`dev.off()` closes the current graphical device.  This clears all of the plots for me in RStudio as long as I don&#39;t have a different graphical device open at the moment.  If you do have other graphical devices open then you can use `dev.list()` to figure out which graphical device is RStudio&#39;s.  The following *should* do that but I haven&#39;t tested it thoroughly.

    dev.off(dev.list()[&quot;RStudioGD&quot;])

But if you aren&#39;t doing anything else then just using `dev.off()` should take care of it.

`dev.off()` only works in an interactive session. If you&#39;re interested in implementing such behavior in a script, you should use

    graphics.off()

instead.

To prevent error message in case there are no plots to clear:

    if(!is.null(dev.list())) dev.off()

I usually use

    while (dev.cur()&gt;1) dev.off()

and since I use RGL a lot, I often add:

    while (rgl.cur()) rgl.close()

I have gone for this which seems to work without reporting any errors:

    # Clear all plots
    try(dev.off(dev.list()[&quot;RStudioGD&quot;]),silent=TRUE)
    try(dev.off(),silent=TRUE)

I merged the instructions from the other answers with an answer on error handling [here][1]: 


  [1]: https://stackoverflow.com/questions/19111956/suppress-error-message-in-r

Is it possible to step backwards through executed code in a debug session?

For example I step over a method called `abc()` expecting to get `12` but after re-checking the value returned I notice it&#39;s `5` instead of `12`. How can I step back to where I was before and step into the method to see what is going on?  I know you can do this in visual studio but I can&#39;t find how to do this in intelliJ.  

How to step one step back in IntelliJ?

Is the runtime complexity defined by the JS standard on common `Array` functions like `push`, `pop`, `shift`, `slice` or `splice`? Esp. I&#39;m interested in removing and inserting entries at random positions. If the complexity is not defined, what can I expect, e.g. in V8?

(This question was inspired by [this](https://stackoverflow.com/questions/1344500/efficient-way-to-insert-a-number-into-a-sorted-array-of-numbers). Also, [this benchmark](http://jsperf.com/array-direct-assignment-vs-push), posted [here](https://stackoverflow.com/questions/614126/why-is-array-push-sometimes-faster-than-arrayn-value/14997768), also makes me curious, but maybe that is some unrelated phenomena.)

(A very related question is [here](https://stackoverflow.com/questions/11514308/big-o-of-javascript-arrays). However, one of the comments on the accepted answer says that it is wrong now. Also, the accepted answer does not have any reference that the standard really defines it that way.).

JavaScript runtime complexity of Array functions

I have code to clear the workspace: `rm(list=ls())` and code to clear the console: `cat(&quot;\014&quot;)`

Is there code to clear all plots from Rstudio?


Code to clear all plots in RStudio

<p>I have code to clear the workspace: <code>rm(list=ls())</code> and code to clear the console: <code>cat("\014")</code></p>
<p>Is there code to clear all plots from Rstudio?</p>


I have a data.table with fields {id, menuitem, amount}.

This is transaction data - so, ids are unique, but menuitem repeats. Now, I want to remove all entries where `menuitem == &#39;coffee&#39;`.

Also, want to delete all rows where `amount &lt;= 0`;

What is the right way to do this in data.table? 

I can use `data$menuitem!=&#39;coffee&#39;` and then index int into data[] - but that is not necessarily efficient and does not take advantage of data.table.

Any pointers in the right direction are appreciated.

Remove rows conditionally from a data.table in R

I would like to fit a model for each hour(the factor variable) using dplyr, I&#39;m getting an error, and i&#39;m not quite sure what&#39;s wrong.

    df.h &lt;- data.frame( 
      hour     = factor(rep(1:24, each = 21)),
      price    = runif(504, min = -10, max = 125),
      wind     = runif(504, min = 0, max = 2500),
      temp     = runif(504, min = - 10, max = 25)  
    )
    
    df.h &lt;- tbl_df(df.h)
    df.h &lt;- group_by(df.h, hour)
    
    group_size(df.h) # checks out, 21 obs. for each factor variable

    # different attempts:
    reg.models &lt;- do(df.h, formula = price ~ wind + temp)
    
    reg.models &lt;- do(df.h, .f = lm(price ~ wind + temp, data = df.h))

I&#39;ve tried various variations, but I can&#39;t get it to work. 


