NEWS

SemNeT 1.4.4 (2023-08-12)

FIX: unequal nodes and edges in 'test.bootSemNeT' (GitHub Issue #3)
UPDATE: tooltips added to network estimation methods in Shiny
UPDATE: associated Shiny packages messages suppressed on Shiny startup
UPDATE: message for Shiny results output
UPDATE: 'test.bootSemNeT' no longer uses number of nodes in ANCOVA
UPDATE: added minimum number ('type = "num"') and proportion ('type = "prop"') of co-occurrences argument to 'NRW'
UPDATE: Shiny with new 'NRW' arguments
UPDATE: Shiny now provides effect sizes for partial eta squared in Bootstrap Network Analyses tab
FIX: 'PF' remove zeros bug (when there were no zero distances, then an empty matrix was given)

UPDATE: output names for 'randwalk'
UPDATE: Shiny interface is condensed and more step-by-step progressive
UPDATE: Shiny includes random walk analysis
UPDATE: Shiny includes spreading activation analysis (thanks to Cythina Siew)
ADD: animation plot for spreading activation analysis in Shiny
FIX: ‘randwalk' bug with ’steps' and 'reps' argument
FIX: Shiny 'Clear Results' for new analyses
UPDATE: progress bar for some Shiny analyses
FIX: output for animation plots in Shiny
UPDATE: S3method for animation plots
UPDATE: citations added to Shiny analyses
ADD: permutation test to SemNeT ('permSemNeT) and Shiny
UPDATE: ANOVAs controlling for the number of nodes and edges is now the statistical test in 'test.bootSemNeT'
ADD: functions to convert data into other softwares format: SNAFU ('convert2snafu') and igraph ('convert2igraph')

FIX: output of two-way ANOVA in 'test.bootSemNeT'
FIX: 'groups' argument in 'test.bootSemNeT'
UPDATE: added integration of SemNetCleaner output into 'SemNeTShiny'
MOVE: 'equate' and 'finalize' moved from SemNetCleaner to SemNeT
REMOVE: foreach and doParallel dependencies were removed (all parallelization is through the pbapply package)
REMOVE: SemNetCleaner dependency was removed to allow SemNeT to operate independently -- all necessary functions from SemNetCleaner have been moved to internal functions
UPDATE: 'compare.nets' has changed to 'compare_nets'
ADD: Several semantic network estimation methods (see 'CN', 'NRW', and 'PF') -- these are included in the Shiny app
CHANGE: 'partboot' is now 'bootSemNeT'
CHANGE: 'plot.partboot' is now 'plot.bootSemNeT'
CHANGE: 'partboot.test' is now 'test.bootSemNeT'
UPDATE: 'cosine' was added to internal functions to remove archived package from dependencies

ADD: Shiny app
FIX: 'groups' argument in 'org.plot'
UPDATE: moved several functions to internal to clean up package
ADD: binary responses matrices from animals verbal fluency data associated with the 'SemNetCleaner' package (open.animals)

fixed bug for weighted modularity in 'semnetmeas'
updated citation (PsyArXiv)
changed y-axis in plots for 'partboot' to read as integers (as added black dot for mean in the scatterplots under the raincloud)
added vignette for analyzing semantic networks
added data for plots in vignette

changed 'semnetmeas' to allow calculation of any combination of measures
'partboot', 'partboot.test', 'plot.partboot', 'randnet.test', and 'compare.nets' now handle groups greater than 2
bug fixes

serious, and I mean serious, revamp of functions (all for the better)
moved most functions over to 'SemNetCleaner' and now only consists of methods and measures for semantic network analysis
added a 'sim.fluency' function for toy examples in CRAN checks
added two datasets 'one.result' and 'two.result' for toy examples in CRAN checks
'partboot.plot' changed to 'plot.partboot' and added to S3 methods
'partboot.test' now outputs a list for each network measure

animals.database: a database for animals was added
animals.misnomer: common misnomers for animals was added
textcleaner: added database functionality, which makes the cleaning process more accurate, efficient, and reproducible
several wrapper functions added to aid textcleaning from a database

autoConverge: significantly improved interface
separated all function files into individual files
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
destr: improved functionality to allow selection of separating character
randwalk: added a function to simulate random walks on the network to examine spontaenous spreading activation
bin2resp: a function to change cleaned binary response data back into character data for each participant

cosine: added cosine similarity
semnetboot: changed name to partboot and added the cosine similarity
semnetmeas: moved from NetworkToolbox
plot.partboot: a function that generates "raindrop" plots for bootstrapped data
org.plot: an organization function for plot.partboot (not for individual use)
convert2cytoscape: added a function to convert a network matrix into a sparse matrix for Cytoscape visualization
added new examples with corresponding data files

autoConverge: created an automated converge function to eliminate the manual converge process
autoDeStr: created an automated de-string function to eliminate most manual de-stringing
fine-tuned most functions
semnetboot: moved from package NetworkToolbox