I run a GLMM_adaptive model (I am doing a resource selection function) and I am using the joint_tests function (emmeans package) to compute joint tests of the terms in the model. The problem is that one of the interactions does not appear in the results.
The model is:
mod.hinc <- mixed_model(fixed = Used ~ scale(ndvi) * season * vegfactor +
scale(ndvi^2) + scale(distance^2) + scale(distance) * season,
random = ~ 1 | id, data = hin.c,
family = binomial(link="logit"))
After running the model I run the joint_tests function:
install.packages("emmeans")
library(emmeans)
joint_tests(mod.hinc)
And this is the result:
joint_tests(mod.hinc)
model term df1 df2 F.ratio p.value
ndvi 1 Inf 36.465 <.0001
season 3 Inf 22.265 <.0001
vegfactor 4 Inf 4.548 0.0011
distance 1 Inf 33.939 <.0001
ndvi:season 3 Inf 13.826 <.0001
ndvi:vegfactor 4 Inf 8.500 <.0001
season:vegfactor 12 Inf 6.544 <.0001
ndvi:season:vegfactor 12 Inf 5.165 <.0001
I cannot find the reason why the interaction scale(distance)*season does not appear in the results.
Any help on that issue is welcome. I can provide more details about the model if is required.
Thank you very much in advance.
Juan
The short answer is that distance:season is not shown because it came up with zero d.f. for the associated interaction contrasts. You could verify this by running joint_tests(mod.hinc, show0df = TRUE).
Why it has 0 d.f. is less clear. However, that is not the only problem here. You have to be extremely careful with numeric predictors when using joint_tests(); it does not do a model ANOVA; instead, as documented, it constructs a reference grid from the fitted model and performs joint tests of interaction contrasts related to the predictors. With numeric predictors, the results depend on the reference grid used.
In this particular instance, the model includes quadratic effects of ndvi and distance; however, the default reference grid is constructed using the range of the covariates -- only two distinct values. Thus, we can pick up the effects of the overall linear trends, but not the curvature effects implied by the quadratic terms. That's why only 1 d.f. of those factors' main effects are tested. There are really 2 d.f. in the effects of ndvi and distance. In order to capture all of those effects, we need to have at least three distinct values of these covariates in the reference grid. One way (not the only way) to accomplish that is to reduce the covariates to their means, plus or minus 1 SD -- which can be accomplished via this code:
meanpm1sd <- function(x)
c(mean(x) - sd(x), mean(x), mean(x) + sd(x))
joint_tests(mod.hinc, cov.reduce = meanpm1sd)
This will yield a different set of joint tests that likely will include 2-d.f. tests of ndvi and distance. But I don't know if you will still have some interactions missing due to zero-d.f. dimensionalities.
You can look directly at the estimates being tested in detail if you have any questions about what those effects are. For example, for season:distance,
### construct the needed reference grid once and for all
RG <- ref_grid(mod.h1nc, cov.reduce = meanpm1sd)
EMM <- emmeans(RG, ~ season * distance)
CON <- contrast(EMM, interaction = "consec")
EMM ### see estimates
CON ### see interaction contrasts
test(CON, joint = TRUE)
I hope this helps shed some light on what is going on.
I am trying to implement a linear mixed effect (LME) regression model for an x-ray imaging quality metric "CNR" (contrast-to-noise ratio) for which I measured for various tube potentials (kV) and filtration materials (Filter). CNR was measured for 3 consecutive slices so I have a standard deviation of the CNR from these independent measurements as well. I am wondering how I can incorporate these multiple independent measurements in my analysis. A representation of the data for a single measurement and my first attempt using fitlme is shown below. I tried looking at online resources but could not find an answer to my specific questions.
kV=[80 90 100 80 90 100 80 90 100]';
Filter={'Al','Al','Al','Cu','Cu','Cu','Ti','Ti','Ti'}';
CNR=[10 9 8 10.1 8.9 7.9 7 6 5]';
T=table(kV,Filter,CNR);
kV Filter CNR
___ ______ ___
80 'Al' 10
90 'Al' 9
100 'Al' 8
80 'Cu' 10.1
90 'Cu' 8.9
100 'Cu' 7.9
80 'Ti' 7
90 'Ti' 6
100 'Ti' 5
OUTPUT
Linear mixed-effects model fit by ML
Model information:
Number of observations 9
Fixed effects coefficients 4
Random effects coefficients 0
Covariance parameters 1
Formula:
CNR ~ 1 + kV + Filter
Model fit statistics:
AIC BIC LogLikelihood Deviance
-19.442 -18.456 14.721 -29.442
Fixed effects coefficients (95% CIs):
Name Estimate SE pValue
'(Intercept)' 18.3 0.17533 1.5308e-09
'kV' -0.10333 0.0019245 4.2372e-08
'Filter_Cu' -0.033333 0.03849 -0.86603
'Filter_Ti' -3 0.03849 -77.942
Random effects covariance parameters (95% CIs):
Group: Error
Name Estimate Lower Upper
'Res Std' 0.04714 0.0297 0.074821
Questions/Issues with current implementation:
How is the fixed effects coefficients for '(Intercept)' with P=1.53E-9 interpreted?
