via Hadley at https://github.com/hadley/ggplot2



&gt;     install.packages(&quot;devtools&quot;)
&gt;     
&gt;     library(devtools)
&gt;     
&gt;     dev_mode(on=T)
&gt;     
&gt;     install_github(&quot;hadley/ggplot2&quot;)
&gt;     
&gt;     # use dev ggplot2 now
&gt;     
&gt;     # when finished do:
&gt;     
&gt;     dev_mode(on=F)  #and you are back to having stable ggplot2

I have the feeling that both previous answers miss the point of your question.  

Consider this:

 - You can control **where to install** packages via arguments to both `R CMD INSTALL` (via `-l`) and `install.packages()`.  

 - At run-time, you can control **where to load packages from** via `.libPaths()`.  

So it really is just a matter of setting a few variables in your `.Rprofile` (or alike) to control this.

for compile binaries install:

    install.packages(&#39;xxx&#39;, repo=&#39;http://repo_adress&#39;)

for source install :

    install.packages(&#39;xxx&#39;, repo=&#39;http://repo_adress&#39;, type=&#39;source&#39;)

    devtools::install_github(&quot;ggplot2&quot;)

If I try this:

    $a = 0;    
    echo $a + ++$a, PHP_EOL;
    echo $a;

I get this output:

    2
    1

Demo: http://codepad.org/ncVuJtJu

###Why is that?

I expect to get this as an output:

    1
    1

###My understanding:

    $a = 0;                    // a === 0    
    echo $a + ++$a, PHP_EOL;   // (0) + (0+1) === 1
    echo $a;                   // a === 1

But why isn&#39;t that the output?

Why is $a + ++$a == 2?

I would like to know the specific difference between `BufferedReader` and `FileReader`. 

I do know that `BufferedReader` is much more efficient as opposed to `FileReader`, but can someone please explain why (specifically and in detail)? Thanks.



Specific difference between bufferedreader and filereader

How can I install a package that is under development directly from a github repository and once installed how can I switch between development and CRAN versions?

The specific package I am interested in installing from git is ggplot2.

How to install development version of R packages github repository

<p>How can I install a package that is under development directly from a github repository and once installed how can I switch between development and CRAN versions?</p>
<p>The specific package I am interested in installing from git is ggplot2.</p>


There are a range of tools available for creating publication quality tables using R, Sweave, and LaTeX.
In particular, there are helper functions like `latex` in the `Hmisc` package, and `xtable` in the `xtable` package. I&#39;ve also often written my own code so that I could have complete control over table formatting (e.g., see [this example](http://jeromyanglim.blogspot.com.au/2010/11/sweave-tutorial-2-individual.html)).

However, when preparing publication quality tables a range of issues often arise:

* how and when to apply numeric formatting
* how to precisely control alignment of columns and cells
* how to precisely control cell borders 
* how to convert variable labels to variable names
* and so on

Beyond the high level issues of specifying the desired table format, there are issues of implementation. 

* When should a helper function such as `xtable` be used? 
* Which helper function should be used in a given situation?
* How can the default output of helper functions be customised to particular requirements?

### Question
It seems to me that the above issues are deserving of a detailed textbook-style introduction.

**Are there any online or offline resources that provide a detailed overview of how to produce publication quality tables using R, Sweave, and LaTeX, and that address the issues discussed above?**



General guide for creating publication quality tables using R, Sweave, and LaTeX

I have a vector like: `a = c(1:10)` and I need to remove multiple values, like: `2, 3, 5`

How to delete those numbers (they are **NOT** the positions in the vector) in the vector?

at the moment i loop the vector and do something like: 
    
    a[!a=NUMBER_TO_REMOVE]

But I think there is a function that does it automatically.


How to delete multiple values from a vector?

Currently, I&#39;m reading a lot about Software Engineering, Software Design, Design Patterns etc. Coming from a totally different background, that&#39;s all new fascinating stuff to me, so please bear with me in case I&#39;m not using the correct technical terminology to describe certain aspects ;-)

I ended up using [Reference Classes][1] (a way of OOP in R) most of the time because object orientation seems to be the right choice for a lot of the stuff that I&#39;m doing. 

