From 5d8a8b753e0f3528d844a46b8d73dee79a1262d6 Mon Sep 17 00:00:00 2001 From: samuel-rosa Date: Thu, 30 Jul 2015 21:55:24 -0300 Subject: [PATCH] updated documentation --- man-roxygen/spSANN_doc.R | 4 ++-- man/optimACDC.Rd | 16 ++++++++-------- man/optimCORR.Rd | 10 +++++----- man/optimDIST.Rd | 10 +++++----- man/optimMKV.Rd | 4 ++-- man/optimMSSD.Rd | 4 ++-- man/optimPPL.Rd | 4 ++-- man/optimSPAN.Rd | 16 ++++++++-------- man/optimUSER.Rd | 4 ++-- 9 files changed, 36 insertions(+), 36 deletions(-) diff --git a/man-roxygen/spSANN_doc.R b/man-roxygen/spSANN_doc.R index ef9840e..ebc612b 100644 --- a/man-roxygen/spSANN_doc.R +++ b/man-roxygen/spSANN_doc.R @@ -1,7 +1,7 @@ # Template documentation for spatial simulated annealing ################################################################################ #' @param iterations Integer. The maximum number of iterations that should be -#' used for the optimization. Defaults to \code{iterations = 100}. IS 100 A GOOD NUMBER? I WOULD THINK IT IS TOO LITTLE. +#' used for the optimization. Defaults to \code{iterations = 100}. #' #' @param acceptance List with two named sub-arguments: \code{initial} -- #' numeric value between 0 and 1 defining the initial acceptance probability, @@ -21,7 +21,7 @@ #' are updated at each 10 iterations. Defaults to \code{plotit = FALSE}. #' #' @param boundary SpatialPolygon. The boundary of the spatial domain. -#' If missing, it is calculated as the bounding box of \code{candi} using \code{\link[sp]{bbox}}. +#' If missing, it is estimated from \code{candi}. #' #' @param progress Logical for printing a progress bar. Defaults to #' \code{progress = TRUE}. diff --git a/man/optimACDC.Rd b/man/optimACDC.Rd index d0d53b6..5ad54f6 100644 --- a/man/optimACDC.Rd +++ b/man/optimACDC.Rd @@ -58,7 +58,7 @@ the projected x- and y-coordinates. If missing, they are estimated from \item{acceptance}{List with two named sub-arguments: \code{initial} -- numeric value between 0 and 1 defining the initial acceptance probability, and \code{cooling} -- a numeric value defining the exponential factor by -witch the acceptance probability decreases at each iteration. Defaults to +which the acceptance probability decreases at each iteration. Defaults to \code{acceptance = list(initial = 0.99, cooling = iterations / 10)}.} \item{stopping}{List with one named sub-argument: \code{max.count} -- @@ -74,7 +74,7 @@ are updated at each 10 iterations. Defaults to \code{plotit = FALSE}.} \item{track}{Logical value. Should the evolution of the energy state and acceptance probability be recorded and returned with the result? If -\code{track = FALSE} (the default), only the starting and ending enery state +\code{track = FALSE} (the default), only the starting and ending energy state values are returned with the result.} \item{boundary}{SpatialPolygon. The boundary of the spatial domain. @@ -252,9 +252,9 @@ The \emph{correlation} between two numeric covariates is measured using the Pearson's r, a descriptive statistic that ranges from $-1$ to $+1$. This statistic is also known as the linear correlation coefficient. -When the set of covariates includes factor covariates, any numeric covariate -is transformed into a factor covariate. The factor levels are defined -using the marginal sampling strata created using one of the two methods +When the set of covariates includes factor covariates, all numeric covariates +are transformed into factor covariates. The factor levels are defined +using the marginal sampling strata created from one of the two methods available (equal-area or equal-range strata). The \emph{association} between two factor covariates is measured using the @@ -270,7 +270,7 @@ of association (weak or strong). Reproducing the marginal distribution of the numeric covariates depends upon the definition of marginal sampling strata. These marginal sampling strata -are also used to define the factor levels of any numeric covariate when they +are also used to define the factor levels of all numeric covariates that are passed together with factor covariates. Two types of marginal sampling strata can be used. \emph{Equal-area} @@ -285,7 +285,7 @@ relatively high frequency in the population of covariate values. The number of repeated break points increases with the number of marginal sampling strata. Only unique break points are used to create marginal sampling strata. -\emph{Equal-range} sampling strata are defined breaking the range of +\emph{Equal-range} sampling strata are defined by breaking the range of covariate values into pieces of equal size. This method usually creates break points that do not occur in the population of