Merge pull request #175 from OHI-Science/dev

Dev

DESCRIPTION

@@ -60,3 +60,4 @@ Collate:
     'trace_git_csv_value.R'
     'write_shortcuts.R'
     'zzz.R'
+RoxygenNote: 5.0.1

NAMESPACE

@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.1.1): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 export(CalculateAll)
 export(CalculateGoalIndex)

R/CalculatePressuresMatrix.R

@@ -1,76 +1,76 @@
-##' Calculate Pressures Matrix
-##' 
-##' The pressures matrix model function computes a pressures weighting matrix
-##' based on regional attributes per category.
-##' 
-##' 
-##' Given:
-##' 
-##' \itemize{
-##' 
-##' \item \emph{g} is the goal or subgoal (e.g., AO, CW, LIV, ECO, ...), \item
-##' \emph{i} is the region (e.g., 1, 2, 3, ...), \item \emph{j} is the
-##' pressures layer or stressor (e.g., \code{cc_acid}, \code{fp_art_lb}, etc.).
-##' \item \emph{k} is the category (e.g., habitat, sector, product, etc.)
-##' 
-##' }
-##' 
-##' There may be a component \emph{k} for a given goal \emph{g} such that
-##' \eqn{p_w(g,i,j,k)} and \eqn{w(g,i,j,k)}.
-##' 
-##' \deqn{p_{w}(g,i,j,k) = w(g,i,j,k) * p(i,j)}
-##' 
-##' In these cases where there is a component \emph{k} for goal \emph{g},
-##' there's an additional aggregation or formula to calculate \eqn{w(g,i,j)}
-##' based on the core rank weight \eqn{\alpha(g,j,k)} from the original
-##' pressures matrix (as written in Halpern et al. (2012)) and some
-##' region-specific data for each category \code{k} \eqn{\beta(i,k)}.
-##' 
-##' This function \code{CalculatePressuresMatrix} will aggregate a
-##' category-specific weighting matrix \eqn{\alpha(g,j,k)} [category x
-##' pressure] using region-specific data \eqn{\beta(g,i,k)} into a [region_id x
-##' pressure] matrix \eqn{w(g,i,j)} used in \code{CalculatePressuresScore}, such
-##' that:
-##' 
-##' \deqn{w(g,i,j) = \frac{\sum_k \alpha({g,j,k}) * \beta({g,i,k})}{\sum_k
-##' \beta({g,i,k})}}
-##' 
-##' \enumerate{
-##' 
-##' \item For the CP, CS goals, the weight depends on the extent \emph{A} of
-##' habitat \emph{k} in region \emph{i}:
-##' 
-##' \deqn{\beta(i,k) = A(i,k)}
-##' 
-##' \item For the HAB goal, the weight depends on the presence of habitat
-##' \emph{k} (i.e., if \eqn{A(i,k)>0}) in region \emph{i}:
-##' 
-##' \deqn{\beta(i,k) = hasHabitat(i,k)}
-##' 
-##' \item For the LIV and ECO goals, the weight depends on the presence of
-##' sector \emph{k} if data available for region \emph{i} and sector \emph{k}:
-##' 
-##' \deqn{\beta(i,k) = hasSector(i,k)}
-##' 
-##' \item For the NP goal, the weight depends on the peak dollar value of each
-##' product \emph{k} across all years (see \eqn{w_p} from SI Equation S27) if
-##' data available for region \emph{i} and product \emph{k}:
-##' 
-##' \deqn{\beta(i,k) = w_p(i,k)} }
-##' 
-##' @param alpha the weighting matrix of the form [category x pressure]. Each
-##' rank weight must be an integer between 0 and 3 inclusive, or NA.
-##' @param beta the aggregation matrix of the form [region_id x category] to
-##' collapse across each category.
-##' @param calc type of calculation, whether avg (default), mean (diff't from
-##' avg?) or presence (results in 1 or 0).
-##' @return Returns a weight matrix \emph{w} [region_id x pressure] suitable
-##' for \code{\link{CalculatePressuresScore}}.
-##' @seealso \code{\link{CalculatePressuresScore}}
-##' @keywords ohi
-##' @export
+#' Calculate Pressures Matrix
+#' 
+#' The pressures matrix model function computes a pressures weighting matrix
+#' based on regional attributes per category.
+#' 
+#' 
+#' Given:
+#' 
+#' \itemize{
+#' 
+#' \item \emph{g} is the goal or subgoal (e.g., AO, CW, LIV, ECO, ...), \item
+#' \emph{i} is the region (e.g., 1, 2, 3, ...), \item \emph{j} is the
+#' pressures layer or stressor (e.g., \code{cc_acid}, \code{fp_art_lb}, etc.).
+#' \item \emph{k} is the category (e.g., habitat, sector, product, etc.)
