This is the code I am using, this creates a summary of stastistical tests I am interested in
library(ape)
library(geiger)
library(caper)
taxatree <- read.tree("newicktest.tre")
LWEVIYRcombodata <- read.csv("LWEVIYR.csv")
LWEVIYRcombodataPGLS <-data.frame(Sum.of.percentage=LWEVIYRcombodata$Sum.of.percentage,OGT=LWEVIYRcombodata$OGT, Species=LWEVIYRcombodata$Species)
LWEVIYRcombodataPGLS$Species<-gsub(" ", "", LWEVIYRcombodataPGLS$Species)
comp.dat <- comparative.data(taxatree, LWEVIYRcombodataPGLS, "Species")
phylo.signal <- pgls((Sum.of.percentage) ~1, data=comp.dat, lambda="ML")
I call this up with the line:
summary(phylo.signal)
And then save it as a variable:
dataforexport <- summary(phylo.signal)
However, this won't let me print it to a regular text file, or even a csv.
When trying something along the lines of this:
write.table(dataforexport, file = "test1.txt", sep = "\t", row.names = FALSE)
I get an error message:
Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) :
cannot coerce class ""summary.pgls"" to a data.frame
I want to be able to save the results of my analysis to a text file, or even a csv (ideally appending the file, but that's another question that's probably been answered somewhere else)
Give this a try -
capture.output(summary(phylo.signal), file = "test1.txt")
Related
I am trying to extract data using the rgbif package for multiple species (once the code works I'll be running a list of about 200 species, so it is important for me to implement a list).
I have tried to adapt code written in following link:
https://github.com/ropensci/rgbif/issues/377
This is what my input file looks like:
csv file
And my code looks as follows:
library("rgbif")
#input <- read.csv("C:/Users/omi30wk/Desktop/TESTsampledata_udi.csv", header = TRUE, fill = TRUE, sep = ",")
#since you guys don't have my csv file here are three samples species I'm using:
# Acanthorrhynchium papillatum, Acrolejeunea sandvicensis, Acromastigum cavifolium
#'taxon' as header, see image posted above of my csv file for clarity
allpts <- vector('list', length(input))
names(allpts) = input
for (taxon in input){
cat(taxon, "\n")
allpts[[taxon]] <- occ_data(scientificName = taxon, limit = 2) #error here
df <- allpts[[taxon]]$data
df$networkKeys = NULL
if (!is.null(df)) {
df <- df[, !apply(df, 2, function(z)
is.null(unlist(z)))]
write.csv(df, paste("/Users/user/Desktop/DATA Bats/allpts_30sept/", gsub(" ", "_", taxon), ".csv", sep = "")) } }
However I get following error message at the moment:
Error in `[[<-`(`*tmp*`, taxon, value = list(`Acanthorrhynchium papillatum` = list( :
no such index at level 1
I'm even happy to try different codes to extract multiple species data. I've already tried many codes (i.e. loops, etc) that also kept giving me error messages and I haven't been able to solve.
Any help is greatly appreciated!
Within R, I am trying to print a series of dataframes into an Excel file using openxlsx. Specifically in this case, I'm using list.files, read.xlsx and write.xlsx.
I'm still unable to write multiple tabs into one Excel file.
Please see my code below, I've tried to approach this problem using a for loop as well as a manual solution to test the feasibility but have had no luck
This is what my code currently looks like. For the length of the file list, pipe each file into a read function which then writes the results.
lapply(
1:length(file.list),
function(x) {
write.xlsx(
read.xlsx(file.list[i]),
file = file_name,
sheetName = file.list[i],
col.names = TRUE,
row.names = FALSE,
append = TRUE)
}
)
A manual solution below also doesn't seem to have any luck for me either
df1 <- read.xlsx(file.list[1])
write.xlsx(df1, file = file_name, sheetName = file.list[1], col.names = TRUE, row.names = FALSE, append = FALSE)
df2 <- read.xlsx(file.list[2])
write.xlsx(df2, file = file_name, sheetName = file.list[2], col.names = TRUE, row.names = FALSE, append = TRUE)
No error messages so far. The final file does see data being written into it, however, it seems only the last file has the results print. I'm thinking that it's almost a cycle of overwrites,
Maybe you could try this:
wb <- createWorkbook(title = "Your_Workbook_Name")
lapply(1:length(file.list), function(y) lapply(1:length(file.list), function(x) writeData(wb,file.list[i],y,col.names = TRUE, row.names = FALSE, append = TRUE)))
Since I don't have a way to replicate this, perhaps you can understand the main idea behind this.
A double loop, in which your traverse all the files you want to write, before writing it you create a sheet with the name of the index, and then you can write in the newly created sheet, the data you want. I hope it's understandable (My knowledge about lapply and sapply is not the best, but the idea still stands)
You can simply use a named list of dataframes in write.xlsx. Something like this should work:
library(openxlsx)
df.list <- lapply(file.list, read.xlsx)
named.df.lst <- setNames(df.list, file.list)
write.xlsx( named.df.lst, file = file_name )
I am trying to read a dat file with ";" separated. I want to read a specific line that starts with certain characters like "B" and the other line are not the matter of interest. Can anyone guide me.
