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  • R: building a simple command line plotting tool/Capturing window close events

    - by user275455
    I am trying to use R within a script that will act as a simple command line plot tool. I.e. user pipes in a csv file and they get a plot. I can get to R fine and get the plot to display through various temp file machinations, but I have hit a roadblock. I cannot figure out how to get R to keep running until the users closes the window. If I plot and exit, the plot disappears immediately. If I plot and use some kind of infinite loop, the user cannot close the plot; he must exit by using an interrupt which I don't like. I see there is a getGraphicsEvent function, but it claims that the device is not supported (X11). Anyway, it doesn't appear to actually support an onClose event, only onMouseDown. Any ideas on how to solve this? edit: Thanks to Dirk for the advice to check out the tk interface. Here is the test code that works: require(tcltk) library(tkrplot) ##function to display plot, called by tkrplot and embedded in a window plotIt<-function(){ plot(x=1:10, y=1:10) } ##create top level window tt<-tktoplevel() ##variable to wait on like a condition variable, to be set by event handler done <- tclVar(0) ##bind to the window destroy event, set done variable when destroyed tkbind(tt,"",function() tclvalue(done) <- 1) ##Have tkrplot embed the plot window, then realize it with tkgrid tkgrid(tkrplot(tt,plotIt)) ##wait until done is true tkwait.variable(done)

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  • Retain numerical precision in an R data frame?

    - by David
    When I create a dataframe from numeric vectors, R seems to truncate the value below the precision that I require in my analysis: data.frame(x=0.99999996) returns 1 (see update 1) I am stuck when fitting spline(x,y) and two of the x values are set to 1 due to rounding while y changes. I could hack around this but I would prefer to use a standard solution if available. example Here is an example data set d <- data.frame(x = c(0.668732936336141, 0.95351462456867, 0.994620622127435, 0.999602102672081, 0.999987126195509, 0.999999955814133, 0.999999999999966), y = c(38.3026509783688, 11.5895099585560, 10.0443344234229, 9.86152339768516, 9.84461434575695, 9.81648333804257, 9.83306725758297)) The following solution works, but I would prefer something that is less subjective: plot(d$x, d$y, ylim=c(0,50)) lines(spline(d$x, d$y),col='grey') #bad fit lines(spline(d[-c(4:6),]$x, d[-c(4:6),]$y),col='red') #reasonable fit Update 1 Since posting this question, I realize that this will return 1 even though the data frame still contains the original value, e.g. > dput(data.frame(x=0.99999999996)) returns structure(list(x = 0.99999999996), .Names = "x", row.names = c(NA, -1L), class = "data.frame") Update 2 After using dput to post this example data set, and some pointers from Dirk, I can see that the problem is not in the truncation of the x values but the limits of the numerical errors in the model that I have used to calculate y. This justifies dropping a few of the equivalent data points (as in the example red line).

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  • Unable to access index for repository error?

    - by Tommy O'Dell
    I've just created a package (RTIO) and a package repository (Q:/Integrated Planning/R), which is a company network drive. I've put my package into the folder: Q:/Integrated Planning/R/bin/windows/contrib/2.15.1/RTIO_0.1-2.zip As per Dirk's instructions in this SO, I've run the following commands: > setwd("Q:/Integrated Planning/R/bin/windows/contrib/2.15.1") > tools::write_PACKAGES(".", type="win.binary") > list.files() [1] "PACKAGES" "PACKAGES.gz" "RTIO_0.1-2.zip" > With the code below, I've added the local repository to my list of repos (and I'll get other users to do the same): options(repos = c(getOption("repos"), RioTintoIronOre = "Q:/Integrated Planning/R")) And now trying to install my package I get an error: > install.packages("RTIO") Installing package(s) into ‘C:/Program Files/R/R-2.15.1/library’ (as ‘lib’ is unspecified) Warning in install.packages : unable to access index for repository Q:/Integrated Planning/R/bin/windows/contrib/2.15 Warning in install.packages : unable to access index for repository Q:/Integrated Planning/R/bin/windows/contrib/2.15 Warning in install.packages : unable to access index for repository Q:/Integrated Planning/R/bin/windows/contrib/2.15 Warning in install.packages : package ‘RTIO’ is not available (for R version 2.15.1) What does unable to access index for repository tell me? And how can I fix it? What I'm really looking to do is to do, under Windows and with RStudio as the IDE, is to let other internal R users add this package repo such that they're able to run commands like install.packages("RTIO") or update.packages() (and presumably use the IDE to manage packages via the GUI)?

