By Clay Ford
Measurement Invariance
Demo (2025-06-26)
Example from Chapter 4 of Latent Variable Modeling Using R
(Beaujean 2014), Latent Variable Models with Multiple Groups. The
example examines if the structure of the WISC-III scale is the same in
children with and without manic symptoms. Book
code
Extracting data from UpSet
Plot (2025-04-10)
How to extract specific interactions from a data frame identified in an
UpSet plot.
Demo of Tukey HSD
(2025-04-02)
Quick demo of how Tukey HSD corrects p-values for multiple
comparisons.
Understanding the log link
in a Poisson model (2025-03-21)
Why we use the log link with Poisson models (i.e.,
family = poisson(link = "log")).
Investigating
Multicolinearity (2025-03-19)
Investigating multicolinearity and challenging idea of inspecting
pairwise correlations before fitting a model and dropping highly
correlated predictors.
analyze correlational
data with treatments (2025-02-03)
Assessing correlation between multiple sets of variables stratified by a
treatment variable. Uses the r.test() function from the
{psych} package.
Repeated Measures
ANOVA examples (2025-01-29)
Two examples of repeated measures ANOVA: (1) Using raw follow-up data as
the outcome with baseline as a covariate, and (2) Using change scores as
the outcome. I prefer the first method.
Comparing self-starting
Michaelis-Menten Models (2025-01-15)
How to compare two fitted curves using an interaction in a
nlme::gnls() model.
Understanding the
{ggeffects} predict_response() margin argument (2025-01-10)
Elaborating on the {ggeffects} vignette, Difference
Between Marginalization Methods: The margin Argument.
Intro to Mixed-Effect
Modeling (2024-12-18)
Introduces mixed-effect modeling using simulated data and compares the
results to wrong and older methods.
Paired t-tests as
mixed-effect model (2024-11-22)
How to run many paired t-tests as a single mixed-effect model. Uses
simulated data.
tidyLPA notes (2024-11-01, Clay Ford
and Lauren Brideau)
Notes on using the {tidyLPA} package and how it relates to the {mclust}
package.
Mixed-Effect Modeling for
ANOVA (2024-10-08)
Demo of implementing ANOVA analysis for multilevel data.
Using polycor::hetcor
(2024-09-27)
Demonstration of using the hetcor() function in the
{polycor} package using simulated data.
Polyserial
and Polychoric Correlation (2024-09-24)
An intro to polyserial and polychoric correlation using the {polycor}
package.
Paired t-test as
linear model (2024-09-05)
How to perform a paired t-test as a linear model and calculate Cohen’s
d. Also includes an example of calculating Cohen’s d following multiple
imputation.
Marginal effects and plots for
2-way and 3-way interactions (2024-08-19)
Demo of Bayesian modeling of 2-way and 3-way interactions (via
{rstanarm}) using the {emmeans} and {ggeffects} packages. Uses simulated
data.
Post-hoc
Comparisons with non-linear models (2024-07-15)
Simple demo of using emmeans() on a non-linear
predictor.
Demo of Term plots
(2024-06-25)
Demonstration of using term plots to detect departures from linearity
for coefficients. Shows the base R termplot() and
car::crPlots() functions.
Assessing residuals with
lineup lots (2024-04-05)
Using lineup plots to better interpret a QQ plot of model
residuals.
Compact Letter Displays (2024-03-24)
How to create and interpret Compact Letter Displays, though some
people don’t like them.
Complex reshaping
example (2024-02-15)
The data set in question had six different sets of variables that needed
to be reshaped into “long” format. Each set was collected over five
waves. This shows how to do the reshaping using
pivot_longer().
Multivariate Paired
Hotelling T Square Test (2024-02-27)
How to implement a Multivariate Paired Hotelling T Square Test in R and
SPSS.
VarCov Matrices
for Random Effects (2024-02-14)
In this note I show how to suppress estimation of covariance random
effects when estimating random effects for a categorical
predictor.
Forced One-way ANOVA
(2023-12-01)
Convert a two-way ANOVA into a one-way ANOVA.
Multilevel Quantile
Regression (2023-10-23)
Example of Multilevel Quantile Regression using {lqmm} and simulated
data.
Data wrangling nc4 files
(2023-10-18)
Example of extracting values from nc4 object (netCDF) and converting to
data frame.
Recoding example
(2023-10-06)
Recoding example using a lookup table.
Multi-level model example using
simulated data (2023-10-03)
Example of multi-level model written for someone who was brand new to R.
Includes demo of {emmeans} and {ggeffects}.
Multilevel model example
with 3 nested levels (2023-09-15)
Example of a multilevel model with 3 levels of nested groups. Uses
simulated data.
