confcurves: Wald Confidence Curves and the Likelihood Confidence Curves

In IPEC: Root Mean Square Curvature Calculation

Wald Confidence Curves and the Likelihood Confidence Curves

Description

Calculates the Wald confidence curves and the likelihood confidence curves of model parameters.

Usage

confcurves( expr, x, y, ini.val, weights = NULL, control=list(), 
            fig.opt = TRUE, fold = 5, np = 20, alpha = seq(1, 0.001, by=-0.001), 
            show.CI = NULL, method = "Richardson", method.args = 
            list(eps = 1e-04, d = 0.11, zero.tol = sqrt(.Machine$double.eps/7e-07), 
            r = 6, v = 2, show.details = FALSE), side = NULL )

Arguments

expr	A given parametric model
x	A vector or matrix of observations of independent variable(s)
y	A vector of observations of response variable
ini.val	A vector or list of initial values of model parameters
weights	An optional vector of weights to be used in the fitting process. weights should be NULL or a numeric vector. If non-NULL, weighted least squares is used with weights weights; otherwise ordinary least squares is used.
control	A list of control parameters for using the optim function in package stats
fig.opt	An option to determine whether to draw the confidence curves of each parameter
fold	The fold of \mbox{SE}\left(\hat{\theta_{i}}\right) for controlling the width of the confidence interval of \hat{\theta_{i}} that represents the estimate of the ith parameter
np	The number of data points for forming the lower or upper bounds of a likelihood confidence interval of \hat{\theta_{i}} , which controlls the step size (i.e., \delta) in the y coordinates of the likelihood confidence curves
alpha	The significance level(s) for calculating the x coordinate(s) of the (1-\alpha)100\% Wald confidence curves, which equals to t_{\alpha/2}\left(n-p\right)
show.CI	The t_{\alpha/2}\left(n-p\right) value(s) associated with the confidence level(s) of each parameter to be showed, i.e., c(0.80, 0.90, 0.95, 0.99)
method	It is the same as the input argument of method of the hessian function in package numDeriv
method.args	It is the same as the input argument of method.args of the hessian function in package numDeriv
side	It is the same as the input argument of side of the jacobian function in package numDeriv

Details

For the (1-\alpha)100\% Wald confidence curves, the corresponding x and y coordinates are:

x = t_{\alpha/2}\left(n-p\right),

and

y = \hat{\theta_{i}} \pm t_{\alpha/2}\left(n-p\right)\,\mbox{SE}\left(\hat{\theta_{i}}\right),

where n denotes the number of the observations, p denotes the number of model parameters, and \mbox{SE}\left(\hat{\theta_{i}}\right) denotes the standard error of the ith model parameter's estimate.

\quad For the likelihood confidence curves (Cook and Weisberg, 1990), the corresponding x and y coordinates are:

x = \sqrt{\frac{\mbox{RSS}\left(\hat{\theta}^{\,\left(-i\right)}\right)-\mbox{RSS}\left(\hat{\theta}\right)}{\mbox{RSS}\left(\hat{\theta}\right)/(n-p)}},

where \mbox{RSS}\left(\hat{\theta}\right) represents the residual sum of squares for fitting the model with all model parameters; \mbox{RSS}\left(\hat{\theta}^{\,\left(-i\right)}\right) represents the residual sum of squares for fitting the model with the ith model parameter being fixed to be \hat{\theta_{i}} \pm k\,\delta. Here, k denotes the kth iteration, and \delta denotes the step size, which equals

\delta = \frac{\hat{\theta_{i}} \pm \mbox{fold}\,\mbox{SE}\left(\hat{\theta_{i}}\right)}{\mbox{np}}.

y = \hat{\theta_{i}} \pm k\,\delta.

Here, fold and np are defined by the user in the arguments.

\quad For other arguments, please see the fitIPEC and parinfo functions for details.

Value

partab	The estimates, standard errors and confidence intervals of model parameters; also see the parinfo function
parlist	A list for the estimate, Wald interval curves and likelihood interval curves of each model parameter.