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  • How do you combine "Revision Control" with "WorkFlow" for R?

    - by Tal Galili
    Hello all, I remember coming across R users writing that they use "Revision control" (e.g: "Source control"), and I am curious to know: How do you combine "Revision control" with your statistical analysis WorkFlow? Two (very) interesting discussions talk about how to deal with the WorkFlow. But neither of them refer to the revision control element: http://stackoverflow.com/questions/1266279/how-to-organize-large-r-programs http://stackoverflow.com/questions/1429907/workflow-for-statistical-analysis-and-report-writing A Long Update To The Question: Following some of the people's answers, and Dirk's question in the comment, I would like to direct my question a bit more. After reading the Wiki article about "revision control" (which I was previously not familiar with), it was clear to me that when using revision control, what one does is to build a development structure of his code. This structure either leads to a "final product" or to several branches. When building something like, let's say, a website. There is usually one end product you work towards (the website), with some prototypes along the way. But when doing a statistical analysis, the work (to my view) is different. Sometimes you know where you want to get to. But more often, you explore. Explore cleaning the dataset. Explore different methods for statistical analysis, and ask various questions of your data (and I am writing this, knowing how Frank Harrell, and other experience statisticians feels about Data dredging). That is way the WorkFlow question with statistical programming is (in my view) a serious and deep question, raising many issues, The simpler ones are technical: Which revision control software do you use (and why) ? Which IDE do you use(and why) ? The more interesting question are about work process: How do you structure your files? What do you keep as a separate file and what as a revision? or asking in a different way - What should be a "branch" and what should be a "sub project" in your code? For example: When starting to explore your data, should a plot be creating and then erased because it didn't lead any where (but kept as a revision) or should there be a backup file of that path? How you solve this tension was my initial curiosity. The second question is "what might I be missing?". What rules (of thumb) should one follow so to avoid common pitfalls doing statistical programming with version control? In my intuition, I feel that statistical programming is inherently different then software development (I am writing this without being a real expert in statistical programming, and even less so in software development). That's way I am unsure which of the lessons I have read here about version control would be applicable. Thanks a lot, Tal

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  • Calling compiled C from R with .C()

    - by Sarah
    I'm trying to call a program (function getNBDensities in the C executable measurementDensities_out) from R. The function is passed several arrays and the variable double runsum. Right now, the getNBDensities function basically does nothing: it prints to screen the values of passed parameters. My problem is the syntax of calling the function: array(.C("getNBDensities", hr = as.double(hosp.rate), # a vector (s x 1) sp = as.double(samplingProbabilities), # another vector (s x 1) odh = as.double(odh), # another vector (s x 1) simCases = as.integer(x[c("xC1","xC2","xC3")]), # another vector (s x 1) obsCases = as.integer(y[c("yC1","yC2","yC3")]), # another vector (s x 1) runsum = as.double(runsum), # double DUP = TRUE, NAOK = TRUE, PACKAGE = "measurementDensities_out")$f, dim = length(y[c("yC1","yC2","yC3")]), dimnames = c("yC1","yC2","yC3")) The error I get, after proper execution of the function (i.e., the right output is printed to screen), is Error in dim(data) <- dim : attempt to set an attribute on NULL I'm unclear what the dimensions are that I should be passing the function: should it be s x 5 + 1 (five vectors of length s and one double)? I've tried all sorts of combinations (including sx5+1) and have found only seemingly conflicting descriptions/examples online of what's supposed to happen here. For those who are interested, the C code is below: #include <R.h> #include <Rmath.h> #include <math.h> #include <Rdefines.h> #include <R_ext/PrtUtil.h> #define NUM_STRAINS 3 #define DEBUG void getNBDensities( double *hr, double *sp, double *odh, int *simCases, int *obsCases, double *runsum ); void getNBDensities( double *hr, double *sp, double *odh, int *simCases, int *obsCases, double *runsum ) { #ifdef DEBUG for ( int s = 0; s < NUM_STRAINS; s++ ) { Rprintf("\nFor strain %d",s); Rprintf("\n\tHospitalization rate = %lg", hr[s]); Rprintf("\n\tSimulation probability = %lg",sp[s]); Rprintf("\n\tSimulated cases = %d",simCases[s]); Rprintf("\n\tObserved cases = %d",obsCases[s]); Rprintf("\n\tOverdispersion parameter = %lg",odh[s]); } Rprintf("\nRunning sum = %lg",runsum[0]); #endif } naive solution While better (i.e., potentially faster or syntactically clearer) solutions may exist (see Dirk's answer below), the following simplification of the code works: out<-.C("getNBDensities", hr = as.double(hosp.rate), sp = as.double(samplingProbabilities), odh = as.double(odh), simCases = as.integer(x[c("xC1","xC2","xC3")]), obsCases = as.integer(y[c("yC1","yC2","yC3")]), runsum = as.double(runsum)) The variables can be accessed in >out.

