Interpreting WinBUGS traps and how to automate the program? - winbugs14

First of all, does anybody know of a developer's guide for WinBUGS? The website is full of detailed examples for Doodles and documentation for the model language, but I have yet to find anything about how to interpret trap windows.
Secondly, has anybody found any ways to streamline the check/load/compile/init/monitor/update cycle? By that I mean, there doesn't seem to be any way to say "don't bother rechecking the model or putting any of the settings back to their defaults (!!!), just keep loading data from these files, inits from those files, and for each generate a new coda". Even the standard Windows shortcuts are neutered here, forcing the user to keep clicking and filling the same fields with the same values over and over. This might seem like a minor issue, but when you are doing many similar analyses one after the other, it gets old fast.
I'm at the point where I'm about to use TRON.EXE to send fake mouseclicks to the program, but before going to that extreme I'm hoping there is some native and more elegant way to automate repetitive WinBUGS tasks.

Well... that's WinBUGS at its normal :-) Unfriendly, showing traps that would scare of an experienced kernel hacker.. :-) I don't think there exist some guide to traps. I mean if WinBUGS creators wanted to put some effort in being more user friendly, they would probably first made the traps more understandable, so that no guide was necessary.
I was trying to do something similar - i.e. to customize WinBUGS behaviour. First, you can call WinBUGS from R using R2WinBUGS. That way you are able to do a lot automatization but not all. For example, I wanted to have something like progress information in WinBUGS. The problem is that WinBUGS UI gets stuck during update cycles. R2WinBUGS creates the script.txt command script and there is command update (<big number of cycles>). What I wanted here was to customize this script.txt to contain a lot of smaller update(..) commands instead of one big one. But, the problem is that R2WinBUGS generates this script itself and you cannot change it.
So the way to customize WinBUGS could be that you create your own wrapper that creates the script.txt and other files. I believe you could do a lot more customization to WinBUGS this way.
However, I'm not sure if WinBUGS is worth it. Its development has stopped and while favorited by many people, it remains rigid. You can try JAGS or CppBugs which seem to have much more promissing future.

For a wrapper around R2WinBUGS that adds lots of functionality to streamline serious WinBUGS use, see my package rube (http://www.stat.cmu.edu/~hseltman/rube/) which is not yet on CRAN.
Among other things, it gives plain English error messages rather than passing your model/data/inits along to WinBUGS when a trap error is certain. It also gives a highly useful summary of your model/data/inits for finding problems that cannot be automatically detected. Of course, it does not catch all trap errors.

Turns out I didn't RTFM enough on the second part of my question. It turns out that the section of the WinBUGS 1.4 manual entitled "Batch-Mode: Scripts" lists all the batch commands. All the important UI functionality has a batch-mode command. There was only a little trial-and-error in getting the arguments right (for example over.relax('true')). What really took me a while to sort out is that WinBUGS seems to have trouble with some Windows paths, but as long as everything is in a subdirectory of the directory where WinBUGS is installed, it runs okay.
It's still kind of messy to have to keep loading all these little files, but I wrote an R-script that uses functions from the BRugs package to create all the files, name them in a consistent pattern, and generate a script that will then initialize the model and load them, over and over again.
I'll leave this question open for a while, though, to see if anybody has any suggestions on where I can learn to make better use of traps.

