Package: TimeTraits 1.2.0

TimeTraits: Functional Data Analysis Pipeline, Extracting Functional Traits from Biological Time-Series Data

Provides a pipeline of tools for analysing circadian time-series data using functional data analysis (FDA). The package supports smoothing of rhythmic time series, functional principle component analysis (FPCA), and extraction of group-level traits from functional representations. Analyses can incorporate multiple curve derivatives and optional temporal segmentation, enabling comparative analysis of circadian dynamics across experimental groups and time windows.

Authors:Sarah Lock [aut, cre]

TimeTraits_1.2.0.tar.gz
TimeTraits_1.2.0.zip(r-4.7)TimeTraits_1.2.0.zip(r-4.6)TimeTraits_1.2.0.zip(r-4.5)
TimeTraits_1.2.0.tgz(r-4.6-any)TimeTraits_1.2.0.tgz(r-4.5-any)
TimeTraits_1.2.0.tar.gz(r-4.7-any)TimeTraits_1.2.0.tar.gz(r-4.6-any)
TimeTraits_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
TimeTraits/json (API)

# Install 'TimeTraits' in R:

install.packages('TimeTraits', repos = c('https://scllock.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/scllock/timetraits/issues

Datasets:

metadata - Example genotype metadata
mydata_example - Arabidopsis thaliana luciferase circadian rhythm dataset

On CRAN:

3.30 score 138 downloads 4 exports 92 dependencies

Last updated from:bc839e0038. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	165
source / vignettes	OK	180
linux-release-x86_64	OK	224
macos-release-arm64	OK	186
macos-oldrel-arm64	OK	290
windows-devel	OK	123
windows-release	OK	122
windows-oldrel	OK	115
wasm-release	OK	134

Exports:filter_curves functional_traits select_basis_lambda_LOOCV smooth_fun

Dependencies:ash askpass base64enc bitops bslib cachem cli cluster colorspace cpp11 crosstalk curl data.table deSolve digest dplyr evaluate farver fastmap fda fdaoutlier fds FNN fontawesome fs generics ggplot2 glue gridExtra gtable hdrcde highr htmltools htmlwidgets httr isoband jquerylib jsonlite kernlab KernSmooth knitr ks labeling later lattice lazyeval lifecycle locfit lomb magrittr MASS Matrix mclust memoise mgcv mime multicool mvtnorm nlme openssl otel pcaPP pillar pkgconfig plotly pracma promises purrr R6 rainbow rappdirs RColorBrewer Rcpp RCurl rlang rmarkdown S7 sass scales stringi stringr sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
TimeTraits: Functional Data Analysis Pipeline, Extracting Functional Traits from Biological Time-Series Data.	TimeTraits-package TimeTraits
Filter, detrend, and quality-control luminescence time-series data	filter_curves
Functional PCA traits for circadian rhythm data	functional_traits
Example genotype metadata	metadata
Arabidopsis thaliana luciferase circadian rhythm dataset	mydata_example
Select optimal number of basis functions and smoothing parameter	select_basis_lambda_LOOCV
Smooth circadian time-series data with optional shape-based outlier detection	smooth_fun