Hi Jeff, But if I do not use setwd(), the current working directory is NOT the project directory. That's what my problem is about... I guess I was not clear in my email... Ivan -- Dr. Ivan Calandra TraCEr, laboratory for Traceology and Controlled Experiments MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution Schloss Monrepos 56567 Neuwied, Germany +49 (0) 2631 9772-243 https://www.researchgate.net/profile/Ivan_Calandra On 02/04/2020 10:37, Jeff Newmiller wrote:> I recommend not using setwd. Then you can always assume your current working directory is your project directory and reference relative to that. > > On April 2, 2020 1:30:29 AM PDT, Ivan Calandra <calandra at rgzm.de> wrote: >> Dear useRs, >> >> I believe this is R code so appropriate for this list, but let me know >> if this relates more to RStudio itself. >> >> I am working on an RStudio project. In that project directory, I have a >> folder called 'analysis' and in there a folder called 'scripts' >> ('~/analysis/scripts'). >> My data files needed for the scripts are in '~/analysis/raw_data' and >> the output should be in '~/analysis/derived_data'. >> >> My scripts are Rmd files, so when I knit them, their working directory >> is where they are located, i.e. '~/analysis/scripts'. The problem I >> then >> have is to specify the path for 'raw_data' and 'derived_data' since >> during the rendering I am not relative to the project directory >> anymore. >> And these folders are not subfolders of the working directory? >> '~/analysis/scripts'. >> I hope I am clear here... >> >> I would like to avoid absolute paths of course, but I do not know how >> to >> proceed. >> What would be nice is a way to get the project directory in the >> scripts, >> rather than their working directory. >> Does that make sense? >> >> Thank you in advance >> Best, >> Ivan
Make it so. Outside R. At the command line, use cd before you start R. This should feel natural. In a GUI file browser, double clicking on a file type assigned to a program by default sets the containing directory to be current directory before kicking off the program, so double-clicking on an empty Project.RData file will do it. Or you can use RStudio Project.Rproj files the same way. On April 2, 2020 1:40:07 AM PDT, Ivan Calandra <calandra at rgzm.de> wrote:>Hi Jeff, > >But if I do not use setwd(), the current working directory is NOT the >project directory. > >That's what my problem is about... I guess I was not clear in my >email... > >Ivan > >-- >Dr. Ivan Calandra >TraCEr, laboratory for Traceology and Controlled Experiments >MONREPOS Archaeological Research Centre and >Museum for Human Behavioural Evolution >Schloss Monrepos >56567 Neuwied, Germany >+49 (0) 2631 9772-243 >https://www.researchgate.net/profile/Ivan_Calandra > >On 02/04/2020 10:37, Jeff Newmiller wrote: >> I recommend not using setwd. Then you can always assume your current >working directory is your project directory and reference relative to >that. >> >> On April 2, 2020 1:30:29 AM PDT, Ivan Calandra <calandra at rgzm.de> >wrote: >>> Dear useRs, >>> >>> I believe this is R code so appropriate for this list, but let me >know >>> if this relates more to RStudio itself. >>> >>> I am working on an RStudio project. In that project directory, I >have a >>> folder called 'analysis' and in there a folder called 'scripts' >>> ('~/analysis/scripts'). >>> My data files needed for the scripts are in '~/analysis/raw_data' >and >>> the output should be in '~/analysis/derived_data'. >>> >>> My scripts are Rmd files, so when I knit them, their working >directory >>> is where they are located, i.e. '~/analysis/scripts'. The problem I >>> then >>> have is to specify the path for 'raw_data' and 'derived_data' since >>> during the rendering I am not relative to the project directory >>> anymore. >>> And these folders are not subfolders of the working directory? >>> '~/analysis/scripts'. >>> I hope I am clear here... >>> >>> I would like to avoid absolute paths of course, but I do not know >how >>> to >>> proceed. >>> What would be nice is a way to get the project directory in the >>> scripts, >>> rather than their working directory. >>> Does that make sense? >>> >>> Thank you in advance >>> Best, >>> Ivan > >______________________________________________ >R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide >http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code.-- Sent from my phone. Please excuse my brevity.
So what you're saying is that I should have scripts in the project directory and not in a subfolder within it, right? But what if I need (or at least want) to? Ivan -- Dr. Ivan Calandra TraCEr, laboratory for Traceology and Controlled Experiments MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution Schloss Monrepos 56567 Neuwied, Germany +49 (0) 2631 9772-243 https://www.researchgate.net/profile/Ivan_Calandra On 02/04/2020 10:56, Jeff Newmiller wrote:> Make it so. Outside R. > > At the command line, use cd before you start R. This should feel natural. > > In a GUI file browser, double clicking on a file type assigned to a program by default sets the containing directory to be current directory before kicking off the program, so double-clicking on an empty Project.RData file will do it. Or you can use RStudio Project.Rproj files the same way. > > On April 2, 2020 1:40:07 AM PDT, Ivan Calandra <calandra at rgzm.de> wrote: >> Hi Jeff, >> >> But if I do not use setwd(), the current working directory is NOT the >> project directory. >> >> That's what my problem is about... I guess I was not clear in my >> email... >> >> Ivan >> >> -- >> Dr. Ivan Calandra >> TraCEr, laboratory for Traceology and Controlled Experiments >> MONREPOS Archaeological Research Centre and >> Museum for Human Behavioural Evolution >> Schloss Monrepos >> 56567 Neuwied, Germany >> +49 (0) 2631 9772-243 >> https://www.researchgate.net/profile/Ivan_Calandra >> >> On 02/04/2020 10:37, Jeff Newmiller wrote: >>> I recommend not using setwd. Then you can always assume your current >> working directory is your project directory and reference relative to >> that. >>> On April 2, 2020 1:30:29 AM PDT, Ivan Calandra <calandra at rgzm.de> >> wrote: >>>> Dear useRs, >>>> >>>> I believe this is R code so appropriate for this list, but let me >> know >>>> if this relates more to RStudio itself. >>>> >>>> I am working on an RStudio project. In that project directory, I >> have a >>>> folder called 'analysis' and in there a folder called 'scripts' >>>> ('~/analysis/scripts'). >>>> My data files needed for the scripts are in '~/analysis/raw_data' >> and >>>> the output should be in '~/analysis/derived_data'. >>>> >>>> My scripts are Rmd files, so when I knit them, their working >> directory >>>> is where they are located, i.e. '~/analysis/scripts'. The problem I >>>> then >>>> have is to specify the path for 'raw_data' and 'derived_data' since >>>> during the rendering I am not relative to the project directory >>>> anymore. >>>> And these folders are not subfolders of the working directory? >>>> '~/analysis/scripts'. >>>> I hope I am clear here... >>>> >>>> I would like to avoid absolute paths of course, but I do not know >> how >>>> to >>>> proceed. >>>> What would be nice is a way to get the project directory in the >>>> scripts, >>>> rather than their working directory. >>>> Does that make sense? >>>> >>>> Thank you in advance >>>> Best, >>>> Ivan >> ______________________________________________ >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code.