I am trying to work with my data set to graph a cluster analysis similar to this example:
Why is the line of wss-plot (for optimizing the cluster analysis) looks so fluctuated?
with a previous related thread (How to draw the plot of within-cluster sum-of-squares for a cluster?)
When I follow along with the exact code of the thread (either the Iris example, or the person asking the question's example data) I get an error when attempting to plot the output:
" Error in xy.coords(x, y, xlabel, ylabel, log) : (list) object cannot be coerced to type 'double' "
The only thing I can think that is going wrong is perhaps the wrap function is not working properly. When I first attempted to do the code wrap was not recognized and so I installed the ggally package and then used the wrap function as presented in the sample codes.
Any help would be appreciated as I feel like there is some obvious and simple fix that I am missing.
Related
I am trying to run the Synthetic Control Method in R. I tried to prepare my data according to Abadie, Diamond and Hainmueller (2011) (https://www.jstatsoft.org/article/view/v042i13).
But when running the dataprep.out function I get the error message that my unit.variables are not nurmeric variables in foo. I don't understand the problem here because my table purely consists of numeric values. The table is also classified as a data.frame. I have attached some pictures to underline my problem. If anyone could help me that would be greatly appreciated!
My code (https://i.stack.imgur.com/7BVYc.png)
My table (https://i.stack.imgur.com/TV1IC.png)
I have tried to reimport my data over and over again. But nothing seems to help.
I am trying to run Kevin Murphy's Bayes Net Toolbox in Octave and encountering some problems. It doesn't help that I'm a novice at Bayesian networks, Matlab and Octave.
This toolbox was originally written for Matlab. There is a large test file called test_BNT.m which runs through all the functionality in the toolbox. Most of the error messages relate to the difference between & and && in Matlab and Octave. This is easy to fix. However, I've now come across a new problem and I don't know what to do about it.
For instance, the qmr1.m script creates an instance of the pearl_inf_engine class, sets some of the member member variables and passes the instance of the class to another function. Later on, the member variables are accessed again in a different script (parallel_protocol.m). But when this happens, the following message appears:
error: invalid index for class
error: evaluating argument list element number 1
It seems that from one script to another, it has forgotten that the class has any member variables and gives the invalid index message when you try to access them.
Is this a common error with an easy solution? Is something wrong with the path or working directory? Maybe someone else has already converted the BNT to octave and knows what to do?
Edit
I was able to get past this error message. The trick was to read the installation instructions (haha) and run addpath(genpathKPM(<BNT base directory)). genpathKPM.m is a script includes in BNT which adds all the required directories to the path.
After doing this, run test_BNT.m and change & to && and | to || at each line where it gives a warning. This will clear up most of the errors.
However, I'm still unable to run mpe1.m, mp2.m, mildew1.m and some others. The new error message I'm stuck on is:
error: invalid empty index list
error: called from:
error: C:\FullBNT-1.0.7\bnt\BNT\inference\static\#var_elim_inf_engine\find_mpe
.m at line 63, column 5
on this line of code:
eval(['sCPT.T(', sargs, num2str(jj), ')=0;']);
If I can get all the scripts to work, I'll post an answer here with the steps I took to do it.
Edit 2
I was able to get past the problem in the previous edit. Replace
eval(['sCPT.T(', sargs, num2str(jj), ')=0;']);
with
eval(['sCPT.T(', sargs, sprintf('%d',jj), ')=0;']);
The next problem is identical. Just replace num2str in the same way.
This file was apparently contributed by a user of BNT, and not written by the original author. Using eval kind of a hack, I think. A better fix would be to just rewrite the code so it doesn't use eval at all.
There is one more error in draw_graph.m, which was apparently also an outside contribution to the project. I just commented out the call to that function since I'm not interested in drawing graphs right now. After doing this, and continuing to fix shortcircuit operators, all of the tests in test_BNT.m will run.
Still, I won't create an answer for this until I can get draw_graph.m to run, too.
