Changes in version 2.1.0

o FIX: group tests in `bootstrap_test_SemNeT` and `test.bootSemNeT` inflated statistics by `sqrt(iter)` (Tu, Chodorow, Brooks, Ezrina, & Valian, under review); recompute any results

o UPDATE: `bootstrap_test_SemNeT` now returns bootstrap intervals of within-iteration group contrasts (`ci_level`, `adjust`, `ci_type`, `power`, `legacy` arguments)

o UPDATE: `bootstrap_test_SemNeT` node bootstraps are summarized descriptively (no interval or p-value)

o UPDATE: `bootstrap_test_SemNeT` legacy parametric tests need `legacy = TRUE` and always warn

o UPDATE: `bootstrap_SemNeT` `$summary` standard error is no longer divided by `sqrt(iter)`; observed (full-data) statistics are stored in `$observed`

o ADD: `bootstrap_test_SemNeT` Wald `z`, `p_value`, and minimal detectable effect `mde` for normal intervals (the default)

o ADD: `bootstrap_test_SemNeT` `bias_se` (|bias| / `se`; above about 0.25 the bootstrap is off-centre from the observed difference), printed as `bias/se`

o ADD: `bootstrap_test_SemNeT` and `permutation_SemNeT` print a note under their summary tables that they should always be run together

o FIX: `cn` `alpha` had no effect

o FIX: `cn` counted co-occurrences on uncleaned responses, so placeholders (`" "`, `"NA"`) emptied the network

o FIX: `nrw` counted every adjacent pair twice per participant; pairs are now counted once (counts are numbers of participants)

o FIX: `pf` dropped zero-distance pairs, leaving identical responses unlinked

o FIX: `binary2responses` ignored response order in an ordered numeric matrix

o FIX: `permutation_SemNeT` computed `q` on the weighted network; all measures are now unweighted

o FIX: `aspl` per-node averages use distances to the other nodes; weighted `aspl` rejects negative weights

o FIX: `similarity` method `"euclid"` returned a distance, which `tmfg` treated as a similarity; it now returns `1 / (1 + d)`

o FIX: `tmfg` stops on undefined similarities and on asymmetric input without `depend = TRUE`

o FIX: `equate` rejects raw responses and duplicated response names

o FIX: `forward_flow` treats `""`, `" "`, and `"NA"` as missing and requires `min_response` of at least 2

o FIX: `q` with `signed = TRUE` weighted the negative term by N / (P - N) instead of N / (P + N) (Gomez et al., 2009); also fixed in {EGAnet}

o FIX: `cohens_d` pools standard deviations by degrees of freedom (agrees with the equal-variance t-test) and handles groups of one

o FIX: `random_walk` 5-unique-node statistic depended on the other network's walk; isolated start nodes and zero variation handled

o FIX: `random_network_test` summed weights for edge counts; networks are binarized, p-values are Monte Carlo, and a degree-preserving null is added

o UPDATE: `cn` gains `cutoff` for `enrich = TRUE` (default `0.50`, was a hardcoded `0.35`) and warns that there is no established value

o UPDATE: `pf` now uses the response-order distance of Paulsen et al. (1996) and needs response order (raw or ordered responses, not 0/1 data)

o UPDATE: `semantic_network_measures` defaults to `weighted = FALSE` (as documented) and gains `na.rm`, `signed`, and `type` (passed to `cc`, `q`, and `aspl`)

o UPDATE: `cc` gains `na.rm` and no longer rounds per-node values; weighted `cc` divides weights by the largest absolute weight

o UPDATE: `similarity` stops on missing or infinite values (and non-0/1 data for `"angular"`, `"faith"`, `"jaccard"`, `"rr"`); `finalize` stops on missing values and non-whole `minimum_cases`

o UPDATE: `q` requires a symmetric network and returns `NaN` for a network without edges

o UPDATE: `seed = 0` means random results, like `NULL`

o UPDATE: `response_analysis` returns `vocabulary` (Jaccard overlap and rarefied richness) and ignores never-given responses in binary input

o UPDATE: `random_walk` no longer reports p-values (they only reflect `iter`); differences, Monte Carlo intervals, and Cohen's d are given instead

o UPDATE: `bootstrap_SemNeT` node bootstrap drops the same nodes from every group in an iteration

o UPDATE: `bootstrap_SemNeT` retries draws only for correlation similarities (`"cor"`, `"phi"`); plot shows the full-data value

o UPDATE: `permutation_SemNeT` tests several measures at once and returns `mde` and `diagnostics`

o UPDATE: `permutation_SemNeT` gains two-sided options `"two_tailed_centered"` and `"two_tailed_doubled"`, tolerates floating-point ties, and aligns samples of different widths or vocabularies

o UPDATE: Shiny Bootstrap tab shows intervals instead of t-test/ANOVA/ANCOVA; labels and captions updated

o ADD: `aspl` `type` argument (`"arithmetic"`, the default and previous behavior, or `"harmonic"`)

