Package 'poisDoubleSamp'

Title: Confidence Intervals with Poisson Double Sampling
Description: Functions to create confidence intervals for ratios of Poisson rates under misclassification using double sampling.
Authors: David Kahle [aut, cre], Phil Young [aut], Dean Young [aut]
Maintainer: David Kahle <[email protected]>
License: GPL-2
Version: 1.1
Built: 2024-11-06 03:55:49 UTC
Source: https://github.com/dkahle/poisdoublesamp

Help Index

Compute the marginal MLE of phi

Description

Compute the marginal MLE of the ratio of two Poisson rates in a two-sample Poisson rate problem with misclassified data given fallible and infallible datasets.

Usage

approxMargMLE(data, N1, N2, N01, N02, l = 0, u = 1000, out = c("par",
  "all"), tol = 1e-10)

Arguments

data

the vector of counts of the fallible data (z11, z12, z21, z22) followed by the infallible data (m011, m012, m021, m022, y01, y02)
N1

the opportunity size of group 1 for the fallible data
N2

the opportunity size of group 2 for the fallible data
N01

the opportunity size of group 1 for the infallible data
N02

the opportunity size of group 2 for the infallible data
l

the lower end of the range of possible phi's (for optim)
u

the upper end of the range of possible phi's (for optim)
out

"par" or "all" (for the output of optim)
tol

tolerance parameter for the rmle EM algorithm

Value

a named vector containing the marginal mle of phi

Examples

## Not run: 

# small example
z11 <- 34; z12 <- 35; N1 <- 10;
z21 <- 22; z22 <- 31; N2 <- 10;
m011 <- 9; m012 <- 1; y01 <- 3; N01 <- 3;
m021 <- 8; m022 <- 8; y02 <- 2; N02 <- 3;
data <- c(z11, z12, z21, z22, m011, m012, m021, m022, y01, y02)

fullMLE(data, N1, N2, N01, N02)
margMLE(data, N1, N2, N01, N02)
approxMargMLE(data, N1, N2, N01, N02)



# big example :
z11 <- 477; z12 <- 1025; N1 <- 16186;
z21 <- 255; z22 <- 1450; N2 <- 18811;
m011 <- 38;  m012 <- 90; y01 <- 15; N01 <- 1500;
m021 <- 41; m022 <- 200; y02 <-  9; N02 <- 2500;
data <- c(z11, z12, z21, z22, m011, m012, m021, m022, y01, y02)

fullMLE(data, N1, N2, N01, N02)
# margMLE(data, N1, N2, N01, N02) # ~1 min
approxMargMLE(data, N1, N2, N01, N02)




## End(Not run)

Compute the profile MLE CI of phi

Description

Compute the profile MLE confidence interval of the ratio of two Poisson rates in a two-sample Poisson rate problem with misclassified data given fallible and infallible datasets. This uses a C++ implemention of the EM algorithm.

Usage

approxMargMLECI(data, N1, N2, N01, N02, conf.level = 0.95, l = 0.001,
  u = 1000, tol = 1e-10)

Arguments

data

the vector of counts of the fallible data (z11, z12, z21, z22) followed by the infallible data (m011, m012, m021, m022, y01, y02)
N1

the opportunity size of group 1 for the fallible data
N2

the opportunity size of group 2 for the fallible data
N01

the opportunity size of group 1 for the infallible data
N02

the opportunity size of group 2 for the infallible data
conf.level

confidence level of the interval
l

the lower end of the range of possible phi's (for optim)
u

the upper end of the range of possible phi's (for optim)
tol

tolerance used in the EM algorithm to declare convergence

Value

a named vector containing the marginal mle of phi

Examples

## Not run: 

# small example
z11 <- 34; z12 <- 35; N1 <- 10;
z21 <- 22; z22 <- 31; N2 <- 10;
m011 <- 9; m012 <- 1; y01 <- 3; N01 <- 3;
m021 <- 8; m022 <- 8; y02 <- 2; N02 <- 3;
data <- c(z11, z12, z21, z22, m011, m012, m021, m022, y01, y02)

waldCI(data, N1, N2, N01, N02)
margMLECI(data, N1, N2, N01, N02)
profMLECI(data, N1, N2, N01, N02)
approxMargMLECI(data, N1, N2, N01, N02)