As a significant amount of time has passed, and the answer to the core problem was provided in the question, I will post it here so it will not stay listed as unanswered:
tl;dr: Change a few operators, solve the remaining bugs specified below, and everything works except the drawing of graphs.
Edit
I was able to get past this error message. The trick was to read the
installation instructions (haha) and run addpath(genpathKPM(<BNT base
directory)). genpathKPM.m is a script includes in BNT which adds
all the required directories to the path.
After doing this, run test_BNT.m and change & to && and | to
|| at each line where it gives a warning. This will clear up most of
the errors.
However, I'm still unable to run mpe1.m, mp2.m, mildew1.m and
some others. The new error message I'm stuck on is:
error: invalid empty index list
error: called from:
error: C:\FullBNT-1.0.7\bnt\BNT\inference\static\#var_elim_inf_engine\find_mpe
.m at line 63, column 5
on this line of code:
eval(['sCPT.T(', sargs, num2str(jj), ')=0;']);
If I can get all the scripts to work, I'll post an answer here with
the steps I took to do it.
Edit 2
I was able to get past the problem in the previous edit. Replace
eval(['sCPT.T(', sargs, num2str(jj), ')=0;']); with
eval(['sCPT.T(', sargs, sprintf('%d',jj), ')=0;']);
The next problem is identical. Just replace num2str in the same way.
This file was apparently contributed by a user of BNT, and not written
by the original author. Using eval kind of a hack, I think. A better
fix would be to just rewrite the code so it doesn't use eval at all.
There is one more error in draw_graph.m, which was apparently also
an outside contribution to the project. I just commented out the call
to that function since I'm not interested in drawing graphs right now.
After doing this, and continuing to fix shortcircuit operators, all of
the tests in test_BNT.m will run.
Let us say that I have a Matlab function and I change its signature (i.e. add parameter). As Matlab does not 'compile' is there an easy way to determine which other functions do not use the right signature (i.e. submits the additional parameter). I do not want to determine this at runtime (i.e. get an error message) or have to do text searches. Hope this makes sense. Any feedback would be very much appreciated. Many thanks.
If I understand you correctly, you want to change a function's signature and find all functions/scripts/classes that call it in the "old" way, and change it to the "new" way.
You also indicated you don't want to do it at runtime, or do text searches, but there is no way to detect "incorrect" calls at "parse-time", so I'm afraid these demands leave no option at all to detect old function calls...
What I would do in that case is temporarily add a few lines to the new function:
function myFunc(param1, param2, newParam) % <-- the NEW signature
if nargin == 2
clc, error('old call detected.'); end
and then run the main script/function/whatever in which this function resides. You'll get one error for each time something calls the function incorrectly, along with the error stack in the Matlab command window.
It is then a matter of clicking on the link in the bottom of the error stack, correct the function call, and repeat from the top until no more errors occur.
Don't forget to remove these lines when you're done, or better, replace the word error with warning just to capture anything that was missed.
Better yet: if you're on linux, a text search would be a matter of
$ grep -l 'myFunc(.*,.*); *.m'
which will list all the files having the "incorrect" call. That's not too difficult I'd say...You can probably do a similar thing with the standard windows search, but I can't test that right now.
This is more or less what the dependency report was invented for. Using that tool, you can find what functions/scripts call your altered function. Then it is just a question of manually inspecting every occurrence.
However, I'd advise to make your changes to the function signature such that backwards compatibility is maintained. You can do so by specifying default values for new parameters and/or issuing a warning in those scenarios. That way, your code will run, and you will get run-time hints of deprecated code (which is more or less a necessary evil in interpreted/dynamic languages).
For many dynamic languages (and MATLAB specifically) it is generally impossible to fully inspect the code without the interpreter executing the code. Just imagine the following piece of code:
x = magic(10);
In general, you'd say that the magic function is called. However, magic could map to a totally different function. This could be done in ways that are invisible to a static analysis tool (such as the dependency report): e.g. eval('magic = 1:100;');.
