Reputation: 97
I am a beginner in R, so please bear with me! I have a csv read into R, it shows the relative abundance of different species at 9 sites. I am trying to get a summation of the rows, however R will not read the numerical values as such, which is going to lead to more issues as I try to run an NMDS ordination analysis. Here are some details about my data:
class(MSBees.spp)
[1] "data.frame"
First few rows of what str()
prints:
str(MSBees.spp)
'data.frame': 9 obs. of 29 variables:
$ X : chr "Site 1" "Site 2" "Site 3" "Site 4" ...
$ COLALG: num 0.02013 0.00997 0 0 0 ...
$ COLCAL: num 0 0 0 0 0 0 0 0 0
$ COLCON: num 0 0 0 0 0 0 0.00339 0 0
$ COLFUL: num 0 0 0 0 0 0.00361 0 0 0
$ COLOBS: num 0.00671 0.00664 0.00755 0.00292 0 ...
What my code looks like so far:
MSBees.spp <- read.csv("data_transposed.csv", header = TRUE)
MSBees.env <- read.csv("data_transposed.env.csv", header = TRUE, row.names = 1)
MSBees_PA.spp <- read.csv("data_transposed.csv", header = TRUE, row.names = 1)
MSBees_abund.spp <- read.csv("data_transposed.csv", header = TRUE, row.names = 1)
sum.of.rows <- apply(MSBees.spp, 1, sum)
which returns:
Error in FUN(newX[, i], ...) : invalid 'type' (character) of argument
I have tried to coerce them to be numeric with:
as.numeric (MSBees.spp)
and
data.frame(lapply(MSBees.spp [2:9, 2:29], as.numeric))
but no luck in being able to run the apply()
function successfully.
Am I sure I am just not reading the csv in properly or coercing them properly, but just can't get it right. Any tips? Please and thank you!
Upvotes: 1
Views: 612
Reputation: 887991
The row wise sum
apply(MSBees.spp, 1, sum)
is an issue because the first column based on the str
is character.
$ X : chr "Site 1" "Site 2" "Site 3" "Site 4" ...
We need to exclude the first column
apply(MSBees.spp[-1], 1, sum)
and get the sum or use vectorized rowSums
rowSums(MSBees.spp[-1], na.rm = TRUE)
Also, there is no need to reconvert the dataset to numeric as the data is correctly read as numeric column types. In addition, as.numeric
expects a vector as input where as MSBees.spp
is a data.frame i.e. as.numeric(MSBees.spp[[2]])
works as it is a vector
Upvotes: 3