Test if col names are in row names in R

0
votes

I would like to test if the column names of a matrix are contained within the rownames of a matrix i.e. if colnames(abun) and contained within rownames(x) in example below

abun <- matrix(c(0.4,0,0.6,0.1,0.4,0.5), 
    nrow = 2, ncol = 3, byrow = TRUE, dimnames = list(c("x", "y"), 
    c("A","B","C")))

 abun
    A   B   C
x 0.4 0.0 0.6
y 0.1 0.4 0.5

x<-data.frame("Trait1" =c(1,1,0,1),
                    "Trait2"=c(1,1,1,1),
                    "Trait3" =c(1,1,0,1),
                    "Trait4" =c(1,0,1,1))
rownames(x)<-c("A","B","C","D") 

x
  Trait1 Trait2 Trait3 Trait4
A      1      1      1      1
B      1      1      1      0
C      0      1      0      1
D      1      1      1      1

UPDATE: I am writing a function and would like an error message to be thrown if a colnames(abun) is not contained within rownames(x). I have tried:

if(colnames(abun) %in% rownames(x) = FALSE)
stop("species names in abun and x do not match")
2
rmatch

2 Answers

1
votes
colnames(abun)[
colnames(abun) %in% rownames(x)
]

colnames(abun) %in% rownames(x) returns a true/false vector indicating which element on colnames(abun) is present in rownames(x).

1
votes

Are you just asking for the intersection of 2 sets?

intersect(c("A","B","C","D") ,
          c("A","B","C"))
[1] "A" "B" "C"

To get the difference use setdiff:

setdiff(c("A","B","C","D") ,
          c("A","B","C"))
[1] "D"