The only way is to go through your whole code base, either inspecting every occurrence manually (which can be found easily with a text search) or by running a test that fully covers your code base.
edit:
There is however a way to access intermediate outputs of the MATLAB parser. This can be accessed using the undocumented and unsupported mtree function (which can be called like this: t = mtree(file, '-file'); for every file in your code base). Using the resulting structure you might be able to find calls with a certain amount of parameters.
In MATLAB 2012a,
I'm trying to save a figure as a .fig file, and all I get is a window with
Title: Error Saving Figure
Message: Object must have an ancestor of type 'figure'.
I googled this error message, and Google was able to predict my search perfectly, meaning other people have searched the same error message before .. however there is not a single page online that actually discusses this error.
I know that I haven't given much information, and I apologize for this, but I can't imagine what other details to give. 2 minutes ago I saved a different figure generated by the exact same program, in the exact same way, as a .fig file with no problems.
What does this error message mean and how do I fix the problem so that I can save figures in .fig format again ?
Edit: I am trying to save the file from the GUI.
Your problem seems to relate to how the GUI builds the figures:
* the parent object is of type 'figure'
* this object has some children of (usually) type 'axis'
* most graphical objects (lines, text, etc) belong to an axis.
It appears to go wrong with figures that have not been built the 'figure;plot(),etc...' way, eg with objects added later to the figure (eg 'legend') or plots that have been made with custom commands ('hist', 'bar3', etc).
My guess is that some GUI object has been added that does not have the figure handle as its 'ancestor'.
Queries about this problem outside StackOverflow seem to involve matlab function
"getproxyvaluefromhandle". Maybe googling that helps. Someone found help decomposing a figure here (seems to be a mix of Matlab, English and German)
If you have no code can you at least please describe what's in the figure? Otherwise the answers will be as hand-wavy as the question...
i want to change function variable at each step in a for loop in matlab.
i take these steps:
i created my mfile function
function [jfun,fun]=air(x,vt,ty,tz,p2,y0)
jfun=[(cos(tz)*cos(ty)*vt/9.81)*(1-exp(-9.81*x(2)/vt)),...
x(1)*cos(tz)*cos(ty)*exp(-9.81*x(1)/vt);
(-vt*sin(tz)*cos(ty)/9.81)*exp(-9.81*x(1)/vt),...
(x(1)*sin(tz)*cos(ty)*+vt)*exp(-9.81*x(1)/vt)];
fun=[(x(1)*cos(ty)*cos(tz)*vt/9.81)*(1-exp(-9.81*x(2)/vt))-p2;...
(vt/9.81)*(x(1)*sin(tz)*cos(ty)+vt)*(1-exp(-9.81*x(2)/vt))-vt*x(2)+y0];
end
and then i used newtonSys command:
ty=rad(-23)
tz=rad(15)
p2=1.8
vt=8.4925
y0=0.2
myfun=#(x)air(x,vt,ty,tz,p2,y0)
x=newtonSys(myfun,[15 5],0.000001,0.000001,500,1)
and matlab answer:
Error in ==> Untitled18 at 7
x=newtonSys(myfun,[15 5],0.000001,0.000001,500,1)
i guess that its because of wrong use of function handle and for my function i have to use another command or i have to use another method for solving 2nonlinear equation.
First, you haven't displayed the entire error. MATLAB should tell you what the actual error is, so unless you tell us that, we won't know what's wrong.
Secondly I don't see newtonSys in my system, or in the online MATLAB documentation. So most likely it is an external program, which most people here might not be familiar with. The closest I found from a quick Google search was this, which is an implementation of Newton's method for approximating the root of a non-linear system of n-equations. Are you using the same file? If so, if you look at the comments, it says that you need to pass the function as a string. So you'd have to pass myfun as 'myfun'.
If not, could you edit your question and add the contents of the function that you're using? Without these, it's near impossible to answer your question.