I only included fixed effects. Should the standard deviation of the ROI measurements somehow be incorporated into the random effects as well?
How do I incorporate the three independent measurements of CNR for three consecutive slices for a give kV/filter combination? Should I just add more rows to the table "T"? This would result in a total of 27 observations.
I am trying to model a wireless channel with following parameters in matlab.
Multipath Fading: Exponential distribution with unit mean
Shadowing: Log-normal distribution with standard deviation 8 dB
Path-loss exponent: 2.4
Path-loss constant: 30
How should I mention shadowing and fading in the channel model in dB?
I tried to use log-normal and exponential distributions in matlab to generate random numbers with given parameters. But I am not sure if it is true or not.
Can anyone help me?
(There is a similar question in Sjaffry question, but it doesn't have any answer and because I don't have enough reputation to comment on that topic, I tried to ask my own question.)
More Information:
I know that:
g_i,j = 10log10(K) - 10log10(B) - 10log10(T) -10alog10(L_i,j);
Where g_i,j is channel gain, B is fading gain, T is shadowing gain, L_i,j is distance between i , j and K is path loss constant.
I wrote this code in matlab:
k = 30;
a = 2.4;
T = 8; % dB
Distance = Dist([i_x, i_y], [j_x,j_y]);
G_dB = 10*log10(k) - 10*log10(exprnd(1)) - 10*log10(random('logn', 0 , (10^(T/10)))) -10 * a * log10(Distance);
The channel gain values (for distances about 300 m) must be more than one or less than one?
How LIBSVM works performs multivariate regression is my generalized question?
In detail, I have some data for certain number of links. (Example 3 links). Each link has 3 dependent variables which when used in a model gives output Y. I have data collected on these links in some interval.
LinkId | var1 | var2 | var3 | var4(OUTPUT)
1 | 10 | 12.1 | 2.2 | 3
2 | 11 | 11.2 | 2.3 | 3.1
3 | 12 | 12.4 | 4.1 | 1
1 | 13 | 11.8 | 2.2 | 4
2 | 14 | 12.7 | 2.3 | 2
3 | 15 | 10.7 | 4.1 | 6
1 | 16 | 8.6 | 2.2 | 6.6
2 | 17 | 14.2 | 2.3 | 4
3 | 18 | 9.8 | 4.1 | 5
I need to perform prediction to find the output of
(2,19,10.2,2.3).
How can I do that using above data for training in Matlab using LIBSVM? Can I train the whole data as input to the svmtrain to create a model or do I need to train each link separate and use the model create for prediction? Does it make any difference?
NOTE : Notice each link with same ID has same value.
This is not really a matlab or libsvm question but rather a generic svm related one.
How LIBSVM works performs multivariate regression is my generalized question?
LibSVM is just a library, which in particular - implements the Support Vector Regression model for the regression tasks. In short words, in a linear case, SVR tries to find a hyperplane for which your data points are placed in some margin around it (which is quite a dual approach to the classical SVM which tries to separate data with as big margin as possible).
In non linear case the kernel trick is used (in the same fashion as in SVM), so it is still looking for a hyperplane, but in a feature space induced by the particular kernel, which results in the non linear regression in the input space.
Quite nice introduction to SVRs' can be found here:
http://alex.smola.org/papers/2003/SmoSch03b.pdf
How can I do that using above data for training in Matlab using LIBSVM? Can I train the whole data as input to the svmtrain to create a model or do I need to train each link separate and use the model create for prediction? Does it make any difference? NOTE : Notice each link with same ID has same value.
You could train SVR (as it is a regression problem) with the whole data, but:
seems that var3 and LinkId are the same variables (1->2.2, 2->2.3, 3->4.1), if this is a case you should remove the LinkId column,
are values of var1 unique ascending integers? If so, these are also probably a useless featues (as they do not seem to carry any information, they seem to be your id numbers),
you should preprocess your data before applying SVM so eg. each column contains values from the [0,1] interval, otherwise some features may become more important than others just because of their scale.
Now, if you would like to create a separate model for each link, and follow above clues, you end up with 1 input variable (var2) and 1 output variable var4, so I would not recommend such a step. In general it seems that you have very limited featues set, it would be valuable to gather more informative features.
I have a dataset 6x1000 of binary data (6 data points, 1000 boolean dimensions).
I perform cluster analysis on it
[idx, ctrs] = kmeans(x, 3, 'distance', 'hamming');
And I get the three clusters. How can I visualize my result?
I have 6 rows of data each having 1000 attributes; 3 of them should be alike or similar in a way. Applying clustering will reveal the clusters. Since I know the number of clusters
I only need to find similar rows. Hamming distance tell us the similarity between rows and the result is correct that there are 3 clusters.
[EDIT: for any reasonable data, kmeans will always finds asked number
of clusters]
I want to take that knowledge
and make it easily observable and understandable without having to write huge explanations.
Matlab's example is not suitable since it deals with numerical 2D data while my questions concerns n-dimensional categorical data.
The dataset is here http://pastebin.com/cEWJfrAR
[EDIT1: how to check if clusters are significant?]
