Aggregate and summarise character object with R

April 4, 2022

I have a breeding productivity dataset:

df1
    # Nest.box Obs.type individual.number Clutch Chick.status
    # 1 Nest1 Egg 1 First NA
    # 2 Nest1 Egg 2 First NA
    # 3 Nest1 Egg 3 First NA
    # 4 Nest2 Egg 1 First NA
    # 5 Nest2 Egg 2 First NA
    # 6 Nest2 Egg 1 First NA
    # 7 Nest1 Chick 1 First Dead
    # 8 Nest1 Chick 2 First Fledged
    # 9 Nest2 Chick 1 First Fledged
    # 10 Nest2 Chick 2 First Fledged
    # 11 Nest2 Chick 1 Second Fledged
    # 12 Nest2 Chick 2 Second UNK

I want to summarise these data by aggregating by Nest.box and Clutch (shows the number of "Fledged" by nest.box, by clutch)

The wanted output would be something like this:

output
        # Nest.box Clutch Fledged
        # 1 Nest1 First 1
        # 2 Nest2 First 2
        # 3 Nest2 Second 1

>Solution :

Here is a potential solution:

library(dplyr)

df <- read.table(text = "Nest.box Obs.type individual.number Clutch Chick.status
1 Nest1 Egg 1 First NA
2 Nest1 Egg 2 First NA
3 Nest1 Egg 3 First NA
4 Nest2 Egg 1 First NA
5 Nest2 Egg 2 First NA
6 Nest2 Egg 1 First NA
7 Nest1 Chick 1 First Dead
8 Nest1 Chick 2 First Fledged
9 Nest2 Chick 1 First Fledged
10 Nest2 Chick 2 First Fledged
11 Nest2 Chick 1 Second Fledged
12 Nest2 Chick 2 Second UNK", header = TRUE)

df %>%
  group_by(Nest.box, Clutch) %>%
  summarise(Fledged = sum(Chick.status == "Fledged", na.rm = TRUE))

#> # A tibble: 3 × 3
#> # Groups:   Nest.box [2]
#>   Nest.box Clutch Fledged
#>   <chr>    <chr>    <int>
#> 1 Nest1    First        1
#> 2 Nest2    First        2
#> 3 Nest2    Second       1

^{Created on 2022-04-04 by the reprex package (v2.0.1)}