Reversible jump step for adding the breakpoints

reversibleJumpBreakPointsAdd(
  res,
  currentSigma,
  currentb,
  currentpi,
  currentbp,
  currentq,
  currentd,
  shape = 1,
  rate = 5,
  logmean = 0,
  logsd = 1,
  shape1 = 1,
  shape2 = 5,
  pishape1 = 1,
  pishape2 = 1,
  dshape = 1,
  drate = 1,
  K,
  R,
  rho,
  lambda,
  multivariate = FALSE,
  cormat = NULL,
  timepoints = timepoints,
  tCoef,
  index,
  numExch,
  density,
  R_lower,
  R_upper,
  phi
)

Arguments

res

data frame of uptake data

currentSigma

numeric current variance parameter

currentb

numeric vector of current rate parameters

currentpi

numeric vector of current mixing parameters

currentbp

numeric vector of current breakpoints

currentq

numeric vector of current stretch parameters

currentd

numeric vector of current rate parameters

shape

numeric shape parameter of the prior gamma distribution

rate

numeric rate parameter of the prior gamma distribution

logmean

numeric mean of the prior lognormal distribution

logsd

numeric standard deviation of the prior lognormal distribution

shape1

numeric shape parameter of the prior beta distribution

shape2

numeric shape parameter of the prior beta distribution

pishape1

numeric shape parameter of the prior beta distribution

pishape2

numeric shape parameter of the prior beta distribution

dshape

numeric shape parameter of the prior gamma distribution

drate

numeric rate parameter of the prior gamma distribution

K

numeric number of breakpoints

R

numeric maximum value of the breakpoints

rho

numeric probability of adding a breakpoint

lambda

numeric the mean number of break points

multivariate

logical flag for multivariate model

cormat

numeric correlation matrix

timepoints

numeric vector of time points

tCoef

numeric vector of scaling variance of time points

index

list of indices for each peptide residues

numExch

list of number of exchangeable amides for each peptide

density

character string of density function

R_lower

numeric lower bound of the breakpoints

R_upper

numeric upper bound of the breakpoints

phi

numeric maximum uptake possible

Value

list of updated parameters