Now, I was wondering if anyone has some good advice or some experience with respect to  implementing the **[MVC][2]** (Model View Controller; also known as **MVP**: Model View Presenter) pattern in R, preferably using Reference Classes.

I&#39;d also be very interested in info regarding other &quot;standard&quot; design patterns such as [observer][3], [blackboard][4] etc., but I don&#39;t want to make this too broad of a question. I guess the coolest thing would be to see some minimal example code, but any pointer, &quot;schema&quot;, diagram or any other idea will also be greatly appreciated!

For those interested in similar stuff, I can really recommend the following books:

 1. [The Pragmatic Programmer][5]
 2. [Design Patterns][6]

**UPDATE 2012-03-12**

I did eventually come up with a small example of my interpretation of MVC (which might not be totally correct ;-)).

## Package Dependencies ##

    require(&quot;digest&quot;)


## Class Definition Observer ##

    setRefClass(
        &quot;Observer&quot;,
        fields=list(
            .X=&quot;environment&quot;
        ),
        methods=list(
            notify=function(uid, ...) {
                message(paste(&quot;Notifying subscribers of model uid: &quot;, uid, sep=&quot;&quot;))
                temp &lt;- get(uid, .self$.X)
                if (length(temp$subscribers)) {
                    # Call method updateView() for each subscriber reference
                    sapply(temp$subscribers, function(x) {
                        x$updateView()        
                    })
                }    
                return(TRUE)
            }
        )
    )

## Class Definition Model ##

    setRefClass(
        &quot;Model&quot;,
        fields=list(
            .X=&quot;data.frame&quot;,
            state=&quot;character&quot;,
            uid=&quot;character&quot;,
            observer=&quot;Observer&quot;
        ),
        methods=list(
            initialize=function(...) {
                # Make sure all inputs are used (&#39;...&#39;)
                .self &lt;- callSuper(...)
                # Ensure uid
                .self$uid &lt;- digest(c(.self, Sys.time()))
                # Ensure hash key of initial state
                .self$state &lt;- digest(.self$.X)
                # Register uid in observer
                assign(.self$uid, list(state=.self$state), .self$observer$.X)
                .self
            },
            multiply=function(x, ...) {
                .self$.X &lt;- .X * x 
                # Handle state change
                statechangeDetect()
                return(TRUE)
            },
            publish=function(...) {
                message(paste(&quot;Publishing state change for model uid: &quot;, 
                    .self$uid, sep=&quot;&quot;))
                # Publish current state to observer
                if (!exists(.self$uid, .self$observer$.X)) {
                    assign(.self$uid, list(state=.self$state), .self$observer$.X)
                } else {
                    temp &lt;- get(.self$uid, envir=.self$observer$.X)
                    temp$state &lt;- .self$state
                    assign(.self$uid, temp, .self$observer$.X)    
                }
                # Make observer notify all subscribers
                .self$observer$notify(uid=.self$uid)
                return(TRUE)
            },
            statechangeDetect=function(...) {
                out &lt;- TRUE
                # Hash key of current state
                state &lt;- digest(.self$.X)
                if (length(.self$state)) {
                    out &lt;- .self$state != state
                    if (out) {
                    # Update state if it has changed
                        .self$state &lt;- state
                    }
                }    
                if (out) {
                    message(paste(&quot;State change detected for model uid: &quot;, 
                       .self$uid, sep=&quot;&quot;))
                    # Publish state change to observer
                    .self$publish()
                }    
                return(out)
            }
        )
    )