Related

What's a good way to navigate code base and find source for a webpage

I'm new to frontend development and thinking about what's a good way to find source code in our code base for a webpage. What I usually do is going to the element tab in chrome dev tool, finding a special class name, and searching that in code base to locate the file. I feel there should be better way for this task. I tried to use source tab in dev tool, but it shows tons of files and folders in navigation column. I also tried to use Components tab since we're using react, but component names are minified to single letters. So want to get suggestions from you folks. How do you usually do this? Thanks!
You have the right idea, the problem is that you are looking at the minified (presumably production) version of the website. In general, while developing a website, you run a development server, in which all of the code (mostly) appears as it is written in your IDE/editor. That way you can find component names and inspect the source code through the chrome dev tools.
You should talk to whoever is currently responsible for the code to help you get a development server running on your machine. Then, you find the component names and then do a "find in files" search through your IDE/editor to see what they are, and where they are used in the code base. There may be many results that you have to sift through. That's par for the course in large code bases until you become more familiar with what goes where. And even afterwards.
I will say; even things that appear simple can be fiendishly complex, so it would be useful for you if the owner of the code could give you a rough outline of how things are organised and why to make navigating the code base easier. But, it will always be a bit hard, and depending on how clean the code is, it might be nearly impenetrable. Good luck.
There are many ways to to find source code or debug Code
①You can use Chrome dev tool
②You can use debbuger in VS
③you can debug your code by puttin debugger in java script code
④browser has good functionality to find
code(For reference please check Image.)

React Navigation and flow-typed

I just started using flow-typed definitions for my popular libraries in a React Native app such as React Navigation, but I find it quite hard to find the documentation on types and how to use them. I'm still getting errors in my IDE and I feel like Flow is more wasting my time than adding value to my developer experience because I've to lookup for the types all the time (and sometimes don't even find an answer). Any advice about that ?
A complex web application using many npm modules is very rarely going to be strongly typed throughout. The goal of strong typing in JS is largely to have as much typing as is feasible or even reasonable. Modules which do not have libdefs will come in as any and that's okay. Obviously it would be great if everything you pulled in had full types, but just given the way that progress is made this is practically impossible. Add to this the fact that the simple act of upgrading flow will often introduce more caught errors to your codebase, and you end up having to accept that typing is a progressive process, it shouldn't really be a blocking one.
Now that that's out of the way, you seem to have a number of different sub-questions:
I've to lookup for the types all the time
Not entirely sure what you mean by this, but you might saying it's hard to find types for the package you're using. Make sure you're familiar with how the flow-typed CLI tool works (npx flow-typed), it will help you with searching for and installing compatible libdefs. If you don't find anything for a module in flow-typed then poke around the source github repo and make sure flow types aren't shipped with the module itself. If you come across a package with a .d.ts (TypeScript) file, try converting it to a libdef with flowgen. If nothing proves fruitful, you should probably just forego types and carry on.
In this case, I would actually start my own libdef (npx flow-typed create-stub <package name>) and fill in some basic types as I went. You can start really simple, I have a libdef currently for react-select that only checks one prop of the component, the options prop (I don't remember why I have this, however :P). Again, progressive typing is the goal. Checking that one prop is actually really nice compared to checking none.
I find it quite hard to find the documentation on types and how to use them
There's generally not real documentation for libdefs in flow-typed unless it's written by the package author somewhere. I usually read the libdefs themselves, but if you find usage confusing I would recommend looking at the tests associated with the libdef. You can also dig through any relevant issues or PRs to find usage examples.
sometimes don't even find an answer
Add a $FlowFixMe and come back to it later if it slows you down too much. All of these things will become much more manageable as you become more accustomed to flow and strong typing in general, and both flow and libdefs are constantly improving.
I'm still getting errors in my IDE
If you can't fix them, add a $FlowFixMe and come back later. Flow actually has a tool included in its source code that has a utility for adding $FlowFixMe for every error, but as it's not currently shipped to npm you have to clone the source to use it.

Recreating KaTeX emulation in La/TeX?

