General
PromptBeginner5 minmarkdownQuality: 24
- Paired test: paired = TRUE uses signed-rank test (Wilcoxon)
not rank-sum (Mann-Whitney).
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General
PromptBeginner5 minmarkdownQuality: 24
- For tables larger than 2x2
uses simulation (simulate.p.value = TRUE) or network algorithm.
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General
PromptBeginner5 minmarkdownQuality: 24
- exact = TRUE by default for small samples with no ties. With ties
normal approximation used.
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General
PromptBeginner5 minmarkdownQuality: 28
- simulate.p.value = TRUE: Monte Carlo with B = 2000 replicates (min p ~ 0.0005). Simulation assumes...
not the chi-sq assumption).
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General
PromptBeginner5 minmarkdownQuality: 24
- Return object includes $expected
$residuals (Pearson)
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General
PromptBeginner5 minmarkdownQuality: 28
- For goodness-of-fit: pass a vector
not a matrix. p must sum to 1 (or set rescale.p = TRUE).
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General
PromptBeginner5 minmarkdownQuality: 28
- uniroot: finds a root of f in `[lower
upper]. Requires f(lower) and f(upper)` to have opposite signs.
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General
PromptBeginner5 minmarkdownQuality: 24
Non-obvious behaviors
gotchas
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General
PromptBeginner5 minmarkdownQuality: 24
- `anova(model1
model2)`: F-test comparing nested models.
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Coding & Debugging
PromptBeginner5 minmarkdownQuality: 28
- SANN (simulated annealing): convergence code is always 0 — it never fails. maxit = total function...
no other stopping criterion.
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General
PromptBeginner5 minmarkdownQuality: 24
- Returns object with predict
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General
PromptBeginner5 minmarkdownQuality: 28
- Default method is Nelder-Mead (no gradients
robust but slow). Poor for 1D — use Brent or optimize().
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General
PromptBeginner5 minmarkdownQuality: 28
- predict.glm with type = response gives predictions on the response scale (e.g.
probabilities for logistic); type = link (default) gives on the link scale.
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General
PromptBeginner5 minmarkdownQuality: 24
- lowess parameter is f (span
default 2/3); loess parameter is span (default 0.75).
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General
PromptBeginner5 minmarkdownQuality: 24
- lowess is the older function; returns `list(x
y)` — cannot predict at new points.
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General
PromptBeginner5 minmarkdownQuality: 24
- Direction: direction = both (default)
forward
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Creative
PromptBeginner5 minmarkdownQuality: 24
- Self-starting models (SSlogis
SSasymp
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Creative
PromptBeginner5 minmarkdownQuality: 28
- aov is a wrapper around lm that stores extra info for balanced ANOVA. For unbalanced designs
Type I SS (sequential) are computed — order of terms matters.
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General
PromptBeginner5 minmarkdownQuality: 24
- For Type III SS
use car::Anova() or set contrasts to contr.sum/contr.helmert.
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General
PromptBeginner5 minmarkdownQuality: 24
- Quasi-families (quasibinomial
quasipoisson) allow overdispersion — no AIC is computed.
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General
PromptBeginner5 minmarkdownQuality: 24
- binomial accepts response as: 0/1 vector
logical
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General
PromptBeginner5 minmarkdownQuality: 28
- `anova(glm_obj
test = Chisq) for deviance-based tests; F` is invalid for non-Gaussian families.
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General
PromptBeginner5 minmarkdownQuality: 28
- weights in glm means prior weights (not frequency weights) — for frequency weights
use the cbind trick or offset.
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General
PromptBeginner5 minmarkdownQuality: 24
- Column names from model.matrix can be surprising: e.g.
factorLevelName concatenation.
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