o ADD: `seed` for `bootstrap_SemNeT` and `permutation_SemNeT`; each resample gets its own seed, so results do not depend on `cores` or `set.seed`

o ADD: `random_network_test` `seed` argument

o ADD: `print` methods for `bootstrap_test_SemNeT` and `permutation_SemNeT`


Changes in version 2.0.0

o FIX: `equate` compared vocabulary size rather than shared words

o FIX: duplicated group names passed via `...` silently hid results

o FIX: weighted `CC` returned `NaN` for negative weights

o FIX: `ASPL` zeroed unreachable pairs, understating ASPL in disconnected networks

o FIX: `TMFG` with 4 nodes iterated backwards and fewer than 4 nodes gave silent `NA`s

o FIX: `NRW` rejected valid ordered response matrices

o FIX: `test.bootSemNeT` errored when all three measures were requested

o FIX: `permSemNeT` dropped `NRW` `threshold` (`thresold` typo), `CN` `enrich`, and passed `threshold` as `window`

o FIX: several `1:n` ranges ran backwards on empty or size-1 inputs

o FIX: `q` is reproducible via `seed` (it depended on R's global RNG through `igraph::cluster_louvain`)

o FIX: `forward_flow` `type = "free"` mismatched or crashed on numeric participant IDs (GitHub Issue #10)

o FIX: Shiny Spreading Activation all-zero output and BRM upload failure (GitHub Issue #11)

o FIX: Shiny app called unexported functions (`responses2binary`, `read_uploaded_file`) that failed under `library(SemNeT)`

o FIX: Shiny background analyses ran sequentially and froze the app; they now run in the background with a live progress bar

o FIX: Shiny progress bar jumped around with `cores > 1`, and `cores` above 1 failed inside background workers

o UPDATE: full rebuild of the package's internals and the Shiny app; every pre-2.0.0 exported name still works

o UPDATE: `TMFG`, `ASPL`, `CC`, `CN`, `NRW`, `PF`, and `Q` are now lowercase (`tmfg`, `aspl`, ...); the old names remain as wrappers

o UPDATE: `bootSemNeT`, `test.bootSemNeT`, `randwalk`, `randnet.test`, `sim.fluency`, `response.analysis`, `semnetmeas`, and `compare_nets` are now `bootstrap_SemNeT`, `bootstrap_test_SemNeT`, `random_walk`, `random_network_test`, `simulate_fluency`, `response_analysis`, `semantic_network_measures`, and `compare_networks`; the old names remain as wrappers

o UPDATE: `bootSemNeT`, `randwalk`, and `randnet.test` default to sequential processing instead of auto-detecting cores

o UPDATE: `finalize` arguments renamed from `rmat` and `minCase` to `data` and `minimum_cases`

o UPDATE: Shiny maximum `cores` is the host's core count minus one

o UPDATE: `bootstrap_SemNeT` and `permutation_SemNeT` no longer hold every resampled network in memory (`keep_networks` argument); `random_network_test` reduces each random network immediately

o UPDATE: dropped `pbapply`, `dplyr`, `plyr`, `magrittr`, `scales`, and `philentropy`; added `future`, `future.apply`, and `progressr`; `ggplot2` is now `Suggests`

o UPDATE: compiled C code (Louvain, signed modularity, xoshiro256++) vendored from {EGAnet}; `NeedsCompilation` is now `yes`

o UPDATE: one file per exported function, a consistent `bootstrap_SemNeT` result schema, vectorized loops, and removal of dead code

o ADD: `permutation_SemNeT` (the old `permSemNeT` was internal and undocumented)

o ADD: `forward_flow` is back, using user-supplied word embeddings (no network access)

o ADD: `responses2binary` and `read_uploaded_file` are exported

o ADD: `find_textcleaner_objects` and a Load Data picker in the Shiny app for {SemNetCleaner} objects


Changes in version 1.4.4

o FIX: minor fix to get back on CRAN

o TODO: major refactor for the entire package to increase future reliability


Changes in version 1.4.3

o FIX: switching to different network estimations in Shiny app


Changes in version 1.4.2

o FIX: bug in reset of Shiny application

o FIX: name ordering of `bootSemNeT` plots

o FIX: p-value bug in random networks tests

o ADD: t-tests to `test.bootSemNeT` and Shiny app


Changes in version 1.4.1

o FIX: unequal nodes and edges in `test.bootSemNeT` (GitHub Issue #3)

o FIX: `PF` remove zeros bug (when there were no zero distances, then an empty matrix was given)

o UPDATE: tooltips added to network estimation methods in Shiny

o UPDATE: associated Shiny packages messages suppressed on Shiny startup

o UPDATE: message for Shiny results output

o UPDATE: `test.bootSemNeT` no longer uses number of nodes in ANCOVA

o UPDATE: added minimum number (`type = "num"`) and proportion (`type = "prop"`) of co-occurrences argument to `NRW`

o UPDATE: Shiny with new `NRW` arguments

o UPDATE: Shiny now provides effect sizes for partial eta squared in Bootstrap Network Analyses tab


