How did researchers calculate the Hazard ratio?

I’m looking at a pdf document and can get the result of the HR. It is actually similiar to calculating the relative risk if I’m right. How do I get the 1.45 HR or 1.20 HR values based on the 3 rows above (ppis users, h2 users, nonusers). I believe I need more parameters which … Read more

Conflicting results of summary() and anova() for a mixed model with interactions in lmer+lmerTest

I recently came across what I think may be a problem in how the anova() function from the lmerTest packages computes its F-statistics and corresponding P-values for fixed effects from mixed-effects models. Let me start by saying that I know of the controversy surrounding calculating P-values from mixed effects models (for reason discussed here). Nonetheless, … Read more

Relation between P-value in a randomness test, number of samples, and entropy

Consider tests of randomness of bit sequences of fixed size $n$ bits as in cryptography (e.g. NIST Special Publication 800-22 page 1-4; notice this uses captital-$P$ for p-values). Define such test as any deterministic function $T$ that accepts a vector $V$ of $n$ bits, and outputs a p-value $p$ in $]0\dots1]$ (with null hypothesis that … Read more

Chi square and p value in GAM results in R

I would like to know how to interpret chi square and p values in GAM. As I understand p values basically tell us a story about the graphs – how low is the probability that there’s just a straight line in the graph, eg. s()=0. Am I correct? But what about the chi square? For … Read more

Interpreting the distribution of the pt function in R

I am attempting to extract p-values for some given t-statistics (calculated from paired t.tests) using the pt function in R. My understanding was that the t-statistic in this case is a measure of how many standard errors away one mean in a pair is from the other. As such I assumed that the further away … Read more

Why use the sample SE when calculating the p value?

In the OpenIntro text book, there is the following example: Globally, the average sleep for a high school student is 7 hours. The researchers at the rural school conducted a simple random sample of n = 110 students on campus. They found that these students averaged 7.42 hours of sleep and the standard deviation of … Read more

t value greater than 1.96 but p value greater than 0.05

When dealing with t statistics, we reject the null hypothesis (H0: β=0) if the t value is greater than 1.96 in absolute value with a level of significance of 0.05. I have run this model, with the factor A with 2 levels and factor B with three levels: ldepvar ~ A * B + (1 … Read more

p-value distribution for enrichment analysis

I am doing a gene ontology enrichment analysis and end up with an unexpected distribution for my p-values. My questions: Why does this happen? Can I anyway use the p-values to interpret if terms are enriched? How can it be corrected? I am not a statistician and appreciate simple answers. HERE ARE THE ANALYSIS DETAILS: … Read more