I just started using the stargazer package to make regression tables in R, but can't figure out how to write table output to a .tex file without either floating or document environments (and preamble in the case of the document environment). That is, I just want the tabular environment. My work flow is to keep the table floating environment - and the associated captions and labels -- in the body of the paper and link to the table's tabular environment with \input{}.
Is this possible?
# bogus data
my.data <- data.frame(y = rnorm(10), x = rnorm(10))
my.lm <- lm(y ~ x, data=my.data)
# if I write to file, then I can omit the floating environment,
# but not the document environment
# (i.e., file contains `\documentclass{article}` etc.)
stargazer(my.lm, float=FALSE, out="option_one.tex")
# if I write to a text connection with `sink`,
# then I can omit both floating and document environments,
# but not commands
# (i.e., log contains `sink` and `stargazer` commands)
con <- file("option_two.tex")
sink(con)
stargazer(my.lm, float=FALSE)
sink()
Save your stargazer results to an object:
res <- stargazer(my.lm, float=FALSE)
If you take a look at the contents of res then you'll see it's just a series of lines of text. Write this to a file using cat() like this
cat(res, file="tab_results.tex", sep="\n")
The sep="\n" is only required because the lines of text in the res object dont contain any line breaks themselves. If we leave use the default sep=" " then your table will be written to the tex file as one long line.
Hope this helps.
Related
I have created an r chunk in an r markdown document, in which I have calculated some parameter values that I am required to find for a homework. Now I would like for my knitted PDF-document to show the sentence "Our estimate of $\beta_1$ is -0.2186". However, the portion of the code for the greek letter beta ($\beta_1$) is being shown in the PDF the same way it's written here, not as the actual greek letter.
I have already tried installing LaTeX-packages in the document header (e.g. \usepackage{mathtools}), which made no difference.
cigs_mean <- mean(smoke$cigs) #find y-bar
educ_mean <- mean(smoke$educ) #find x-bar
beta1_hat <- (cov(smoke$educ,smoke$cigs))/(var(smoke$educ)) #find beta1-hat
beta0_hat <- (cigs_mean-(beta1_hat*educ_mean)) #find beta0-hat
print(paste0("Our estimate of $\beta_1$ is ", round(beta1_hat, digits=4)))
I just want for the document to show a greek letter beta with subscript 1, rather than replicating the code I have written ($\beta_1$)
Backslashes in R character strings have a special meaning as escape characters, and must themselves be escaped. Otherwise, your string '$\beta$' is read by R as '$' ‹backspace› 'e' 't' 'a' '$'.
Furthermore, print is the wrong function to use here: its purpose is to provide output in the interactive R console, never for actual output to a document. Use cat instead.
Finally, if you haven’t already done so, you need to tell knitr to interpret the results of this code chunk as-is instead of rendering them as a result:
```{r results = 'asis'}
…
cat(paste0("Our estimate of $\\beta_1$ is ", round(beta1_hat, digits=4), "\n"))
```
I have written an executable script in R that will simply plot a graph given an input file in a tab delimited format. However, the script I wrote is specific to a single file in terms of what to use as x and y. I want to have this script be able to plot whatever file I give it. All files I will be using for this script will be in the same format: Tab delimited with 4 headers with labels a, b, c, d. Labels b,c, and d have a different name for each file. My x values for the graph will be the values under header b and y values for the graph will be the values under header c. How can I plot a graph that will use whatever is under header b and c?
My script is posted below.
#!/usr/bin/env Rscript
args = commandArgs(trailingOnly=TRUE)
data = read.table((args[1]), header=TRUE, fill=TRUE, sep="\t")
attach (data)
jpeg(args[2])
plot (RPMb, RPMc)
dev.off()
Instead of using attach() (which is almost never recommended), use data frame indexing to extract the relevant variables from your data variable.
#!/usr/bin/env Rscript
args = commandArgs(trailingOnly=TRUE)
data = read.table((args[1]), header=TRUE, fill=TRUE, sep="\t")
jpeg(args[2])
x <- names(data)[2]
y <- names(data)[3]
plot (data[[x]], data[[y]],xlab=x,ylab=y)
dev.off()
You could also just use plot(data[,2],data[,3]) ...
A couple of other details/comments:
it's generally best to avoid naming variables for built-in functions such as data. It will usually work, but occasionally it will bite you.
are you sure you want JPEG output? Either PNG or PDF are usually best for line graphs, depending on whether you need a raster or a vector format ...
I'm sure this is very simple, but I'm new to doing my own programming in R and haven't quite gotten a hang of the syntax for looping.
I have code like this:
mydata1 <- read.table("ph001.txt", header=TRUE)
# ... series of formatting and merging steps
write.table(mydata4, "ph001_anno.txt", row.names=FALSE, quote=FALSE, sep="\t")
png("manhattan_ph001.png"); manhattan(mydata4); dev.off()
png("qq_ph001.png"); qq(mydata4$P); dev.off()
The input file ph001.txt is output from a linear regression algorithm, and from that file, I need to output ph001_anno.txt, manhattan_ph001.png, and qq_ph001.png. The latter two are using the qqman package.
