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musclesyneRgies 1.2.5.9008 (development version)

How to install

install.packages("remotes")
remotes::install_github("alesantuz/musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • Improved robustness of function classify_kmeans, which can now deal with trial names containing dots.

musclesyneRgies 1.2.5.9007 (development version)

How to install

install.packages("remotes")
remotes::install_github("alesantuz/musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • Improved robustness of function filtEMG.

musclesyneRgies 1.2.5.9006 (development version)

How to install

install.packages("remotes")
remotes::install_github("alesantuz/musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • Performance improvement in function classify_kmeans
  • Use of previously unused variable in function sMLE.

musclesyneRgies 1.2.5.9005 (development version)

How to install

install.packages("remotes")
remotes::install_github("alesantuz/musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • The function synsNMF is now faster.

musclesyneRgies 1.2.5.9004 (development version)

How to install

install.packages("remotes")
remotes::install_github("alesantuz/musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • Back to original synsNMF function, with l2-norm applied to weights M and then scaling P accordingly.

musclesyneRgies 1.2.5.9003 (development version)

How to install

install.packages("remotes")
remotes::install_github("alesantuz/musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • Faster synsNMF function, l2-norm is applied only to weights M.

musclesyneRgies 1.2.5.9002 (development version)

How to install

install.packages("remotes")
remotes::install_github("alesantuz/musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • Faster sMLE function.
  • Faster CoA function
  • Improved l2-norm in function synsNMF.

musclesyneRgies 1.2.5.9001 (development version)

How to install

install.packages("remotes")
remotes::install_github("alesantuz/musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • New function cossim allows to calculate the cosine similarity between two vectors.

musclesyneRgies 1.2.5.9000 (development version)

How to install

install.packages("remotes")
remotes::install_github("alesantuz/musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • Customisable y-axis limits in plot_classified_syns
  • Number of clusters can be imposed in classify_kmeans
  • Modules and primitives are now called muscle weights and activation patterns, respectively.

musclesyneRgies 1.2.5

How to install

install.packages("musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • Removed dependency from gtools
  • Removed JOSS paper folder
  • CRAN release.

musclesyneRgies 1.2.4

How to install

install.packages("remotes")
remotes::install_github("alesantuz/musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • Increased robustness of subsetEMG
  • Added tests for subsetEMG
  • Updated CITATION files
  • synsNMF now saves the synergy-vs-quality data.

musclesyneRgies 1.2.3

How to install

install.packages("remotes")
remotes::install_github("alesantuz/musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • Removed ISBNs from JOSS paper bibliography.

musclesyneRgies 1.2.2

How to install

install.packages("remotes")
remotes::install_github("alesantuz/musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • Corrected JOSS paper bibliography.

musclesyneRgies 1.2.1

How to install

install.packages("remotes")
remotes::install_github("alesantuz/musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • Version ready for JOSS paper after spell check.

musclesyneRgies 1.2.0

How to install

install.packages("remotes")
remotes::install_github("alesantuz/musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • Version ready for JOSS paper.

musclesyneRgies 1.1.3.9006 (development version)

How to install

install.packages("remotes")
remotes::install_github("alesantuz/musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • Cleaned and adjusted code according to goodpractice::gp() suggestions (thanks @fabian_s for the hint!)
  • Added more tests for classify_kmeans, synsNMF, subsetEMG, sMLE, normEMG, Hurst, HFD, filtEMG, plot_classified_syns_UMAP, plot_meanEMG, plot_rawEMG.

musclesyneRgies 1.1.3.9005 (development version)

How to install

install.packages("remotes")
remotes::install_github("alesantuz/musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • Added to README the possibility to download a full data set from Zenodo
  • Added definition of muscle synergies to README
  • Added definition of motor modules and motor primitives to README
  • Improved documentation of classify_kmeans, HFD and Hurst
  • Added test for classify_kmeans.

musclesyneRgies 1.1.3.9004 (development version)

How to install

install.packages("remotes")
remotes::install_github("alesantuz/musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • Updated tests to check for compatibility with single-column cycles.

musclesyneRgies 1.1.3.9003 (development version)

How to install

install.packages("devtools")
devtools::install_github("alesantuz/musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • Improved robustness of EMG pre-processing functions for one-column cycle times.

musclesyneRgies 1.1.3.9002 (development version)

How to install

install.packages("devtools")
library(devtools)
install_github("alesantuz/musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • Removed emg data frame row names in RAW_DATA list
  • Updated JOSS paper draft
  • rawdata can now handle RData files saved with save().

musclesyneRgies 1.1.3.9001 (development version)

How to install

install.packages("devtools")
library(devtools)
install_github("alesantuz/musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • Added Open Journals PDF Generator GitHub Action
  • First JOSS paper draft.

musclesyneRgies 1.1.3.9000 (development version)

How to install

install.packages("devtools")
library(devtools)
install_github("alesantuz/musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • Improved robustness of normEMG function.

musclesyneRgies 1.1.3

How to install

install.packages("musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • Faster examples and tests for CRAN
  • Removed classify_NMF function.

musclesyneRgies 1.1.2

How to install

install.packages("musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • Removed all progress bars.

musclesyneRgies 1.1.1

How to install

install.packages("musclesyneRgies")

How to use

README and vignettes are available both on CRAN and on GitHub.