I'm working on a site that is using KaTeX for rendering math. However, the interface for entering the math content is (really) not ideal, so it is actually faster for me to work in an editor, like Sublime Text 3 and import the work; however, an issue I run into is that when I import, I discover various functions / environments aren't supported (i.e. emulated) by KaTeX.
If it were just me working on the material, I would simply learn as I go and consult the KaTeX documentation page; however, I have several contractors working on digitizing content who do not have access to the site (and I don't have the ability to give them access), and so cannot learn by trial-and-error. Instead, I end up with piles of documents that all need to be manually adjusted, to render as desired with KaTeX.
As such, I wanted to assemble a preamble for a LaTeX document that would recreate the abilities (i.e. functions and environments) KaTeX can emulate, and was wondering if such a preamble / package already exists? I have tried a few quick searches, but because I'm looking for something that imitates an emulator, I'm finding it tricky to find the right choice of words to get relevant results.
I wasn't sure if this were best posted here or on the TeX.se - I suspect it falls in-between the two - so I apologize if my guess was wrong and I should've tried there first. Any suggestions would be very much appreciated, as this is creating a substantial bottle-neck in my workflow but is also just outside of my ability to solve on my own.
Supported functions is one thing. To tackle that you might actually stand a fair chance of just tokenizing the input, looking for backslash name sequences and checking them against a list extracted from KaTeX sources to see which are supported.
I guess one could even try to remove all other functions from LaTeX. Or rather hide them, such that the user input can't access them but third party libraries can. Getting rid of language features (as opposed to macros) such as \def would probably be even harder. Better askn on the TeX stack exchange for details of you really want to follow this route.
As an alternative I guess you might be able to perform the check I described above in TeX. Write a macro which reads the current file as plain text instead of TeX source, to perform this analysis. Or some such. But a separate stand-alone tool would be much easier.
If you are going for a separate tool, you might as well write it in JavaScript for Node, and have it run KaTeX on the input. That way you can at least tell whether it will get typeset to something or error out.
Whether the rendering is what you expect from LaTeX may be another question. In general KaTeX aims to reproduce LaTeX behaviour, so any difference might indicate a bug. But bugs exist, so all of this might not avoid the need for checks. How about you just processing the math part of the input with KaTeX to some HTML which authors can check without access to the site?
As for existing tools or macro packages, I know of none, but tool or library questions are off topic on stack exchange anyway.

Why is overshadowing not supported with Codename One?

I've been trying to work with Codename One for years, but I still find errors that prevent me from releasing my apps.
Locally I can fix errors by I overshadowing erroneous classes. This works but for some reason it doesn't work when I send my apps to the build server.
If I could overshadow faulty classes would be good in many ways:
I'd better get on with my work
I could check how my corrections work on the different platforms
I could contribute to the further development of Codename One
I suffer much from not being able to publish my apps because I see no way how I can fix basic problems.
I love iPhones and do not like the Mac. Therefore I do not own a Mac and prefer to work with Linux and use the Codename One build server.
What are the reasons for not supporting overloading classes like com.codename1.ui.Component? Can You see that it would be beneficial?
This isn't the first time people asked for that but we won't deliver it. Doing this creates huge problems:
Developers don't file issues or submit fixes instead they make local fixes
Developers break things due to complex behaviors then try to get support and blame us for the issues
We have a process of submitting patches to Codename One, patches are always accepted quickly when they are valid. If something needs fixing that's what you need to do. If you need a hack then submit a patch that defines the extension point that you need. That's why we are open source...
In the past this might have been painful as you would need to wait until we updated the servers, but since changes go in every week in recent revisions this is no longer an issue. Don't think of it as "contributing", think of it as free code reviews where the entire community pulls together to improve your work...

