Problem with saving the output of a simple loop in R

Question

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I'm having a frustrating problem collecting the output of a simple loop that I can't crack.

Here is the loop, which calculates the same summary statistic many times using different upper limits of my data. This gives me correct values and prints them with no issues.

> for (i in maxdist) + { + homo_sax <- sum(W_distances$distance > 0 & W_distances$distance < i & W_distances$concat_ID=="saxatilis_saxatilis") ## count all sax_sax pairs + homo_arc <- sum(W_distances$distance > 0 & W_distances$distance < i & W_distances$concat_ID=="arcana_arcana") ## count all the arc_arc pairs + hetero <- sum(W_distances$distance > 0 & W_distances$distance < i & W_distances$concat_ID=="arcana_saxatilis") ## count all the arc_sax pairs + total_homo = homo_sax + homo_arc ## calculate the total number of homo observations + temp_RI <- 1-2*hetero/(total_homo+hetero) ### calculate RI according to equation RI4 from Sobel & Chen (2013) + print(temp_RI) + } [1] 0.2046285 [1] 0.1603105 [1] 0.1195596 [1] 0.01857161 [1] 0.01784158 [1] 0.01498829 >

The problem arises when I try and save these values to an empty vector, as I obtain numbers that are different, and are not correct:

> maxdist <- seq(from = 0.5, to = 3, by = 0.5) ## the max distance for each bin RI_bins <- vector("numeric",length(maxdist)) for (i in maxdist) { homo_sax <- sum(W_distances$distance > 0 & W_distances$distance < i & W_distances$concat_ID=="saxatilis_saxatilis") ## collect all sax_sax pairs homo_arc <- sum(W_distances$distance > 0 & W_distances$distance < i & W_distances$concat_ID=="arcana_arcana") ## collect all the arc_arc pairs hetero <- sum(W_distances$distance > 0 & W_distances$distance < i & W_distances$concat_ID=="arcana_saxatilis") total_homo = homo_sax + homo_arc temp_RI <- 1-2*hetero/(total_homo+hetero) ### equation RI4 from Sobel & Chen (2013) RI_bins[i]<-temp_RI } > RI_bins [1] 0.11955961 0.01784158 0.01498829 0.00000000 0.00000000 0.00000000

I'd be very grateful if someone could help me to understand what I am missing here. Thanks in advance!!

Sean

r2evans · Accepted Answer · 2020-03-27 16:26:06Z

maxdist is a floating point number, not to be used as the index in a vector. By trying that, the fractional number is truncated and inserted there.

vec <- numeric(5) vec # [1] 0 0 0 0 0 vec[2.5] <- 3 vec # [1] 0 3 0 0 0 vec[2.1] <- 2 vec # [1] 0 2 0 0 0 vec[2.9] <- 1 vec # [1] 0 1 0 0 0

Instead, try this code. The two changes are: using seq_along to count along the length of maxdist, and then assign to and use md for comparison using this index.

maxdist <- seq(from = 0.5, to = 3, by = 0.5) ## the max distance for each bin RI_bins <- vector("numeric",length(maxdist)) for (i in seq_along(maxdist)) { md <- maxdist[i] homo_sax <- sum(W_distances$distance > 0 & W_distances$distance < md & W_distances$concat_ID=="saxatilis_saxatilis") ## collect all sax_sax pairs homo_arc <- sum(W_distances$distance > 0 & W_distances$distance < md & W_distances$concat_ID=="arcana_arcana") ## collect all the arc_arc pairs hetero <- sum(W_distances$distance > 0 & W_distances$distance < md & W_distances$concat_ID=="arcana_saxatilis") total_homo = homo_sax + homo_arc temp_RI <- 1-2*hetero/(total_homo+hetero) ### equation RI4 from Sobel & Chen (2013) RI_bins[i]<-temp_RI }

(Untested, as we don't have your data.)

Thanks so much for taking the time to look at this and for your explanation.

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