I have a folder that contains ph001 through ph138, and would like a loop function that reads these files individually and creates the corresponding output files for each file. As I said, I'm sure there is an easy way to do this as a loop function, but the part that's tripping me up is modifying the output filenames.
You can use the stringr package to do a lot of the string manipulation you want in order to generate your file names, like so:
f <- function(i) {
num <- str_pad(i, 3, pad = "0")
a <- str_c("ph", num, "_anno.txt")
m <- str_c("manhattan_ph", num, ".png")
q <- str_c("qq_ph", num, ".png")
# Put code to do stuff with these file names here
}
sapply(1:138, f)
In the above block of code, for each number in 1:138 you create the name of three files. You can then use those file names in calls to read.table or ggsave or whatever you want.
Hi I am performing a task on a text file chosen from file.choose which just separates out the lines and then adds a new number to each separation.
I would like to name the outputted file the same as file.choose but instead of .txt I would like it to be called .fa. So far I have
fileConn<-file("outputtbb.txt")
longlist <- readLines(file.choose())
lvls1 <- unique(longlist)
cat(paste0("Sequence>", seq_along(lvls1), "\n", lvls1, collapse="\n"), file=fileConn)
close(fileConn)
I know its something to do with changing file=fileConn but cant figure out how to manipulate it and all I get is outputtbb.
Please help!
You could seperate the readLines(file.choose()) to two lines.
filename <- file.choose()
longlist <- readLines(filename)
You now have file name available as a variable and you can bend it, you can twist it all day long (no reference to iPhone 6 bending intended).
To change endings, assuming no ".txt" appears anywhere else in the file name, this would work
x <- "file.txt"
sub(".txt", replacement = ".fa", x = x)
[1] "file.fa"
I'm facing a challenge in R. I'm writing a code that incorporates another code written in C++ called MHX.
MHX is used for chemical data analysis by inputting some concentrations, etc. The integration between R and MHX works fine. So I'm able to write my MHX code definitions in the form of cat(CODE HERE) then calling a bash command to run MHX from terminal.
Now the results from MHX are given as tab delimited data tables that I am able to read without a problem in R. The problem is that I use R to simulate a large number of MHX calculations using loops.
Hence the need to write dynamic variables and here were I'm stuck. Let me give you more information with examples of my R code:
for (i in 1:100) {
fin <- file.create("input/ex1") #MHX input file
fout <- file.create("output/ex1.out") #MHX output file
FNM <- paste0("table_data/pH", i, ".txt") #filename used inside MHX definition
file.create(FNM) #this is used to create FNM table in R
fXY <- file.create(paste0("table_data/ECOMXY", i, ".txt"))
ifelse (HERE SOME MATHEMATICAL DEFINITIONS OF SOME VARIABLES)
ksource(MHXCode) #THIS CALLS MY MHX CODE which is inside another R code called `MHXCode` using a custom function KSOURCE. No problem here.
Up to here I don't have major problems. Now I need to setup the dynamic variables:
First I am creating variables PHL1 to PHL100
assign(paste("PHL", i, sep=""), read.table(paste0("table_data/pH", i, ".txt") ,skip=0, sep="\t", head=TRUE, na.strings = "-Inf"))
Each PHL table contains two rows and about 20 columns. Now I am interested in creating data frames from the second row for each column. Take for example row number 1 which is called EMF, ideally I need to do the following for all tables from PHLto PHL100 which is very tedious:
EMFT <- cbind(PHL1$EMF[2], PHL2$EMF[2], PHL3$EMF[2], PHL4$EMF[2], PHL5$EMF[2], PHL6$EMF[2],PHL7$EMF[2], PHL8$EMF[2], PHL9$EMF[2], PHL10$EMF[2], ....... etc up to PHL100! )
I tried many things to achieve the above, but I was not successful, including:
XX <- assign(paste0("PHL", i, "$EMF[2]"), cat(paste0("PHL", i, "$EMF[2]")))
I will need to do the same for other variables in order to be able to create some complicated plots. I hope anyone would be able to help.
I must mention that the main problem with assign is that I get qouted names of variables hence cannot return their values. Also for cat, you cannot use it to return a value, you will get NULL in the example above. Simple I am stuck!!
Please help.
Thanks to Justin he gave me a clue to answer my question. Here is what I have done:
files <- list.files(path="table_data", pattern=".dat", full.names=T); files
FRM <- NULL
for (f in files){
dat <- read.table(f, skip=0, header=TRUE, sep="\t", na.strings="",quote="", colClasses="character")[2,]
note that the [2, ] argument means that you skip all lines except line number 2 while keeping header which exactly what I was looking for.
Now I can bind it all in one table for my plots.
FRM <- rbind(FRM, dat)
This is a short answer and I think it is neat, sorted!