existing covariate values. Such break points are replaced by the nearest existing covariate @@ -302,7 +302,7 @@ some of them with different area/size. Because the goal is to have a sample that reproduces the marginal distribution of the covariate, each marginal sampling strata will have a different number of sample points. The wanted distribution of the number of sample points per marginal strata is estimated -empirically computing the proportion of points of the population of existing +empirically as the proportion of points in the population of existing covariate values that fall in each marginal sampling strata. } \examples{ diff --git a/man/optimCORR.Rd b/man/optimCORR.Rd index 23c6b3f..d79e986 100644 --- a/man/optimCORR.Rd +++ b/man/optimCORR.Rd @@ -55,7 +55,7 @@ the projected x- and y-coordinates. If missing, they are estimated from \item{acceptance}{List with two named sub-arguments: \code{initial} -- numeric value between 0 and 1 defining the initial acceptance probability, and \code{cooling} -- a numeric value defining the exponential factor by -witch the acceptance probability decreases at each iteration. Defaults to +which the acceptance probability decreases at each iteration. Defaults to \code{acceptance = list(initial = 0.99, cooling = iterations / 10)}.} \item{stopping}{List with one named sub-argument: \code{max.count} -- @@ -71,7 +71,7 @@ are updated at each 10 iterations. Defaults to \code{plotit = FALSE}.} \item{track}{Logical value. Should the evolution of the energy state and acceptance probability be recorded and returned with the result? If -\code{track = FALSE} (the default), only the starting and ending enery state +\code{track = FALSE} (the default), only the starting and ending energy state values are returned with the result.} \item{boundary}{SpatialPolygon. The boundary of the spatial domain. @@ -240,9 +240,9 @@ The \emph{correlation} between two numeric covariates is measured using the Pearson's r, a descriptive statistic that ranges from $-1$ to $+1$. This statistic is also known as the linear correlation coefficient. -When the set of covariates includes factor covariates, any numeric covariate -is transformed into a factor covariate. The factor levels are defined -using the marginal sampling strata created using one of the two methods +When the set of covariates includes factor covariates, all numeric covariates +are transformed into factor covariates. The factor levels are defined +using the marginal sampling strata created from one of the two methods available (equal-area or equal-range strata). The \emph{association} between two factor covariates is measured using the diff --git a/man/optimDIST.Rd b/man/optimDIST.Rd index 9ec3eb1..ce21b1f 100644 --- a/man/optimDIST.Rd +++ b/man/optimDIST.Rd @@ -55,7 +55,7 @@ the projected x- and y-coordinates. If missing, they are estimated from \item{acceptance}{List with two named sub-arguments: \code{initial} -- numeric value between 0 and 1 defining the initial acceptance probability, and \code{cooling} -- a numeric value defining the exponential factor by -witch the acceptance probability decreases at each iteration. Defaults to +which the acceptance probability decreases at each iteration. Defaults to \code{acceptance = list(initial = 0.99, cooling = iterations / 10)}.} \item{stopping}{List with one named sub-argument: \code{max.count} -- @@ -71,7 +71,7 @@ are updated at each 10 iterations. Defaults to \code{plotit = FALSE}.} \item{track}{Logical value. Should the evolution of the energy state and acceptance probability be recorded and returned with the result? If -\code{track = FALSE} (the default), only the starting and ending enery state +\code{track = FALSE} (the default), only the starting and ending energy state values are returned with the result.} \item{boundary}{SpatialPolygon. The boundary of the spatial domain. @@ -238,7 +238,7 @@ function B. Reproducing the marginal distribution of the numeric covariates depends upon the definition of marginal sampling strata. These marginal sampling strata -are also used to define the factor levels of any numeric covariate when they +are also used to define the factor levels of all numeric covariates that are passed together with factor covariates. Two types of marginal sampling strata can be used. \emph{Equal-area} @@ -253,7 +253,7 @@ relatively high frequency in the population of covariate values. The number of repeated break points increases with the number of marginal sampling strata. Only unique break points are used to create marginal sampling strata. -\emph{Equal-range} sampling strata are defined breaking the range of +\emph{Equal-range} sampling