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…ion to 1.25.0, and fix exposure rownames issue
…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.
aoliveram
changed the title
Avoid masking epiworldR::get_transmissions() when both packages are loaded. No behavior change; exported name and docs renamed, tests updated accordingly. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
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>
Adds adoption_model = c("threshold", "logit") and adoption_pars
arguments to rdiffnet(). In logit mode, node i adopts at step t with
probability plogis(beta0 + beta_expo * exposure_i), drawn from
runif() each step. Threshold stays the default so fixed-seed calls
that omit the new argument remain bit-identical.
15 new tests cover backward compatibility, parameter validation,
saturation / suppression extremes, and multi-behaviour runs. Full
suite: 665 pass, 0 fail.
…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.
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The milestones tabla have been updated, following @gvegayon's comments:
Order of execution: M6 → M5 → M7 → M8 → M9 → M10+. |
…M4 -adoption_model = c('deterministic', 'stochastics'). Bumps version 1.25.0 -> 1.26.0
…ix (M6 follow-up, #78)
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Refs #78.
This draft PR tracks the implementation of epidemiological analysis capabilities in
netdiffuseR, addressing the four gaps identified in the internal gap report:tod) / reinfection episodes.stochastic-transmissionbranch, now integrated here).This branch starts from
masterand has already integrated two upstream feature branches:issue-75-epigames-dynamic-attrs— dynamic behavioral attributes for Epigames.stochastic-transmission—mode = "stochastic"forexposure()/rdiffnet().No new dependencies will be added to
DESCRIPTION.Implementation milestones
\$todslot,\$transmissionslot, validators, coercionsR/diffnet-class.r,R/adjmat.r, newR/transmission.Rlink_funinexposure()R/stats.Rtests/testthat/adoption_model = \"logit\"inrdiffnet()R/rdiffnet.rR/epi_metrics.Rhazard_rate(),plot_adopters()under\$todR/stats.R,R/diffnet-methods.rrepr_number()+ plot methodR/epi_metrics.Rhistories.csv → \$transmissiondata-raw/vignettes/epidemiological-analysis.Rmdtests/testthat/,.github/workflows/