Fitting several regression models with dplyr

I am using the `mtcars` dataset. I want to find the number of records for a particular combination of data. Something very similar to the `count(*)` group by clause in SQL. `ddply()` from *plyr* is working for me 

    library(plyr)
    ddply(mtcars, .(cyl,gear),nrow)

has output

      cyl gear V1
    1   4    3  1
    2   4    4  8
    3   4    5  2
    4   6    3  2
    5   6    4  4
    6   6    5  1
    7   8    3 12
    8   8    5  2

Using this code

    library(dplyr)
    g &lt;- group_by(mtcars, cyl, gear)
    summarise(g, length(gear))

has output

      length(cyl)
    1          32

I found various functions to pass in to `summarise()` but none seem to work for me. One function I found is `sum(G)`, which returned

    Error in eval(expr, envir, enclos) : object &#39;G&#39; not found

Tried using `n()`, which returned 

    Error in n() : This function should not be called directly

What am I doing wrong? How can I get `group_by()` / `summarise()` to work for me?


Count number of rows by group using dplyr

I am trying to predict weekly sales using &lt;strike&gt; ARMA &lt;/strike&gt; ARIMA models. I could not find a function for tuning the order(p,d,q) in `statsmodels`. Currently R has a function `forecast::auto.arima() ` which will tune the (p,d,q) parameters. 

How do I go about choosing the right order for my model? Are there any libraries available in python for this purpose?

auto.arima() equivalent for python

I am attempting to reproduce one of the examples in the dplyr package but am getting this error message. I am expecting to see a new column n produced with the frequency of each combination.  What am I missing?  I triple checked that the package is loaded.

     library(dplyr)
    # summarise peels off a single layer of grouping
    by_vs_am &lt;- group_by(mtcars, vs, am)

    by_vs &lt;- summarise(by_vs_am, n = n())

&gt; Error in n() : This function should not be called directly

dplyr: &quot;Error in n(): function should not be called directly&quot;

So here is how my data set looks like :

    In [1]: df1=pd.DataFrame(np.random.rand(4,2),index=[&quot;A&quot;,&quot;B&quot;,&quot;C&quot;,&quot;D&quot;],columns=[&quot;I&quot;,&quot;J&quot;])
    
    In [2]: df2=pd.DataFrame(np.random.rand(4,2),index=[&quot;A&quot;,&quot;B&quot;,&quot;C&quot;,&quot;D&quot;],columns=[&quot;I&quot;,&quot;J&quot;])
    
    In [3]: df1
    Out[3]: 
              I         J
    A  0.675616  0.177597
    B  0.675693  0.598682
    C  0.631376  0.598966
    D  0.229858  0.378817
    
    In [4]: df2
    Out[4]: 
              I         J
    A  0.939620  0.984616
    B  0.314818  0.456252
    C  0.630907  0.656341
    D  0.020994  0.538303

**I want to have stacked bar plot for each dataframe but since they have same index, I&#39;d like to have 2 stacked bars per index.**

I&#39;ve tried to plot both on the same axes :

    In [5]: ax = df1.plot(kind=&quot;bar&quot;, stacked=True)
    
    In [5]: ax2 = df2.plot(kind=&quot;bar&quot;, stacked=True, ax = ax)

But it overlaps.

Then I tried to concat the two dataset first :

    pd.concat(dict(df1 = df1, df2 = df2),axis = 1).plot(kind=&quot;bar&quot;, stacked=True)

but here everything is stacked

My best try is :

     pd.concat(dict(df1 = df1, df2 = df2),axis = 0).plot(kind=&quot;bar&quot;, stacked=True)

Which gives :

![enter image description here][1]

This is basically what I want, except that I want the bar ordered as
 
(df1,A) (df2,A) (df1,B) (df2,B) etc...

I guess there is a trick but I can&#39;t found it !

-------

After @bgschiller&#39;s answer I got this :

![enter image description here][2] 

Which is almost what I want. I would like the bar to be **clustered by index**, in order to have something visually clear.

*Bonus* : Having the x-label not redundant, something like : 

    df1 df2    df1 df2
    _______    _______ ...
       A          B


Thanks for helping.