## Class Definition Controller and Views ##

    setRefClass(
        &quot;Controller&quot;,
        fields=list(
            model=&quot;Model&quot;,
            views=&quot;list&quot;
        ),
        methods=list(
            multiply=function(x, ...) {
                # Call respective method of model
                .self$model$multiply(x) 
            },
            subscribe=function(...) {
                uid     &lt;- .self$model$uid
                envir   &lt;- .self$model$observer$.X 
                temp &lt;- get(uid, envir)
                # Add itself to subscribers of underlying model
                temp$subscribers &lt;- c(temp$subscribers, .self)
                assign(uid, temp, envir)    
            },
            updateView=function(...) {
                # Call display method of each registered view
                sapply(.self$views, function(x) {
                    x$display(.self$model)    
                })
                return(TRUE)
            }
        )
    )
    setRefClass(
        &quot;View1&quot;,
        methods=list(
            display=function(model, x=1, y=2, ...) {
                plot(x=model$.X[,x], y=model$.X[,y])
            }
        )
    )
    setRefClass(
        &quot;View2&quot;,
        methods=list(
            display=function(model, ...) {
                print(model$.X)
            }
        )
    )

## Class Definition For Representing Dummy Data ##

    setRefClass(
        &quot;MyData&quot;,
        fields=list(
            .X=&quot;data.frame&quot;
        ),
        methods=list(
            modelMake=function(...){
                new(&quot;Model&quot;, .X=.self$.X)
            }
        )
    )

## Create Instances ##

    x &lt;- new(&quot;MyData&quot;, .X=data.frame(a=1:3, b=10:12))

Investigate model characteristics and observer state

    mod &lt;- x$modelMake()
    mod$.X

    &gt; mod$uid
    [1] &quot;fdf47649f4c25d99efe5d061b1655193&quot;
    # Field value automatically set when initializing object.
    # See &#39;initialize()&#39; method of class &#39;Model&#39;.

    &gt; mod$state
    [1] &quot;6d95a520d4e3416bac93fbae88dfe02f&quot;
    # Field value automatically set when initializing object.
    # See &#39;initialize()&#39; method of class &#39;Model&#39;.

    &gt; ls(mod$observer$.X)
    [1] &quot;fdf47649f4c25d99efe5d061b1655193&quot;

    &gt; get(mod$uid, mod$observer$.X)
    $state
    [1] &quot;6d95a520d4e3416bac93fbae88dfe02f&quot;

Note that the object&#39;s uid has automatically been registered in the observer upon initialization. That way, controllers/views can subscribe to notifications and we have a 1:n relationship.

Instantiate views and controller

    view1 &lt;- new(&quot;View1&quot;)
    view2 &lt;- new(&quot;View2&quot;)
    cont  &lt;- new(&quot;Controller&quot;, model=mod, views=list(view1, view2))

## Subscribe ##

Controller subscribes to notifications of underlying model

    cont$subscribe()

Note that the subscription has been logged in the observer

    get(mod$uid, mod$observer$.X)

## Display Registered Views ##

    &gt; cont$updateView()
      a  b
    1 1 10
    2 2 11
    3 3 12
    [1] TRUE

There&#39;s also a plot window that is opened.

## Modify Model ##

    &gt; cont$model$multiply(x=10)
    State change detected for model uid: fdf47649f4c25d99efe5d061b1655193
    Publishing state change for model uid: fdf47649f4c25d99efe5d061b1655193
    Notifying subscribers of model uid: fdf47649f4c25d99efe5d061b1655193
       a   b
    1 10 100
    2 20 110
    3 30 120
    [1] TRUE

Note that both registered views are automatically updated as the underlying model published its state change to the observer, which in turn notified all subscribers (i.e., the controller).

## Open Questions ##

Here&#39;s what I feel like I&#39;m not fully understanding yet:

 1. Is this a somewhat correct implementation of the MVC pattern? If not, what did I do wrong?
 2. Should &quot;processing&quot; methods (e.g. aggregate data, take subsets etc.) for the model &quot;belong&quot; to the model or the controller class . So far, I always defined everything a specific object can &quot;do&quot; as methods of this very object. 
 3. Should the controller be sort of a &quot;proxy&quot; controlling every interaction between model and views (sort of &quot;both ways&quot;), or is it only responsible for propagating user input to the model (sort of &quot;one way&quot;?

