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)
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!
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.
Related
I am trying to get abundance estimates of rodents for my survey area using capture mark recapture. I am using the package "marked" but keep running into a problem where my capture histories are changed to numbers eg. 0010 becomes 10.
I have tried csv's, txt files, changing numbers to text in excel and can't seem to come right. When I am able to get data into R as a capture history as opposed to a number I get "Incorrect ch values in data:10;FMU".
I think the error lies in the input data, and I'm wondering if anyone perhaps has an example of their input data for something similar?
Any suggestions, would be greatly appreciated.
So I've used the decompose function and I want to export all the lists it generates not just the plot it creates. I tried converting the lists into either a matrix or data frame but then that gets rid of the date header and year columns so if someone knows how to convert it and keep the list formatting that would solve my issue I think.
Anyway, The closest I've got to being able to do this keeping the list format is by doing
capture.output(decompose, file = "filename.csv")
As you can see from the image attached though:
Sometimes the months arent all together in a row which is really not helpful or what I want. It also just puts it in one column and I'm having to go into the excel after and do the text to column option which is going to get old really quickly.
Any help would be greatly appriciated. I'm really new to R so apologise if there is an obvious fix I'm missing.
I'm brand new to programming and an picking up Rstudio as a stats tool.
I have a dataset which includes multiple questionnaires divided by weeks, and I'm trying to organize the data into meaningful chunks.
Right now this is what my code looks like:
w1a=table(qwest1,talm1)
w2a=table(qwest2,talm2)
w3a=table(quest3,talm3)
Where quest and talm are the names of the variable and the number denotes the week.
Is there a way to compress all those lines into one line of code so that I could make w1a,w2a,w3a... each their own object with the corresponding questionnaire added in?
Thank you for your help, I'm very new to coding and I don't know the etiquette or all the vocabulary.
This might do what you wanted (but not what you asked for):
tbl_list <- mapply(table, list(qwest1, qwest2, quest3),
list(talm1, talm2, talm3) )
names(tbl_list) <- c('w1a', 'w2a','w3a')
You are committing a fairly typical new-R-user error in creating multiple similarly named and structured objects but not putting them in a list. This is my effort at pushing you in that direction. Could also have been done via:
qwest_lst <- list(qwest1, qwest2, quest3)
talm_lst <- list(talm1, talm2, talm3)
tbl_lst <- mapply(table, qwest_lst, talm_lst)
names(tbl_list) <- paste0('w', 1:3, 'a')
There are other ways to programmatically access objects with character vectors using get or wget.
I have a data frame loaded using the CSV Library in R, like
mySheet <- read.csv("Table.csv", sep=";")
I now can print a summary on that mySheet object
summary(mySheet)
and it will show me a summary for each column, for example, one column named Diagnose has the unique values RCM, UCM, HCM and it shows the number of occurences of each of these values.
I now filter by a diagnose, like
subSheet <- mySheet[mySheet$Diagnose=='UCM',]
which seems to be working, when I just type subSheet in the console it will print only the rows where the value has been matched with 'UCM'
However, if I do a summary on that subSheet, like
summary(subSheet)
it still 'knows' about the other two possibilities RCM and HCM and prints those having a value of 0. However, I expected that the new created object will NOT know about the possible values of the original mySheet I initially loaded.
Is there any way to get rid of those other possible values after filtering? I also tried subset but this one just seems to be some kind of shortcut to '[' for the interactive mode... I also tried DROP=TRUE as option, but this one didn't change the game.
Totally mind squeezing :D Any help is highly appreciated!
What you are dealing with here are factors from reading the csv file. You can get subSheet to forget the missing factors with
subSheet$Diagnose <- droplevels(subSheet$Diagnose)
or
subSheet$Diagnose <- subSheet$Diagnose[ , drop=TRUE]
just before you do summary(subSheet).
Personally I dislike factors, as they cause me too many problems, and I only convert strings to factors when I really need to. So I would have started with something like
mySheet <- read.csv("Table.csv", sep=";", stringsAsFactors=FALSE)
I'm a total newbie with R, and I'm trying to create a histogram (with value and frequency as the axises) from a csv file (just one row of values). Any idea how I can do this?
I'm also an R newbie, and I ran into the same thing. I made two separate mistakes, actually, so I'll describe them both here.
Mistake 1: Passing a frequency table to hist(). Originally I was trying to pass a frequency table to hist() instead of passing in the raw data. One way to fix this is to use the rep() ("replicate") function to explode your frequency table back into a raw dataset, as described here:
Creating a histogram using aggregated data
Simple R (histogram) from counted csv file
Instead of that, though, I just decided to read in my original dataset instead of the frequency table.
Mistake 2: Wrong data type. My raw data CSV file contains two columns: hostname and bookings (idea is to count the number of bookings each host generated during some given time period). I read it into a table.
> tbl <- read.csv('bookingsdata.csv')
Then when I tried to generate a histogram off the second column, I did this:
> hist(tbl[2])
This gave me the "'x' must be numeric" error you mention in a comment. (It was trying to read the "bookings" column header in as a data value.)
This fixed it:
> hist(tbl$bookings)
You should really start to read some basic R manual...
CRAN offers a lot of them (look into the Manuals and Contributed sections)
In any case:
setwd("path/to/csv/file")
myvalues <- read.csv("filename.csv")
hist(myvalues, 100) # Example: 100 breaks, but you can specify them at will
See the manual pages for those functions for more help (accessible through ?read.table, ?read.csv and ?hist).
To plot the histogram, the values must be of numeric class i.e the data must be of numeric value. Here the value of x seems to be of some other class.
Run the following command and see:
sapply(myvalues[1,],class)