Incorrect values when summing values in a column according to other 3 columns

I am working on the output file from phyloseq object. I calculated the rel.abundance and extracted the columns I am interested in as follows: this is how I calculate the rel_abund

dat <- read_excel("selected_data.xlsx")%>% group_by(OTU)%>% mutate(rel_abund = Abundance/sum(Abundance))
dat

OTU Abundance SampleID Genotype rel_abund ASV2 4988 P35 genotype1 0.2801617614 ASV4 3894 1P-GH-R2 genotype2 0.9660133962 ASV7 3681 P53 genotype1 0.5047305636 ASV3 2149 P16 genotype4 0.3943842907

Then I need to calculate the summed relative abundance of each ASV in each genotype. Each genotype is represented by 1-5 samples, and I have 44 ASVs of 2,464 rows according to their occurrences in samples

To display each ASV along with its rel_abund across genotypes including sampleIDs, I tried this

dat %>%
  count(OTU, SampleID, rel_abund, Genotype) %>%
  pivot_wider(names_from = SampleID, values_from = n)

results in

OTU rel_abund Genotype 1P-R1 1P-R2 P1 ....... ASV1 0.0000000000 genotype11 1 1 NA NA NA NA NA
ASV1 0.0000000000 genotype2 NA NA 1 NA NA NA NA

Then,

dat %>%
  group_by(OTU, Genotype) %>%
  summarize(Summed_rel_abund = sum(rel_abund >= 0, na.rm = TRUE))

gives:

OTU Genotype Summed_rel_abund ASV1 genotype1 1
ASV1 genotype3 3
ASV1 genotype2 1
ASV1 genotype5 3
ASV1 genotype6 2
ASV10 genotype7 5
ASV10 genotype8 5

I do not how the sum is integers and the summed values are decimal fractions. I doubt the last step and I need a correction, please! Thanks

Solution

Currently, sum(rel_abund >= 0) is summing the TRUE values of the >= 0 test, counting each as 1, therefore effectively just counting. To sum the values where the value >= 0 try sum(rel_abund[rel_abund >= 0], na.rm = TRUE):

dat %>%
  group_by(OTU, Genotype) %>%
  summarize(Summed_rel_abund = sum(rel_abund[rel_abund >= 0], na.rm = TRUE)) 

#> # A tibble: 4 x 3
#> # Groups:   OTU [4]
#>   OTU   Genotype  Summed_rel_abund
#>   <chr> <chr>                <dbl>
#> 1 ASV2  genotype1            0.280
#> 2 ASV3  genotype4            0.394
#> 3 ASV4  genotype2            0.966
#> 4 ASV7  genotype1            0.505

^{Created on 2022-03-18 by the reprex package (v2.0.1)}