What's changed

  • musclesyneRgies is on CRAN!
  • Adjusted test-CoA.R to pass on M1mac and noLD.

musclesyneRgies 1.1.0

How to install

install.packages("devtools")
library(devtools)
install_github("alesantuz/musclesyneRgies")

How to use

Follow the README for a breakdown of the typical workflow.

What's changed

  • This version was submitted to CRAN for checks
  • Added tests
  • Added NEWS.md to track changes to the package
  • Function plot_rawEMG can now plot muscle activities in custom grid (arguments row_number and col_number)
  • Line thickness and colour can now be specified in function plot_rawEMG (arguments line_size and line_col)
  • Added dark mode to plot_rawEMG, plot_meanEMG, plot_syn_trials and plot_classified_syns
  • Function plot_syn_trials partially rewritten with new native pipes |> and lapply instead of for loops
  • Updated README
  • Added CITATION.cff using R package cffr
  • Simplified all plot functions, which now exports gtable objects rather tan saving to file
  • Added tests for plot functions
  • Added vignettes (workflow, plots, analysis and pro_tips).

musclesyneRgies 1.0.1

How to install

install.packages("devtools")
library(devtools)
install_github("alesantuz/musclesyneRgies")

How to use

Follow the README for a breakdown of the typical workflow.

What's changed

  • Rectification can now be avoided in filtEMG if needed with rectif = "none"
  • Functions plot_rawEMG and plot_meanEMG partially rewritten with new native pipes |> and lapply instead of for loops
  • Fixed a bug in synsNMF that didn't L2-normalise M and P in iteration "zero".

musclesyneRgies 1.0.0

How to install

install.packages("devtools")
library(devtools)
install_github("alesantuz/musclesyneRgies")

What's changed

  • The short-term maximum Lyapunov exponents of motor primitives can now be calculated with the new function sMLE
  • Zero- or negative values in relevant matrices are now replaced with the smallest non-zero around twice as fast
  • L2-normalisation within synsNMF is now 1.5-2x faster
  • All code re-styled in tidyverse style using styler
  • Fixed a bug in filtEMG that didn't allow to avoid low-pass filtering if needed.

musclesyneRgies 0.9.4-beta

  • All code re-styled with tidyverse style using styler, plus new logo!

v1.0.0 coming soon with function for calculating the short-term maximum Lyapunov exponents of motor primitives.

musclesyneRgies 0.9.3-beta

  • Improved robustness of functions subsetEMG and normEMG when cycle times are given as data frames.

musclesyneRgies 0.9.2-beta

  • This not-so-minor update allows the user to extract synergies with a fixed rank.

musclesyneRgies 0.9.1-beta

  • musclesyneRgies is now a R package. Follow the README for a breakdown of the typical workflow. This is the first release, still in beta.

musclesyneRgies 0.8.7-alpha

  • Fixed a bug in the UMAP plots.

musclesyneRgies 0.8.6-alpha

  • Housekeeping and UMAP plots of mean filtered EMG.

musclesyneRgies 0.8.5-alpha

  • UMAP plots of classified synergies are saved in the NMF folder for advanced visualisation of factorisation/classification outcomes.

UMAP details: McInnes, Leland, John Healy, and James Melville. "Umap: Uniform manifold approximation and projection for dimension reduction." arXiv preprint arXiv:1802.03426 (2018).

R-package: https://cran.r-project.org/web/packages/umap/

musclesyneRgies 0.8.4-alpha

  • Raw EMG plots are now saved for each trial. The last raw_pl (see line 133) seconds of the trial are considered for plots.

musclesyneRgies 0.8.3-alpha

  • When reordering synergies manually during classification, the user can now repeat endlessly the classification if mistakes are made during input.

musclesyneRgies 0.8.2-alpha

  • A bit of housekeeping and now the clusters found by k-means classification are saved in one plot per condition.

musclesyneRgies 0.8.1-alpha

  • The robustness of k-means classification is improved and can now better deal with special cases of clusters with similar CoA and FWHM.

musclesyneRgies 0.7.3-alpha

  • Now the classification method is saved in the SYNS_classified list and can be used by step 4 (graph creation) to save the classification method in the file name.

musclesyneRgies 0.7.2-alpha

  • Now the classification method is saved in the file name when producing graph in step 4.

musclesyneRgies 0.7.1-alpha

  • First public API of musclesyneRgies
  • Fixed a bug in section 4