Version Control for a total newbie

I'm totally new to the world of programming and understand very little in terms of jargon and typical methodology.
A while ago I was writing some code, but accidentally deleted some good code while I was deleting bad code. From then on I started creating versions of my files, I would name each file with the date and a version number.
However, this is a pain in the ass, having to give an unique name to each file and then going to my core file and changing the reference to the name of the new file.
And then, just the other day I accidentally over wrote something important even with this method, probably because of a typo in naming.
Needless to say, this method sucks.
I'm looking for suggestions on better practices, better tools. I've been looking at version control, but a lot of them, git svn look really complicated. The idea is to speed up the whole versioning process, not make it harder by having to do command line.
Right now I'm hoping that there's a tool that would save an unique version of the file every time I hit ctrl-s, and give me one button to create a finalized version.
Of course if there are suggestions for totally different ways of doing things, that would be more awesome.
Thanks everyone.
There are two approaches to this problem:
Versioning on demand. This is the model used by subversion, CVS, etc., etc. When you have made a 'significant' change, you decide to tell the system "keep this version".
Automatic versioning. This is the model used by some old VAXen, Eclipse, IDEA, every wiki ever, and a few writer's tools. Every time you save, a new version is implicitly created. At some remove, old versions may be culled (e.g., only one version is kept from work performed a week ago, rather than every save).
It sounds like you would prefer #2, because it is "fool-proof" -- you never have to go, "oops, I should have 'checked in' / 'kept' my work before making this change." You can always roll back. One downside is that you have to manually step through the old versions to find something, because unlike with #1 you generally are not giving a description of each change.
Another downside is that for large files, or ones that are not easily diff'd/patched (i.e. binary files), you will start burning through disk space pretty fast..
As an aside, it sounds like you don't need 90% of the features in a standard SCM system -- branching, labeling, etc. -- but you might find uses for them eventually. So learning one may be a win in the long run. You can do this with svn, etc. but it will take some customizing. If you use a scriptable editor (emacs, vi, TextMate, whatever) you could redefine the "Save" command as "Save and make a new version".
Subversion is more or less the gold standard.
I'd suggest (especially for a newbie) that you check out BeanStalk (www.Beanstalkapp.com) to run your subversion server and TortoiseSVN for your client.
Good luck!
Whatever you do, if someone mentions Visual SourceSafe -- run as fast as you can. VSS was created by Satan himself and handed down to torment developers the world over.
I think you're in a position where you have to get a little bit out of your comfort zone and take some time to learn git. It's pretty easy to learn and use.
Believe me, it's really worth it. Time spent learning git is time well spent.
If you are not working in a team, you could use something like Eclipse's local history feature. It stores versions of your files locally, and you can revert to previous versions whenever you feel like it. More details here: http://help.eclipse.org/ganymede/index.jsp (Search for "local history"). I am pretty sure other IDEs have such a feature too.
If you are collaborating with others on your code, there probably is no way around learning one of the standard tools like SVN, CVS or git. For most of them, there are plugins for many IDEs available, so you don't have to use the command line.
I currently use Subversion, but my source control experience is limited.
I would however suggest reading the tutorial by Eric Sink.
http://www.ericsink.com/scm/source_control.html
Its best to learn how to use an existing 'industry standard' versioning tool like Subversion. Even if you're new to programming and version control, SVN isn't that hard to learn and will serve you well. I personally use and recommend VisualSVN Server and TortoiseSVN for Windows. Both are free and quite simple to use.
For a system that creates a revision on every save, perhaps you should look into a Versioning File System.
I think TortoiseSVN would be a good Subversion client for you to try if you're in Windows. It won't do what you're looking for with every-time-I-save-I-get-a-new-version--you'll have to manually "commit" versions to the repository. When you do a commit, that creates a new version, essentially saving your progress at that point. TortoiseSVN is pretty user-friendly, and it's a GUI, so you won't be working at the command line. You'll be able to do things like right-click a file in Windows Explorer and choose Commit to save your progress. Plus, TortoiseSVN is free and open source.
Subversion is not really complicated. If you are using Windows, TortiseSVN will help a lot, if you are using Eclipse, subclipse plug-in is awesome. (You probably should be using eclipse regardless :) )
Some of the others are a bit complicated, but you just have to know the pattern with eclipse. Maybe you could "Try it out" with an open source project or some existing subversion server.
The cycle would be:
First you "Check out" a repository. This fills up your specified directory with the contents from the repository.
