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  • R: ggplot2, how to get the parameters from a plotted linear model smoother?

    - by John
    I have a data.frame with 3 time series in it, shown below. When I plot them with a smoother time series, I want to be able to get the parameters of the linear model that I plot, but I can't see how to do that? > data day od series_id 1 1 0.10 A1 2 3 1.00 A1 3 5 0.50 A1 4 7 0.70 A1 5 1 1.70 B1 6 3 1.60 B1 7 5 1.75 B1 8 7 1.70 B1 9 1 2.10 C1 10 3 2.30 C1 11 5 2.50 C1 12 7 2.70 C1 data = data.frame (day = c(1,3,5,7,1,3,5,7,1,3,5,7), od = c(0.1,1.0,0.5,0.7 ,1.7,1.6,1.75,1.7 ,2.1,2.3,2.5,2.7), series_id = c("A1", "A1", "A1","A1", "B1", "B1","B1", "B1", "C1","C1", "C1", "C1")) r <- ggplot(data = data, aes(x = day, y = od)) r + stat_smooth(aes(group = series_id, color = series_id),method="lm")

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  • Wireshark Dissector: How to Identify Missing UDP Frames?

    - by John Dibling
    How do you identify missing UDP frames in a custom Wireshark dissector? I have written a custom dissector for the CQS feed (reference page). One of our servers gaps when receiving this feed. According to Wireshark, some UDP frames are never received. I know that the frames were sent because all of our other servers are gap-free. A CQS frame consists of multiple messages, each having its own sequence number. My custom dissector provides the following data to Wireshark: cqs.frame_gaps - the number of gaps within a UDP frame (always zero) cqs.frame_first_seq - the first sequence number in a UDP frame cqs.frame_expected_seq - the first sequence number expected in the next UDP frame cqs.frame_msg_count - the number of messages in this UDP frame And I am displaying each of these values in custom columns, as shown in this screenshot: I tried adding code to my dissector that simply saves the last-processed sequence number (as a local static), and flags gaps when the dissector processes a frame where current_sequence != (previous_sequence + 1). This did not work because the dissector can be called in random-access order, depending on where you click in the GUI. So you could process frame 10, then frame 15, then frame 11, etc. Is there any way for my dissector to know if the frame that came before it (or the frame that follows) is missing? The dissector is written in C. (See also a companion post on serverfault.com)

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  • Unescape _xHHHH_ XML escape sequences using Python

    - by John Machin
    I'm using Python 2.x [not negotiable] to read XML documents [created by others] that allow the content of many elements to contain characters that are not valid XML characters by escaping them using the _xHHHH_ convention e.g. ASCII BEL aka U+0007 is represented by the 7-character sequence u"_x0007_". Neither the functionality that allows representation of any old character in the document nor the manner of escaping is negotiable. I'm parsing the documents using cElementTree or lxml [semi-negotiable]. Here is my best attempt at unescapeing the parser output as efficiently as possible: import re def unescape(s, subber=re.compile(r'_x[0-9A-Fa-f]{4,4}_').sub, repl=lambda mobj: unichr(int(mobj.group(0)[2:6], 16)), ): if "_" in s: return subber(repl, s) return s The above is biassed by observing a very low frequency of "_" in typical text and a better-than-doubling of speed by avoiding the regex apparatus where possible. The question: Any better ideas out there?

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  • SVN Tree Conflict Errors

    - by John
    I seem to see such errors quite often in our SVN 1.6 repo. We got these quite a lot while we used to just work on /trunk so I don't think it's due to merge/branching confusion. It seems that a cleup and marking the conflict resolved always works, but it's a little concerning to see errors in your version control system when you're just adding/updating/deleting files. What causes it?

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  • Calculating a Sample Covariance Matrix for Groups with plyr