Data wrangling
consultation (2023-08-28)
Data wrangling tasks: (1) drop any groups with less than 10 rows, (2)
drop rows with runs of zeroes greater than or equal to 5.
Examples of emmeans
(2023-03-24)
Examples of using emmeans after fitting mixed-effect model, including
estimating differences in differences.
Various t-test
alternatives (2023-02-21)
Shows alternatives to t-tests, including log-transformed t-tests,
Wilcoxon, permutation tests, and bootstrap.
Dummy coding versus
effects coding (2023-01-07)
Demonstrates differences in coefficient interpretations for dummy coding
versus effects coding. Uses simulated data.
Multilevel model
for discrete ordered data (2022-11-04)
Demo of fitting a multilevel model for an ordered categorical outcome.
Uses the {ordinal} and {emmeans} packages.
Split violin plots
(2022-10-18)
Demo of how to create split violin plots using
introdataviz::geom_split_violin()
The stats::filter()
function (2022-10-12)
How to use the the base R filter() function to calculate
moving averages.
Logistic
regression interactions (2022-09-19)
How to interpret and visualize 2-level categorical variable interactions
in a logistic regression model.
Nested Factorial Experiment
(2022-09-19)
Example of a Nested Factorial Experiment from Statistical Models in
S.
How to adjust p-values using
R (2022-09-13)
Quick demo of how to use Holm method to adjust p-values.
EFA with binary data
(2022-07-28)
Example of performing exploratory factor analysis with binary data. Uses
simulated data.
Three
approaches to logistic regression in R (2022-07-18)
Demo of three ways to fit a logistic regression model in R.
Comparing a mediation
analysis and with a t-test (2022-05-25)
The difference in means from a t-test is the “Total Effect” in mediation
analysis.
Dangers of only looking at R-squared
(2022-05-09)
Demo of how R-squared can be misleadingly high despite a poor-fitting
model. Includes demonstrations of non-linear models.
Mediation Analysis with Multiple
Imputation (2022-04-25)
An attempt at mediation analysis with multiply imputed data using the
{mice} and {mediation} packages.
Plotting
logistic regression probabilities in Python (2022-04-15)
How to create an effect plot for a binary predictor using a logistic
regression model in Python. Uses matplotlib and statsmodels.
Splines in
mixed-effect models (2022-04-13)
Demo of fitting splines in mixed-effect models. Also includes demo of
piecewise splines using the {segmented} package. Uses simulated
data.
Explaining large confidence
intervals (2022-04-05)
Student wondered why confidence intervals on marginal means were so
large. Due to small estimated degrees of freedom.
Nomogram demo (2022-03-31)
This demonstration is a modification of the example available on the
nomogram() help page from the {rms} package. It
demonstrates a nomogram for a logistic regression model using simulated
data.
mixed-effect proportional odds
model (2022-02-25)
An example of a mixed-effect proportional odds model using simulated
data and the clmm() function from the {ordinal}
package.
Robustness of t-test
(2022-01-07)
Simulation demonstrating robustness of t-test to non-normal
data.
ANCOVA example
(2022-01-07)
Quick demo of using Analysis of Covariance to compare trends over
time.
Identifying peaks in a line plot
(2021-06-14)
One possible method of identifying peaks in a line plot using the
findpeaks() function in the {pracma} package.
Bootstrapped diff in means
(2021-12-11)
Example of implementing a bootstrapped difference in means as an
alternative to a t-test using the {boot} package in R.
Multilevel Model power
analysis (2021-10-04)
Power analysis for a multilevel model with a Likert outcome ranging from
1-5 and a simple binary treatment variable. Presents two approaches: (1)
manual simulation, and (2) the {simr} package.
logistic regression
for a 2x2 table (2021-06-09)
Example of using logistic regression to get odds ratio, confidence
interval on OR, and the p-value testing null if OR is 1.
Plotting Derivatives
(2021-05-17)
Calculating and plotting first and second derivatives.
Comparing Trends with ANCOVA
(2021-04-22)
Comparing slopes via ANCOVA and {emmeans} using simulated data.
Demo of Generalized Linear Mixed Model
(2021-02-12)
A demonstration of binomial GLMM using simulated data.
CIs for Cramer’s V
(2021-01-20)
Demo of calculating CIs for Cramer’s V for a small sample.
Normality is for
Residuals (2020-11-02)
The normality assumption in linear modeling (multiple regression) is on
the residuals, not the dependent or independent variables.
Stepwise Model Selection
performing poorly (2020-09-01)
Demo of stepwise model selection performing poorly in the presence of
collinearity. Stepwise
selection should be avoided anyway.