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  • Top Tweets SOA Partner Community – March 2012

    - by JuergenKress
    Send your tweets @soacommunity #soacommunity and follow us at http://twitter.com/soacommunity SOA Community ?SOA Community Newsletter February 2012 wp.me/p10C8u-o0 Marc ?Reading through the #OFM 11.1.1.6 , patchset 5 documentation. What is the best way to upgrade your whole dev…prd street. SOA Community Thanks for the successful and super interesting #sbidays ! Wonderful discussions around the Integration, case management and security tracks Torsten Winterberg Schon den neuen Opitz Technology-Blog gebookmarked? The Cattle Crew bit.ly/yLPwBD wird ab sofort regelmäßig Erkenntnisse posten. OTNArchBeat ? Unit Testing Asynchronous BPEL Processes Using soapUI | @DanielAmadei bit.ly/x9NsS9 Rolando Carrasco ?Video de Human Task en BPM 11g. Por @edwardo040. bit.ly/wki9CA cc @OracleBPM @OracleSOA @soacommunity View video Marcel Mertin SOA Security Hands-On by Dirk Krafzig and Mamoon Yunus at #sbidays is also great! SOA Community Workshop day #sbidays #BPMN2.0 by Volker Stiehl from #SAP great training – now I can model & execute in #bpmsuite #soacommunity Simone Geib ?Just updated our advanced #soasuite #otn page with a number of very interesting @orclateamsoa blog posts: bit.ly/advancedsoasui… OTNArchBeat ? Start Small, Grow Fast: SOA Best Practices article by @biemond, @rluttikhuizen, @demed bit.ly/yem9Zv Steffen Miller ? Nice new features in SOA Suite Business Rules #PS5 Testing rules with scenarios and output validation bit.ly/zj64Q3 @SOACOMMUNITY OTNArchBeat ? Reply SOA Blackbelt training by David Shaffer, April 30th–May 4th 2012 bit.ly/xGdC24 OTNArchBeat ? What have BPM, big data, social tools, and business models got in common? | Andy Mulholland bit.ly/xUkOGf SOA Community ? Live hacking at #sbidays – cheaper shopping, bias cracking, payment systems, secure your SOA! pic.twitter.com/y7YaIdug SOA Community Future #BPM & #ACM solutions can make use of ontology’s, based on #sqarql #sbidays pic.twitter.com/xLb1Z5zs Simone Geib ? @soacommunity: SOA Blackbelt training by David Shaffer, April 30th–May 4th 2012 wp.me/p10C8u-nX Biemond Changing your ADF Connections in Enterprise Manager with PS5: With Patch Set 5 of Fusion Middleware you can fina… bit.ly/zF7Rb1 Marc ? HUGE (!) CPU and Heap improvement on Oracle Fusion Middleware tinyurl.com/762drzp @wlscommunity @soacommunity #OSB #SOA #WLS SOA Community ?Networking @ SOA & BPM Partner Community blogs.oracle.com/soacommunity/e… #soacommunity #otn #opn #oracle SOA Community ?Published the SOA Partner Community newsletter February edition – READ it. Not yet a member? oracle.com/goto/emea/soa #soacommunity #otn #opn AMIS, Oracle & Java Blog by Lucas Jellema: "Book Review: Do More with SOA Integration: Best of Packt (december 2011, various authors)" bit.ly/wq633E Jon petter hjulstad @SOASimone Excellent summary! Lots of new features! Simone Geib ?Do you want to know what’s new in #soasuite #PS5? Go to bit.ly/xBX06f and let me know what you think SOA Community ? Unit Testing Asynchronous BPEL Processes Using soapUI oracle.com/technetwork/ar… #soacommunity #soa #otn #oracle #bpel Retweeted by SOA Community View media Retweeted by SOA Community Eric Elzinga ? Oracle Fusion Middleware Partner Community Forum Malage, The Overview, bit.ly/AA9BKd #ofmforum SOA&Cloud Symposium ? The February issue of the Service Technology Magazine is now published. servicetechmag.com SOA Community ? Oracle SOA Suite 11g Database Growth Management – must read! oracle.com/technetwork/da… #soacommunity #soa #purging demed ? Have you exposed internal processes to mobile devices using #oraclesoa? Interested in an article? DM me! #osb #rest #multichannel #mobile