  [1]: http://stat.ethz.ch/R-manual/R-devel/library/methods/html/refClass.html
  [2]: http://en.wikipedia.org/wiki/Model%E2%80%93view%E2%80%93controller
  [3]: http://en.wikipedia.org/wiki/Observer_pattern
  [4]: http://en.wikipedia.org/wiki/Blackboard_system
  [5]: http://www.amazon.com/The-Pragmatic-Programmer-Journeyman-Master/dp/020161622X/ref=sr_1_1?s=books&amp;ie=UTF8&amp;qid=1331597257&amp;sr=1-1
  [6]: http://www.amazon.com/Design-Patterns-Elements-Reusable-Object-Oriented/dp/0201633612

Implementing standard software design patterns (focus on MVC) in R

I have a data frame with several columns; some numeric and some character. **How to compute the&#160;sum of a specific column?** I’ve googled for this and I see numerous functions (`sum`, `cumsum`, `rowsum`, `rowSums`, `colSums`, `aggregate`, `apply`) but I can’t make sense of it all.

For example suppose I have a data frame `people` with the following columns


    people &lt;- read(
      text = 
        &quot;Name Height Weight
        Mary 65     110
        John 70     200
        Jane 64     115&quot;, 
      header = TRUE
    )
    …

How do I get the sum of all the weights?

How to sum data.frame column values?

I would like install R on my laptop Mac OS X version 10.7.3

I downloaded the last version and I double click on it and it was installed, when i start up I get the following error, I searched in internet but I could not solve the problem, any help would be appreciated 

the errors are 
&gt;During startup - Warning messages:  
1: Setting LC_CTYPE failed, using &quot;C&quot;   
2: Setting LC_COLLATE failed, using &quot;C&quot;   
3: Setting LC_TIME failed, using &quot;C&quot;   
4: Setting LC_MESSAGES failed, using &quot;C&quot;   
5: Setting LC_PAPER failed, using &quot;C&quot;   
[R.app GUI 1.50 (6126) x86_64-apple-darwin9.8.0]  

&gt;WARNING: You&#39;re using a non-UTF8 locale, therefore only ASCII characters will work.
Please read R for Mac OS X FAQ (see Help) section 9 and adjust your system preferences accordingly.
[History restored from /Users/nemo/.Rapp.history]

Installing R on Mac - Warning messages: Setting LC_CTYPE failed, using &quot;C&quot;

I  currently have a local Git repository, which I push to a Github repository.

The local repository has ~10 commits, and the Github repository is a synchronised duplicate of this.

What I&#39;d like to do is remove ALL the version history from the local Git repository, so the current contents of the repository appear as the only commit (and therefore older versions of files within the repository are not stored). 

I&#39;d then like to push these changes to Github.

I have investigated Git rebase, but this appears to be more suited to removing specific versions.
Another potential solution is to delete the local repo, and create a new one - though this would probably create a lot of work!

ETA: There are specific directories / files that are untracked - if possible I would like to maintain the untracking of these files.

Make the current commit the only (initial) commit in a Git repository?

I have cloned a Git project into a local Git repository. Then I have done something nasty to one of the files and in that panic I deleted file physically from the drive (`rm style.css`) and also removed it from Git (`git rm style.css`).

I want to get the original `style.css` file back from origin to my development branch. Unfortunately my Git thinks it is up-to-date and won&#39;t do anything.

    cd ~/project.me
    git status

    # On branch dev
    nothing to commit (working directory clean)

    git pull origin dev

    Password for &#39;https://someone@github.com&#39;:
    From https://github.com/somewhere/project.me
    * branch            dev        -&gt; FETCH_HEAD
    Already up-to-date.

What do I need to do to tell git that I want to download original `style.css` file back into my dev branch?




How do I pull a missing file back into my branch?

It happens every now and then. Some library depends on another and a user opens an issue that belongs to the wrong repo. Can I move the issue to the other repo?

You could argue that the issue could be seen as being both repos&#39; issue because one depends on the other and as long as one doesn&#39;t work properly both don&#39;t. But I&#39;d rather talk about solutions to the issue in the repo it belongs in.

