How to get presence/absence summary by month for each taxa to create ggplot bar plot?-CodePudding

I have fish stomach contents/diet data and I would like to get presence/absence information for each taxa in my df by month. Each observation (row) has information on the taxa absent (== 0) or present (== 1) in each fish's stomach. I have already transformed my original data to presence/absence values, however, I am not sure how to obtain a summary of what taxa was present or absent by month.

    structure(list(id = c("607_6", "808_4", "801_3", "807_11", "801_16", 
"724_13", "1030_40", "723_78", "701_4", "634_2", "1023_2", "1031_2", 
"643_4", "606_3", "723_79", "801_4", "629_4", "642_10", "801_10", 
"801_11", "1001_35", "616_4", "701_9", "627_2", "601_5"), Daphnia = c(0, 
0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0), Byths = c(0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 
1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1), Chiro.Pupae = c(0, 1, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0
), Empty = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), Chiro.Larvae = c(0, 
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 0, 0), Amphipod = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0), Isopod = c(0, 0, 0, 0, 0, 
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), 
    Chironomidae = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Hemimysis = c(0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0), Copepoda = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0), Sphaeriidae = c(0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0), Chiro.Adult = c(0, 0, 0, 0, 0, 0, 0, 1, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Trichopteran = c(0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 1, 0, 0, 0), UID.Fish = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Chydoridae = c(0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0), Cyclopoid = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Fish.Eggs = c(0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0), EggMass = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Dreissena = c(0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0), Goby = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Eurycercidae = c(0, 
    0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0), Hirudinea = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), totalnumPrey = c(0, 
    5, 0, 0, 102, 7, 220, 45, 0, 0, 0, 25, 116, 49, 119, 0, 7, 
    5, 0, 0, 0, 595, 105, 58, 20), MONTH = c(6L, 8L, 8L, 8L, 
    8L, 7L, 11L, 7L, 7L, 6L, 11L, 11L, 6L, 6L, 7L, 8L, 6L, 6L, 
    8L, 8L, 11L, 6L, 7L, 6L, 6L), empty = c("Empty", "Not_empty", 
    "Empty", "Empty", "Not_empty", "Not_empty", "Not_empty", 
    "Not_empty", "Empty", "Empty", "Empty", "Not_empty", "Not_empty", 
    "Not_empty", "Not_empty", "Empty", "Not_empty", "Not_empty", 
    "Empty", "Empty", "Empty", "Not_empty", "Not_empty", "Not_empty", 
    "Not_empty")), row.names = c(NA, -25L), class = c("data.table", 
"data.frame"))

I looked online and various SO posts like

Originally, the data was in long format but this results in multiple rows per fish. I changed to wide format to end up with one observation(row) per fish.

How can I achieve this to ultimately plot presence/absence by month? Thank you!

CodePudding user response：

Maybe you want something like with your selected column converted to a longer format. After that to show the zeros bars, you can say that there is a bar by giving it a small negative number (if you want to show zero bars). At last, the y-axis has a binary format. You can use the following code:

library(dplyr)
library(ggplot2)
library(tidyr)
library(lubridate)

df %>%
  select(MONTH, Daphnia, Byths, Chiro.Pupae, Isopod, Goby) %>%
  mutate(MONTH = month.name[MONTH]) %>%
  pivot_longer(cols = -c(MONTH), values_transform = as.numeric) %>%
  ggplot(aes(x = MONTH, y = sapply(value, FUN=function(x) ifelse(x==0,-0.1,x)), fill = name))  
  geom_bar(position = "dodge", stat = "identity")  
  scale_y_continuous(breaks = c(0,1))  
  labs(y = "Absence", x = "Month")

^{Created on 2022-07-30 by the reprex package (v2.0.1)}