For more information please visit the following link:
https://chat.stackoverflow.com/rooms/32090/discussion-between-oleg-komarov-and-justcurious
If the question is not clear ask, for anything you are missing.
For representing the differences between high-dimensional vectors or clusters, I have used Matlab's dendrogram function. For instance, after loading your dataset into the matrix x I ran the following code:
l = linkage(a, 'average');
dendrogram(l);
and got the following plot:
The height of the bar that connects two groups of nodes represents the average distance between members of those two groups. In this case it looks like (5 and 6), (1 and 2), and (3 and 4) are clustered.
If you would rather use the hamming distance rather than the euclidian distance (which linkage does by default), then you can just do
l = linkage(x, 'average', {'hamming'});
although it makes little difference to the plot.
You can start by visualizing your data with a 'barcode' plot and then labeling rows with the cluster group they belong:
% Create figure
figure('pos',[100,300,640,150])
% Calculate patch xy coordinates
[r,c] = find(A);
Y = bsxfun(#minus,r,[.5,-.5,-.5, .5])';
X = bsxfun(#minus,c,[.5, .5,-.5,-.5])';
% plot patch
patch(X,Y,ones(size(X)),'EdgeColor','none','FaceColor','k');
% Set axis prop
set(gca,'pos',[0.05,0.05,.9,.9],'ylim',[0.5 6.5],'xlim',[0.5 1000.5],'xtick',[],'ytick',1:6,'ydir','reverse')
% Cluster
c = kmeans(A,3,'distance','hamming');
% Add lateral labeling of the clusters
nc = numel(c);
h = text(repmat(1010,nc,1),1:nc,reshape(sprintf('%3d',c),3,numel(c))');
cmap = hsv(max(c));
set(h,{'Background'},num2cell(cmap(c,:),2))
Definition
The Hamming distance for binary strings a and b the Hamming distance is equal to the number of ones (population count) in a XOR b (see Hamming distance).
Solution
Since you have six data strings, so you could create a 6 by 6 matrix filled with the Hamming distance. The matrix would be symetric (distance from a to b is the same as distance from b to a) and the diagonal is 0 (distance for a to itself is nul).
For example, the Hamming distance between your first and second string is:
hamming_dist12 = sum(xor(x(1,:),x(2,:)));
Loop that and fill your matrix:
hamming_dist = zeros(6);
for i=1:6,
for j=1:6,
hamming_dist(i,j) = sum(xor(x(i,:),x(j,:)));
end
end
(And yes this code is a redundant given the symmetry and zero diagonal, but the computation is minimal and optimizing not worth the effort).
Print your matrix as a spreadsheet in text format, and let the reader find which data string is similar to which.
This does not use your "kmeans" approach, but your added description regarding the problem helped shaping this out-of-the-box answer. I hope it helps.
Results
0 182 481 495 490 500
182 0 479 489 492 488
481 479 0 180 497 517
495 489 180 0 503 515
490 492 497 503 0 174
500 488 517 515 174 0
Edit 1:
How to read the table? The table is a simple distance table. Each row and each column represent a series of data (herein a binary string). The value at the intersection of row 1 and column 2 is the Hamming distance between string 1 and string 2, which is 182. The distance between string 1 and 2 is the same as between string 2 and 1, this is why the matrix is symmetric.
Data analysis
Three clusters can readily be identified: 1-2, 3-4 and 5-6, whose Hamming distance are, respectively, 182, 180, and 174.
Within a cluster, the data has ~18% dissimilarity. By contrast, data not part of a cluster has ~50% dissimilarity (which is random given binary data).
Presentation
I recommend Kohonen network or similar technique to present your data in, say, 2 dimensions. In general this area is called Dimensionality reduction.
I you can also go simpler way, e.g. Principal Component Analysis, but there's no quarantee you can effectively remove 9998 dimensions :P
scikit-learn is a good Python package to get you started, similar exist in matlab, java, ect. I can assure you it's rather easy to implement some of these algorithms yourself.
Concerns
I have a concern over your data set though. 6 data points is really a small number. moreover your attributes seem boolean at first glance, if that's the case, manhattan distance if what you should use. I think (someone correct me if I'm wrong) Hamming distance only makes sense if your attributes are somehow related, e.g. if attributes are actually a 1000-bit long binary string rather than 1000 independent 1-bit attributes.
Moreover, with 6 data points, you have only 2 ** 6 combinations, that means 936 out of 1000 attributes you have are either truly redundant or indistinguishable from redundant.
K-means almost always finds as many clusters as you ask for. To test significance of your clusters, run K-means several times with different initial conditions and check if you get same clusters. If you get different clusters every time or even from time to time, you cannot really trust your result.
I used a barcode type visualization for my data. The code which was posted here earlier by Oleg was too heavy for my solution (image files were over 500 kb) so I used image() to make the figures
function barcode(A)
B = (A+1)*2;
image(B);
colormap flag;
set(gca,'Ydir','Normal')
axis([0 size(B,2) 0 size(B,1)]);
ax = gca;
ax.TickDir = 'out'
end