Help for package paramGUI

Title:

A Shiny GUI for some Parameter Estimation Examples

Version:

2.2.0

Description:

Allows specification and fitting of some parameter estimation examples inspired by time-resolved spectroscopy via a Shiny GUI.

URL:

https://github.com/glotaran/paramGUI/

License:

GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]

Depends:

R (≥ 3.0.0)

Imports:

shiny, shinydashboard, TIMP, fields

BugReports:

https://github.com/glotaran/paramGUI/issues

Encoding:

UTF-8

Language:

en-US

LazyData:

true

RoxygenNote:

7.2.3

NeedsCompilation:

Packaged:

2022-12-25 01:33:23 UTC; jsnel

Author:

Joris Snellenburg [cre, aut], Katharine Mullen [aut], Ivo van Stokkum [aut]

Maintainer:

Joris Snellenburg <j.snellenburg@vu.nl>

Repository:

CRAN

Date/Publication:

2023-01-08 15:00:07 UTC

Calculates a matrix in which each column is a skewed Gaussian

Description

Calculates a matrix in which each column is a skewed Gaussian. Like calcEhiergaus from TIMP package but uses a vector not a list of parameter estimates.

Usage

calcE(theta, lambda)

Arguments

theta

vector of parameter estimates

lambda

wavelengths at which to calculate model

Value

matrix

This is an example dataset included in this package

Description

Dispersion corrected time-resolved transient-absorption data of the peridinin chlorophyll protein (PCP) excited with 490 nm laser light from the publication of Stokkum et.al. (2009)

Author(s)

Ivo van Stokkum i.h.m.van.stokkum@vu.nl

References

doi:10.1016/j.chemphys.2008.10.005

is_compressed

Description

Helper function for is_rdata, checks if the file is a compressed (gzip) file. Does not (yet) check for bzip2 or xz compression.

Usage

is_compressed(filename, magic.number = as.raw(c("0x1f", "0x8b")))

Arguments

filename

The filename of the file to test for magic compression codes

magic.number

The magic numbers in as a vector of strings with the hexadecimal numbers (e.g. "0x1f")

Value

boolean, TRUE if the file is compressed

is_rdata

Description

Checks a file is a rdata file by inspecting the file for so called magic bytes

Usage

is_rdata(filename)

Arguments

filename

The filename of the file to test if it is an rdata file

Value

boolean, TRUE if the file is an rdata file

kroneckercol: column-wise kronecker product

Description

The column-wise kronecker product is also called the Khatri–Rao product

Usage

kroneckercol(A, B)

Arguments

A

numerical matrix

B

numerical matrix

Value

column-wise kronecker product of A and B

Generate linlog tics for a linear-logarithmic axis

Description

Generate linlog tics for a linear-logarithmic axis

Usage

linlogtics(x, mu, alpha)

Arguments

x

values for which to calculate a linlog axis

mu

center of axis in the original x axis

alpha

linear part

Value

Returns matrix with new x values in first column and the corresponding labels in the second column.

paramGUI

Description

Allows specification and fitting of some parameter estimation examples inspired by time-resolved spectroscopy via a Shiny GUI.

Master plot function for paramGUI

Description

Master plot function for paramGUI

Usage

plotterforGUI(
  modtype = "kin",
  X = matrix(),
  data,
  model,
  theta = vector(),
  result,
  lin = NA,
  mu = 0,
  guessIRF = FALSE
)

Arguments

modtype

either 'kin', 'spec' or 'spectemp'

X

matrix of conditionally linear parameters, if any

data

object of class dat containing data

model

object of class dat containing data

theta

object of class theta containing parameters

result

object returned by fitModel or in the case modtype=='spectemp', by nls

lin

The linear range for the concentration plot

mu

The center of the lin-log axis is lin is specified

guessIRF

Boolean to indicate whether to try and guess the location of the IRF

Value

graphics

Run paramGUI

Description

Runs the shiny paramGUI app.

Usage

runGUI()

Examples

## Not run: 
runGUI()

## End(Not run)

Simulate data

Description

Calculates an object of class 'kin'. <TODO>

Usage

simndecay_gen_paramGUI(
  kinpar,
  tmax,
  deltat,
  specpar = vector(),
  lmin,
  lmax,
  deltal,
  sigma,
  irf = FALSE,
  irfpar = vector(),
  seqmod = FALSE,
  dispmu = FALSE,
  nocolsums = FALSE,
  disptau = FALSE,
  parmu = list(),
  partau = vector(),
  lambdac = 0,
  fullk = FALSE,
  kmat = matrix(),
  jvec = vector(),
  specfun = "gaus",
  nupow = 1,
  irffun = "gaus",
  kinscal = vector(),
  lightregimespec = list(),
  specdisp = FALSE,
  specdisppar = list(),
  parmufunc = "exp",
  specdispindex = list(),
  amplitudes = vector(),
  specref = 0,
  nosiminfo = TRUE
)

Arguments

kinpar

vector of rate constants

tmax

last time point

deltat

time step

specpar

vector of spectral parameters for location, width, skewness

lmin

minimum wavelength (nm)

lmax

maximum wavelength (nm)

deltal

wavelength step

sigma

noise level

irf

logical for IRF usage

irfpar

vector of IRF parameters for location, width

seqmod

logical for sequential model

dispmu

logical for dispersion of IRF location mu

nocolsums

logical for <TODO>

disptau

logical for dispersion of IRF width tau

parmu

vector of dispersion parameters for IRF location mu

partau

vector of dispersion parameters for IRF width tau

lambdac

center wavelength for dispersion

fullk

logical for full K matrix

kmat

K matrix

jvec

input vector

specfun

function for spectral shape

nupow

power of nu in spectral model

irffun

function for IRF

kinscal

vector of kinetic scaling parameters

lightregimespec

<TODO>

specdisp

logical for dispersion parameters of spectral parameters

specdisppar

vector of dispersion parameters of spectral parameters

parmufunc

<TODO>

specdispindex

<TODO>

amplitudes

amplitudes of components

specref

<TODO>

nosiminfo

logical for hiding simulation information

Value

an object of class 'kin'

Author(s)

Katharine M. Mullen

Ivo H. M. van Stokkum

Spectrotemporal model

Description

Spectrotemporal model

Usage

spectemp(sim, model, iter, kroncol = FALSE, lin = NA, l_posk = FALSE)

Arguments

sim

object of class dat representing data

model

object of class dat representing a model

iter

integer number of iterations

kroncol

object of class logical that is TRUE if the kroneckcol function should be used to formulate the model and FALSE if the standard kronecker is to be used instead

lin

defines the range to plot linearly (from -lin to +lin)

l_posk

object of class logical indicating whether positivity-constraints are enforced on the rate parameters

Start paramGUI

Description

The same as runGUI(), starts the shiny paramGUI app.

Usage

startGUI()