  [1]: http://i.stack.imgur.com/dSSsI.png
  [2]: http://i.stack.imgur.com/8Uk5l.png
  [3]: http://i.stack.imgur.com/9ywt2.png

How to have clusters of stacked bars with python (Pandas)

When I try to plot a graph on GNU Octave, and try to use plot, it gives me the following output 

    set terminal aqua enhanced title &quot;Figure 1&quot; size 560 420  font &quot;*,6&quot; dashlength 1
                      ^
         line 0: unknown or ambiguous terminal type; type just &#39;set terminal&#39; for a list

I am using Mac OS X 10.9.2. 
I have tried using 

    octave:79&gt; setenv(&quot;GNUTERM&quot;,&quot;X11&quot;)

but I still get the same error.

Octave does not plot

I have the following dataframe:

    uniq &lt;- structure(list(year = c(1986L, 1987L, 1991L, 1992L, 1993L, 1994L, 1995L, 1996L, 1997L, 1998L, 1999L, 2000L, 2001L, 2002L, 2003L, 2004L, 2005L, 2006L, 2007L, 2008L, 2009L, 2010L, 2011L, 2012L, 2013L, 2014L, 1986L, 1987L, 1991L, 1992L, 1993L, 1994L, 1995L, 1996L, 1997L, 1998L, 1999L, 2000L, 2001L, 2002L, 2003L, 2004L, 2005L, 2006L, 2007L, 2008L, 2009L, 2010L, 2011L, 2012L, 2013L, 2014L, 1986L, 1987L, 1991L, 1992L, 1993L, 1994L, 1995L, 1996L, 1997L, 1998L, 1999L, 2000L, 2001L, 2002L, 2003L, 2004L, 2005L, 2006L, 2007L, 2008L, 2009L, 2010L, 2011L, 2012L, 2013L, 2014L), uniq.loc = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), .Label = c(&quot;u.1&quot;, &quot;u.2&quot;, &quot;u.3&quot;), class = &quot;factor&quot;), uniq.n = c(1, 1, 1, 2, 5, 4, 2, 16, 16, 10, 15, 14, 8, 12, 20, 11, 17, 30, 17, 21, 22, 19, 34, 44, 56, 11, 0, 0, 3, 3, 7, 17, 12, 21, 18, 10, 12, 9, 7, 11, 25, 14, 11, 17, 12, 24, 59, 17, 36, 50, 59, 12, 0, 0, 0, 1, 4, 6, 3, 3, 9, 3, 4, 2, 5, 2, 12, 6, 8, 8, 3, 2, 9, 5, 20, 7, 10, 8), uniq.p = c(100, 100, 25, 33.3, 31.2, 14.8, 11.8, 40, 37.2, 43.5, 48.4, 56, 40, 48, 35.1, 35.5, 47.2, 54.5, 53.1, 44.7, 24.4, 46.3, 37.8, 43.6, 44.8, 35.5, 0, 0, 75, 50, 43.8, 63, 70.6, 52.5, 41.9, 43.5, 38.7, 36, 35, 44, 43.9, 45.2, 30.6, 30.9, 37.5, 51.1, 65.6, 41.5, 40, 49.5, 47.2, 38.7, 0, 0, 0, 16.7, 25, 22.2, 17.6, 7.5, 20.9, 13, 12.9, 8, 25, 8, 21.1, 19.4, 22.2, 14.5, 9.4, 4.3, 10, 12.2, 22.2, 6.9, 8, 25.8)), .Names = c(&quot;year&quot;, &quot;uniq.loc&quot;, &quot;uniq.n&quot;, &quot;uniq.p&quot;), class = &quot;data.frame&quot;, row.names = c(NA, -78L))

When I make an area-plot with:

    ggplot(data = uniq) + 
      geom_area(aes(x = year, y = uniq.p, fill = uniq.loc), stat = &quot;identity&quot;, position = &quot;stack&quot;) +
      scale_x_continuous(limits=c(1986,2014)) +
      scale_y_continuous(limits=c(0,101)) +
      theme_bw()

I get this result:

![enter image description here][1]

However, I want to remove the space between the axis and the actual plot. When I add `theme(panel.grid = element_blank(), panel.margin = unit(-0.8, &quot;lines&quot;))` I get the following error message:

&gt;     Error in theme(panel.grid = element_blank(), panel.margin = unit(-0.8,  : 
&gt;       could not find function &quot;unit&quot;

Any suggestions on how to solve this problem?

