probsens.irr.conf: Probabilistic sensitivity analysis for unmeasured confounding...

In episensr: Basic Sensitivity Analysis of Epidemiological Results

Probabilistic sensitivity analysis for unmeasured confounding of person-time data and random error.

Description

Probabilistic sensitivity analysis to correct for unmeasured confounding when person-time data has been collected.

Usage

probsens.irr.conf(
  counts,
  pt = NULL,
  reps = 1000,
  prev.exp = list(dist = c("constant", "uniform", "triangular", "trapezoidal",
    "logit-logistic", "logit-normal", "beta"), parms = NULL),
  prev.nexp = list(dist = c("constant", "uniform", "triangular", "trapezoidal",
    "logit-logistic", "logit-normal", "beta"), parms = NULL),
  risk = list(dist = c("constant", "uniform", "triangular", "trapezoidal",
    "log-logistic", "log-normal"), parms = NULL),
  corr.p = NULL,
  discard = TRUE,
  alpha = 0.05
)

Arguments

counts	A table or matrix where first row contains disease counts and second row contains person-time at risk, and first and second columns are exposed and unexposed observations, as: Exposed Unexposed Cases a b Person-time N1 N0
pt	A numeric vector of person-time at risk. If provided, counts must be a numeric vector of disease counts.
reps	Number of replications to run.
prev.exp	List defining the prevalence of exposure among the exposed. The first argument provides the probability distribution function (constant,uniform, triangular, trapezoidal, logit-logistic, logit-normal, or beta) and the second its parameters as a vector. Logit-logistic and logit-normal distributions can be shifted by providing lower and upper bounds. Avoid providing these values if a non-shifted distribution is desired. constant; value, uniform: min, max, triangular: lower limit, upper limit, mode, trapezoidal: min, lower mode, upper mode, max. logit-logistic: location, scale, lower bound shift, upper bound shift, logit-normal: location, scale, lower bound shift, upper bound shift, beta: alpha, beta.
prev.nexp	List defining the prevalence of exposure among the unexposed.
risk	List defining the confounder-disease relative risk or the confounder-exposure odds ratio. The first argument provides the probability distribution function (constant,uniform, triangular, trapezoidal, log-logistic, or log-normal) and the second its parameters as a vector: constant: value, uniform: min, max, triangular: lower limit, upper limit, mode, trapezoidal: min, lower mode, upper mode, max. log-logistic: shape, rate. Must be strictly positive, log-normal: meanlog, sdlog. This is the mean and standard deviation on the log scale.
corr.p	Correlation between the exposure-specific confounder prevalences.
discard	A logical scalar. In case of negative adjusted count, should the draws be discarded? If set to FALSE, negative counts are set to zero.
alpha	Significance level.

Value

A list with elements:

obs.data	The analyzed 2 x 2 table from the observed data.
obs.measures	A table of observed incidence rate ratio with exact confidence interval.
adj.measures	A table of corrected incidence rate ratios.
sim.df	Data frame of random parameters and computed values.

References

Lash, T.L., Fox, M.P, Fink, A.K., 2009 Applying Quantitative Bias Analysis to Epidemiologic Data, pp.117–150, Springer.

Examples

set.seed(123)
# Unmeasured confounding
probsens.irr.conf(matrix(c(77, 10000, 87, 10000),
dimnames = list(c("D+", "Person-time"), c("E+", "E-")), ncol = 2),
reps = 20000,
prev.exp = list("trapezoidal", c(.01, .2, .3, .51)),
prev.nexp = list("trapezoidal", c(.09, .27, .35, .59)),
risk = list("trapezoidal", c(2, 2.5, 3.5, 4.5)),
corr.p = .8)

episensr documentation built on Aug. 30, 2023, 5:09 p.m.