+#' 
+#' }
+#' 
+#' There may be a component \emph{k} for a given goal \emph{g} such that
+#' \eqn{p_w(g,i,j,k)} and \eqn{w(g,i,j,k)}.
+#' 
+#' \deqn{p_{w}(g,i,j,k) = w(g,i,j,k) * p(i,j)}
+#' 
+#' In these cases where there is a component \emph{k} for goal \emph{g},
+#' there's an additional aggregation or formula to calculate \eqn{w(g,i,j)}
+#' based on the core rank weight \eqn{\alpha(g,j,k)} from the original
+#' pressures matrix (as written in Halpern et al. (2012)) and some
+#' region-specific data for each category \code{k} \eqn{\beta(i,k)}.
+#' 
+#' This function \code{CalculatePressuresMatrix} will aggregate a
+#' category-specific weighting matrix \eqn{\alpha(g,j,k)} [category x
+#' pressure] using region-specific data \eqn{\beta(g,i,k)} into a [region_id x
+#' pressure] matrix \eqn{w(g,i,j)} used in \code{CalculatePressuresScore}, such
+#' that:
+#' 
+#' \deqn{w(g,i,j) = \frac{\sum_k \alpha({g,j,k}) * \beta({g,i,k})}{\sum_k
+#' \beta({g,i,k})}}
+#' 
+#' \enumerate{
+#' 
+#' \item For the CP, CS goals, the weight depends on the extent \emph{A} of
+#' habitat \emph{k} in region \emph{i}:
+#' 
+#' \deqn{\beta(i,k) = A(i,k)}
+#' 
+#' \item For the HAB goal, the weight depends on the presence of habitat
+#' \emph{k} (i.e., if \eqn{A(i,k)>0}) in region \emph{i}:
+#' 
+#' \deqn{\beta(i,k) = hasHabitat(i,k)}
+#' 
+#' \item For the LIV and ECO goals, the weight depends on the presence of
+#' sector \emph{k} if data available for region \emph{i} and sector \emph{k}:
+#' 
+#' \deqn{\beta(i,k) = hasSector(i,k)}
+#' 
+#' \item For the NP goal, the weight depends on the peak dollar value of each
+#' product \emph{k} across all years (see \eqn{w_p} from SI Equation S27) if
+#' data available for region \emph{i} and product \emph{k}:
+#' 
+#' \deqn{\beta(i,k) = w_p(i,k)} }
+#' 
+#' @param alpha the weighting matrix of the form [category x pressure]. Each
+#' rank weight must be an integer between 0 and 3 inclusive, or NA.
+#' @param beta the aggregation matrix of the form [region_id x category] to
+#' collapse across each category.
+#' @param calc type of calculation, whether avg (default), mean (diff't from
+#' avg?) or presence (results in 1 or 0).
+#' @return Returns a weight matrix \emph{w} [region_id x pressure] suitable
+#' for \code{\link{CalculatePressuresScore}}.
+#' @seealso \code{\link{CalculatePressuresScore}}
+#' @keywords ohi
+#' @export
 CalculatePressuresMatrix <- function(alpha, beta, calc='avg') {
-  #' Parameters:
+  # Parameters:
   #' @param alpha weighting matrix of the form [category x pressure]
      #' @param beta aggregation matrix of the form [region_id x category] to collapse across each category
      #' @param calc type of calculation, whether avg (default), mean (diff't from avg?) or presence (results in 1 or 0)

R/CalculatePressuresScore.R

@@ -187,18 +187,18 @@
 ##' 
 ##' @export
 CalculatePressuresScore <- function(p, w, GAMMA=0.5, browse=F, pressures_categories=list(environmental=c('po','hd','fp','sp','cc'), social='ss')) {
-  #' Computation of pressure
-  #'
-  #' The weighting matrix and the pressure scores matrix are of the form
-  #' [region_id] x [pressure]
-  #'
-  #' The pressure names must be of the form "category"_"pressure". 
-  #' Use "ss" to denote the social category.
-  #'    
-  #' Parameters:
+  # Computation of pressure
+  #
+  # The weighting matrix and the pressure scores matrix are of the form
+  # [region_id] x [pressure]
+  #
+  # The pressure names must be of the form "category"_"pressure". 
+  # Use "ss" to denote the social category.
+  #    
+  # Parameters:
   #' @param p is the pressures value matrix [region_id x pressure]
      #' @param w is the weighting matrix of the form [region_id x pressure]
-     #'
+     #
      #' @return pressures scores as a named vector.
 
      # verify parameters