  [1]: http://i.stack.imgur.com/ndT43.png



Remove space between plotted data and the axes

I&#39;ve looked in different questions for a solution and I&#39;ve tried what was suggested but I have not found a solution to make it work.

Everytime I want to run this code it always says: 
&gt;Error in plot.new() : figure margins too large

and I don&#39;t know how to fix it. Here is my code:

    par(mfcol=c(5,3))
    hist(RtBio, main=&quot;Histograma de Bio Pappel&quot;)
    boxplot(RtBio, main=&quot;Diagrama de Caja de Bio Pappel&quot;)
    stem(RtBio)
    plot(RtBio, main=&quot;Gr&#225;fica de Dispersi&#243;n&quot;)
    
    hist(RtAlsea, main=&quot;Histograma de Alsea&quot;)
    boxplot(Alsea, main=&quot;Diagrama de caja de Alsea&quot;)
    stem(RtAlsea)
    plot(RtTelev, main=&quot;Gr&#225;fica de distribuci&#243;n de Alsea&quot;)
    
    hist(RtTelev, main=&quot;Histograma de Televisa&quot;)
    boxplot(telev, main=&quot;Diagrama de Caja de Televisa&quot;)
    stem(Telev)
    plot(Telev, main=&quot;Gr&#225;fica de dispersi&#243;n de Televisa&quot;)
    
    hist(RtWalmex, main=&quot;Histograma de Walmex&quot;)
    boxplot(RtWalmex, main=&quot;Diagrama de caja de Walmex&quot;)
    stem(RtWalmex)
    plot(RtWalmex, main=&quot;Gr&#225;fica de dispersi&#243;n de Walmex&quot;)
    
    hist(RtIca, main=&quot;Histograma de Ica&quot;)
    boxplot(RtIca, main=&quot;Gr&#225;fica de caja de Ica&quot;)
    stem(RtIca)
    plot(RtIca, main=&quot;Gr&#225;fica de dispersi&#243;n de Ica&quot;)

What can I do?


Error in plot.new() : figure margins too large, Scatter plot

I&#39;m trying to make a plot in matplotlib with transparent markers which have a fixed color edge . However, I can&#39;t seem to achieve a marker with transparent fill. 

I have a minimum working example here:

    import numpy as np
    import matplotlib.pyplot as plt

    x = np.arange(10)
    y1 = 2*x + 1
    y2 = 3*x - 5

    plt.plot(x,y1, &#39;o-&#39;, lw=6, ms=14)
    plt.plot(x,y2, &#39;o&#39;, ms=14, markerfacecolor=None, alpha=0.5, markeredgecolor=&#39;red&#39;, markeredgewidth=5)

    plt.show()

I tried two techniques I found online to achieve this:
1) Setting alpha parameter. However, this makes the marker edge transparent too, which is not the desired effect.
2) Setting markerfacecolor=None, although this has no effect on my plot

Is there a solution to this please?


Plotting with a transparent marker but non-transparent edge

I have a simple script file called `test.R`. It&#39;s saved in the working directory. When I go to `File &gt; Open &gt; test.R`, it opens the file in the editor (without executing the code, which is what I want). 

How do I do this by typing a command in the console window? To be clear, I just want to open (**not** execute) the file.

How do I open a script file in RStudio using an R command?

I am using Rstudio and not sure how options &quot;run&quot; and &quot;source&quot; are different.

I tried googling these terms but &#39;source&#39; is a very common word and wasn&#39;t able to get good search results :(

![enter image description here][1]


  [1]: http://i.stack.imgur.com/2GHjV.jpg

Rstudio difference between run and source

I am using RStudio for writing markdown documents and want to add Table of Contents (TOC) at top of the documents so that the user could click the relevant section for reading. There were some relevant examples on rpubs but now I can&#39;t seem to find them. Please note that I don&#39;t use `pandoc` and am quite new to `Rmd` &amp; `knitr`. Is there any way to add TOCs without using `pandoc`? If using `pandoc` is must then which functions are relevant?