I have tried using the read_delim, read.table and read.csv2.But since some lines are not of equal length. So, I am getting errors.
file <- read.table(file = '~/file.DAT',header = FALSE, quote = "\"'",dec = ".",numerals = c("no.loss"),sep = ';',text)
I am expecting a r dataframe out of this file which I can write it to a csv file again.
You should be able to do that through readLines
allLines <- readLines(con = file('~/file.DAT'), 'r')
grepB <- function(x) grepl('^B',x)
BLines <- filter(grepB, allLines)
df <- as.data.frame(strsplit(BLines, ";"))
And if your file contains header, then you can specify
names(df) <- strsplit(allLines[1], ";")[[1]]
I would be delighted and most grateful if anyone can explain to me why I am having a problem exporting some data from a function which extracts coefficients from a linear model. I have hundreds to do so I’m hoping to build a loop to handle it but have fallen at an earlier hurdle.
I am using methods borrowed from someone much smarter at this stuff:
https://stat.ethz.ch/pipermail/r-sig-ecology/2008-May/000062.html
The relevant bits (data creation, the function and finally my attempt to export my data are below) but firstly I will mention that the data, “export”, is exported to the experiment.csv file as a single COLUMN. I am told that the Append property of the write.table function only works with rows. Consequently it overwrites previous runs of the same sets of commands rather than successfully appending it.
The error messages are of the form below: (they are all the same, one for each piece of information).
Warning messages:
1: In write.csv(export, file = "experiment.csv", append = TRUE, quote = TRUE, :
attempt to set 'append' ignored
#DATA CREATION
# create an empty list
mod <- list()
# start a loop for create 5 objects of class 'lm'
for (i in 1:5) {
x <- rnorm(i*10)
y <- rnorm(i*10)
mod[[paste("run",i,sep="")]] <- lm(y ~ x)
}
# FUNCTION TO EXTRACT DATA
myFun <-
function(lm)
{
out <- c(lm$coefficients[1],
lm$coefficients[2],
length(lm$model$y),
summary(lm)$coefficients[2,2],
pf(summary(lm)$fstatistic[1], summary(lm)$fstatistic[2],
summary(lm)$fstatistic[3], lower.tail = FALSE),
summary(lm)$r.squared)
names(out) <- c("intercept","slope","n","slope.SE","p.value","r.squared")
return(out)}
# FAILED ATTEMPT TO EXPORT
export <-myFun(mod$run1)
write.csv(export, file = "experiment.csv", append = TRUE, quote = TRUE, sep = " ",
eol = "\n", na = "NA", dec = ".", row.names = FALSE,
col.names = FALSE, qmethod = c("escape", "double"),
fileEncoding = "")
I have a simple for loop to write the past 100 tweets of a few usernames to .csv files:
library(twitteR)
mclist <- read.table('usernames.txt')
for (mc in mclist)
{
tweets <- userTimeline(mc, n = 100)
df <- do.call("rbind", lapply(tweets, as.data.frame))
write.csv(df, file=paste("Desktop/", mc, ".csv", sep = ""), row.names = F)
}
I mostly followed what I've read on StackOverflow but I continue to get this error message:
Error in file(file, ifelse(append, "a", "w")) :
invalid 'description' argument
In addition: Warning message:
In if (file == "") file <- stdout() else if (is.character(file)) { :
the condition has length > 1 and only the first element will be used
Where did I go wrong?
I just cleaned up the code a bit, and everything started working.
Step 1: Let's set the working directory and load the 'twitteR' package.
library(twitteR)
setwd("C:/Users/Dinre/Desktop") # Replace with your desired directory
Step 2: First, we need to load a list of user names from a flat text file. I'm assuming that each line in the text file has one username, like so:
[contents of usernames.txt]
edclef
notch
dkanaga
Let's load it using the 'scan' function to read each line into an array:
mclist <- scan("usernames.txt", what="", sep="\n")
Step 3: We'll loop through the usernames, just like you did before, but we're not going to refer to the directory, since we're going to use the same directory for output as input. The original code had a syntax error in attempting to referring to the desktop directory, and we're just going to sidestep that.
for (mc in mclist){
tweets <- userTimeline(mc, n = 100)
df <- do.call("rbind", lapply(tweets, as.data.frame))
write.csv(df, file=paste(mc, ".csv", sep = ""), row.names = F)
}
I end up with three files on the desktop, and all the data seems to be correct.
edclef.csv
notch.csv
dkanaga.csv
Update: If you really want to refer to different directories within your code, use the '.' character to refer to the parent directory. For instance, if your working directory is your Windows user profile, you would refer to the 'Desktop' folder like so:
setwd("C:/Users/Dinre")
...
write.csv(df, file=paste("./Desktop/". mc, ".csv", sep = ""), row.names = F)
There's a convenience function in the package twListToDF which will handle the conversion of the list of tweets to a data.frame.
Since your mclist is a data.frame, you can replace your for by apply
apply( mclist, 1,function(mc){
tweets <- userTimeline(mc, n = 100)
df <- do.call("rbind", lapply(tweets, as.data.frame))
write.csv(df, file=paste("Desktop/", mc, ".csv", sep = ""), ##!! Change Desktop to
## something like Desktop/tweets/
row.names = F)
})
PS :
The userTimeline function will only work if the user requested has a
public timeline, or you have previously registered a OAuth object
using registerTwitterOAuth