strata are defined by breaking the range of covariate values into pieces of equal size. This method usually creates break points that do not occur in the population of existing covariate values. Such break points are replaced by the nearest existing covariate @@ -270,7 +270,7 @@ some of them with different area/size. Because the goal is to have a sample that reproduces the marginal distribution of the covariate, each marginal sampling strata will have a different number of sample points. The wanted distribution of the number of sample points per marginal strata is estimated -empirically computing the proportion of points of the population of existing +empirically as the proportion of points in the population of existing covariate values that fall in each marginal sampling strata. } \examples{ diff --git a/man/optimMKV.Rd b/man/optimMKV.Rd index 4f431e9..56a7b42 100644 --- a/man/optimMKV.Rd +++ b/man/optimMKV.Rd @@ -63,7 +63,7 @@ the projected x- and y-coordinates. If missing, they are estimated from \item{acceptance}{List with two named sub-arguments: \code{initial} -- numeric value between 0 and 1 defining the initial acceptance probability, and \code{cooling} -- a numeric value defining the exponential factor by -witch the acceptance probability decreases at each iteration. Defaults to +which the acceptance probability decreases at each iteration. Defaults to \code{acceptance = list(initial = 0.99, cooling = iterations / 10)}.} \item{stopping}{List with one named sub-argument: \code{max.count} -- @@ -79,7 +79,7 @@ are updated at each 10 iterations. Defaults to \code{plotit = FALSE}.} \item{track}{Logical value. Should the evolution of the energy state and acceptance probability be recorded and returned with the result? If -\code{track = FALSE} (the default), only the starting and ending enery state +\code{track = FALSE} (the default), only the starting and ending energy state values are returned with the result.} \item{boundary}{SpatialPolygon. The boundary of the spatial domain. diff --git a/man/optimMSSD.Rd b/man/optimMSSD.Rd index e6fc076..29f8f5b 100644 --- a/man/optimMSSD.Rd +++ b/man/optimMSSD.Rd @@ -43,7 +43,7 @@ the projected x- and y-coordinates. If missing, they are estimated from \item{acceptance}{List with two named sub-arguments: \code{initial} -- numeric value between 0 and 1 defining the initial acceptance probability, and \code{cooling} -- a numeric value defining the exponential factor by -witch the acceptance probability decreases at each iteration. Defaults to +which the acceptance probability decreases at each iteration. Defaults to \code{acceptance = list(initial = 0.99, cooling = iterations / 10)}.} \item{stopping}{List with one named sub-argument: \code{max.count} -- @@ -59,7 +59,7 @@ are updated at each 10 iterations. Defaults to \code{plotit = FALSE}.} \item{track}{Logical value. Should the evolution of the energy state and acceptance probability be recorded and returned with the result? If -\code{track = FALSE} (the default), only the starting and ending enery state +\code{track = FALSE} (the default), only the starting and ending energy state values are returned with the result.} \item{boundary}{SpatialPolygon. The boundary of the spatial domain. diff --git a/man/optimPPL.Rd b/man/optimPPL.Rd index 29705a0..3f184b5 100644 --- a/man/optimPPL.Rd +++ b/man/optimPPL.Rd @@ -81,7 +81,7 @@ the projected x- and y-coordinates. If missing, they are estimated from \item{acceptance}{List with two named sub-arguments: \code{initial} -- numeric value between 0 and 1 defining the initial acceptance probability, and \code{cooling} -- a numeric value defining the exponential factor by -witch the acceptance probability decreases at each iteration. Defaults to +which the acceptance probability decreases at each iteration. Defaults to \code{acceptance = list(initial = 0.99, cooling = iterations / 10)}.} \item{stopping}{List with one named sub-argument: \code{max.count} -- @@ -97,7 +97,7 @@ are updated at each 10 iterations. Defaults to \code{plotit = FALSE}.} \item{track}{Logical value. Should the evolution of the energy state and acceptance probability be recorded and returned with the result? If -\code{track = FALSE} (the default), only the starting and ending enery state +\code{track = FALSE} (the default), only the starting and ending energy state values are returned with the result.