Changes in version 1.4.0

o FIX: `randwalk` bug with 'steps' and 'reps' argument

o FIX: Shiny 'Clear Results' for new analyses

o FIX: output for animation plots in Shiny

o UPDATE: output names for `randwalk`

o UPDATE: Shiny interface is condensed and more step-by-step progressive

o UPDATE: Shiny includes random walk analysis

o UPDATE: Shiny includes spreading activation analysis (thanks to Cythina Siew)

o UPDATE: progress bar for some Shiny analyses

o UPDATE: S3method for animation plots

o UPDATE: citations added to Shiny analyses

o UPDATE: ANOVAs controlling for the number of nodes and edges is now the statistical test in `test.bootSemNeT`

o ADD: animation plot for spreading activation analysis in Shiny

o ADD: permutation test to SemNeT (`permSemNeT) and Shiny

o ADD: functions to convert data into other softwares format: SNAFU (`convert2snafu`) and igraph (`convert2igraph`)


Changes in version 1.3.0

o FIX: output of two-way ANOVA in `test.bootSemNeT`

o FIX: 'groups' argument in `test.bootSemNeT`

o UPDATE: added integration of SemNetCleaner output into `SemNeTShiny`

o UPDATE: `compare.nets` has changed to `compare_nets`

o UPDATE: `cosine` was added to internal functions to remove archived package from dependencies

o ADD: Several semantic network estimation methods (see `CN`, `NRW`, and `PF`) -- these are included in the Shiny app

o MOVE: `equate` and `finalize` moved from SemNetCleaner to SemNeT

o REMOVE: foreach and doParallel dependencies were removed (all parallelization is through the pbapply package)

o REMOVE: SemNetCleaner dependency was removed to allow SemNeT to operate independently -- all necessary functions from SemNetCleaner have been moved to internal functions

o CHANGE: `partboot` is now `bootSemNeT`

o CHANGE: `plot.partboot` is now `plot.bootSemNeT`

o CHANGE: `partboot.test` is now `test.bootSemNeT`


Changes in version 1.2.0

o FIX: 'groups' argument in `org.plot`

o UPDATE: moved several functions to internal to clean up package

o ADD: Shiny app

o ADD: binary responses matrices from animals verbal fluency data associated with the 'SemNetCleaner' package (open.animals)


Changes in version 1.1.3

o added extended ANOVA capabilities to `partboot.test` (e.g., two-way ANOVA)


Changes in version 1.1.2

o fixed bug for weighted modularity in `semnetmeas`

o updated citation (PsyArXiv)

o changed y-axis in plots for `partboot` to read as integers (as added black dot for mean in the scatterplots under the raincloud)

o added vignette for analyzing semantic networks

o added data for plots in vignette


Changes in version 1.1.1

o updated citation


Changes in version 1.1.0

o bug fixes

o changed `semnetmeas` to allow calculation of any combination of measures

o `partboot`, `partboot.test`, `plot.partboot`, `randnet.test`, and `compare.nets` now handle groups greater than 2


Changes in version 1.0.0

o serious, and I mean serious, revamp of functions (all for the better)

o moved most functions over to 'SemNetCleaner' and now only consists of methods and measures for semantic network analysis

o added a `sim.fluency` function for toy examples in CRAN checks

o added two datasets 'one.result' and 'two.result' for toy examples in CRAN checks

o `partboot.plot` changed to `plot.partboot` and added to S3 methods

o `partboot.test` now outputs a list for each network measure


Changes in version 0.9.9

o animals.database: a database for animals was added

o animals.misnomer: common misnomers for animals was added

o textcleaner: added database functionality, which makes the cleaning process more accurate, efficient, and reproducible

o several wrapper functions added to aid textcleaning from a database


Changes in version 0.1.2

o autoConverge: significantly improved interface

o separated all function files into individual files

o semnetcleaner (changed to textcleaner): added argument to input participants by row or column; ids now included for output; added output to show what spellcheck changed

o destr: improved functionality to allow selection of separating character

o randwalk: added a function to simulate random walks on the network to examine spontaenous spreading activation

o bin2resp: a function to change cleaned binary response data back into character data for each participant


Changes in version 0.1.1

o cosine: added cosine similarity

o semnetboot: changed name to partboot and added the cosine similarity

o semnetmeas: moved from NetworkToolbox

o plot.partboot: a function that generates "raindrop" plots for bootstrapped data

o org.plot: an organization function for plot.partboot (not for individual use)

o convert2cytoscape: added a function to convert a network matrix into a sparse matrix for Cytoscape visualization

o added new examples with corresponding data files


Changes in version 0.1.0

o autoConverge: created an automated converge function to eliminate the manual converge process

o autoDeStr: created an automated de-string function to eliminate most manual de-stringing

o fine-tuned most functions

o semnetboot: moved from package NetworkToolbox