Hello all,
I have a question regarding the definition of restrictions in a Wald test statistics. I have the following linear model:
Y = \alpha + \beta X + \delta M + e
I would like to test whether \beta=c and \delta=c (two restrictions and also the null hypothesis), I can re-write it to be \beta-\delta=0 (one restriction). I first impose two restrictions (one on each parameter) or I can collapse the two conditions into one restriction (i.e \beta= \delta).
Can I understand the latter statement (\beta=\delta) to be one restriction and thus have a t-test (special case of Wald test)? And the former statement ( \beta=c and \delta=c) to be a Wald test with two degrees of freedom under the null hypothesis?
I am making the assumption that the two tests should give me the same answer. However I am not sure if I understand how restrictions are defined in a Wald test.
Thank you!
My understanding of type II testing is that you compare a model with each tested factor, and all equivalent or lower-order terms, with a model excluding that factor. For example for y ~ a+b + ab, a type II significance test of a would involve comparing y ~ a + b with y ~b. The fact that the full model under consideration includes an additional term (ab) appears irrelevant to that test. From what I understand then, including higher order interactions in the model should not affect type II tests of lower interaction terms. The way I imagine doing a likelihood ratio, you would fit the sub-models mentioned above and compare their likelihoods with no reference to the full model. I understand the Wald test to be an approximation of the likelihood ratio. However, when I check the results for type II Wald tests in R on mixed models with and without interaction terms, I see some small differences in results for the lower order terms when an interaction is included, as shown below.
Is my understanding of type II testing correct? If so, I assume the differences introduced by the interaction term are due to numerical issues, or the Wald test being an approximation?
library(lme4) library(car)
#Wald type II chi square tests on model including interaction term
m <- lmer(angle ~ recipe * temperature + (1|replicate), cake)
Anova(m)
#Wald type II chi square tests on model excluding interaction term
m2 <- lmer(angle ~ recipe + temperature + (1|replicate), cake)
Anova(m2)Hi everybody, my issue is that i’m not even sure if i should use wald test after ologit, so for an ordinal logistic regression. I tried it out but it didn’t work.
I have a question about what is meant by Wald tests. Based on the contexts of where I have read it, as well as some notes like the Wikipedia entry, my understanding is any test that is formulated by a measure of distance between the estimated value and hypothesized value is a Wald Test?
So the distribution of the test is not relevant, just if it is a distance it can be called a Wald Test? so a T test, F test, z -test, chi-square etc. are all types of Wald Tests, that have a particular distribution?
I want to test whether there is an effect of group for a three level variable using a Wald_test:
yi ~ 0 + Group + Group:Variable
How can I write the matrix?
I tried the following but it states that it should be a q*6 matrix
Wald_test(model, constraints = matrix(c(1,0,0,0,1,0,0,0,1, vcov = "CR2")]
Does anyone have a good grasp or resources of how to go about this?
I’m taking and adv econometrics class and my professor said that the Wald test is the asynthotic equivalent of the F test.
I get that a F distribution can be approximated to a chi square as the sample size increases. However in the F test formula has at the denominator the sample variance (s^2) divided by degrees of freedom of the chi square: number of restrictions r and the N-K (N is the sample size and K number of parameters to be tested). I don’t get why in the Wald test we correct only for r degrees of freedom and and if the variance estimator we use is same s^2 we used for the F-test. I hope I was clear enough, sorry for the mistakes and thank you redditors!
#waldtest
So I have this quadratic regression with two parameters. One of these parameters is squared and have a coefficient of 0.15 (b2) and the other is -1.17 (b1). My constant/intercept is 140 (b0). So my question is: based on a degree 2 polynomial model, do the wald test that was run to test association between X and mean outcome Y, take into account both coefficients or only one of them (either b1 or b2)? Also the test stat that I obtained, gave a t stat of -5.45 (P>t 0.000) for b1 and 1.83 (P>t 0.07) for b2. My second question is, does the wald test (5% level) still reject my null hypothesis of no linearity, despite the bigger p-value obtained for b2?
input <- mtcars[,c("am","cyl","hp","wt")]
fit <- glm(formula = am ~ cyl + hp + wt, data = input, family =
binomial)
summary(fit)
column Pr(>|z|) is the result of the wald test correct?
I am testing the association between a gene and a binary disease
The gene has many different "versions". These versions are called alleles.
I am also including covariates for sex, age, etc.
Right now I am doing omnibus test for the gene like this (pseudocode):
full<- "disease ~ sex + age + allele1 + allele2 + allele3"
null<- "disease ~ sex + age"
lr_test <- anova(null, full, test='Chisq')
I realize that after this I could use the wald test results to determine how significant each allele of the gene is, but I am wondering if this is best done with the LR test, which would allow me to account for the covariates on each allele comparisons, sort of like this:
full1<- "disease ~ sex + age + allele1"
null<- "disease ~ sex + age"
lr_test1 <- anova(null, full1, test='Chisq')
full2<- "disease ~ sex + age + allele2"
null<- "disease ~ sex + age"
lr_test2 <- anova(null, full2, test='Chisq'), etc.
