How to get R to read my first column as a "header"?-CodePudding

I want to calculate diversity indices of different sampling sites in R. I have sites in the first row and the different species in the first column. However, R is reading the first column as normal data (not as a header so to speak).

Pics:

https://imgur.com/a/iBsFtbe

Code:

>Macro<-read.csv("C:\\Users\\Carly\\OneDrive\\Desktop\\Ecology >Projects\\Macroinvertebrates & Water >Quality\\Macro_RData\\Macroinvert\\MacroR\\MacroCSV.csv", header = T)

CodePudding user response：

You need to add row.names = 1 to your command. This will indicate that row names are stored in column number 1.

Macro <- read.csv("<...>/MacroCSV.csv", header = TRUE, row.names = 1)

I sense that you are frustrated. As r2evans said, it is easier for people to help you if you provide them with the data in text form and not with screenshots - because we can't recreate the problem or try to solve it by loading a screenshot into R.

CSV files are just text, so you can open them with a text editor such as NotePad and copy and paste it here. You don't need the whole text - the columns and lines needed to reproduce the problem are enough. This was what we were looking for:

Site,Aeshnidae,Amnicolidae,Ancylidae,Asellidae
AN0119A,0,0,0,6,0
AN0143,0,0,0,0,0

Programming for many people is very frustrating when they start out, don't let this discourage you!

CodePudding user response：

It looks like your data is in the wrong orientation for analysis in vegan - your species are the rows, and sites are columns. From your pics, it looks like you've spotted this issue and tried transposing, but are having issues with the placement of the headers.

Try reading your csv in, and specifying that the first column should be row names:

MacroDataDataFinal <- read.csv("Path/to/file.csv",
                                row.names=1)

Then transpose the data

MacroDataDataFinal_transposed <- t(MacroDataDataFinal)

Then try running the specaccum function:

library(vegan)
speccurve <- specaccum(comm=MacroDataDataFinal_transposed,
                       method="random",
                       permutation=1000)

Hopefully this will work. If you get any errors please let us know the code you typed, and the precise error message.