I am doing an html document from R Markdown (RStudio) and I think I am following the right instructions to show it up. I read the R's Bookdown (https://bookdown.org/yihui/rmarkdown) and there says this is the way, or at least this is what I get from it. I am using this only script line to make the image calling:
.
When knitting I get this error message: "File Macintosh HD/Usuarios/ivanmendivelso/Dropbox/Escuela/IntroR Vids/HW.jpeg not found in resource path
Error: pandoc document conversion failed with error 99
Execution halted".
Does anybody know what am I doing wrong? Why I can not see images in my documents?
Thanks in advance.
It looks like your path is not correct.
If the image can be moved, put it in the same directory as your .Rmd file. If you can't move it to the file directory and if you don't speak UNIX, you can get the path by:
Finding the file with the finder
Right click on it
hold the option key on your keyboard and you will see the menu change from Copy "HW.jpg" to say Copy "HW.jpeg" as pathname
Paste that path into your code.
When you have file spaces in your file path you need to put single quotes around to make them strings
What about this below
.
notice the / at the begining of the file path. on Mac the very first / is meaning from the root of your hard drive
Related
Whenever I knit to a PDF in RStudio, the error "The system cannot find the file specified."
Here is the code that I'm using:
##importing data
library(readr)
Quiz1data_2 <- read_csv("C:/Users/erinp/Downloads/Quiz1data-2.csv")
I have restarted RStudio multiple times and I have copied and pasted the exact link that my file is saved to and it's still not working.
What am I not seeing or what am I not thinking?
Some suggestions/questions:
Without knitting, when you run the line reading in the csv, does it work?
Also, are you sure that the error is referring to the data csv? Could it be referring to the (I'm assuming) markdown file you are writing your code in? Have you moved that file since you started working in it?
Are you able to knit other documents to pdf? You need MiKTeX on a windows machine. Does knitting to html work?
I've found R to be a little tricky reading in files. I usually use the base function like this:go to the environment tab>import dataset>from text(base)> (select the file you want, hit open)>(select settings so that the dataframe preview looks right>import. Code that does this will run in the console, and I copy it into my markdown file so that every time it knits, it replicates that successful process.
I figured it out. It's because I forgot to assign a value to an object so it wouldn't knit into a PDF. I made a comment earlier, but it's small so I thought I would add this to the answer section.
I am doing my current project in RStudio Desktop. I am doing RMarkdown to later transfer. I am having some trouble getting an error of the system cannot find the file specified RMarkdown. At first, it says that the combined_databike was not found, but I literally did it in the same file already also you can see in the upper right all of the data frames which mention "combined_databike." This being said when I am trying to hit knit it gives me the error. Now the error says is at the tripdata_202006, which I cannot understand because I imported every file from tripdata_202006 to tripdata_202105 using the "import dataset."
I want to understand why is not working and how I bring a solution.
That's because the file you want to read is not in the folder where your project or in this case your rmarkdown file is.
As you can see in the file list of your console, in your directory you have 4 files, and you don't have the folder "Bike data" where the file 202006-divvy-tripdata.csv is located, according to the path that is in line 83 of your code.
Maybe to solve that, I think you have two options, the first one is to write the whole path to the folder location and then to the file. And the second option is to move the folder "Bike data" with the files you have in it, where your rmarkdown file is located.
I'm on RStudio, just wanting to read a csv file:
newdata <- read_csv("Nameofdata.csv",
col_names = TRUE)
But it keeps telling me that the file doesn't exist. It does exist. I'm staring DIRECTLY at it, underneath the file path that RStudio insists is wrong. I can open it in another tab, I can open in in excel, it's EXACTLY where RStudio says it's not existing. Please help.
Looking very closely at your screen shot, commenters are suggesting that you have an extra space at the beginning of your file name.
Also, I see that the working directory appears to be correct (the error message lists it as C:/users/mdavi/Desktop/School/Research/Sc, which appears to match what is listed in the Files pane
A couple of strategies for trouble-shooting file-locating problems:
use getwd() and list.files() to confirm your working directory and what files R can see from there (you can read this introduction to get more background on working directories):
use file.choose() to select a file interactively; it's generally a bad idea to use this in production code, as it will add an interactive step when you usually want to be able to run all of your code start to finish without needing manual steps, but it's quite useful for debugging.
If you wanted R to list files that approximately matched your specified filename, you could use
L <- list.files(pattern="*.csv")
agrep("myfile.csv", L, value=TRUE)
You need to set your working directly correctly, either via setwd("~/Desktop/School/Research/SC") in the R Console (that's what I think I see in your screenshot: ~ stands for your home directory, i.e "Users/Whoever") or via Session > Set Working Directory > To File Pane in the RStudio menus.
You can read a variety of Stack Overflow questions about setting the working directory for more complete context ... web searching on "R 'working directory'" might help too.
I am using R Studio and I want to save my script (i.e., the upper left panel). However, the only ways that I can find to do it are by either clicking the blue floppy disk icon to save or using the drop down menu File > Save > name.R
Is there any way besides using these shortcuts to save the script to a .R file or is the shortcut the only way?
Thanks.
You can use rstudioapi::documentSave() to save the currently open script file to disk.
From the source documentation, one can see that it can be used in conjunction with the id returned with getActiveDocumentContext()$id to make sure the document saved is the one running the script.
For your intended use, try:
rstudioapi::documentSave(rstudioapi::getActiveDocumentContext()$id)
For future reference, here is the reference manual of rstudioapi:
https://cran.rstudio.com/web/packages/rstudioapi/rstudioapi.pdf
I'm not yet allowed to comment, but this refers to the comment above that this does not work with .rmd files:
rstudioapi::documentSave(rstudioapi::getActiveDocumentContext()$id)
I tried and in Rstudio Version 1.2.5042 it does seem to work.
Every new tab in R(created by ctrl+shift+n) can be independently saved by using ctrl+s in the respective tab. If you intend to rename the file though, you may do it as you would rename any file in windows(goto the file location and single click on the filename). Hope my answer was of some help!
I'm making a simple line in r to automatically open my generated plots.
I output the plots to a file called "plots.pdf" in the same directory as my r file, and at the end i use this two lines to try to open it:
dir <- paste("/Applications/Skim.app/Contents/MacOS/Skim ",getwd(),"/plots.pdf",sep="")
system(dir)
Basically, dir concatenates the full path of the skim app and the full path of the generated plot.
If i run the string stored at dir in a shell it works perfect, it opens the pdf file in Skim, but when i run it with system() from inside R it doesn't work (Skim says 'The document “plots.pdf” could not be opened.').
I believe this is a very little mistake somewhere in the syntax regarding the absolute/relative paths, but haven't managed to find it... Any advice is welcome! (Or a better way to achieve the same)
I found a way to bypass that problem, i just changed the path to Skim for the 'open' command and i let the system to assign the default app for pdf viewing. So:
dir <- paste("open ",getwd(),"/plots.pdf",sep="")
And it works.