My gut feeling is that the LR approach for the pairwise allele comparisons would be better than wald. Is this the case?
Hi,
Sorry if this has been asked before, I tried searching and couldn't find an answer (At least one that I could understand).
I'm having trouble understanding how DEseq2 prepares the data to perform the Wald test. I tried reading the DESeq2 paper and the vignette as well as looking through various tutorials. I've found an illustration of the Wald test that makes sense to me but I'm having trouble putting it in the context of RNA seq analysis. According to (1) the Wald test calculates the probability of a_0 given the data which has been fit with maximum likelihood a-hat.
So in RNA-seq data the a-hat is the maximum likelihood for the fold change of a gene between two groups, say Control and Treated. a_0 is the null hypothesis that the fold change is zero (No change in expression for that gene). What I'm wondering about is how this model takes into account the variability in the data. Both the Treated and Control groups will have a standard error, how are both of these used in the analysis?
Let's say I have two biological replicates for the Control group and two for the Treated group, is it fair to think of it like I've illustrated in (2) where I calculate the fold change for all possible combinations of Control to Treatment samples (C1/T1, C1/T2, C2/T1, C2/T2). Then I can set a_0 to 0 and a-hat to the maximum likelihood for these pairwise fold changes.
I know this is probably convoluted and confusing. I'm working on improving my literacy in statistics but it's a process, so for now pictures help me. Thanks for reading and any help you can provide!
How can I prove that the Wald test is consistent? We have been given as hint that we need to find an estimator for sigma squared under the null hypothesis, alternative hypothesis and the whole parameter space. Then we need to find how the sigma under the alternative hypothesis corresponds with the other two.
P.S. With the wald test I mean ni(\hat{\theta}_n)(\hat{\theta}_n - \theta_0)^2
Hi everyone,
Im preparing for my econometrics exam and im currently studying the chapter on linear hypothesis.
The thing that confuses me is that we define a test on multiple parameters as a wald statistic. We showed this thing converges in distribution to a normal distribution with mean 0 and some variance (under the null). But then we want to transform the statistic to make the coefficient independent (or something along those lines). After many pages of algebra we showed the new statistic is distributed as a chi squared distribution with degrees of freedom equal to the number of restricttions.
My question is why... why do we want to make the betas independent? Is it just because we want to use the Chi squared distribution to test the restrictions or is there some other reason?
I have some bernoulli trials and was testing for randomness. I used the Wald-Wolfowitz runs test and got a p value of .003162 for a one-sided test. Curiously, when I simulated 10000 simulations I found that 452 of my simulations had less runs than my data set indicating a much higher p value. To run my simulations I call rbinom(3247, 1, .7717).
The mean number of runs from my monte carlo is 1144.436 which is incredibly close to the runs test mean of 1144.79. What am I missing here? Thanks
I am trying to get differential transcript/gene expression using sleuth on my dataset which consist of 3 replicates of well watered and not watered plants. I am using kallisto/sleuth pipeline. I realized I am getting more significant hits (qval <= 0.05) after running LRT test compared to Wald test. Isn't it supposed to be opposite? I read that LRT is a more stringent test. There is a difference of over 5000 transcripts between them!
Here's the code I am running:
so <- sleuth_prep(s2c, target_mapping = t2g, ~ condition, extra_bootstrap_summary = TRUE)
so <- sleuth_fit(so, ~condition, 'full')
so <- sleuth_fit(so, ~1, 'reduced')
so <- sleuth_lrt(so, 'reduced', 'full')
so <- sleuth_wt(so,'conditionwater','full')
results_table_lrt <- sleuth_results(so, 'reduced:full', 'lrt', show_all = FALSE)
results_lrt_significant <- results_table_lrt$target_id[which(results_table_lrt$qval <= 0.05)]
results_table_wald <- sleuth_results(so, 'conditionwater','full', test_type = 'wt')
results_wald_significant <- results_table_wald$target_id[which(results_table_wald$qval <= 0.05)]
table(results_table_lrt$qval<=0.05)
FALSE TRUE
53234 32237
table(results_table_wald$qval<=0.05)
FALSE TRUE
57549 27922
I would appreciate any help.
Say I have 3 different coefficients in my regression, the 1st one is non significant, the second and third are significant
How do I test whether all 3 together are significant? I’ve been proposed to use the Wald test, but I don’t quite understand it.
How should I formulate the null hypothesis to know whether c1, c2, and c3 are jointly significant?
Please help :)
Dear Community,
I'm conducting a meta-analysis with robumeta and most examples I see conduct a Wald test after the meta analysis.
Two questions:
1)Why do they do that
2)What are constraints in the context of a Wald test?
Thank you for your time.
Is there any reason for using them, when we can simply use k-fold cross validation on couple on models and then select the best one?