    - by John A. Ramey
    I'm going to use the sample code from http://gettinggeneticsdone.blogspot.com/2009/11/split-apply-and-combine-in-r-using-plyr.html for this example. So, first, let's copy their example data: mydata=data.frame(X1=rnorm(30), X2=rnorm(30,5,2), SNP1=c(rep("AA",10), rep("Aa",10), rep("aa",10)), SNP2=c(rep("BB",10), rep("Bb",10), rep("bb",10))) I am going to ignore SNP2 in this example and just pretend the values in SNP1 denote group membership. So then, I may want some summary statistics about each group in SNP1: "AA", "Aa", "aa". Then if I want to calculate the means for each variable, it makes sense (modifying their code slightly) to use: > ddply(mydata, c("SNP1"), function(df) data.frame(meanX1=mean(df$X1), meanX2=mean(df$X2))) SNP1 meanX1 meanX2 1 aa 0.05178028 4.812302 2 Aa 0.30586206 4.820739 3 AA -0.26862500 4.856006 But what if I want the sample covariance matrix for each group? Ideally, I would like a 3D array, where the I have the covariance matrix for each group, and the third dimension denotes the corresponding group. I tried a modified version of the previous code and got the following results that have convinced me that I'm doing something wrong. > daply(mydata, c("SNP1"), function(df) cov(cbind(df$X1, df$X2))) , , = 1 SNP1 1 2 aa 1.4961210 -0.9496134 Aa 0.8833190 -0.1640711 AA 0.9942357 -0.9955837 , , = 2 SNP1 1 2 aa -0.9496134 2.881515 Aa -0.1640711 2.466105 AA -0.9955837 4.938320 I was thinking that the dim() of the 3rd dimension would be 3, but instead, it is 2. Really this is a sliced up version of the covariance matrix for each group. If we manually compute the sample covariance matrix for aa, we get: [,1] [,2] [1,] 1.4961210 -0.9496134 [2,] -0.9496134 2.8815146 Using plyr, the following gives me what I want in list() form: > dlply(mydata, c("SNP1"), function(df) cov(cbind(df$X1, df$X2))) $aa [,1] [,2] [1,] 1.4961210 -0.9496134 [2,] -0.9496134 2.8815146 $Aa [,1] [,2] [1,] 0.8833190 -0.1640711 [2,] -0.1640711 2.4661046 $AA [,1] [,2] [1,] 0.9942357 -0.9955837 [2,] -0.9955837 4.9383196 attr(,"split_type") [1] "data.frame" attr(,"split_labels") SNP1 1 aa 2 Aa 3 AA But like I said earlier, I would really like this in a 3D array. Any thoughts on where I went wrong with daply() or suggestions? Of course, I could typecast the list from dlply() to a 3D array, but I'd rather not do this because I will be repeating this process many times in a simulation. As a side note, I found one method (http://www.mail-archive.com/[email protected]/msg86328.html) that provides the sample covariance matrix for each group, but the outputted object is bloated. Thanks in advance.

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  • Compiled Haskell libraries with FFI imports are invalid when imported into GHCI

    - by John Millikin
    I am using GHC 6.12.1, in Ubuntu 10.04 When I try to use the FFI syntax for static storage, only modules running in interpreted mode (ie GHCI) work properly. Compiled modules have invalid pointers, and do not work. I'd like to know whether anybody can reproduce the problem, whether this an error in my code or GHC, and (if the latter) whether it's a known issue. I'm using sys_siglist because it's present in a standard library on my system, but I don't believe the actual storage used matters (I discovered this while writing a binding to libidn). If it helps, sys_siglist is defined in <signal.h> as: extern __const char *__const sys_siglist[_NSIG]; I thought this type might be the problem, so I also tried wrapping it in a plain C procedure: #include<stdio.h> const char **test_ffi_import() { printf("C think sys_siglist = %X\n", sys_siglist); return sys_siglist; } However, importing that doesn't change the result, and the printf() call prints the same pointer value as show siglist_a. My suspicion is that it's something to do with static and dynamic library loading. Update: somebody in #haskell suggested this might be 64-bit specific; if anybody tries to reproduce it, can you mention your architecture and whether it worked in a comment? Code as follows: -- A.hs {-# LANGUAGE ForeignFunctionInterface #-} module A where import Foreign import Foreign.C foreign import ccall "&sys_siglist" siglist_a :: Ptr CString -- -- B.hs {-# LANGUAGE ForeignFunctionInterface #-} module B where import Foreign import Foreign.C foreign import ccall "&sys_siglist" siglist_b :: Ptr CString -- -- Main.hs {-# LANGUAGE ForeignFunctionInterface #-} module Main where import Foreign import Foreign.C import A import B foreign import ccall "&sys_siglist" siglist_main :: Ptr CString main = do putStrLn $ "siglist_a = " ++ show siglist_a putStrLn $ "siglist_b = " ++ show siglist_b putStrLn $ "siglist_main = " ++ show siglist_main peekSiglist "a " siglist_a peekSiglist "b " siglist_b peekSiglist "main" siglist_main peekSiglist name siglist = do ptr <- peekElemOff siglist 2 str <- maybePeek peekCString ptr putStrLn $ "siglist_" ++ name ++ "[2] = " ++ show str I would expect something like this output, where all pointer values identical and valid: $ runhaskell Main.hs siglist_a = 0x00007f53a948fe00 siglist_b = 0x00007f53a948fe00 siglist_main = 0x00007f53a948fe00 siglist_a [2] = Just "Interrupt" siglist_b [2] = Just "Interrupt" siglist_main[2] = Just "Interrupt" However, if I compile A.hs (with ghc -c A.hs), then the output changes to: $ runhaskell Main.hs siglist_a = 0x0000000040378918 siglist_b = 0x00007fe7c029ce00 siglist_main = 0x00007fe7c029ce00 siglist_a [2] = Nothing siglist_b [2] = Just "Interrupt" siglist_main[2] = Just "Interrupt"

