General
PromptBeginner5 minmarkdown
> Non-obvious behaviors
gotchas
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General
PromptBeginner5 minmarkdown
- **Lognormal**: `meanlog` and `sdlog` are mean/sd of the **log**
not of the distribution itself.
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General
PromptBeginner5 minmarkdown
- Returns `$estimate`
`$p.value`
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General
PromptBeginner5 minmarkdown
- **`n` argument in `r*()` functions**: if `length(n) > 1`
uses `length(n)` as the count
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General
PromptBeginner5 minmarkdown
- **Beta**: `shape1` (alpha)
`shape2` (beta) — no `mean`/`sd` parameterization.
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General
PromptBeginner5 minmarkdown
- `names = TRUE` by default
adding 0%
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General
PromptBeginner5 minmarkdown
- **Nine** `type` options (1-9). Default `type = 7` (R default
linear interpolation). Type 1 = inverse of empirical CDF (SAS default). Types 4-9 are continuous; 1-3 are discontinuous.
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General
PromptBeginner5 minmarkdown
- `prcomp` uses **SVD** (numerically superior); `princomp` uses `eigen` on covariance (less stable
N-1 vs N scaling).
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General
PromptBeginner5 minmarkdown
- `method = euclidean` (default). Other options: `manhattan`
`maximum`
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Creative
PromptBeginner5 minmarkdown
- `nstart > 1` recommended (e.g.
`nstart = 25`): runs algorithm from multiple random starts
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General
PromptBeginner5 minmarkdown
- Methods: `holm` (default)
`BH` (Benjamini-Hochberg FDR)
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General
PromptBeginner5 minmarkdown
- For tables larger than 2x2
uses simulation (`simulate.p.value = TRUE`) or network algorithm.
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General
PromptBeginner5 minmarkdown
- `exact = TRUE` by default for small samples with no ties. With ties
normal approximation used.
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General
PromptBeginner5 minmarkdown
- Paired test: `paired = TRUE` uses signed-rank test (Wilcoxon)
not rank-sum (Mann-Whitney).
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General
PromptBeginner5 minmarkdown
- `simulate.p.value = TRUE`: Monte Carlo with `B = 2000` replicates (min p ~ 0.0005). Simulation assumes **fixed marginals** (Fisher-style sampling
not the chi-sq assumption).
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General
PromptBeginner5 minmarkdown
- Return object includes `$expected`
`$residuals` (Pearson)
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General
PromptBeginner5 minmarkdown
- 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 minmarkdown
- `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 minmarkdown
- `anova(model1
model2)`: F-test comparing nested models.
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General
PromptBeginner5 minmarkdown
> Non-obvious behaviors
gotchas
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Coding & Debugging
PromptBeginner5 minmarkdown
- `SANN` (simulated annealing): convergence code is **always 0** — it never fails. `maxit` = total function evals (default 10000)
no other stopping criterion.
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General
PromptBeginner5 minmarkdown
- Default method is Nelder-Mead (no gradients
robust but slow). Poor for 1D — use `Brent` or `optimize()`.
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General
PromptBeginner5 minmarkdown
- Returns object with `predict`
`print`
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General
PromptBeginner5 minmarkdown
- `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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