NEWS.md

SemNeT 2.0.0

Full rebuild of the package's internals (see REFACTOR_PLAN.md for the phase-by-phase development record). Every pre-2.0.0 exported name still works -- see "Backward compatibility" below -- so existing scripts do not need to change. The Shiny app (SemNeTShiny()) is not part of this rebuild and remains on the pre-2.0.0 code path.

New functions

• permutation_SemNeT() -- the old permSemNeT() was an internal, undocumented, unexported function with three real argument-passing bugs (see "Bug fixes" below). It is now fully validated, documented, and exported for the first time.
• forward_flow() -- re-added after being dropped entirely in 1.4.4's CRAN resurrection (its ff_function() helper called googledrive::drive_auth()/ drive_download() to silently fetch pretrained semantic-space vectors at runtime, a hard CRAN policy violation). This version never touches the network: pass your own word-embedding matrix (embeddings, rows named by vocabulary term) instead of naming a built-in space. Internals were otherwise rewritten to match the rest of the 2.0.0 codebase -- validated arguments, parallel_process() instead of a hand-managed parallel::makeCluster(), and the existing cosine() helper instead of a new LSAfun dependency.

Real bugs fixed

• equate(): two groups were compared by vocabulary size, not actual shared words -- two similarly-sized groups with almost no overlap could receive zero equating. Fixed to compute the true shared vocabulary directly, with a consistent column order across every group.
• bootSemNeT()/bootstrap_SemNeT(), test.bootSemNeT()/ bootstrap_test_SemNeT(), equate(), response.analysis()/ response_analysis(), randnet.test()/random_network_test(), compare_nets()/compare_networks(): every function taking named groups via ... validated that names were present but not unique -- a duplicate name silently hid or corrupted a result via $/[[ access (R always returns only the first match). Now rejected outright where a duplicate is a real user mistake, or disambiguated via make.unique() where two distinct objects can legitimately share a label.
• CC()/cc(): the weighted branch's cube root (A^(1/3)) returned NaN for every negative edge weight, silently breaking weighted clustering coefficient on any signed network. Fixed with a real-valued signed cube root.
• ASPL()/aspl(): distance() silently zeroed unreachable node-pair distances before averaging, understating ASPL for any disconnected network. Unreachable pairs now correctly propagate Inf and are excluded from the average.
• TMFG()/tmfg(): for(e in 5:n) iterated backwards whenever n == 4, corrupting the result; n < 4 produced silent NA corruption instead of an error. Both fixed.
• NRW()/nrw(): the numeric-response detection heuristic (max(range(data)) >= 1) rejected virtually every valid ordered response matrix. Fixed with a correct, shared heuristic (also used by CN()/cn()).
• test.bootSemNeT()/bootstrap_test_SemNeT(): match.arg(measures) was missing several.ok = TRUE, so requesting the function's own documented default (all three measures at once) errored.
• permSemNeT()/permutation_SemNeT(): a thresold typo silently dropped NRW's threshold argument; enrich <- args$enrich (assignment used as a bare call argument) silently dropped CN's enrich argument; one sample's NRW call passed its threshold into a parameter named window instead of threshold. All three shared one root cause (hand-duplicated per-method argument-passing code) and are structurally impossible now, via one shared dispatcher.
• Several 1:n-style ranges that silently ran backwards or indexed out of bounds on degenerate (empty/size-1) inputs, in both inherited and newly-written code -- see REFACTOR_PLAN.md's "Phase 0-2 line-by-line review" section for the full list.
• q()'s modularity is now reproducible via an explicit seed argument, instead of depending on R's global RNG state via igraph::cluster_louvain() (which meant the same call could return different results depending on unrelated code executed earlier in a session).
• forward_flow()'s type = "free" path silently mismatched or crashed on numeric participant IDs (e.g. 7, 12, 20): [[ on a list indexes positionally for a bare number, not by name, so result_index_by_id[[id]]/ response_flow_list[[id]] either threw "subscript out of bounds" (an ID exceeding the participant count) or silently returned another participant's results. Found by re-running GitHub issue #10's actual reported dataset through the rebuilt function. Fixed by indexing with as.character(id).

Verification against real user-reported data

• GitHub issue #10 ("node stack overflow" in forward_flow()) and issue #11 (Shiny Spreading Activation producing all-zero output / BRM upload failing) were re-tested end to end using the actual data files attached to those issues, not synthetic data. Both are resolved. See REFACTOR_PLAN.md's "Post-rebuild addition: forward_flow()" section for the full investigation and results.
• distance(A, weighted = TRUE) (a from-scratch Dijkstra implementation reachable via aspl(A, weighted = TRUE)) and cc(A, weighted = TRUE)'s geometric-mean formula had no prior correctness tests (only type validation) -- verified against an independent reference (igraph for distance(), hand-derived values including negative edge weights for cc()) and found correct; permanent regression tests added either way.
• q()'s vendored Louvain modularity was cross-checked against igraph::modularity() computing the same partition independently, and matched to floating-point precision.

