Details}
 #' @param similarity (optional) two-dimensional \code{matrix} of mode 
 #' \code{numeric}, with rows as types, columns as types, and elements 
-#' containing the pairwise similarity between types.
+#' containing the pairwise similarity between types
 #' 
 #' @return \code{metacommunity()} returns an object of class 
 #' \code{metacommunity} (see \emph{Fields}).

R/powermean.R

@@ -1,16 +1,45 @@
 #' Calculate power mean
 #'
-#' Functions to check if an object is a \code{powermean}, or coerse an object 
-#' into a \code{powermean}; for \code{raw_alpha()}, \code{norm_alpha()}, 
-#' \code{raw_rho()}, \code{norm_rho()}, or  \code{raw_gamma()}. 
+#' Functions to coerse an object into a \code{powermean} (\code{raw_alpha()}, 
+#' \code{norm_alpha()}, \code{raw_rho()}, \code{norm_rho()}, and/or  
+#' \code{raw_gamma()}). 
 #' 
-#' @param tag measure
-#' @param results \code{matrix} of mode \code{numeric}; contains values 
-#' calculated from diversity-term functions \code{norm_alpha()}, 
-#' \code{raw_alpha()}, \code{raw_rho()}, \code{norm_rho()}, and 
-#' \code{raw_gamma()}
-#' @param meta object of class \code{metacommunity}; contains proportional
-#' abundance of types, pair-wise similarity, and other associated variables.
+#' @param results \code{data.frame} containing rdiversity outputs associated 
+#' with \code{norm_alpha()}, \code{raw_alpha()}, \code{raw_rho()}, 
+#' \code{norm_rho()}, and/or \code{raw_gamma()}
+#' @param meta object of class \code{metacommunity} containing the proportional
+#' abundance of types, pair-wise similarity, and other associated variables
+#' @param tag object of class \code{character} naming the diversity measure
+#' being calculated
+#' 
+#' @field results \code{data.frame} containing rdiversity outputs associated 
+#' with \code{norm_alpha()}, \code{raw_alpha()}, \code{raw_rho()}, 
+#' \code{norm_rho()}, and/or \code{raw_gamma()}
+#' @field measure object of class \code{character} naming the diversity
+#' measure being calculated
+#' @field type_abundance two-dimensional \code{matrix} of mode \code{numeric}; 
+#' contains proportional abundance of \emph{types} in the subcommunity 
+#' as a fraction of the metacommunity as a whole (in the phylogenetic case, 
+#' this corresponds to the proportional abundance of historic species, which
+#' is calculated from the proportional abundance of present day species)
+#' @field ordinariness two-dimensional \code{matrix} of mode \code{numeric} 
+#' with rows as types, columns as subcommunities, and elements containing the
+#' ordinariness of types within subcommunities 
+#' @field subcommunity_weights \code{vector} of mode \code{numeric} containing
+#' subcommunity weights
+#' @field type_weights two-dimensional \code{matrix} of mode \code{numeric}, 
+#' with rows as types, columns as subcommunities, and elements containing 
+#' weights of types within a subcommunity
+#' @field datID object of class \code{character} describing the class of 
+#' distance / similarity being used, e.g. "naive", "taxonomic", and so on
+#' @field similarity_components list containining the components necessary to 
+#' calculate similarity. This list is empty when \code{precompute_dist = TRUE} 
+#' when calculating distance. When a pairwise distance matrix is too large and  
+#' \code{precompute_dist = FALSE}, this list contains all the information 
+#' required to calculate pairwise distance between types
+#' @field similarity_parameters list containining parameters associated with
+#' converting pairwise distances to similarities (the \code{dist2sim()} 
+#' arguments)
 #'
 #' @return \code{powermean(x)} returns an object of class \code{powermean}.
 #' @include class-powermean.R