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

Question

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)

Please do not post (only) an image of code/data/errors: it breaks screen-readers and it cannot be copied or searched (ref: https://meta.stackoverflow.com/a/285557 and https://xkcd.com/2116/). Please include the code, console output, or data (e.g., `data.frame(...)` or the output from `dput(head(x))`) directly. — r2evans, Mar 20 '22 at 04:10
This may be a duplicate question https://stackoverflow.com/questions/23209330/how-to-change-the-first-row-to-be-the-header-in-r — bcstryker, Mar 20 '22 at 04:13
Sadly @bcstryker I don't think so, Carly is asking the same question now a third time. According to the [previous](https://stackoverflow.com/questions/71534679/transposed-data-in-r-now-my-top-column-has-v-listed-above-them-why-wont-it) [two](https://stackoverflow.com/questions/71543562/r-is-not-reading-my-data-can-someone-please-help-me-understand-what-i-am-doing) questions, it seems as if Carly is either using incorrect headers or the wrong `read.*` function. We can't really know for sure, the questions (despite requests) only include images of partial code. — r2evans, Mar 20 '22 at 04:15
There is no code. I just want the data frame to recognize the first column as a header. — , Mar 20 '22 at 04:15
To r2evans: I have no idea what any of that means in that question. I literally just started learning this stuff last week. — , Mar 20 '22 at 04:16
Do you mean "row as a header"? ***Please***, just open the data file (csv?) in notepad or some other text editor, copy the first 3-4 lines, and then [edit] your question and paste the contents into a [code block](https://stackoverflow.com/editing-help). And ***please*** show the `read.*` code/expression you are trying to use to read in this data. ***Please*** not images of such. — r2evans, Mar 20 '22 at 04:18
Carly, I do agree that this site is often difficult for "noobs", but ... we've asked several times for you to clarify certain things, and you have ignored the requests. We're trying to help you improve the way your question is framed so that we have a chance of helping you. — r2evans, Mar 20 '22 at 04:20
I can't help with code I cannot see. I see some *images* of what your data *might* look like in its raw form, so I can guess with a simple `dat — r2evans, Mar 20 '22 at 04:21
You were close, I edited a suggested fix. Code blocks require *backticks* `\`\`\``, not single-quotes `'''`, and they need to be on lines by themselves (both before your code and after it). There is also inline code formatting. Please see the link I provided above about "code block", it talks a bit about all of that, and while it may be hard to see some of the differences between quotes and backticks and such, the differences are important. — r2evans, Mar 20 '22 at 04:25
But it would still be really really helpful see the first few lines of the *raw file*, not open in Excel or such. (Thanks for the code edit, btw.) — r2evans, Mar 20 '22 at 04:27
are you using rstudio? maybe it would be best to try `file > import dataset > from text (base)` then play around with the options until the preview looks correct, then study the code it generates to give you the correct data set — rawr, Mar 20 '22 at 04:51

score 2 · Answer 1 · edited Mar 20 '22 at 09:05

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!

score 1 · Answer 2 · edited Mar 20 '22 at 09:10

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.

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

2 Answers2