orclateamsoa ? A-Team SOA Blog: Enhanced version of Thread Dump Analyzer (TDA A-Team) ow.ly/1hpk7l SOA Community Reply BPM Suite #PS5 (11.1.1.6) available for download soacommunity.wordpress.com/2012/02/22/soa… Send us your feedback! #soacommunity #bpmsuite #opn SOA Community ? SOA Suite #PS5 (11.1.1.6) available for download soacommunity.wordpress.com/2012/02/22/soa… Send us your feedback! #soacommunity #soasuite SOA Community BPM Suite #PS5 1(1.1.1.6) available for download. List of new BPM features blogs.oracle.com/soacommunity/e… #soacommunity #bpm #bpmsuite #opn OracleBlogs BPM in Utilties Industry ow.ly/1hC3fp Retweeted by SOA Community OTNArchBeat ? Demystifying Oracle Enterprise Gateway | Naresh Persaud bit.ly/xtDNe2 OTNArchBeat ? Architect’s Guide to Big Data; Test BPEL Processes Using SoapUI; Development Debate bit.ly/xbDYSo Frank Nimphius ? Finished my book review of "Do More with SOA Integration: Best of Packt ". Here are my review comments: bit.ly/x2k9OZ Lucas Jellema ? That is my one stop-and-go download center for #PS5 : edelivery.oracle.com/EPD/Download/g… Lucas Jellema ? Interesting piece of documentation: Fusion Applications Extensibility Guide – docs.oracle.com/cd/E15586_01/f… source for design time @ run time inspira Lucas Jellema ? Strongly improved support for testing Business Rules at Design Time in #PS5 see docs.oracle.com/cd/E23943_01/u… Lucas Jellema ? SOA Suite 11gR1 PS5: new BPEL Component testing – docs.oracle.com/cd/E23943_01/d… Lucas Jellema ? PS5 available for CEP (Complex Event Processing) – a personal favorite of mine : oracle.com/technetwork/mi… Lucas Jellema ?What’s New in Fusion Developer’s Guide 11gR1 PS5: docs.oracle.com/cd/E23943_01/w… Lucas Jellema ? BPMN Correlation (FMW 11gR1 PS5): docs.oracle.com/cd/E23943_01/d… Lucas Jellema ? Modifying running BPM Process instances (FMW 11gR1 PS5): docs.oracle.com/cd/E23943_01/d… Lucas Jellema ? SOA Suite 11gR1 PS5 – new aggregation pattern: docs.oracle.com/cd/E23943_01/d… routing multiple messages to same instance Melvin van der Kuijl ? Automating Testing of SOA Composite Applications in PS5. docs.oracle.com/cd/E23943_01/d… Cato Aune ? SOA suite PS5 Enterprise Deployment Guide is available in ePub docs.oracle.com/cd/E23943_01/c… . Much better than pdf on Galaxy Note SOA Community ?JDeveloper 11.1.1.6 is available for download bit.ly/wGYrwE #soacommunity SOA Community ? Your first experience #PS5 – let us know @soacommunity – send us your tweets and blog posts! #soacommunity Jon petter hjulstad ? WLS 10.3.6 New features, ex better logging of jdbc use: docs.oracle.com/cd/E23943_01/w… Heidi Buelow ? Get it now! RT @soacommunity: BPM Suite PS5 11.1.1.6 available for download bit.ly/AgagT5 #bpm #soacommunity Jon petter hjulstad ?SOA Suite PS5 EDG contains OSB! docs.oracle.com/cd/E23943_01/c… Jon petter hjulstad ? Testing Oracle Rules from JDeveloper is easier in PS5: docs.oracle.com/cd/E23943_01/u… Biemond® ? What’s New in Oracle Service Bus 11.1.1.6.0 oracle.com/technetwork/mi… Jon petter hjulstad ? Adminguide New and Changed Features for PS5, ex GridLink data sources: docs.oracle.com/cd/E23943_01/c… Retweeted by SOA Community Andreas Koop ? Unbelievable! #OFM Doc Lib growth from 11gPS4->11gPS5 by 1.2G! View media SOA Community ?ODI PS5 is available oracle.com/technetwork/mi… #odi #soacommunity 22 Feb View media SOA Community Service Bus 11g Development Cookbook soacommunity.wordpress.com/2012/02/20/ser… #osb #soacommunity #ace #opn View media For regular information on Oracle SOA Suite become a member in the SOA Partner Community for registration please visit  www.oracle.com/goto/emea/soa (OPN account required) Blog Twitter LinkedIn Mix Forum Technorati Tags: soacommunity,twitter,Oracle,SOA Community,Jürgen Kress,OPN,SOA,BPM

