Integrate functions for depth integrated species abundance - r

Question

Hei,
I am trying to calculate the organisms quantity per class over the entire depth range (e.g., from 10 m to 90 m). To do that I have the abundance at certain depths (e.g., 10, 30 and 90 m) and I use the integrate function which calculate:
the average of abundance between each pair of depths, multiplied by the difference of the pairs of depths. The values are summed up over the entire depth water column to get a totale abundance over the water column.
See an example (only a tiny part of bigger data set with several locations and year, more class and depths):
View(df)
Class Depth organismQuantity
1 Ciliates 10 1608.89
2 Ciliates 30 2125.09
3 Ciliates 90 1184.92
4 Dinophyceae 10 0.00
5 Dinoflagellates 30 28719.60
6 Dinoflagellates 90 4445.26
integrate = function(x) {
averages = (x$organismQuantity[1:length(x)-1] + x$organismQuantity[2:length(x)]) / 2
sum(averages * diff(x$Depth))
}
result = ddply(df, .(Class), integrate)
print(result)
But I got these result and warning message for lines with NA value :
Class V1
1 Ciliates 136640.1
2 Dinoflagellates NA
3 Dinophyceae 0.0
Warning messages:
1: In averages * diff(x$Depth) :
longer object length is not a multiple of shorter object length
I don't understand why Dinoflagellates got NA value... It is the same for several others class in my complete data set (for some class abundance the integration equation applies for others I got the warning message).
thank you for the help!!
Cheers,
Lucie

Answer 1

Here is a way using function trapz from package caTools, adapted to the problem.
#
# library(caTools)
# Author(s)
# Jarek Tuszynski
#
# Original, adapted
trapz <- function(DF, x, y){
x <- DF[[x]]
y <- DF[[y]]
idx <- seq_along(x)[-1]
as.double( (x[idx] - x[idx-1]) %*% (y[idx] + y[idx-1]) ) / 2
}
library(plyr)
ddply(df, .(Class), trapz, x = "Depth", y = "organismQuantity")
# Class V1
#1 Ciliates 136640.1
#2 Dinoflagellates 994945.8
#3 Dinophyceae NA
Data
df <- read.table(text = "
Class Depth organismQuantity
1 Ciliates 10 1608.89
2 Ciliates 30 2125.09
3 Ciliates 90 1184.92
4 Dinophyceae 10 0.00
5 Dinoflagellates 30 28719.60
6 Dinoflagellates 90 4445.26
", header = TRUE)