sum and conditionally count based on a second column - r

Question

I have gotten frustrated trying to solve this seemingly simple problem. I have a dataset (df) like this:
structure(list(Year = c(2015L, 2015L, 2015L, 2015L, 2015L, 2015L,
2015L, 2015L, 2015L, 2015L, 2015L, 2015L, 2015L, 2015L, 2015L,
2015L, 2015L, 2015L, 2015L, 2015L), Unknown = c(1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L
), Temp = c(21L, 21L, 21L, 23L, 23L, 21L, 21L, 22L, 21L, 23L,
23L, 22L, 21L, 21L, 22L, 22L, 21L, 21L, 23L, 23L), Obs = structure(c(1L,
1L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 1L,
1L, 2L, 2L), .Label = c("mdk", "sde"), class = "factor"), State = structure(c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L), .Label = "ma", class = "factor"), Zone = c(2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L), Segment = c(8L, 7L, 4L, 17L, 18L, 7L, 2L, 12L, 1L, 17L,
18L, 12L, 9L, 7L, 13L, 11L, 8L, 9L, 17L, 18L), Subseg = c(1L,
3L, 3L, 2L, 2L, 2L, 4L, 0L, 10L, 4L, 2L, 0L, 1L, 1L, 3L, 1L,
2L, 2L, 1L, 1L), Wdir = structure(c(2L, 2L, 1L, 3L, 3L, 2L, 2L,
1L, 2L, 3L, 3L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L), .Label = c("na",
"ne", "nw"), class = "factor"), Wvel = structure(c(1L, 1L, 2L,
1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L,
2L), .Label = c("5", "na"), class = "factor"), Clouds = structure(c(1L,
1L, 3L, 1L, 1L, 1L, 1L, 3L, 1L, 1L, 1L, 3L, 1L, 1L, 3L, 3L, 1L,
1L, 3L, 3L), .Label = c("1", "4", "na"), class = "factor"), Temp.1 = structure(c(1L,
1L, 3L, 1L, 1L, 1L, 1L, 3L, 1L, 1L, 1L, 3L, 1L, 1L, 3L, 3L, 1L,
1L, 3L, 3L), .Label = c("20", "25", "na"), class = "factor"),
Species = structure(c(7L, 21L, 1L, 21L, 16L, 4L, 16L, 6L,
1L, 17L, 5L, 7L, 5L, 1L, 1L, 6L, 7L, 7L, 24L, 5L), .Label = c("ABDU",
"ABDU", "ABDU", "ABDU", "ABDU", "CAGO", "CAGO", "CAGO", "CAGO",
"CAGO", "GOLD", "GOLD", "GOLD", "GOLD", "GOLD", "MERG", "MERG",
"MERG", "MERG", "MERG", "SCOT", "SCOT", "SCOT", "SCOT",
"SCOT", "SCOT", "SCOT"), class = "factor"), Count = c(5L,
1L, 150L, 3L, 20L, 8L, 5L, 10L, 5L, 1L, 20L, 10L, 2L, 2L,
80L, 40L, 1L, 1000L, 2L, 20L)), .Names = c("Year", "Unknown",
"Temp", "Obs", "State", "Zone", "Segment", "Subseg", "Wdir",
"Wvel", "Clouds", "Temp.1", "Species", "Count"), row.names = c(666L,
614L, 2060L, 1738L, 1459L, 536L, 197L, 2467L, 98L, 1794L, 1449L,
2464L, 696L, 483L, 2644L, 2350L, 686L, 844L, 2989L, 2934L), class = "data.frame")
With a header that looks like this:
Year Unknown Temp Obs State Zone Segment Subseg Wdir Wvel
666 2015 1 21 mdk ma 2 8 1 ne 5
614 2015 1 21 mdk ma 2 7 3 ne 5
2060 2015 1 21 sde ma 2 4 3 na na
1738 2015 1 23 mdk ma 2 17 2 nw 5
1459 2015 1 23 mdk ma 2 18 2 nw 5
536 2015 1 21 mdk ma 2 7 2 ne 5
Clouds Temp.1 Species Count
666 1 20 CAGO 5
614 1 20 SCOT 1
2060 na na ABDU 150
1738 1 20 SCOT 3
1459 1 20 MERG 20
536 1 20 ABDU 8
Among other things within dplyr, I want to get a sum of each species as a new column, when I am grouping by segment. This is the final code I have tried with many variations.
df_group = df %>%
group_by(Segment) %>%
summarise(temp = round(mean(Temp)),
WDir = round(mean(Wdir)),
ABDU = sum(which(Species=="ABDU"),Count),
CAGO = sum(which(Species=="CAGO"),Count),
GOLD = sum(which(Species=="GOLD"),Count),
MERG = sum(which(Species=="MERG"),Count),
SCOT = sum(which(Species=="SCOT"),Count))
And this is what I get (to show correct format):
Segment temp WDir ABDU CAGO GOLD MERG SCOT
1 1 21 2 6 5 5 5 5
2 2 21 2 5 5 5 6 5
3 4 21 1 151 150 150 150 150
4 7 21 2 16 11 11 11 12
5 8 21 2 6 9 6 6 6
6 9 21 2 1003 1004 1002 1002 1002
The format and general idea are what I want, but the numbers are not adding up the way I want them to. I'm sure it is simple but need some help! Thanks.

Answer 1

The problem is that which returns a vector of the positions, but you're not using those to subset. So the sum you are getting is of the positions which are true in addition to the count variable. e.g.
x <- c("a", "b", "b")
count <- c(10, 11, 12)
sum(which(c("a", "b", "b") == "b"), count)
# 38 because it is 2 + 3 + 10 + 11 + 12
I believe what you want is (or at least one way of writing it):
sum(ifelse(x == "b", count, 0))
# 23 because it is equal to 0 + 11 + 12
Translating into dplyr syntax, your example could look like this:
df_group = df %>%
group_by(Segment) %>%
summarise(temp = round(mean(Temp)),
WDir = round(mean(Wdir)),
ABDU = sum(ifelse(Species=="ABDU", Count, 0L)),
CAGO = sum(ifelse(Species=="CAGO", Count, 0L)),
GOLD = sum(ifelse(Species=="GOLD", Count, 0L)),
MERG = sum(ifelse(Species=="MERG", Count, 0L)),
SCOT = sum(ifelse(Species=="SCOT", Count, 0L)))

Answer 2

Another approach, in case you don't want to type out the sum for all your species:
library(reshape2)
library(dplyr)
# I had a problem with duplicate factor levels from your dput,
# so I re-factored species
df$Species = as.factor(as.character(df$Species))
species.counts = select(df, Segment, Species, Count) %>%
dcast(formula = Segment ~ Species, value.var = "Count", fun.aggregate = sum)
> head(species.counts)
Segment ABDU CAGO MERG SCOT
1 1 5 0 0 0
2 2 0 0 5 0
3 4 150 0 0 0
4 7 10 0 0 1
5 8 0 6 0 0
6 9 2 1000 0 0
df %>% group_by(Segment) %>%
summarise(temp = round(mean(Temp))) %>%
left_join(species.counts)
Source: local data frame [11 x 6]
Segment temp ABDU CAGO MERG SCOT
1 1 21 5 0 0 0
2 2 21 0 0 5 0
3 4 21 150 0 0 0
4 7 21 10 0 0 1
5 8 21 0 6 0 0
6 9 21 2 1000 0 0
I also couldn't do the wind direction average, because your dput data only has that as a factor with the directions, not like the head() you showed, but the technique generalizes.