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  • SQL Server and Table-Valued User-Defined Function optimizations

    - by John Leidegren
    If I have an UDF that returns a table, with thousands of rows, but I just want a particular row from that rowset, will SQL Server be able to handle this effciently? SELECT * FROM dbo.MyTableUDF() WHERE ID = 1 To what extent is the query optimizer capable of reasoning about this type of query? How are Table-Valued UDFs different from traidtional views if they take no parameters? Any gotchas I should know about?

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  • Writing a simple RSpec test to check that Rake tasks are correct

    - by John Feminella
    I'm trying to be diligent about checking my rake tasks with RSpec tests, but in the process of feeling my way around I seem to have hit a wall. I've got a really simple RSpec test that looks like this: # ./test/meta_spec.rb describe "Rake tasks" do require 'rake' before(:each) do @rake = Rake::Application.new @rake.load_rakefile # => Error here! Rake.application = @rake end after(:each) do Rake.application = nil end it "should have at least one RSpec test to execute" do Rake.application["specs"].spec_files.size.should > 0 end end I have a simple task called "specs" defined in ./Rakefile.rb which has an RSpec task that includes all the *_spec.rb files. If I put the @rake.load_rakefile method in, I want that Rakefile to load. But instead it just bombs out. If I comment it out, however, the test fails because the "specs" task is (understandably) not defined. Where am I going wrong?

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  • All words in a trie data-structure

    - by John Smith
    I'm trying to put all words in a trie in a string, a word is detonated by the eow field being true for a certain character in the trie data structure, hence a trie can could have letters than lead up to no word, for ex "abc" is in the trie but "c"'s eow field is false so "abc" is not a word Here is my Data structure struct Trie { bool eow; //when a Trie field isWord = true, hence there is a word char letter; Trie *letters[27]; }; and here is my attemped print-all function, basically trying to return all words in one string seperated by spaces for words string printAll( string word, Trie& data) { if (data.eow == 1) return word + " "; for (int i = 0; i < 26; i++) { if (data.letters[i] != NULL) printAll( word + data.letters[i]->letter, *(data.letters[i])); } return ""; } Its not outputting what i want, any suggestions?

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  • jquery load links not clickable

    - by john morris
    ok i am loading a separate page with links in it, into a page named index.php. it loads fine, but when i click one of the links inside the loaded content, nothing happens. they dont act as links. but if i do a alert('hi'); after the load('page.html'); then it will work. any ideas on getting this to work without alerting something after it loads? oh also i cant use a callback, unless there is a way to update the get variable because the page loading, has a $_GET variable, and the links inside the loaded page are supposed to update the $_GET variable. anyways is there a way to make the links clickable after loading the page?

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  • jQuery returning two elements for each one it finds?

