Good day. I am new to R and am currently using R studio. I managed to import my CSV data into R studio, but when I try using R to determine the alpha diversity, B-diversity and other analyses, I get the error "Error in "104D0"shannon : operator is invalid for atomic vectors"
hist("104D0"$shannon, main="Shannon diversity", xlab="", breaks=10)
Error in "104D0"shannon : operator is invalid for atomic vectors
hist("104D0"$simpson, main="Simpson diversity", xlab="", breaks=10)
Error in "104D0"simpson : operator is invalid for atomic vectors
hist("104D0"$chao, main="Chao richness", xlab="", breaks=15)
Error in "104D0"chao : operator is invalid for atomic vectors
hist("104D0"$ace, main="ACE richness", xlab="", breaks=15)
Error in "104D0"ace : operator is invalid for atomic vectors
I will thus be happy to get help on how to convert my csv data into an appropriate vector format in which the various statistical computations can be done.
Thank you sir, I just tried that and it returned this:
hist(104D0$shannon, main="Shannon diversity", xlab="", breaks=10)
Error in hist(104D0$shannon, main = "Shannon diversity", xlab = "", :
object '104D0' not found
hist(104D0.csv$shannon, main="Shannon diversity", xlab="", breaks=10)
The 104D0 is my CSV file containing two columns: the first column is the species column and the 2nd column is the abundance column. So I want to calculate alpha diversity, Beta diversity, and principal component analyses. I do not know if the problem is with my data format.
You specifically forgot to add the backticks as specified in my solution. I am not sure what kind of keyboard you use, but the backtick is the following symbol in parentheses: (`). You must use it:
But, the easiest solution is to change the name of your variable. When you import your dataset, just store it into a different variable name. Assuming that your data is in a csv file, you can just import it into a variable called, for example, my_data.
mydata1
Species.Abundance
1 Streptococcus;46927
2 Mycobacterium;11077
3 Atopobium;8951
4 Granulicatella;4685
5 Actinomyces;4016
6 Catonella;1904
7 Homo;1000
8 Macaca;688
9 unclassified (derived from Bacteria);568
10 Eubacterium;530
11 Clostridium;259
12 Gemella;253
13 Lactobacillus;124
14 Sorghum;115
15 Rothia;112
16 Bifidobacterium;99
17 unclassified (derived from Clostridiales);85
18 Bacillus;81
19 Canis;81
20 Ruminococcus;80
21 Schistosoma;80
22 Enterococcus;77
23 Danio;72
24 Neisseria;67
25 Pan;64
26 Lactococcus;62
27 unclassified (derived from Siphoviridae);62
28 Staphylococcus;61
29 unclassified (derived from Clostridiales Family XI. Incertae Sedis);58
30 Ciona;56
31 Mobiluncus;54
32 Veillonella;54
33 Prevotella;45
34 Peptostreptococcus;44
35 Olsenella;41
36 Loa;39
37 Nonionella;38
38 Oribacterium;37
39 Oryza;34
40 Shuttleworthia;33
41 Fusobacterium;32
42 Rattus;32
43 Moniezia;31
44 Collinsella;27
45 unclassified (derived from Erysipelotrichaceae);27
46 Bacteroides;24
47 Xylosandrus;23
48 Slackia;22
49 Coprococcus;22
50 Pongo;22
hist(mydata1$shannon, main="Shannon diversity", xlab="", breaks=10)
Error in hist.default(mydata1$shannon, main = "Shannon diversity", xlab = "", :
'x' must be numeric
I used the (`) symbol instead of the (") symbol and it did not work. However, when I re-imported the CSV file and named it as mydata1, it did not return the same error....it's now stating that the 'x' must be numeric. Could you please be of help here?
@jod14139 Your data is in a very odd format. Let's do this then. Can you upload your file to any cloud storage service (Google drive, dropbox, onedrive, ...) and then share the link here. I think that'll be easier.
There is a problem with the column names. You only have one column called Species.Abundance when it looks like you need two columns named Species and Abundance
Have a look at the csv file and see if it is using a (.) rather than a ( as a separator in the first line.
I manually edited the earlier data you supplied and changed Species.Abundance to Species;Abundance
@jrkrideau,
You're right. I actually have the data in two columns, species and abundance. I then saved it from excel into csv format. So am quiet surprised that it came out that way after I imported in into R. However, when I check the original files, it still shows as Species;Abundance.
What could be the cause for this and how do i change it as you did? Do i use the command you just showed in your response, because the original files look OK....or I should revert the files to excel format?
I am trying to calculate diversity, abundance, and richness of my species in my microbiome data. To do this, I need to find their alpha & beta diversities as well as principal component analyses.
I am following tutorials for doing this from this website: Microbiota Analysis in R
It's the only website I have now.
You're very welcome. Don't hesitate to post new questions on RStudio Community if you have any. Also, it would greatly help to learn how to post code in your questions. You can do so by moving to a new line and pressing: Ctrl + Shift + C
as a separator in the first line.