invest: Inverse estimation for linear, nonlinear, and generalized...

In bgreenwell/investr: Inverse Estimation/Calibration Functions

Inverse estimation for linear, nonlinear, and generalized linear models

Description

Provides point and interval estimates for the unknown predictor value that corresponds to an observed value of the response (or vector thereof) or specified value of the mean response. See the references listed below for more details.

Usage

invest(object, y0, ...)

## S3 method for class 'lm'
invest(
  object,
  y0,
  interval = c("inversion", "Wald", "percentile", "none"),
  level = 0.95,
  mean.response = FALSE,
  x0.name,
  newdata,
  data,
  boot.type = c("parametric", "nonparametric"),
  nsim = 999,
  seed = NULL,
  progress = FALSE,
  lower,
  upper,
  extendInt = "no",
  tol = .Machine$double.eps^0.25,
  maxiter = 1000,
  adjust = c("none", "Bonferroni"),
  k,
  ...
)

## S3 method for class 'glm'
invest(
  object,
  y0,
  interval = c("inversion", "Wald", "percentile", "none"),
  level = 0.95,
  lower,
  upper,
  x0.name,
  newdata,
  data,
  extendInt = "no",
  tol = .Machine$double.eps^0.25,
  maxiter = 1000,
  ...
)

## S3 method for class 'nls'
invest(
  object,
  y0,
  interval = c("inversion", "Wald", "percentile", "none"),
  level = 0.95,
  mean.response = FALSE,
  data,
  boot.type = c("parametric", "nonparametric"),
  nsim = 1,
  seed = NULL,
  progress = FALSE,
  lower,
  upper,
  extendInt = "no",
  tol = .Machine$double.eps^0.25,
  maxiter = 1000,
  adjust = c("none", "Bonferroni"),
  k,
  ...
)

## S3 method for class 'lme'
invest(
  object,
  y0,
  interval = c("inversion", "Wald", "percentile", "none"),
  level = 0.95,
  mean.response = FALSE,
  data,
  lower,
  upper,
  q1,
  q2,
  extendInt = "no",
  tol = .Machine$double.eps^0.25,
  maxiter = 1000,
  ...
)

Arguments

object	An object that inherits from class lm, glm, nls, or lme.
y0	The value of the observed response(s) or specified value of the mean response. For glm objects, y0 should be on the scale of the response variable (e.g., a number between 0 and 1 for binomial families).
...	Additional optional arguments. At present, no optional arguments are used.
interval	The type of interval required.
level	A numeric scalar between 0 and 1 giving the confidence level for the interval to be calculated.
mean.response	Logical indicating whether confidence intervals should correspond to an individual response (FALSE) or a mean response (TRUE). For glm objects, this is always TRUE.
x0.name	For multiple linear regression, a character string giving the name of the predictor variable of interest.
newdata	For multiple linear regression, a data.frame giving the values of interest for all other predictor variables (i.e., those other than x0.name).
data	An optional data frame. This is required if object$data is NULL.
boot.type	Character string specifying the type of bootstrap to use when interval = "percentile". Options are "parametric" and "nonparametric".
nsim	Positive integer specifying the number of bootstrap simulations; the bootstrap B (or R).
seed	Optional argument to set.seed.
progress	Logical indicating whether to display a text-based progress bar during the bootstrap simulation.
lower	The lower endpoint of the interval to be searched.
upper	The upper endpoint of the interval to be searched.
extendInt	Character string specifying if the interval c(lower, upper) should be extended or directly produce an error when the inverse of the prediction function does not have differing signs at the endpoints. The default, "no", keeps the search interval and hence produces an error. Can be abbreviated. See the documentation for the base R function uniroot for details.
tol	The desired accuracy passed on to uniroot. Recommend a minimum of 1e-10.
maxiter	The maximum number of iterations passed on to uniroot.
adjust	A logical value indicating if an adjustment should be made to the critical value used in calculating the confidence interval.This is useful for when the calibration curve is to be used multiple, say k, times.
k	The number times the calibration curve is to be used for computing a confidence interval. Only needed when adjust = "Bonferroni".
q1	Optional lower cutoff to be used in forming confidence intervals. Only used when object inherits from class lme. Defaults to stats::qnorm((1+level)/2).
q2	Optional upper cutoff to be used in forming confidence intervals. Only used when object inherits from class lme. Defaults to stats::qnorm((1-level)/2).