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  • Sorting the columns of an HTML table using JQuery

    - by nikolaosk
    In this post I will show you how easy is to sort the columns of an HTML table. I will use an external library,called Tablesorter which makes life so much easier for developers. ?here are other posts in my blog regarding JQuery.You can find them all here. You can find another post regarding HTML tables and JQuery here. We will demonstrate this with a step by step example. I will use Visual Studio 2012 Ultimate. You can also use Visual Studio 2012 Express Edition. You can also use VS 2010 editions.   1) Launch Visual Studio. Create an ASP.Net Empty Web application. Choose an appropriate name for your application. 2) Add a web form, default.aspx page to the application. 3) Add a table from the HTML controls tab control (from the Toolbox) on the default.aspx page 4) Now we need to download the JQuery library. Please visit the http://jquery.com/ and download the minified version.Then we need to download the Tablesorter JQuery plugin. Please donwload it, here. 5) We need to reference the JQuery library and the external JQuery Plugin. In the head section ? add the following lines.   <script src="jquery-1_8_2_min.js" type="text/javascript"></script>  <script src="jquery.tablesorter.js" type="text/javascript"></script>6) We need to type the HTML markup, the HTML table and its columns <body>    <form id="form1" runat="server">    <div>        <h1>Liverpool Legends</h1>        <table style="width: 50%;" border="1" cellpadding="10" cellspacing ="10" class="liverpool">            <thead>                <tr><th>Defenders</th><th>MidFielders</th><th>Strikers</th></tr>            </thead>            <tbody>            <tr>                <td>Alan Hansen</td>                <td>Graeme Souness</td>                <td>Ian Rush</td>            </tr>            <tr>                <td>Alan Kennedy</td>                <td>Steven Gerrard</td>                <td>Michael Owen</td>            </tr>            <tr>                <td>Jamie Garragher</td>                <td>Kenny Dalglish</td>                <td>Robbie Fowler</td>            </tr>            <tr>                <td>Rob Jones</td>                <td>Xabi Alonso</td>                <td>Dirk Kuyt</td>            </tr>                </tbody>        </table>            </div>    </form></body> 7) Inside the head section we also write the simple JQuery code.   <script type="text/javascript"> $(document).ready(function() { $('.liverpool').tablesorter(); }); </script> 8) Run your application.This is how the HTML table looks before the table is sorted on the basis of the selected column.   9) Now I will click on the Midfielders header.Have a look at the picture below  Tablesorter is an excellent JQuery plugin that makes sorting HTML tables a piece of cake. Hope it helps!!!

