# demo/NorthShore.R In CollocInfer: Collocation Inference for Dynamic Systems

## Groundwater level measurements as a function of rainfall.
#
# The data were collected in North Vancouver near a site of a
# mud slide that caused two fatalities in 2004.
#
# The groundwater levels are a relatively smooth process with a
# rather high signal to noise ratio.  Rainfall events, however,
# are sporadic and can be considered as events with times and
# intensities, called a marked point process in statistical theory.
#
# Groundwater level is modeled by a first order linear differential
# equation forced by rainfall.
#
# A constant coefficient version of the equation is
#
# $$\dot{G}(t) = - \beta G(t) + \alpha R(t - \delta) + \mu$$
#
# and a variable coefficient version is
#
# $$\dot{G}(t) = - \beta(t) G(t) + \alpha(t) R(t - \delta) + \mu(t)$$
#
# Coefficient \beta controls the speed of the response
# of groundwater to a rainfall event.
#
# Coefficient \alpha controls the size of the response
# of groundwater to a rainfall event.   The gain in the system
# is defined as K = \alpha / \beta.
#
# Constant \mu is an adjustment to the overall level of
# groundwater required because the origin of the measurements
# can be viewed as arbitrary or irrelevant.
#
# Lag constant \delta allows a time lapse before groundwater
# begins to respond to a rainfall event.  It was estimated by
# inspecting plots to be three hours for the purposes of these
# analyses, and is therefore not actually estimated by these
# analyses themselves.
#
# The following code allows for each of the remaining three
# parameters to be either constant, or themselves functions
# of time.  That is,
#
# Although the constant model does a fair job of
# describing the data, allowing for a mild time-variation in
# these parameters substantially improved the fit.  We used
# five order 4 B-splines to model this time dependency.
#
#
## Setting up the data
#

library("CollocInfer")

# Input the data to be analyzed.

#  rainfall should be lagged by about three hours

#Ninput = length(rainfall)
#lag    = 3
#rainfall = c(rep(0,2*lag), rainfall[1:(Ninput-2*lag)])

#  a subset of the data are selected, running from day 79 into day 92
#  if all the data are used, R has to allocate additional storage

# index = 1597:3024
#index = 1907:2221  #  here we select a smaller set of data
#yobs = as.matrix(groundwater[index])
#zobs = as.matrix(rainfall[index])
#N = length(yobs)
#tobs = (index - index)

data(NSdata)

yobs = NSgroundwater
zobs = NSrainfall
tobs = NStimes

N    = length(tobs)
rangeval = c(0,N-1)

#  plot the groundwater data

par(mfrow = c(2,1))
plot(tobs, yobs, "p",  xlab="Time (hours)",
ylab="Groundwater level (metres)")
plot(tobs, zobs, "p",  xlab="Time (hours)",
ylab="Hourly rainfall (millimetres)")

#  set up cumulative rainfall

#  Set up a basis for rainfall itself:
#     An order 1 or piece-wise constant spline

norder = 1
nbasis = N + norder - 2
rainbasis  = create.bspline.basis(rangeval, nbasis, norder)
rainfd = smooth.basis(tobs, zobs, rainbasis)$fd # plot the data plotfit.fd(zobs, tobs, rainfd, nfine=N) ## The basis for representing groundwater: G(t) # Define the knot sequence. A knot is placed at each mid-hour # point, giving maximum capacity to fit the data. Variable # rangeval is a vector of length 2 containing the lower and # upper time limits of the observations, and is in file # NorthShoreData.mat knots = c(rangeval, seq(rangeval+0.5, rangeval-0.5, len=N-1), rangeval) norder = 3 nbasis = length(knots) + norder - 2 basisobj = create.bspline.basis(rangeval, nbasis, norder, knots) # The constant coefficient basis is required for constant beta and alpha. conbasis = create.constant.basis(rangeval) ## Definition of functional basis objects for the coefficient functions # Set up the basis for the coefficient function \beta(t) or # \beta(G) determining the speed of response and recovery # # select the command that specifies the argument of \beta # # This basis is for \beta(t) as a function of time. You may # change the number of basis functions that are used. # # Here we use a constant basis for each coefficient, but at end # we can do that analysis again with five order 5 B-spline basis functions. nbetabasis = 1 #nbetabasis = 5 if (nbetabasis > 1) { betabasis = create.bspline.basis(rangeval, nbetabasis) } else { betabasis = conbasis } # Set up the basis for the coefficient function \alpha(t) # multiplying rainfall nalphabasis = 1 #nalphabasis = 5 if (nalphabasis > 1) { alphabasis = create.bspline.basis(rangeval, nalphabasis) } else { alphabasis = conbasis } # store the bases and rainfall object in a list "more" more = vector("list",0) more$betabasis  = betabasis
more$alphabasis = alphabasis more$rainfd     = rainfd