# EDIT

Here&#39;s a small sample page:

    ---
    title: &quot;Sample Document&quot;
    output:
      html_document:
        toc: true
        theme: united
    ---

    Header 1
    ---------------
    This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see &lt;http://rmarkdown.rstudio.com&gt;.
        
    ## Header 2
    When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
        
    ```{r}
    summary(cars)
    ```
    
    You can also embed plots, for example:
    
    ```{r, echo=FALSE}
    plot(cars)
    ```
    ### Header 3
    Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.

I tried running this in RStudio v 0.98.864 and it worked! but sadly it didn&#39;t work on 0.98.501 and 0.98.507. I am working on my thesis in 0.98.501 and after updating RStudio, some of my analyses didn&#39;t work. So, I reverted back to 0.98.501.
What should I do now? I really want TOCs but without harming the outputs of other analyses.


How to add table of contents in Rmarkdown?

I wonder how to use `rmarkdown` to generate a pdf which has both portrait and landscape layout in the same document. If there is a pure `rmarkdown` option that would be even better than using latex.

Here&#39;s a small, reproducible example. First, rendering this `.Rmd` in RStudio (press **Knit PDF** button) results in a pdf with all pages in landscape layout:

    ---
    title: &quot;All pages landscape&quot;
    output: pdf_document
    classoption: landscape
    ---
      
    ```{r}
    summary(cars)
    ```
    
    \newpage
    ```{r}
    summary(cars)
    ```

Then an attempt to create a document which mixes portrait and landscape layout. The basic setup in the `YAML` is done according to the &#39;Includes&#39; section [**here**](http://rmarkdown.rstudio.com/pdf_document_format.html). The `in_header` file &#39;header.tex&#39; only contains `\usepackage{lscape}`, a package suggested for `knitr` landscape layout [**here**](https://github.com/yihui/knitr-examples/blob/master/030-landscape.Rnw). The `.tex` file is in the same directory as the `.Rmd` file.  

    ---
    title: &quot;Mixing portrait and landscape&quot;
    output:
        pdf_document:
            includes:
                in_header: header.tex
    ---
    
    Portrait:
    ```{r}
    summary(cars)
    ```
    
    \newpage
    \begin{landscape}
    Landscape:
    ```{r}
    summary(cars)
    ```
    \end{landscape}
    
    \newpage
    More portrait:
    ```{r}
    summary(cars)
    ```

However, this code results in an error:

    # ! You can&#39;t use `macro parameter character #&#39; in horizontal mode.
    # l.116 #
    
    # pandoc.exe: Error producing PDF from TeX source
    # Error: pandoc document conversion failed with error 43

Any help is much appreciated.

Rstudio rmarkdown: both portrait and landscape layout in a single PDF

I&#39;m trying to follow [this pandoc example](http://johnmacfarlane.net/pandoc/demo/example9/pandocs-markdown.html#yaml-metadata-block) to add multiple authors to an Rmarkdown file in the [yaml metadata block](http://rmarkdown.rstudio.com/authoring_pandoc_markdown.html#yaml-metadata-block). The pdf will generate in RStudio (Version 0.98.932), but there is no author information. 

    ---
    title:  &#39;This is the title: it contains a colon&#39;
    author:
    - name: Author One
      affiliation: University of Somewhere
    - name: Author Two
      affiliation: University of Nowhere
    date: &quot;`r format(Sys.time(), &#39;%d %B %Y&#39;)`&quot;
    tags: [nothing, nothingness]
    abstract: |
      This is the abstract.
    
      It consists of two paragraphs.
    output: pdf_document
    ---

I&#39;d also like to customize the heading a bit more and add a subtitle. Possible?

Content Type	Original Author	Original Content on Stackoverflow
Question	dpel	View Question on Stackoverflow
Solution 1 - R	Dason	View Answer on Stackoverflow
Solution 2 - R	Waldir Leoncio	View Answer on Stackoverflow
Solution 3 - R	Patrícia Gonçalves	View Answer on Stackoverflow
Solution 4 - R	Tom	View Answer on Stackoverflow
Solution 5 - R	MattG	View Answer on Stackoverflow

Code to clear all plots in RStudio

R Problem Overview

R Solutions

Solution 1 - R

Solution 2 - R

Solution 3 - R

Solution 4 - R

Solution 5 - R

JavaScript runtime complexity of Array functions

How to step one step back in IntelliJ?

Attributions