CODEWITHSUNDEEP
rfor-loop
Sean18
Sean18

Reputation: 1

Problem with saving the output of a simple loop in R

Hope this email finds you safe and healthy!

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

Upvotes: 0

Views: 26

Answers (1)

r2evans
r2evans

Reputation: 160447

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.)

Upvotes: 1

Related Questions