Commit 760e7072 authored by Facundo Muñoz's avatar Facundo Muñoz ®️
Browse files

rasterize_geonetwork(): improve doc

parent 1f903689
Package: mapMCDA
Title: Produce an epidemiological risk map by weighting multiple risk
factors
Version: 0.4.12
Version: 0.4.13
Date: 2019-06-12
Authors@R: c( person("Andrea", "Apolloni", email =
"andrea.apolloni@cirad.fr", role = c("ctb"), comment = "Animal
......
......@@ -178,6 +178,10 @@ setOldClass("geonetwork")
#' If you want the unweighted importance, remove the weight attribute
#' from the graph with \code{igraph::delete_edge_attr(x, "weight")}.
#'
#' The importance of each node is computed as the relative
#' contribution to the Potential for Transmision \eqn{R_0} of the
#' graph. I.e., \eqn{R_{0k}/R_0}. See \code{\link{epidemic_threshold}}.
#'
#' @param x a geographic network (a geonetwork object with node attributes
#' "Lon" and "Lat" in the WGS84 reference system)
#' @param y a Raster* or a SpatialPolygons* object.
......@@ -278,11 +282,11 @@ setMethod(
#' context of a network. It thus quantifies the potential for
#' transmission of an infection throughout the contact network. It is
#' computed in terms of the incoming-outgoing rates from the network's
#' nodes: \deqn{R_0 = \beta \frac{\hat{k_\mathrm{in}
#' k_\mathrm{out}}}{\hat{k_\mathrm{in}}},}{R_0 = \beta <k_in*k_out>/<k_in>,}
#' nodes: \deqn{R_0 = \beta \frac{\overline{k_\mathrm{in}\cdot
#' k_\mathrm{out}}}{\overline{k_\mathrm{in}}},}{R_0 = \beta <k_in*k_out>/<k_in>,}
#' where \eqn{\beta} is the transmission coefficient among animals,
#' \eqn{k_\mathrm{in/out}}{k_in/out} are the in/out-degrees of a node
#' and the \eqn{<·>} symbol represents the average value
#' and the \eqn{\overline{\cdot}}{<·>} symbol represents the average value
#' across all nodes in the graph.
#'
#' The unweighted value computed above is most appropriate for a
......@@ -296,7 +300,7 @@ setMethod(
#' contacts.
#'
#' The default value of 1 for the probability of transmission
#' \code{beta} implies that every infectious contact leads to
#' \eqn{\beta} implies that every infectious contact leads to
#' transmission.
#'
#' @param x an \code{igraph} object
......
......@@ -33,11 +33,11 @@ the Basic Reproduction Number \eqn{R_0} of an epidemy to the
context of a network. It thus quantifies the potential for
transmission of an infection throughout the contact network. It is
computed in terms of the incoming-outgoing rates from the network's
nodes: \deqn{R_0 = \beta \frac{\hat{k_\mathrm{in}
k_\mathrm{out}}}{\hat{k_\mathrm{in}}},}{R_0 = \beta <k_in*k_out>/<k_in>,}
nodes: \deqn{R_0 = \beta \frac{\overline{k_\mathrm{in}\cdot
k_\mathrm{out}}}{\overline{k_\mathrm{in}}},}{R_0 = \beta <k_in*k_out>/<k_in>,}
where \eqn{\beta} is the transmission coefficient among animals,
\eqn{k_\mathrm{in/out}}{k_in/out} are the in/out-degrees of a node
and the \eqn{<·>} symbol represents the average value
and the \eqn{\overline{\cdot}}{<·>} symbol represents the average value
across all nodes in the graph.
The unweighted value computed above is most appropriate for a
......@@ -51,7 +51,7 @@ transmission probability is assumed proportional to the number of
contacts.
The default value of 1 for the probability of transmission
\code{beta} implies that every infectious contact leads to
\eqn{\beta} implies that every infectious contact leads to
transmission.
}
\examples{
......
......@@ -41,4 +41,8 @@ in the WGS84 reference system.
If the graph is weighted, the weighted importance will be computed.
If you want the unweighted importance, remove the weight attribute
from the graph with \code{igraph::delete_edge_attr(x, "weight")}.
The importance of each node is computed as the relative
contribution to the Potential for Transmision \eqn{R_0} of the
graph. I.e., \eqn{R_{0k}/R_0}. See \code{\link{epidemic_threshold}}.
}
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