Memory

• bootstrap_SemNeT()/permutation_SemNeT() no longer keep every bootstrapped/permuted network in memory by default -- a full set of iter dense N x N networks per group/sample (the default is iter = 1000) could reach gigabyte scale for realistic network sizes, and the only documented downstream consumer (bootstrap_test_SemNeT()'s ANCOVA covariate) only ever needed a single scalar (edge count) per network. Both functions gained a keep_networks argument, defaulting to FALSE: bootstrap_SemNeT() now always computes each network's edge count at generation time regardless of this setting, and bootstrap_test_SemNeT() reads that instead of the (now usually absent) full networks; permutation_SemNeT()'s previous = reuse (testing a second measure without re-simulating) now requires the original call to have used keep_networks = TRUE, since that's the only case needing the networks kept around afterward.
• random_network_test() no longer materializes an entire batch of iter random networks before reducing them to measures -- each one is reduced immediately, since nothing it returns ever needed the raw random networks in the first place. No change in behavior or return shape, only in peak memory during the call.

Backward compatibility

Every pre-2.0.0 exported name is kept working via R/legacy.R, translating old-style arguments/call conventions into a call to the new implementation:

Old name	New name
TMFG()	tmfg()
ASPL()	aspl()
CC()	cc()
CN()	cn()
NRW()	nrw()
PF()	pf()
Q()	q()
bootSemNeT()	bootstrap_SemNeT()
test.bootSemNeT()	bootstrap_test_SemNeT()
plot.bootSemNeT()	plot.bootstrap_SemNeT()
randwalk()	random_walk()
randnet.test()	random_network_test()
sim.fluency()	simulate_fluency()
response.analysis()	response_analysis()
semnetmeas()	semantic_network_measures()
compare_nets()	compare_networks()

similarity(), finalize(), equate(), convert2igraph(), and convert2cytoscape() keep their original names -- no wrapper needed.

A few narrow, documented behavior changes come with this compatibility layer (see each wrapper's own ?help page for details):

• bootSemNeT()'s method/type arguments never actually had a working default in the original (an unresolved multi-value default reaching switch()/if() would error) -- omitting them now cleanly falls through to bootstrap_SemNeT()'s own defaults ("tmfg"/"case") instead of erroring.
• bootSemNeT()/randwalk()/randnet.test() no longer auto-detect and use half/most of the machine's CPU cores by default; they now default to sequential processing, matching their new-named replacements. Pass cores = explicitly for parallel execution.
• finalize()'s argument names changed from rmat/minCase to data/ minimum_cases -- positional calls are unaffected, but a call naming these arguments explicitly will need updating.

Dependency changes

• Dropped: pbapply, dplyr, plyr, magrittr, ggplot2, scales, philentropy. Plotting (plot.bootstrap_SemNeT()) now uses base graphics::boxplot(); Chebyshev distance (pf()) uses stats::dist(method = "maximum"); parallelism uses future/ future.apply/progressr with guaranteed cleanup, replacing several leak-prone parallel::makeCluster()/pbapply::pblapply() blocks.
• Added: future, future.apply, progressr, stats, graphics, utils (all either new parallelism infrastructure or previously-implicit base-package usage now declared explicitly).
• Unchanged: igraph, qgraph (used by compare_networks()'s plotting), car, broom, effects (used by bootstrap_test_SemNeT()'s ANOVA/ANCOVA), methods.
• This package now vendors a small amount of compiled C (src/, from {EGAnet}) for Louvain community detection and signed modularity, replacing igraph::cluster_louvain() for q(). NeedsCompilation is now yes.

Internal

• One file per exported function (function + its own input validation), matching {EGAnet}'s conventions -- replaces the previous single 1,800+ line utils-SemNeT.R and several large, multi-function files.
• bootstrap_SemNeT() (and everything downstream of it) uses one consistent result schema (list(groups = list(<name> = list(networks, measures, summary)), meta = list(...)), class "bootstrap_SemNeT") instead of the previous fragile "XNet"/"XMeas"/"XSumm" string-splicing convention that three different files independently regex-parsed.
• Numerous hot loops vectorized (similarity(), tmfg(), cn(), random_walk(), and others) -- see REFACTOR_PLAN.md's optimization-pass sections for benchmarked, verified details.
• R/methods.R (verified 100% dead/shadowed code) removed.