How do I move an issue on github to another repo?

Is it possible to generate an automatic Table of Contents using [Github Flavoured Markdown][1]?

  [1]: http://github.github.com/github-flavored-markdown/

Automatic TOC in github-flavoured-markdown

For example, `https://github.com/vanillaforums/Garden` is the GitHub repository. But I only want to &#39;watch&#39; this directory `https://github.com/vanillaforums/Garden/tree/master/plugins` in the repository.

How do I do that? There doesn&#39;t seem to be a way.

How to &#39;Watch&#39; only a directory in a GitHub repository?

Is there a way to extract the values of the fitted line returned from stat_smooth?

The code I am using looks like this:

    p &lt;- ggplot(df1, aes(x=Days, y= Qty,group=Category,color=Category))
    p &lt;- p + stat_smooth(method=glm, fullrange=TRUE)+ geom_point())

This new r user would greatly appreciate any guidance.



Method to extract stat_smooth line fit

Is it possible to insert a raster image or a pdf image underneath a `geom_line()` on a `ggplot2` plot?

I wanted to be quickly able to plot data over a previously calculated plot that takes a long time to generate as it uses a large amount of data.

I read through this [example][1]. However, as it is over one year old I thought there might be a different way of doing this now.


  [1]: https://kohske.wordpress.com/2010/12/26/use-image-for-background-in-ggplot2/

Inserting an image to ggplot2

I&#39;m making a straightforward barchart in R using the ggplot2 package.  Rather than the grey default I&#39;d like to divide the background into five regions, each a different (but similarly understated) colour.  How do I do this?

More specifically, I&#39;d like the five coloured regions to run from 0-25, 25-45, 45-65, 65-85 and 85-100 where the colours represent worse-than-bronze, bronze, silver, gold and platinum respectively.  Suggestions for a colour scheme very welcome too.



Make the background of a graph different colours in different regions

Is it possible to group by two columns? So the cross product is drawn
by `geom_point()` and `geom_smooth()`?

As example:

    frame &lt;- data.frame(
     series &lt;- rep(c(&#39;a&#39;, &#39;b&#39;), 6), 
     sample &lt;- rep(c(&#39;glass&#39;,&#39;water&#39;, &#39;metal&#39;), 4), 
     data &lt;- c(1:12))

    ggplot(frame, aes()) # ...

Such that the points `6` and `12` share a group, but not with `3`.


group by two columns in ggplot2

I created several simple ggplot2 plots and saved them to PDF files using the following commands:

    p &lt;- ggplot(plotobject, aes(x=Pos, y=Pval),res=300)
    ggsave(plot=p,height=6,width=6,dpi=200, filename=&quot;~/example.pdf&quot;)

If I now open this example.pdf in Adobe Illustrator I get the following error:

&gt; The font AdobePiStd is missing.  Affected text will be displayed using
&gt; a substitute font.

Is there a way in ggplot2 to specify a font (I presume this is for the dots/points) that Adobe will understand or otherwise is there a way to get this font working in Adobe? 

/edit just to clarify, the text/labels/titles are all just fine its the dots that are missing for the font 
/edit2 I got a working solution by just using the EPS output in ggsave, but still would love to find out a way to also be able to just open/import ggplot2 plots in PDF format directly in AI

Content Type	Original Author	Original Content on Stackoverflow
Question	Etienne Low-Décarie	View Question on Stackoverflow
Solution 1 - R	Seth	View Answer on Stackoverflow
Solution 2 - R	Dirk Eddelbuettel	View Answer on Stackoverflow
Solution 3 - R	b_rousseau	View Answer on Stackoverflow
Solution 4 - R	ferrelwill	View Answer on Stackoverflow

How to install development version of R packages github repository

R Problem Overview

R Solutions

Solution 1 - R

Solution 2 - R

Solution 3 - R

Solution 4 - R

Specific difference between bufferedreader and filereader

Why is $a + ++$a == 2?

Attributions