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  • Highlighting rows and columns in an HTML table using JQuery

    - by nikolaosk
    A friend of mine was seeking some help regarding HTML tables and JQuery. I have decided to write a few posts demonstrating the various techniques I used with JQuery to achieve the desired functionality. ?here are other posts in my blog regarding JQuery.You can find them all here.I have received some comments from visitors of this blog that are "complaining" about the length of the blog posts. I will not write lengthy posts anymore...I mean I will try not to do so..We will demonstrate this with a step by step example. I will use Visual Studio 2012 Ultimate. You can also use Visual Studio 2012 Express Edition. You can also use VS 2010 editions. 1) Launch Visual Studio. Create an ASP.Net Empty Web application. Choose an appropriate name for your application.2) Add a web form, default.aspx page to the application.3) Add a table from the HTML controls tab control (from the Toolbox) on the default.aspx page4) Now we need to download the JQuery library. Please visit the http://jquery.com/ and download the minified version.5) We will add a stylesheet to the application (Style.css)5) Obviously at some point we need to reference the JQuery library and the external stylesheet. In the head section ? add the following lines.   <link href="Style.css" rel="stylesheet" type="text/css" />       <script src="jquery-1_8_2_min.js" type="text/javascript"></script> 6) Now we need to highlight the rows when the user hovers over them.7) First we need to type the HTML markup<body>    <form id="form1" runat="server">    <div>        <h1>Liverpool Legends</h1>        <table style="width: 50%;" border="1" cellpadding="10" cellspacing ="10">            <thead>                <tr><th>Defenders</th><th>MidFielders</th><th>Strikers</th></tr>            </thead>            <tbody>            <tr>                <td>Alan Hansen</td>                <td>Graeme Souness</td>                <td>Ian Rush</td>            </tr>            <tr>                <td>Alan Kennedy</td>                <td>Steven Gerrard</td>                <td>Michael Owen</td>            </tr>            <tr>                <td>Jamie Garragher</td>                <td>Kenny Dalglish</td>                <td>Robbie Fowler</td>            </tr>            <tr>                <td>Rob Jones</td>                <td>Xabi Alonso</td>                <td>Dirk Kuyt</td>            </tr>                </tbody>        </table>            </div>    </form></body>8) Now we need to write the simple rules in the style.css file.body{background-color:#eaeaea;}.hover { background-color:#42709b; color:#ff6a00;} 8) Inside the head section we also write the simple JQuery code.  <script type="text/javascript"> $(document).ready(function() { $('tr').hover( function() { $(this).find('td').addClass('hover'); }, function() { $(this).find('td').removeClass('hover'); } ); }); </script>9) Run your application and see the row changing background color and text color every time the user hovers over it. Let me explain how this functionality is achieved.We have the .hover style rule in the style.css file that contains some properties that define the background color value and the color value when the mouse will be hovered on the row.In the JQuery code we do attach the hover() event to the tr elements.The function that is called when the hovering takes place, we search for the td element and through the addClass function we apply the styles defined in the .hover class rule in the style.css file.I remove the .hover rule styles with the removeClass function. Now let's say that we want to highlight only alternate rows of the table.We need to add another rule in the style.css.alternate { background-color:#42709b; color:#ff6a00;} The JQuery code (comment out the previous JQuery code) follows  <script type="text/javascript">        $(document).ready(function() {                     $('table tr:odd').addClass('alternate');        });    </script>  When I run my application through VS I see the following result You can do that with columns as well. You can highlight alternate columns as well.The JQuery code (comment out the previous JQuery code) follows  <script type="text/javascript">        $(document).ready(function() {                      $('td:nth-child(odd)').addClass('alternate');        });    </script>  In this script I use the nth-child() method in the JQuery code.This method retrieves all the elements that are nth children of their parent.Have a look at the picture below to see the resultsYou can also change color to each individual cell when hovered on.The JQuery code (comment out the previous JQuery code) follows    <script type="text/javascript">        $(document).ready(function() {          $('td').hover(                  function() {                 $(this).addClass('hover');               },                function() {                    $(this).removeClass('hover');                }                );        });    </script> Have a look at the picture below to see the results. Hope it helps!!!

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