…ion to 1.25.0, and fix exposure rownames issue

…ormalization

…ormalization

…Issue #75)

- Add data-raw/epigames.R: bundles epigames_hourly + dynamic_attrs_hourly.csv
  into epigames list with new $dyn_attrs slot (long format, 201,366 rows)
- Add data-raw/epigamesDiffNet.R: collapses hourly attrs to 15 daily windows,
  populates vertex.dyn.attrs with mask/med/quarantine proportions per day
- Regenerate data/epigames.rda and data/epigamesDiffNet.rda

Dynamic attributes (mask, med, quarantine) now visible in print(epigamesDiffNet):
  Dynamic attributes: mask, med, quarantine (3)

Validated: exposure(epigamesDiffNet, attrs = 'mask') works with time-varying
data. Correlation with static proxy = 0.88, confirming dynamic attrs
capture additional temporal variation.

- Removed redundant comments and sanity checks for better readability
- Simplified as_diffnet call structure
- Regenerated .rda files to match clean scripts

- new_diffnet() gains a -tod- argument (single-behavior vector) with
  validation (element-wise tod > toa, NA where toa is NA, length match).
- When -tod- is supplied, cumadopt is reconstructed from the intervals
  [toa, tod - 1] via cumadopt_from_intervals() in R/adjmat.r.
- New $transmission slot plus exported helpers as_transmission_tree()
  and get_transmissions() (R/transmission.R) storing the directed
  infection forest as a data.frame with columns date, source, target,
  source_exposure_date, virus_id, virus. Docs cite Lloyd-Smith et al.
  (2005) and White & Pagano (2008).
- Tests cover interval reconstruction, validation errors, coercion,
  and the transmission slot round-trip.

No new package dependencies.

Adds link_fun + link_pars arguments to exposure(). Supported named
kernels: identity (default), linear (min(beta*w, 1)), sigmoid
(plogis((w-h)/scale)), wells-riley (1 - exp(-beta*w)). Custom user
functions are accepted with either signature function(w) or
function(w, pars). Non-identity kernels force valued = TRUE with a
warning. Default behavior unchanged; 639 pre-existing tests still pass.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

…ange weights (M3, #78)

Adds four test_that blocks to tests/testthat/test-stochastic-exposure.R
covering each link kernel under seconds-scale weights, the
degree-denominator fix, and zero-weight self-loop handling. Small code
changes in R/stats.R: (1) warn when stochastic mode sees post-kernel
weights outside [0, 1] -- the sampler silently saturated before;
(2) denominator now counts non-zero-weight neighbours instead of every
stored entry, so link kernels that zero out some edges no longer
inflate the normaliser. No NAMESPACE / Rd changes. 652 tests pass.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Drop the dual signature for user-supplied link_fun. The helper now
always calls `link_fun(W@x)` with a single argument; parameters are
expected to be baked into the closure. `link_pars` remains relevant
only for the named kernels ("linear", "sigmoid", "wells-riley").
Simpler API, simpler docs, simpler tests.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

…tic/stochastic (M4 follow-up, #78)

Renames the two values accepted by adoption_model in rdiffnet() so
the vocabulary matches the existing exposure.mode (which already
uses deterministic/stochastic). No behavior change:
  - adoption_model = c("deterministic", "stochastic"), default
    "deterministic" (was "threshold")
  - "stochastic" keeps the same plogis(beta0 + beta_expo * exposure)
    Bernoulli draw previously called "logit"
  - Error message, roxygen doc and man page updated to match
  - Test file renamed test-rdiffnet-logit.R -> test-rdiffnet-stochastic.R;
    all 15 existing expectations updated to use the new names

Full suite: 665 passed, 0 failed.

…ix (M6 follow-up, #78)

<noreply@anthropic.com>

…e status helpers

…78)”

…D check WARNING

…ract extension (M8, #78)

…llow-up, #78)

)

…nt/plot (M12 follow-up, #78)

…int/plot (M12 follow-up, #78)

…M12.2, #78)

… events (M13, #78)

…+ summary survival line (#78)

…ticity (M14, #78)

… follow-up, #78)