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.
Where did this false dichotomy come from? The rmarkdown::render function has quite flexible parameters for compiling rmarkdown files in subdirectories without changing the current directory. And RStudio has a Global configuration to enable compiling using the Project directory as "current" under the RMarkdown settings. On April 2, 2020 1:59:03 AM PDT, Ivan Calandra <calandra at rgzm.de> wrote:>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. > >______________________________________________ >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.
Thanks Jeff, I was just completely unaware of these options! Now I know. Best, 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 15:40, Jeff Newmiller wrote:> Where did this false dichotomy come from? The rmarkdown::render function has quite flexible parameters for compiling rmarkdown files in subdirectories without changing the current directory. And RStudio has a Global configuration to enable compiling using the Project directory as "current" under the RMarkdown settings. > > On April 2, 2020 1:59:03 AM PDT, Ivan Calandra <calandra at rgzm.de> wrote: >> 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. >> ______________________________________________ >> 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.