Function curve_area

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: Lexiguel
-Version: 0.0.0.9008
+Version: 0.0.0.9009
 Date: 2016-10-27
 Title: Miscellaneous Functions
 Authors@R: person("Miguel", "Alvarez", email="[email protected]",

NAMESPACE

@@ -8,6 +8,7 @@ importFrom("stats", "terms")
 
 ## Export regular function names
 export(
+	curve_area,
     error_bars,
     gap_id,
     gap_fill,

R/sloss.R

@@ -4,9 +4,9 @@
 ################################################################################
 
 # Internal function calculating area below the curve (trapezoids)
-curve_area <- function(x, y) {
-    D1 <- c(0, diff(x))
-    D2 <- c(0, diff(y))
+curve_area <- function(x, y, bottom=0) {
+    D1 <- c(bottom, diff(x))
+    D2 <- c(bottom, diff(y))
     Area <- sum(D1*y + D1*D2/2)
     return(Area)
 }

man/curve_area.Rd

@@ -0,0 +1,47 @@
+\name{curve_area}
+\alias{curve_area}
+
+\title{Calculation of area below a curve.}
+\description{
+This function calculates the area below a curve by the trapezoidal rule.
+}
+\usage{
+curve_area(x, y, bottom=0)
+}
+\arguments{
+	\item{x}{A numerical vector with the ordinate values.}
+	\item{y}{A numerical vector with the abscissa values.}
+	\item{bottom}{A numerical value indicating the bottom for area calculation.}
+}
+\details{
+The argument \code{bottom} can be adjusted to the minimum observed values an
+will be particularly useful when values of \code{y} are negative.
+
+Curves going bellow the \code{bottom} value will get a negative value of area
+and therefore subtracted when \code{y} cuts the bottom value.
+
+This function was originally written as internal function for the calculations
+done by \code{\link{sloss}}.
+}
+\value{
+A numeric value.
+}
+\author{
+Miguel Alvarez (\email{malvarez@uni-bonn.de}).
+}
+\examples{
+## Load gaps from the Robinson Crusoe Island
+library(Lexiguel)
+data(rc_gaps)
+data(rc_gaps.env)
+
+## Calculation of curves
+rc_curves <- sloss(rc_gaps, rc_gaps.env, area)
+
+## Area calculated by function
+rc_curves$Index
+
+## Cross-check
+with(rc_curves$SL, curve_area(area, species))/with(rc_curves$LS,
+	curve_area(area, species))
+}

man/gap_fill.Rd

@@ -35,6 +35,8 @@ is the vector \code{x} with NAs replaced by custom values.
 Miguel Alvarez (\email{malvarez@uni-bonn.de}).
 }
 \examples{
+library(Lexiguel)
+
 ## A vector with two gaps
 A <- c(1:5, NA, NA, 7:10, NA, NA, NA, 16:20)
 A