I could imagine using them for getting some kind of feature importance and confidence intervals, but I still can't make up solid argument, why CV would not be more reliable.
I am currently estimating a seemingly unrelated regression to test the effect of IV1 on DV1 and DV2 (errors for DV1 and DV2 are theoretically correlated), following the procedures outlined here:
https://stats.idre.ucla.edu/r/faq/how-can-i-perform-seemingly-unrelated-regression-in-r/
After I run the regression, I use the Wald test to see if IV1 in model1 is equal to IV1 in model2. I only do this because the help page shows me that it is possible. In my stats classes we never learned SUR models so I guess my first question is, does it actually make sense to use the Wald test to compare the size of IV1 effect in model1 and model2? It seems weird to me that this is possible but again I don't have much experience with simultaneous models.
My second question is does it matter that DV1 and DV2 have different scales? I can reject the null that the two effect sizes are the same, but my scales are not the same. Should I rescale my variables or does the Wald test take that into consideration? Thanks!
When testing the null hypothesis of a parameter in a mixed model being equal to 0 against the alternative hypothesis that it is not equal to 0, why must a test like the Wald, Score, or LR be used?
In simple linear regression, I understand that one can use something simple like a t-test to test whether a regression coefficient for a fixed effect is significant in the model (ie. whether it is not equal to 0 and therefore not contributing to the model).
However, testing the same hypotheses (as mentioned above) in mixed models, I only see Wald, Score, and LR tests being used. Why? (in the case of fixed effects)
From what I have been able to gather, it seems to have something to do with the fact that maximum likelihood is often used to estimate parameters in the mixed model...I also don't understand why in mixed model inference, model fits are tested...I'm not interested in a model fit, but in a single parameter of the model.
I'm not a statistician; I have minimal knowledge of the math behind these things. I ask here in hope of someone being able to provide a clear (relatively simple) answer, so that I can intuitively understand what is going on, even if I do not understand the math behind it.
While there exists a lot of literature about mixed models and inference, I have not been able to find anything that specifically addresses (in terms I can understand) why we can't use a t-test to test significance of a model parameter in a mixed model, but can in a simple linear model.
For a binomial, the estimated p is y/n. Since the standard error using the Wald test statistic for p is sqrt(p(1-p)/n), the maximum SE occurs at p=0.5. As p nears 0 or 1 the standard error obviously gets close to 0, but what does that really mean? Is the Wald statistic more accurate since the SE becomes so small, and creating a smaller confidence interval? Or does it just not work correctly near 0 and 1?
Hey guys, I'm trying to work on the proof from Wald form to F-test stat form from this page.
However, I can't seem solve it with the linear projection matrix.
Would appreciate some guidance or advice!
ps. _hat is unrestricted model. _tilda is restricted model under null hypothesis.
Hi!
I am working on a project on the effects of gasoline prices on personal consumer expenditures and we are trying to test for symmetry in the responses to upticks and downticks in fuel prices. The paper that our work builds on (Edelstein and Killian 2007) talks about using Wald tests. Can anyone give me a basic rundown on how these work and how to apply them in R? Thanks!
I use OxMetrics that is based on Ox.
(I have reduced my question to 2 regimes)
I need to test if my variable are insignificant (zero) across both regimes (MSR)(H0: X1=X2=0) I was easy with a LR-test by just removing the parameter. But I am having trouble setting up the Wald test, if this can even be used for this purpose. Ox doesn't let me test X1=X2=0, and X1-X2=0 tests if they are equal across both regimes, which is not what I want to test. Any suggestions? Thanks
The t-values are both insignificant (-0,75 and 0,791)
[Question]Why there is no denominator in the Wald test?
I’m taking and adv econometrics class and my professor said that the Wald test is the asynthotic equivalent of the F test.
I get that a F distribution can be approximated to a chi square as the sample size increases. However in the F test formula has at the denominator the sample variance (s^2) divided by degrees of freedom of the chi square: number of restrictions r and the N-K (N is the sample size and K number of parameters to be tested). I don’t get why in the Wald test we correct only for r degrees of freedom and and if the variance estimator we use is same s^2 we used for the F-test. I hope I was clear enough, sorry for the mistakes and thank you redditors!
#waldtest
How can I prove that the Wald test is consistent? We have been given as hint that we need to find an estimator for sigma squared under the null hypothesis, alternative hypothesis and the whole parameter space. Then we need to find how the sigma under the alternative hypothesis corresponds with the other two.
P.S. With the wald test I mean ni(\hat{\theta}_n)(\hat{\theta}_n - \theta_0)^2
How can I prove that the Wald test is consistent? We have been given as hint that we need to find an estimator for sigma squared under the null hypothesis, alternative hypothesis and the whole parameter space. Then we need to find how the sigma under the alternative hypothesis corresponds with the other two.
P.S. With the wald test I mean ni(\hat{\theta}_n)(\hat{\theta}_n - \theta_0)^2