If you are doing it from the command line--it's "svn co"--there is enough help there to figure out the rest.
Second you edit your files. You don't have to lock them or anything.
if you add a new file, you use "svn add filename" as soon as you add it. This won't actually change the repository until you commit your changes.
When a group of edits are done, you check them in with "svn ci" (also svn commit works).
This one has a SLIGHT twist that you'll always forget--every commit needs a comment. You don't have to specify the files you are committing or anything, but you do need to be in the top level of your project (it will commit everything below your directory.
So the procedure here is, go to the "root" of your project tree and type:
svn ci -m "comment"
piece of cake.
Finally, IF someone else is checking stuff in things get SLIGHTLY stranger. before you commit, you should "update" and get their changes. "svn up" is all it takes, but it may warn you that there were merges. This only happens when both of you edited the same file, and 90% of the time, the merges will go okay. the rest of the time, it will put little markers in your file telling you what you changed and what they changed. The "up" command will tell you which files it did this to. Go look at them and clean the file up before you check the file in.
Always test between "svn up" and "svn ci", you never know if their crappy changes busted your pristine code.
That's really it. It's so easy from the CLI, that the graphics environments are hardly worth it (but subclipse is really nice if you are in eclipse anyway because it will visually show you modified files that need to be checked in).
If you ever forget, svn's command line help is extremely terse and useful, tells you JUST what you need to know, and has help on all the sub-commands and options.
If you're looking for an easy-to-set-up version control system for Windows, I highly recommend TortoiseHg, an easy-to-use Mercurial frontend for Windows. You don't have to worry about setting up and keeping track of a repository separate from your files, but you always can do so if you'd like to. Mercurial is a great tool because it can grow with your needs. It has all the usual features like easy merging, etc. and is quite a bit easier to wrap your head around than Git in my experience.
I think Git is really easy to use especially when you use GitHub. They also provide lots of good guides to get up and running.
http://github.com
http://github.com/guides/home
I've used Git, SVN, CVS, and Perforce. On both Windows and Unix environments.
My vote is definitely for SVN, as it's ease of use, and flexibility. I prever to use command-line now, but at one time I was using TortoiseSVN for Windows, which we were able to get non-technical people to use without a hitch.
Use SVN.
You're definitely on the right track with recognizing the need for version control, but sound unsure what that might mean to you and your work. Once you learn the concepts behind version control systems, you will really come to appreciate them.
The concepts are simple: a source code control system is a piece of software designed to help you store and manage your code. How you get code into and out of it differ based on which system you choose: one paradigm is that you deliberately "check out" a file, make your changes to it, test it and make sure it's good, then check it back in. Another is that you simply save every change you make because disk space is dirt cheap, much cheaper than your time and effort spent to create the source in the first place.
Another important concept is the "baseline" or "label". When your product is in a ready-to-ship state, you tell the source code control system to create a "label" and tag every current item your entire source code base with that label. That way, when someone reports a bug in version 4.1 you can go to your system, request all the files with the "Version 4.1" label and get exactly the source code they're having a problem with.
Having a source control tool integrated with your development environment makes the whole process much easier than having to mess with command lines. (Don't discount command line because of their complexity, they deliver elegant control to an experienced user, and you eventually will become an experienced user.) But for now, I'd recommend a source code tool that can automate the process as much as possible.
Some things to consider: are you now, or are you planning to share the development with another developer? That might make a difference on how you want to set up a server. If you're developing alone on your own box, you can set it all up locally, but that's probably not the best approach for a team. (If you're unsure, git is very flexible in that arena.) Are you going to be storing large multimedia files, or just source code? Some source code systems are designed to efficiently store only text files, and will not handle movies, sounds or image files very well.
Something else to know is that most newer source control systems require some kind of "daemon" program running on the server (Subversion, git, Perforce, Microsoft Team Foundation Server) while the older, simpler systems just use the file system directly (Visual Source Safe, cvs) and don't require a server program.
If you don't want to learn much and your demands are low, the simpler solutions should suffice. Microsoft's Visual Source Safe used to come with their visual studio products, and was a very simple to use tool. It's not very robust, it's Microsoft-only, and it can't handle large files well, but it's very, very easy to set up and use. If you don't want to spend money, Subversion and git are two stellar open source solutions, and there is a lot of documentation for both on the web.
