Package: TemporalGSSA
Type: Package
Title: Outputs Temporal Profile of Molecules Undergoing Stochastic
Simulations
Version: 1.0.0
Author: Siddhartha Kundu
Maintainer: Siddhartha Kundu <siddhartha_kundu@aiims.edu>
Description: The data that is generated from consecutive 'GillespieSSA' runs for a generic biochemical network
is formatted as "rows". The first column of each row constitutes the computed timestep. Subsequent
columns are used for the participating molecules of a generic biochemical network. In this way 'TemporalGSSA',
may be considered a wrapper for the R-package 'GillespieSSA'. The number of observations must be at least 30.
This will generate data that is statistically significant. The user must also enter an integer from 1-4.
These specify the statistical modality utilized to compute a representative timestep (mean, median, random, all).
These arguments are mandatory and will be checked. Whilst, the numeric indicator "0" indicates suitability,
"1" prompts the user to revise and re-enter their data. An optional logical argument controls the output to the
console with the default being "TRUE" (curtailed) whilst "FALSE" (verbose). The temporal profile of a molecule
is necessary to comprehend its' behaviour within the cell. This is accomplished by selecting a representative
timestep for a set of observations or consecutive runs (n >= 30). A linear model of the numbers of each molecule is
created with the associated timestep from these observations. The coefficients of this model (slope, constant) are then
incorporated into a second linear regression model. Here, the independent variable is the representative timestep
chosen previously. The generated data is the imputed molecule number for an in silico experiment with (n >=30)
observations. These steps can be replicated with multiple set of observations or runs. The generated "technical
replicates" can be averaged and will constitute the time-dependent data point of each molecule for a particular simulation
time. For varying simulation times these data will generate time-dependent trajectories for each molecule
of the biochemical network under study. The algorithm has been deployed effectively in previous publications Kundu, S
(2021, Heliyon) <doi:10.1016/j.heliyon.2021.e07466> and (2016, Journal of Theoretical Biology) <doi:10.1016/j.jtbi.2016.07.002>.
License: GPL-3
Encoding: UTF-8
Depends: stats
Suggests: testthat (>= 3.0.0)
RoxygenNote: 7.1.2
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2022-03-01 13:02:21 UTC; Siddhartha
Repository: CRAN
Date/Publication: 2022-03-02 08:50:15 UTC