Short Asynchronous Time-Series Analysis
Calculate the Akaike Information Criterion for a smooth.spline
Calculate the Akaike Information Criterion Corrected for small observa...
Calculate the Bayesian Information Criterion for a smooth.spline
Compute the optimal df and weighted-df using 5 spline fitting metric
Plot for each eigenSpline the automatically fitted spline, splines for...
Compute eigenSplines across a dataset
Generate a Ind x Time + Var data.frame concatenating all variables fro...
Generate a matrix of group membership for all individuals
Generate a Ind x Time DataFrame from input data
Compute the value of different fitting metrics over all possible df fo...
Calculate the penalised loglikelihood of a smooth.spline
Plot an histogram of the number of time-trajectories with a given numb...
Plot the evolution of different fitting parameters across all possible...
santaR: A package for Short AsyNchronous Time-series Analysis in R
Automate all steps of santaR fitting, Confidence bands estimation and ...
Summarise, report and save the results of a santaR analysis
Compute Group Mean Curve Confidence Bands
Generate a SANTAObj for a variable
Plot a SANTAObj
Evaluate difference in group trajectories based on the comparison of d...
Evaluate difference between a group mean curve and a constant model
Evaluate difference in group trajectories based on the comparison of m...
Evaluate difference between a group mean curve and a constant model us...
santaR Graphical User Interface
Mean scaling of each column
Unit-Variance scaling of each column
A graphical and automated pipeline for the analysis of short time-series in R ('santaR'). This approach is designed to accommodate asynchronous time sampling (i.e. different time points for different individuals), inter-individual variability, noisy measurements and large numbers of variables. Based on a smoothing splines functional model, 'santaR' is able to detect variables highlighting significantly different temporal trajectories between study groups. Designed initially for metabolic phenotyping, 'santaR' is also suited for other Systems Biology disciplines. Command line and graphical analysis (via a 'shiny' application) enable fast and parallel automated analysis and reporting, intuitive visualisation and comprehensive plotting options for non-specialist users.
Useful links