Value

Returns an object of class "invest" or, if interval = "percentile", of class c("invest", "bootCal"). The generic function {plot} can be used to plot the output of the bootstrap simulation when interval = "percentile".

An object of class "invest" containing the following components:

• estimate The estimate of x0.

• lwr The lower confidence limit for x0.

• upr The upper confidence limit for x0.

• se An estimate of the standard error (Wald and percentile intervals only).

• bias The bootstrap estimate of bias (percentile interval only).

• bootreps Vector of bootstrap replicates (percentile interval only).

• nsim The number of bootstrap replicates (percentile interval only).

• interval The method used for calculating lower and upper (only used by {print} method).

References

Greenwell, B. M. (2014). Topics in Statistical Calibration. Ph.D. thesis, Air Force Institute of Technology. URL https://apps.dtic.mil/sti/pdfs/ADA598921.pdf

Greenwell, B. M., and Schubert Kabban, C. M. (2014). investr: An R Package for Inverse Estimation. The R Journal, 6(1), 90–100. URL http://journal.r-project.org/archive/2014-1/greenwell-kabban.pdf.

Graybill, F. A., and Iyer, H. K. (1994). Regression analysis: Concepts and Applications. Duxbury Press.

Huet, S., Bouvier, A., Poursat, M-A., and Jolivet, E. (2004) Statistical Tools for Nonlinear Regression: A Practical Guide with S-PLUS and R Examples. Springer.

Norman, D. R., and Smith H. (2014). Applied Regression Analysis. John Wiley & Sons.

Oman, Samuel D. (1998). Calibration with Random Slopes. Biometrics 85(2): 439–449. doi:10.1093/biomet/85.2.439.

Seber, G. A. F., and Wild, C. J. (1989) Nonlinear regression. Wiley.

Examples

#
# Dobson's beetle data (generalized linear model)
#

# Complementary log-log model
mod <- glm(cbind(y, n-y) ~ ldose, data = beetle, 
           family = binomial(link = "cloglog"))
plotFit(mod, pch = 19, cex = 1.2, lwd = 2, 
        xlab = "Log dose of carbon disulphide",
        interval = "confidence", shade = TRUE, 
        col.conf = "lightskyblue")

# Approximate 95% confidence intervals and standard error for LD50
invest(mod, y0 = 0.5)
invest(mod, y0 = 0.5, interval = "Wald")

#
# Nasturtium example (nonlinear least-squares with replication)
#

# Log-logistic model
mod <- nls(weight ~ theta1/(1 + exp(theta2 + theta3 * log(conc))),
           start = list(theta1 = 1000, theta2 = -1, theta3 = 1),
           data = nasturtium)
plotFit(mod, lwd.fit = 2)
           
# Compute approximate 95% calibration intervals
invest(mod, y0 = c(309, 296, 419), interval = "inversion")
invest(mod, y0 = c(309, 296, 419), interval = "Wald")  

# Bootstrap calibration intervals. In general, nsim should be as large as 
# reasonably possible (say, nsim = 9999).
boo <- invest(mod, y0 = c(309, 296, 419), interval = "percentile", 
              nsim = 300, seed = 101)
boo  # print bootstrap summary
plot(boo)  # plot results

#
# Bladder volume example (random coefficient model)
#

# Load required packages
library(nlme)

# Plot data
plot(HD^(3/2) ~ volume, data = bladder, pch = 19,
       col = adjustcolor("black", alpha.f = 0.5))
       
# Fit a random intercept and slope model
bladder <- na.omit(bladder)
ris <- lme(HD^(3/2) ~ volume, data = bladder, random = ~volume|subject)
invest(ris, y0 = 500)
invest(ris, y0 = 500, interval = "Wald")

bgreenwell/investr documentation built on April 7, 2022, 5:01 a.m.