Note

In the value of parlist, there are the estimate (pari), the Wald interval curves (WaldCI), and the likelihood interval curves (lhCI) of the ith model parameter. In WaldCI, there are three columns. The first column, tc, represents t_{\alpha/2}\left(n-p\right) , the second and third columns, LCI and UCI, represent the lower and upper bounds of the (1-\alpha)100\% Wald confidence intervals, respectively. In lhCI, there are six columns. The first and second columns, x.lower and lhLCI, represent the lower bounds of the likelihood confidence intervals the and corresponding x values, respectively; the third and fourth columns, x.upper and lhUCI, represent the upper bounds of the likelihood confidence intervals and the corresponding x values, respectively; the fifth and sixth columns, RSS.lower and RSS.upper, represent the values of the residual sum of squares of the lower bounds and those of the upper bounds, respectively. Please see Cook and Weisberg (1990) for details.

Author(s)

Peijian Shi [e-mail], Peter M. Ridland [e-mail], David A. Ratkowsky [e-mail], Yang Li [e-mail].

References

Cook, R.D. and Weisberg, S. (1990) Confidence curves in nonlinear regression. J. Am. Statist. Assoc. 82, 221-230. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1080/01621459.1990.10476233")}

Nelder, J.A. and Mead, R. (1965) A simplex method for function minimization. Comput. J. 7, 308-313. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/comjnl/7.4.308")}

Ratkowsky, D.A. (1990) Handbook of Nonlinear Regression Models, Marcel Dekker, New York.

See Also

parinfo, fitIPEC, optim in package stats

Examples

#### Example 1 ###################################################################################
# Weight of cut grass data (Pattinson 1981)
# References:
#   Clarke, G.P.Y. (1987) Approximate confidence limits for a parameter function in nonlinear 
#       regression. J. Am. Stat. Assoc. 82, 221-230.
#   Gebremariam, B. (2014) Is nonlinear regression throwing you a curve? 
#       New diagnostic and inference tools in the NLIN Procedure. Paper SAS384-2014.
#       http://support.sas.com/resources/papers/proceedings14/SAS384-2014.pdf
#   Pattinson, N.B. (1981) Dry Matter Intake: An Estimate of the Animal
#       Response to Herbage on Offer. unpublished M.Sc. thesis, University
#       of Natal, Pietermaritzburg, South Africa, Department of Grassland Science.

# 'x4' is the vector of weeks after commencement of grazing in a pasture
# 'y4' is the vector of weight of cut grass from 10 randomly sited quadrants

x4 <- 1:13
y4 <- c(3.183, 3.059, 2.871, 2.622, 2.541, 2.184, 
        2.110, 2.075, 2.018, 1.903, 1.770, 1.762, 1.550)

# Define the first case of Mitscherlich equation
MitA <- function(P, x){    
    P[3] + P[2]*exp(P[1]*x)
}

# Define the second case of Mitscherlich equation
MitB <- function(P2, x){
    if(P2[3] <= 0)
        temp <- mean(y4)
    if(P2[3] > 0)
       temp <- log(P2[3]) + exp(P2[2] + P2[1]*x)
    return( temp )
}

# Define the third case of Mitscherlich equation
MitC <- function(P3, x, x1=1, x2=13){
    theta1 <- P3[1]
    beta2  <- P3[2]
    beta3  <- P3[3]
    theta2 <- (beta3 - beta2)/(exp(theta1*x2)-exp(theta1*x1))
    theta3 <- beta2/(1-exp(theta1*(x1-x2))) - beta3/(exp(theta1*(x2-x1))-1)
    theta3 + theta2*exp(theta1*x)
}

ini.val3 <- c(-0.1, 2.5, 1)
RESU1    <- confcurves( MitA, x=x4, y=y4, ini.val=ini.val3, fig.opt = TRUE, 
                        fold=5, np=20, alpha=seq(1, 0.001, by=-0.001), 
                        show.CI=c(0.8, 0.9, 0.95, 0.99) )

ini.val4 <- c(-0.10, 0.90, 2.5)
RESU2    <- confcurves( MitB, x=x4, y=y4, ini.val=ini.val4, fig.opt = TRUE, 
                        fold=5, np=200, alpha=seq(1, 0.001, by=-0.001), 
                        show.CI=c(0.8, 0.9, 0.95, 0.99) )

ini.val6 <- c(-0.15, 2.5, 1)
RESU3    <- confcurves( MitC, x=x4, y=y4, ini.val=ini.val6, fig.opt = TRUE, 
                        fold=5, np=20, alpha=seq(1, 0.001, by=-0.001), 
                        show.CI=c(0.8, 0.9, 0.95, 0.99) )
##################################################################################################

graphics.off()

IPEC documentation built on May 29, 2024, 8:14 a.m.