Motivation | Load packages | Culcita example: near-complete separation | Gopher tortoise example: mitigate singular fit | Zero-inflation | TO DO/FIX ME | Development issues | References

Motivation | Workflow in DHARMa | Installing, loading and citing the package | Calculating scaled residuals | Plotting the scaled residuals | Goodness-of-fit tests on the scaled residuals | Simulation options | Refit | Conditional vs. unconditional simulations | Integer treatment / randomization | Calculating residuals for groups or subsets | Reproducibility notes, random seed and random state | Interpreting residuals and recognizing misspecification problems | General remarks on interpreting residual patterns and tests | Recognizing over/underdispersion | Residual patterns of over/underdispersion | Formal tests for over/underdispersion | Zero-inflation / k-inflation or deficits | Residual patterns | Formal tests for zero-inflation | Testing generic summary statistics, e.g. for k-inflation or deficits | Heteroscedasticity | Detecting missing predictors or wrong functional assumptions | Residual correlation structures (temporal, spatial, phylogenetic) | Case studies and examples | Budworm example (count-proportion n/k binomial) | Owl example (count data) | Notes on particular data types | Poisson data | Proportional data | Binomial data | Supported packages and frameworks | lm and glm | lme4 | mgcv | gamm4 | glmmTMB | spaMM | GLMMadaptive | phylolm | phyr | brms | Unsupported packages | Importing external simulations (e.g. from Bayesian software or unsupported packages)

Basic workflow | Example in Jags | Exercise | Conditional vs. unconditional simulations in hierarchical models | Statistical differences between Bayesian vs. MLE quantile residuals

Overview | The AR(1) covariance structure | Demonstration on simulated data | Increasing the sample size | The unstructured covariance | The Toeplitz structure | Compound symmetry | Anova tables | Adding coordinate information | Ornstein–Uhlenbeck | Spatial correlations | Matérn | Gaussian | Exponential | A spatial covariance example | Mappings | Unstructured | Generalized latent variable model | Reduced-rank | Proportional | Equal | Construction of structured covariance matrices | References

Warnings | Model convergence problem; non-positive-definite Hessian matrix; NA values for likelihood/AIC/etc. | Example 1. | Example 2. | Example 3. | Model convergence problem: eigenvalue problems | NA/NaN function evaluation | false convergence | Errors | NA/NaN gradient evaluation | gradient length

Overview | Setup | Salamander example | Metropolis-Hastings (DIY) | tmbstan | Sleep study example

Compare to digest

Secure Random Numbers

Simulating from a fitted model | Simulating from scratch (de novo) | example 1: linear regression | example 2: random effects (including correlations) | example 3: AR1 model | FIXME/TO DO

Adding a family | C++ | modify glmmTMB.cpp | R code | modifying family.R | modifying glmmTMB.R | updating NAMESPACE | updating enum.R | Finishing up | Reinstall | Test | Additional distributional parameters | Adding a covariance structure | C++ code | Structure of a glmmTMB object

Notes on OpenMP support | System information

Adding headers

Adding headers | Combining tables | Formatting tables | Merged header columns | Alternative pipe syntax

Formatting tables | Merged header columns | Alternative pipe syntax | Working with colors | Data generation | Table construction

Modelling titanic survival | Data preparation | Table construction

Beta dispersion model

RSA key generation | How RSA encryption works

Overview | Prerequisites | Overview of Nightingale blood biomarker data | Rename alternative biomarker names | Association analysis | Join the blood biomarker data with other variables | Linear regression | Forest plot | Statistical significance for multiple testing | Cox proportional hazards regression | A forestplot for all Nightingale blood biomarkers | Final remarks | References

Overview | Installation | Usage | Adding information on statistical significance | Comparing several traits | Grouping the biomarkers | Plotting odds / hazard ratios

Downloading Data | Example

The DER format | The PEM format | The OpenSSH format | The JSON Web Key (JWK) format