From 6fd049b11e32048071e2a3d1924b18eb4d57dd8f Mon Sep 17 00:00:00 2001
From: Miguel Alvarez <malvarez@uni-bonn.de>
Date: Fri, 28 Oct 2016 00:10:24 +0200
Subject: [PATCH] Function curve_area

---
 DESCRIPTION       |  2 +-
 NAMESPACE         |  1 +
 R/sloss.R         |  6 +++---
 man/curve_area.Rd | 47 +++++++++++++++++++++++++++++++++++++++++++++++
 man/gap_fill.Rd   |  2 ++
 5 files changed, 54 insertions(+), 4 deletions(-)
 create mode 100644 man/curve_area.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 28040a2..5194ddb 100644
--- a/DESCRIPTION
+++ b/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="malvarez@uni-bonn.de",
diff --git a/NAMESPACE b/NAMESPACE
index a7b1e9c..5fb4367 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -8,6 +8,7 @@ importFrom("stats", "terms")
 
 ## Export regular function names
 export(
+	curve_area,
     error_bars,
     gap_id,
     gap_fill,
diff --git a/R/sloss.R b/R/sloss.R
index d57a3bc..df65cf1 100644
--- a/R/sloss.R
+++ b/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)
 }
diff --git a/man/curve_area.Rd b/man/curve_area.Rd
new file mode 100644
index 0000000..9d20a73
--- /dev/null
+++ b/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))
+}
diff --git a/man/gap_fill.Rd b/man/gap_fill.Rd
index 70018f5..792fbc6 100644
--- a/man/gap_fill.Rd
+++ b/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