NEWS

musclesyneRgies 1.2.5.9009

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 function CoA with non-duplicated angles and robust quadrant handling.

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.

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.

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.

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

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

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

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

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

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 (2022-07-19)

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

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

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

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

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

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

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

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 (2022-02-10)

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 (2022-02-09)

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

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

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

musclesyneRgies 0.9.2

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

musclesyneRgies 0.9.1

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

Fixed a bug in the UMAP plots.

musclesyneRgies 0.8.6

Housekeeping and UMAP plots of mean filtered EMG.

musclesyneRgies 0.8.5

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

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

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

musclesyneRgies 0.8.2

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

musclesyneRgies 0.8.1

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

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

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

musclesyneRgies 0.7.1

First public API of musclesyneRgies
Fixed a bug in section 4