If you like to spend money, Perforce is considered an excellent choice for professional development teams (and I believe they have a free single-developer version.) If you really like to spend lots of money and want to make Bill Gates happy, Microsoft's Team Foundation Server is a complete software development lifecycle manager, is extremely easy to use in the Windows environment, and very powerful; but you'd probably want to devote an entire Windows server (plus SQL Server) instance to host it, and it will cost you several thousand dollars just on licenses. Unfortunately it is not the right tool for a one-man shop, or if you have no Windows admin experience.
If you have the budget or the connections, bringing in an experienced software engineer to help you get things started might be the quickest path to success. Otherwise, you'll have to do some more research to learn which systems best fit your situation.
Whatever VCS you use, if you choose versioning on demand instead of automatic versioning (to borrow terms from Alex's post), you will have to go through some ceremony to:
-create,
-rename,
-move,
-copy, or
-delete
a file that is under source control.
When you create a new file, you have to Add it to source control before you Commit your changes to the repository.
When you rename, move, copy, or delete a file under source control, do so with your VCS client. In TortoiseSVN and TortoiseGit, the move and copy operations are done with a right-click-and-drag, whereas the rename and delete operations are available via a right-click.
As you can imagine, changing things like the name of a project can be quite the hassle, hence the case for automatic versioning.
Ordinary file edits and any changes to files not under source control, do not require you to tell your VCS client about them.
Finally, for one-man projects, I prefer git over SVN because SVN requires at least 2 copies of everything: a repository (the "master" copy of the files and history) and a working copy (the copy you do your work on). With git, the repository and working copy are the same thing, which makes my experience simpler.
We use SourceGear Vault, which has great integration with Visual Studio, and is free for a single user. Depending on what framework and languages you're using, though, Subversion is a great free solution.
First of all, please read these articles by Eric Sink. Eric sink runs a company that creates a Source Control system called Vault. He explains in a newbie friendly manner how to do source control, best practices etc:
Introduction to Source Control
I found it invaluable when I first wanted to understand Source Control.
SourceGear Vault is FREE for a single user. It's interface is intuitive and integrates well with Visual Studio.
If it's just you, you might want to try Bazaar. It's distributed like Git (so it'll be nice for a single person--no server to deal with), but one of their main goals was to make it it much easier to use than Git.
Also, there is a handy gui tool that should make it amazingly easy to use called ToroiseBzr. http://bazaar-vcs.org/TortoiseBzr
There is in fact such a tool. It is called emacs.
Just create yourself a "~/.emacs" file and put the following lines in it:
(setq kept-new-versions 5)
(setq kept-old-versions 5)
And then restart emacs.
This tells emacs to save your 5 oldest and 5 newest versions of that file. They will be kept in files named filename~n~ where "filename" is your file's normal name, and "n" is the backup number.
If you develop your project alone (don't need ane server for collaboration) Mercurial might be you system of choice. I personally value one of its features: it only uses one place to save its information, it is the .hg directory in the root of your project. It doesn't put its data into every directory (like SVN). This way the archive and the project directory is easy to manage.
I've used Visual Source Safe, Perforce, and Subversion. They were all fine, but I would have to say that the support and extensions for Subversion just seemed slightly better. If you're planning on entering/staying in the software industry, you MUST know the fundamentals to source control, and I would highly recommend setting up one of the source control services. Subversion would be my recommendation and is free as well. It will be complicated at first, but you really should use a SVN client to add a GUI to increase utility and cut down on all the complication you're observing.
I quick google of "dreamweaver svn" reveals that many people are working with Subversion in Dreamweaver. I'm a advocate of version control, and SVN in particular, so I would recommend you look into that :)
If you don't want to use a full on version control system (as noted above), you may be able to improve your lot by refining and automating the procedure you described originally. Depending on your comfort with the tools you should be able to put together a script in DreamWeaver itself or in Windows Scripting ( Powershell, VBA, Perl, etc ) that will at least make date-named copies of the folder you are working in every so often. This will keep you from having to do it and make sure there aren't any typo-related problems. Further down that path you can have your script put a copy of your work on a backup drive or remote server, and then you'd have a back up, too.
I'm afraid I don't know much about DreamWeaver, but if it has much scripting support built-in you may even be able to "hook" into the Save/ Auto-Save functions and have them do exactly what you want.
Hope this helps,
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