# Definition of the required named list containing the right side
#  evaluation functions.

NSfn = make.NS()

## Prepare the constant coefficient analysis

# Set up the functional parameter object that defines the
# roughness penalty.  Here an important choice must be made:
# how large should the smoothing parameter \lambda be?
# One may be advised to begin with a lowish value, such as
# \lambda = 1, complete the analysis with this value, then
# increase the value to something like \lambda = 100, using
# as starting values for the parameter array pars at this stage
# the array newpars computed at the profiled estimation analysis
# for the previous smaller value.

lambdaDE = 1e0  # A good value for the initial analysis.
penorder = 1    # The penalty is first order

# Smooth the data with this roughness penalty to get initial
# values for coefficients defining G(t).

DEfd0 = smooth.basis(tobs, yobs, GfdPar)$fd # plot the data and the fit plotfit.fd(yobs, tobs, DEfd0, xlab="Time (hours)", ylab="Groundwater level (metres)", title="") # extract the coefficient array coefs0 = DEfd0$coefs

# Initial parameter values for constant bases

pars0 = matrix(0, nbetabasis + nalphabasis, 1)

#pars0 = matrix(c(rep(res1$pars,nbetabasis), # rep(res1$pars,nalphabasis)),
#                 nbetabasis + nalphabasis, 1)

## Profiled estimation step

control.out = list()
control.out$trace = 6 control.out$tol    = 1e-6

# This is the main optimization for profiled estimation.
# It uses initial values for parameters and coefficients that
# are set up above.  This requires a lot of computation, and
# will take a number of minutes per iteration.  Find something
# else to do in the meantime.

lambda = 1e0

#  estimate the parameters using differencing

res0 = Profile.LS(make.NS()$fn, yobs, tobs, pars0, coefs0, basisobj, lambda, more = more, out.meth='ProfileGN', control.out=control.out) res0$pars  #  display the parameter estimates

res0$outer.result$value  # display the final function value

#  estimate the parameters using the derivative evaluation functions

lambda = 1e0

res1 = Profile.LS(NSfn, yobs, tobs, pars0, coefs0, basisobj, lambda,
more=more, out.meth='ProfileGN',
control.out=control.out)

res1$pars # display the parameter estimates res1$outer.result$value # display the final function value # set up the functional data object for the fit DEfd1 = fd(res1$coefs, basisobj)

#  increase lambda a few times, starting each time with
#  parameters estimated from the last value

lambda = 1e2

res2 = Profile.LS(NSfn, yobs, tobs, res1$pars, res1$coefs, basisobj, lambda,
more = more, out.meth='ProfileGN',
control.out=control.out)

res2$pars # display the parameter estimates DEfd2 = fd(res2$coefs, basisobj)

lambda = 1e4

res3 = Profile.LS(NSfn, yobs, tobs, res2$pars, res2$coefs, basisobj, lambda,
more = more, out.meth='ProfileGN',
control.out=control.out)

res3$pars # display the parameter estimates DEfd3 = fd(res3$coefs, basisobj)

lambda = 1e6

res4 = Profile.LS(NSfn, yobs, tobs, res3$pars, res3$coefs, basisobj, lambda,
more = more, out.meth='ProfileGN',
control.out=control.out)

res4$pars # display the parameter estimates DEfd4 = fd(res4$coefs, basisobj)

lambda = 1e8

res5 = Profile.LS(NSfn, yobs, tobs, res4$pars, res4$coefs, basisobj, lambda,
more = more, out.meth='ProfileGN',
control.out=control.out)

res5$pars # display the parameter estimates DEfd5 = fd(res5$coefs, basisobj)

#  compare fits to the data

par(mfrow=c(1,1))
plotfit.fd(yobs, tobs, DEfd1,
xlab="Time (hours)", ylab="Groundwater level (metres)",
title="")
lines(DEfd2)
lines(DEfd3)
lines(DEfd4)
lines(DEfd5, lty=2)

#  By the time we get to res4, the fit to the data is essentially
#  a soluton to the differential equation.  We see that it has
#  rather less capacity to fit the data, but still captures some
#  of the shapes in the data.


## Try the CollocInfer package in your browser

Any scripts or data that you put into this service are public.

CollocInfer documentation built on May 2, 2019, 4:03 a.m.