When doing logistic regression in SPSS, is there a way to remove the reference category in the independent variables so they're all compared against each other equally rather than against the reference category?
When you have a categorical predictor variable, the most fundamental way to encode it for modeling, sometimes referred to as the canonical representation, is to use a 0-1 indicator for each level of the predictor, where each case takes on a value of 1 for the indicator corresponding to its category, and 0 for all the other indicators. The multinomial logistic regression procedure in SPSS (NOMREG) uses this parameterization.
If you run NOMREG with a single categorical predictor with k levels, the design matrix is built with an intercept column and the k indicator variables, unless you suppress the intercept. If the intercept remains in the model, the last indicator will be redundant, linearly dependent on the intercept and the first k-1 indicators. Another way to say this is that the design matrix is of deficient rank, since any of the columns can be predicted given the other k columns.
The same redundancy will be true of any additional categorical predictors entered as main effects (only k-1 of k indicators can be nonredundant). If you add interactions among categorical predictors, an indicator for each combination of levels of the two predictors is generated, but more than one of these will also be redundant given the intercept and main effects preceding the interaction(s).
The fundamental or canonical representation of the model is thus overparameterized, meaning it has more parameters than can be uniquely estimated. There are multiple ways commonly used to deal with this fact. One approach is the one used in NOMREG and most other more recent regression-type modeling procedures in SPSS, which is to use a generalized inverse of the cross-product of the design matrix, which has the effect of aliasing parameters associated with redundant columns to 0. You'll see these parameters represented by 0 values with no standard errors or other statistics in the SPSS output.
The other way used in SPSS to handle the overparameterized nature of the basic model is to reparameterize the design matrix to full rank, which involves creating k-1 coded variables instead of k indicators for each main effect, and creating interaction variables from these. This is the approach taken in LOGISTIC REGRESSION.
Note that the overall model fit and predicted values from a logistic regression (or other form of linear or generalized linear model) will be the same regardless of what choices are made about parameterization, as long as the appropriate total number of unique columns are in the design matrix. Particular parameter estimates are of course highly dependent upon the particular parameterization used, but you can derive the results from any of the valid approaches using the results from any other valid approach.
If there are k levels in a categorical predictor, there are k-1 degrees of freedom for comparing those k groups, meaning that once you'd made k-1 linearly independent or nonredundant comparisons, any others can be derived from those.
So the short answer is no, you can't do what you're talking about, but you don't need to, because the results for any valid parameterization will allow you to derive those for any other one.
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I have previously been told that -- for reasons that make complete sense -- one shouldn't run OLS regressions when the outcome variable is binary (i.e. yes/no, true/false, win/loss, etc). However, I often read papers in economics/other social sciences in which researchers run OLS regressions on binary variables and interpret the coefficients just like they would for a continuous outcome variable. A few questions about this:
Why do they not run a logistic regression? Is there any disadvantage/limitation to using logit models? In economics, for example, I very often see papers using OLS regression for binary variable and not logit. Can logit only be used in certain situations?
In general, when can one run an OLS regression on ordinal data? If I have a variable that captures "number of times in a week survey respondent does X", can I - in any circumstance - use it as a dependent variable in a linear regression? I often see this being done in literature as well, even though we're always told in introductory statistics/econometrics that outcome variables in an OLS regression should be continuous.
The application of applying OLS to a binary outcome is called Linear Probability Model. Compared to a logistic model, LPM has advantages in terms of implementation and interpretation that make it an appealing option for researchers conducting impact analysis. In LPM, parameters represent mean marginal effects while parameters represent log odds ratio in logistic regression. To calculate the mean marginal effects in logistic regression, we need calculate that derivative for every data point and then
calculate the mean of those derivatives. While logistic regression and the LPM usually yield the same expected average impact estimate[1], researchers prefer LPM for estimating treatment impacts.
In general, yes, we can definitely apply OLS to an ordinal outcome. Similar to the previous case, applying OLS to a binary or ordinal outcome result in violations of the assumptions of OLS. However, within econometrics, they believe the practical effect of violating these assumptions is minor and that the simplicity of interpreting an OLS outweighs the technical correctness of an ordered logit or probit model, especially when the ordinal outcome looks quasi-normal.
Reference:
[1] Deke, J. (2014). Using the linear probability model to estimate impacts on binary outcomes in randomized controlled trials. Mathematica Policy Research.
I'm trying to understand the technical part of Latent Dirichlet Allocation (LDA), but I have a few questions on my mind:
First: Why do we need to add alpha and gamma every time we sample the equation below? What if we delete the alpha and gamma from the equation? Would it still be possible to get the result?
Second: In LDA, we randomly assign a topic to every word in the document. Then, we try to optimize the topic by observing the data. Where is the part which is related to posterior inference in the equation above?