} \item{boundary}{SpatialPolygon. The boundary of the spatial domain. diff --git a/man/optimSPAN.Rd b/man/optimSPAN.Rd index 3d083cf..99fa599 100644 --- a/man/optimSPAN.Rd +++ b/man/optimSPAN.Rd @@ -92,7 +92,7 @@ the projected x- and y-coordinates. If missing, they are estimated from \item{acceptance}{List with two named sub-arguments: \code{initial} -- numeric value between 0 and 1 defining the initial acceptance probability, and \code{cooling} -- a numeric value defining the exponential factor by -witch the acceptance probability decreases at each iteration. Defaults to +which the acceptance probability decreases at each iteration. Defaults to \code{acceptance = list(initial = 0.99, cooling = iterations / 10)}.} \item{stopping}{List with one named sub-argument: \code{max.count} -- @@ -108,7 +108,7 @@ are updated at each 10 iterations. Defaults to \code{plotit = FALSE}.} \item{track}{Logical value. Should the evolution of the energy state and acceptance probability be recorded and returned with the result? If -\code{track = FALSE} (the default), only the starting and ending enery state +\code{track = FALSE} (the default), only the starting and ending energy state values are returned with the result.} \item{boundary}{SpatialPolygon. The boundary of the spatial domain. @@ -280,9 +280,9 @@ The \emph{correlation} between two numeric covariates is measured using the Pearson's r, a descriptive statistic that ranges from $-1$ to $+1$. This statistic is also known as the linear correlation coefficient. -When the set of covariates includes factor covariates, any numeric covariate -is transformed into a factor covariate. The factor levels are defined -using the marginal sampling strata created using one of the two methods +When the set of covariates includes factor covariates, all numeric covariates +are transformed into factor covariates. The factor levels are defined +using the marginal sampling strata created from one of the two methods available (equal-area or equal-range strata). The \emph{association} between two factor covariates is measured using the @@ -298,7 +298,7 @@ of association (weak or strong). Reproducing the marginal distribution of the numeric covariates depends upon the definition of marginal sampling strata. These marginal sampling strata -are also used to define the factor levels of any numeric covariate when they +are also used to define the factor levels of all numeric covariates that are passed together with factor covariates. Two types of marginal sampling strata can be used. \emph{Equal-area} @@ -313,7 +313,7 @@ relatively high frequency in the population of covariate values. The number of repeated break points increases with the number of marginal sampling strata. Only unique break points are used to create marginal sampling strata. -\emph{Equal-range} sampling strata are defined breaking the range of +\emph{Equal-range} sampling strata are defined by breaking the range of covariate values into pieces of equal size. This method usually creates break points that do not occur in the population of existing covariate values. Such break points are replaced by the nearest existing covariate @@ -330,7 +330,7 @@ some of them with different area/size. Because the goal is to have a sample that reproduces the marginal distribution of the covariate, each marginal sampling strata will have a different number of sample points. The wanted distribution of the number of sample points per marginal strata is estimated -empirically computing the proportion of points of the population of existing +empirically as the proportion of points in the population of existing covariate values that fall in each marginal sampling strata. } diff --git a/man/optimUSER.Rd b/man/optimUSER.Rd index 2b9c690..3ad5a02 100644 --- a/man/optimUSER.Rd +++ b/man/optimUSER.Rd @@ -47,7 +47,7 @@ the projected x- and y-coordinates. If missing, they are estimated from \item{acceptance}{List with two named sub-arguments: \code{initial} -- numeric value between 0 and 1 defining the initial acceptance probability, and \code{cooling} -- a numeric value defining the exponential factor by -witch the acceptance probability decreases at each iteration. Defaults to +which the acceptance probability decreases at each iteration. Defaults to \code{acceptance = list(initial = 0.99, cooling = iterations / 10)}.} \item{stopping}{List with one named sub-argument: \code{max.count} -- @@ -63,7 +63,7 @@ are updated at each 10 iterations. Defaults to \code{plotit = FALSE}.} \item{track}{Logical value. Should the evolution of the energy state and acceptance probability be recorded and returned with the result? If -\code{track = FALSE} (the default), only the starting and ending enery state +\code{track = FALSE} (the default), only the starting and ending energy state values are returned with the result.} \item{boundary}{SpatialPolygon. The boundary of the spatial domain.