    - by John Rudy
    I'll start by saying I'm fairly new to jQuery. For the most part, I've found it intuitive and powerful, but this one circumstance has me thoroughly stumped. In the following method, the call to .each() returns two elements for every one found. It iterates over a set of table rows given IDs starting with the word, "communication," and followed by an ID number. For each row it returns, it processes twice. Using Firebug, I've validated that the DOM only has a single instance of each table row in question. Also using Firebug, I've validated that the method is not being called twice; the iteration in .each() is truly going over each returned table row twice. By the time all the AJAX call goodness is done, I'll have two entries in the database for each row created in the table. This is the code that's causing the issues: function getCommunications() { var list = $('[id^=communication]'); var communications = new Array(); list.each(function () { var communication = { ID: $(this).find('.commCompanyID').val(), /* * SNIP: more object properties here that are * unnecessary to this discussion */ }; communications.push(communication); }); return communications; } At the point of return communications, the Array returned will contain twice as many elements as there are table rows. I should note that nearly identical code (but going against specific lists of divs) is working on the same page. It's just the table that's suffering the issues. I'm using jQuery 1.4.1, the version which shipped with Visual Studio .NET 2010. The table markup is fully dynamic -- that is, aside from the header row, it's dependent on data either returned at page load or created by the user via a dialog box. I'll drop in just the code for what's created at page load; again using Firebug I've validated that what I create dynamically when an end user creates a row with the dialog box matches. (This should be readable by anyone, but for the record this is an ASP.NET MVC 2.0 project.) <table id="commTable"> <tr> <th></th> <th> Date / Time </th> <th> Contact </th> <th> Type </th> <th> Duration </th> <th> Notes </th> </tr> <% foreach (var item in Model) { %> <tr id="communication<%: item.ID %>"> <td> <a href="#" onclick="showEditCommunicationForm(<%: item.ID %>"> Edit</a> <span class="commDeleteButton"> <a href="#" onclick="deleteCommunication(<%: item.ID %>)"> Delete</a> </span> </td> <td> <span class="commDateTime"><%: item.DateTime %></span> <input type="hidden" class="commID" value="<%: item.ID %>" /> <input type="hidden" class="commIsDeleted" value="<%: item.IsDeleted %>" /> </td> <td> <span class="commSourceText"><%: item.Company.CompanyName %></span> <input type="hidden" class="commCompanyID" value="<%: item.CompanyID %>" /> </td> <td> <%: item.CommunicationType.CommunicationTypeText %> <input type="hidden" class="commTypeID" value="<%: item.CommunicationTypeID %>" /> </td> <td> <span class="commDuration"><%: item.DurationMinutes %></span> Minutes </td> <td> <span class="commNotes"><%: item.Notes %></span> </td> </tr> <% } %> </table>

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  • What's the official Microsoft way to track counts of dynamic controls to be reconstructed upon Postback?

    - by John K
    When creating dynamic controls based on a data source of arbitrary and changing size, what is the official way to track exactly how many controls need to be rebuilt into the page's control collection after a Postback operation (i.e. on the server side during the ASP.NET page event lifecycle) specifically the point at which dynamic controls are supposed to be rebuilt? Where is the arity stored for retrieval and reconstruction usage? By "official" I mean the Microsoft way of doing it. There exist hacks like Session storage, etc but I want to know the bonafide or at least Microsoft-recommended way. I've been unable to find a documentation page stating this information. Usually code samples work with a set of dynamic controls of known numbers. It's as if doing otherwise would be tougher. Update: I'm not inquiring about user controls or static expression of declarative controls, but instead about dynamically injecting controls completely from code-behind, whether they be mine, 3rd-party or built-in ASP.NET controls.

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  • Set title of SplitViewController

    - by John
    I am using the SplitViewController template. How do I set the title on the topbar in the detailview? Been trying to work this out for hours. Tried simple: detailViewController.title = @"String"; but no luck. Any help appreciated. Thanks.

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  • Benefits of migrating my work to a new web development framework?

    - by John
    When I first started programming with PHP, I was ignorant of other php frameworks (like code igniter, cake php, etc...). So I fell into the trap of re-inventing wheels, which had the benefit of being "fun" and "educational". Overtime, I discovered other open source products that I found useful, like smarty templating engine, jquery library, tcpdf library, fdf etc...so I started bundling these technologies along with things I've built over the years into a LAMP development framework to make life easier for myself. This pass year, I've been having fun developing on the code igniter framework. It does many of the things I do in my framework. Coding in CI feels natural because the MVC and ORM feels similar to the MVC and ORM of my framework. So now I'm contemplating migrating a lot of the plugins in my framework over to CI. The pros and cons I can think of for such a project are: Pros: benefit from the vast community of CI developers lots of other developers will be familiar with it better documentation Cons: I've built a lot of useful plugins against my own framework, and it will take a lot of time to move even just the essential ones at the moment, I still, work faster against my own framework than CI, just because I'm more familiar with it even if I did migrate to CI, there will always be newer and better frameworks in the near future, and i'll be contemplating this scenario again So my question is the following: perhaps I should leave my old framework as is, and for each new project I receive, I make a decision on whether the requirements are best served by developing with CI or my own framework. Is this the right approach?

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  • Alternative to BerkeleyDB?

    - by John
    I'm looking for a dbm-like library that I can use in place of Berkeley DB, which I'm currently using. My main reason for switching is the licensing fees for BDB are pretty high (free for open source apps, but my employer does not want to open source this particular app for various reasons). I've looked briefly at qdbm but it doesn't look like it will fill my needs -- lots of keys (several million) and large data items ( 1-5 megabytes). Before I continue my search I figured I'd ask because it seems there are tons of dbm-like libraries out there.