If you look at the inference derivation on Wiki, the alpha and beta are introduced simply because the theta and phi are both drawn from Dirichlet distribution uniquely determined by them separately. The reason of choosing Dirichlet distribution as the prior distribution (e.g. P(phi|beta)) are mainly for making the math feasible to tackle by utilizing the nice form of conjugate prior (here is Dirichlet and categorical distribution, categorical distribution is a special case of multinational distribution where n is set to one, i.e. only one trial). Also, the Dirichlet distribution can help us "inject" our belief that doc-topic and topic-word distribution are centered in a few topics and words for a document or topic (if we set low hyperparameters). If you remove alpha and beta, I am not sure how it will work.
The posterior inference is replaced with joint probability inference, at least in Gibbs sampling, you need joint probability while pick one dimension to "transform the state" as the Metropolis-Hasting paradigm does. The formula you put here is essentially derived from the joint probability P(w,z). I would like to refer you the book Monte Carlo Statistical Methods (by Robert) to fully understand why inference works.
Here's a simplified example of what I'm trying to figure out from a report. All analyses are being run in SPSS, which I don't have and don't use (my experience is with SAS and R).
They were running a regression to predict overall meal satisfaction from food type ordered, self-reported food flavor, and self-reported food texture.
But food flavor and texture are highly correlated, so they conducted a factor analysis, found food flavor and texture load on one factor, and used the factor scores in the regression.
However, about 40% of respondents don't have responses on self-reported food texture, so they used pairwise deletion while making the factors.
My question is when SPSS calculates the factor scores and outputs them as new variables in the data set, what does it do with people who had an input for a factor that was pairwise deleted?
How does it calculate (if it calculates it at all) factor scores for those people who had a response pairwise deleted during the creation of the factors and who therefore have missing data for one of the variables?
Factor scores are a linear combination of their scaled inputs. That is, given normalized variables X1, ..., Xn, we have the following (where LaTeX formatting isn't supported and the L's indicate the loadings)
f = \sum_{i=1}^n L_i X_i
In your case n = 2. Now suppose one of the X_i is missing. How do you take a sum involving a missing value? Clearly, you cannot... unless you impute it.
I don't know what the analyst who created your report did. I suggest you ask them.
I have a conceptual question about numerical methods. What is the difference among finite element, continuous finite element, discontinuous finite element, continuous galerkin and discontinuous galerkin methods? Are some of them just the same thing?
Thanks in advance
Finite element methods are a subset of numerical methods (which also include finite volume, finite difference, Monte Carlo and a lot more).
Simply put, in finite element methods, one tries to approximate the solution to a problem with a linear combination of pre-defined basis functions. These basis functions can be chosen to be either continuous or discontinuous. The resulting numerical methods are called CG/DG (continuous/discontinuous Galerkin) methods. In a DG method, the basis functions are only piecewise continuous: each basis function is zero everywhere in the domain, except in one element. See also this excellent Wikipedia article, which features some very nice figures.
Discontinuous Garlerkin methods were originally popularised in the field of particle transport long ago, but they have recently gained ground in other fields as well. (This is mostly because it wasn't clear at first how discontinuous basis functions would work well in equations that involve diffusion, but that problem has been solved now.)
Just a small pedantic correction to #A. Hennink's answer - In DG methods, the state variable is not piece-wise continuous between basis functions. There is a non-physical jump in the state variable between basis functions, hence the discontinuous part in the name. This can be visualized in the following figure displaying (dis)continuous basis functions of CG and DG:
In CG methods, the basis functions are piece-wise continuous, meaning continuous in the state variable itself, but the derivative may not be continuous (i.e. there may be a discontinuity in the derivative of the state variable between basis functions). This means that the solution to what ever problem you're solving can have non-physical kinks in the solution. Note the 'kinks' in the following solution
Some basis functions are not always discontinuous in the derivative though (see Hermite basis functions). See how the following Hermite basis function has a derivative of zero at both the end points. If all basis functions are composed using Hermite polynomials, then the derivative is continuous between basis functions because it's zero at the boundaries. Below, Psi_1 is the derivate of Psi_0, and Psi_3 is the derivative of Psi_2:
I have a variable X and and 16 groups of samples. I would like to know which group is the most associated to this variable (the one with the lowest values actually). I performed an ANOVA and a TukeyHSD/post-hoc but that only highlight which groups are different for variable X.
Is there a way to determine which group is significantly associated at lowest values for variable X ?
Thanks for your help
With the post-hoc comparisons already in place, and with the information which groups differ from one another, all you need to know is the mean of X within each group.
The group means are easily calculated in standard statistical software. You already know, which of those means are significantly different from one another.
Alternatively you can use a dummy coding for the group variable (i.e., 5 indicator variables with one reference group that replace the 6-level factor). A regression model that regresses X on the dummy variables is equivalent to the ANOVA model (in most parts) and allows for most pairwise comparisons (depending on the coding).
The regression coefficients will indicate the difference between groups, and the test for the coefficients will indicate whether or not these are significant on some level of confidence.