How can I check if a value of a column in a dataframe in r corresponds to a single occurence of another columns for each row of the dataframe?

Question

I have a dataframe like this with the names of marine fish species in one of the column and their respective BIN in another column (which is a sort of ID for each species). Sometimes a single BIN number can correspond to more than one species and I want to check which species correspond to a single BIN and which ones have more than one BIN for each single species in each row. I'm sorry if I'm being confusing but I'm very lost in how I can do this. Thank you in advance for any suggestion

 1.  species          BIN
 2. Tilapia guineensis BOLD:AAL5979
 3. Tilapia zillii BOLD:AAB9042
 4. Fundulus rubrifrons BOLD:AAI7245
 5. Eutrigla gurnardus BOLD:AAC0262
 6.  Sprattus sprattus BOLD:AAE9187
 7.  Gadus morhua BOLD:ACF1143
 8. Clupea harengus BOLD:AAB7944
 (...)

Answer 1

With dplyr , you can do (I used sample data with a species having two BINs):

df %>%
 group_by(species) %>%
 summarise(occurrence = n_distinct(BIN),
           BIN = paste(unique(BIN), collapse = ","))

  species             occurrence BIN                      
  <chr>                    <int> <chr>                    
1 Clupea_harengus              1 BOLD:AAB7944             
2 Eutrigla_gurnardus           2 BOLD:AAC0262,BOLD:AAE9187
3 Fundulus_rubrifrons          1 BOLD:AAI7245             
4 Gadus_morhua                 1 BOLD:ACF1143             
5 Sprattus_sprattus            1 BOLD:AAE9187             
6 Tilapia_guineensis           1 BOLD:AAL5979             
7 Tilapia_zillii               1 BOLD:AAB9042 

It counts the number of BINs per "species" and combines together the name of unique BINs belonging to a species.

Sample data:

df <- read.table(text = "species          BIN
 2 Tilapia_guineensis BOLD:AAL5979
 3 Tilapia_zillii BOLD:AAB9042
 4 Fundulus_rubrifrons BOLD:AAI7245
 5 Eutrigla_gurnardus BOLD:AAC0262
 6 Eutrigla_gurnardus BOLD:AAE9187
 7  Sprattus_sprattus BOLD:AAE9187
 8  Gadus_morhua BOLD:ACF1143
 9 Clupea_harengus BOLD:AAB7944", header = TRUE,
                 stringsAsFactors = FALSE)

Answer 2

Another option in tidyverse would be to get the distinct rows, grouped by 'species', summarise the 'occurrence' as number of rows ( n() ) and use str_c (from stringr - part of the tidyverse packages - which would also give a different behavior when there is NA element) to collapse the elements into a single string

library(dplyr)
library(stringr)
df %>% 
    distinct() %>%
    group_by(species) %>%
    summarise(occurrence = n(),
       BIN = str_c(unique(BIN), collapse = ","))
# A tibble: 7 x 3
#  species             occurrence BIN                      
#  <chr>                    <int> <chr>                    
#1 Clupea_harengus              1 BOLD:AAB7944             
#2 Eutrigla_gurnardus           2 BOLD:AAC0262,BOLD:AAE9187
#3 Fundulus_rubrifrons          1 BOLD:AAI7245             
#4 Gadus_morhua                 1 BOLD:ACF1143             
#5 Sprattus_sprattus            1 BOLD:AAE9187             
#6 Tilapia_guineensis           1 BOLD:AAL5979             
#7 Tilapia_zillii               1 BOLD:AAB9042 

---

If there are NA elements, the behavior is slightly different (unless we take care of the NA s first)

paste(c(NA, 'a', 'b'), collapse=",")
#[1] "NA,a,b"
str_c(c(NA, 'a', 'b'), collapse=",")
#[1] NA

data

df <- structure(list(species = c("Tilapia_guineensis", "Tilapia_zillii", 
"Fundulus_rubrifrons", "Eutrigla_gurnardus", "Eutrigla_gurnardus", 
"Sprattus_sprattus", "Gadus_morhua", "Clupea_harengus"), BIN = c("BOLD:AAL5979", 
"BOLD:AAB9042", "BOLD:AAI7245", "BOLD:AAC0262", "BOLD:AAE9187", 
"BOLD:AAE9187", "BOLD:ACF1143", "BOLD:AAB7944")),
class = "data.frame", row.names = c("2", 
"3", "4", "5", "6", "7", "8", "9"))