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  • I want to combine my www and non www and keep the link jucie from both.

    - by John Ray
    My website shows up for some keywords in the www and some in the non www. Seaquake shows more links to the non www version. It is a PR2 either way. I would like to combine the link juice of the two versions into the non www version. Does anyone know the best way to combine the two and keep the link juice of both. It is as simple as a 301 redirect and if so does the 301 need to be handled in any specific way.

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  • unable to get into windows 7 or ubuntu after system file back on a dual boot system

    - by John Jiang
    I installed ubuntu on my dell xps 9000 which originally has a window 7 installed. So after I did system file back up as told by windows 7 and restarted my computer, I received the following message right after restarting in the black screen: roughly like this: ubuntu grub error, " " symbol cannot be found. I was wondering how I can get access into windows 7 and uninstall ubuntu all together. I actually had the same booting problem after system backup before and the solution was to install two extra ubuntus but I'd prefer not to do that. I'd highly appreciate any help!

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  • Store a byte[] stored in a SQL XML parameter to a varbinary(MAX) field in SQL Server 2005. Can it be

    - by Mikey John
    Store a byte[] stored in a SQL XML parameter to a varbinary(MAX) field in SQL Server 2005. Can it be done ? Here's my stored procedure: set ANSI_NULLS ON set QUOTED_IDENTIFIER ON GO ALTER PROCEDURE [dbo].[AddPerson] @Data AS XML AS INSERT INTO Persons (name,image_binary) SELECT rowWals.value('./@Name', 'varchar(64)') AS [Name], rowWals.value('./@ImageBinary', 'varbinary(MAX)') AS [ImageBinary] FROM @Data.nodes ('/Data/Names') as b(rowVals) SELECT SCOPE_IDENTITY() AS Id In my schema Name is of type String and ImageBinary is o type byte[].

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  • How Do You Profile & Optimize CUDA Kernels?

    - by John Dibling
    I am somewhat familiar with the CUDA visual profiler and the occupancy spreadsheet, although I am probably not leveraging them as well as I could. Profiling & optimizing CUDA code is not like profiling & optimizing code that runs on a CPU. So I am hoping to learn from your experiences about how to get the most out of my code. There was a post recently looking for the fastest possible code to identify self numbers, and I provided a CUDA implementation. I'm not satisfied that this code is as fast as it can be, but I'm at a loss as to figure out both what the right questions are and what tool I can get the answers from. How do you identify ways to make your CUDA kernels perform faster?

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  • How to update a custom dependency property when the datasource list changes

    - by John
    Hi We have a user control with a custom dependency property (DP). The DP is bound to an ObservableCollection. When a new item is added to the collection programatically, the databinding does not update the target DP. Why? We think it's because, unfortunately, in our case the target is not a ListBox or ListView, but a Canvas. The DP, when changed or initialized, is supposed to draw a Shape (!) onto the Canvas, and the shape's position and size is bound to the collection item's two properties: WIDTH, LEFT. Ideally we don't want to clear the Canvas and redraw all items just becasue one has been added (or deleted). But how? So: How can the custom DP take care of drawing the shape for the new collection item? What callback do we need, at what point in time does this have to happen, and what specific MetaDataOptions might there? Also, are there any good resources out there concerning all these dependency property options. They are quite confusing. MSDN does not really help with what we're trying to do. Thanks!

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  • UNIX-style RegExp Replace running extremely slowly under windows. Help? EDIT: Negative lookahead ass

    - by John Sullivan
    I'm trying to run a unix regEXP on every log file in a 1.12 GB directory, then replace the matched pattern with ''. Test run on a 4 meg file is took about 10 minutes, but worked. Obviously something is murdering performance by several orders of magnitude. Find: ^(?!.*155[0-2][0-9]{4}\s.*).*$ -- NOTE: match any line NOT starting 155[0-2]NNNN where in is a number 0-9. Replace with: ''. Is there some justifiable reason for my regExp to take this long to replace matching text, or is the program I am using (this is windows / a program called "grepWin") most likely poorly optimized? Thanks. UPDATE: I am noticing that searching for ^(155[0-2]).$ takes ~7 seconds in a 5.6 MB file with 77 matches. Adding the Negative Lookahead Assertion, ?=, so that the regExp becomes ^(?!155[0-2]).$ is causing it to take at least 5-10 minutes; granted, there will be thousands and thousands of matches. Should the negative lookahead assertion be extremely detrimental to performance, and/or a large quantity of matches?

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