# big example :
z11 <- 477; z12 <- 1025; N1 <- 16186;
z21 <- 255; z22 <- 1450; N2 <- 18811;
m011 <- 38;  m012 <- 90; y01 <- 15; N01 <- 1500;
m021 <- 41; m022 <- 200; y02 <-  9; N02 <- 2500;
data <- c(z11, z12, z21, z22, m011, m012, m021, m022, y01, y02)

waldCI(data, N1, N2, N01, N02)
margMLECI(data, N1, N2, N01, N02)
profMLECI(data, N1, N2, N01, N02)
approxMargMLECI(data, N1, N2, N01, N02)




## End(Not run)

Compute the full MLEs

Description

Compute the MLEs of a two-sample Poisson rate problem with misclassified data given fallible and infallible datasets.

Usage

fullMLE(data, N1, N2, N01, N02)

Arguments

data

the vector of counts of the fallible data (z11, z12, z21, z22) followed by the infallible data (m011, m012, m021, m022, y01, y02)
N1

the opportunity size of group 1 for the fallible data
N2

the opportunity size of group 2 for the fallible data
N01

the opportunity size of group 1 for the infallible data
N02

the opportunity size of group 2 for the infallible data

Details

These are the closed-form expressions for the MLEs.

Value

a named vector containing the mles of each of the parameters (phi, la12, la21, la22, th1, and th2)

Examples

## Not run: 

# small example
z11 <- 34; z12 <- 35; N1 <- 10;
z21 <- 22; z22 <- 31; N2 <- 10;
m011 <- 9; m012 <- 1; y01 <- 3; N01 <- 3;
m021 <- 8; m022 <- 8; y02 <- 2; N02 <- 3;
data <- c(z11, z12, z21, z22, m011, m012, m021, m022, y01, y02)

fullMLE(data, N1, N2, N01, N02)



# big example :
z11 <- 477; z12 <- 1025; N1 <- 16186;
z21 <- 255; z22 <- 1450; N2 <- 18811;
m011 <- 38;  m012 <- 90; y01 <- 15; N01 <- 1500;
m021 <- 41; m022 <- 200; y02 <-  9; N02 <- 2500;
data <- c(z11, z12, z21, z22, m011, m012, m021, m022, y01, y02)

fullMLE(data, N1, N2, N01, N02)



## End(Not run)

Compute the marginal MLE of phi

Description

Compute the marginal MLE of the ratio of two Poisson rates in a two-sample Poisson rate problem with misclassified data given fallible and infallible datasets.

Usage

margMLE(data, N1, N2, N01, N02, l = 0.001, u = 1000, out = c("par",
  "all"))

Arguments

data

the vector of counts of the fallible data (z11, z12, z21, z22) followed by the infallible data (m011, m012, m021, m022, y01, y02)
N1

the opportunity size of group 1 for the fallible data
N2

the opportunity size of group 2 for the fallible data
N01

the opportunity size of group 1 for the infallible data
N02

the opportunity size of group 2 for the infallible data
l

the lower end of the range of possible phi's (for optim)
u

the upper end of the range of possible phi's (for optim)
out

"par" or "all" (for the output of optim)

Value

a named vector containing the marginal mle of phi

Examples

## Not run: 

# small example
z11 <- 34; z12 <- 35; N1 <- 10;
z21 <- 22; z22 <- 31; N2 <- 10;
m011 <- 9; m012 <- 1; y01 <- 3; N01 <- 3;
m021 <- 8; m022 <- 8; y02 <- 2; N02 <- 3;
data <- c(z11, z12, z21, z22, m011, m012, m021, m022, y01, y02)

fullMLE(data, N1, N2, N01, N02)
margMLE(data, N1, N2, N01, N02)



# big example :
z11 <- 477; z12 <- 1025; N1 <- 16186;
z21 <- 255; z22 <- 1450; N2 <- 18811;
m011 <- 38;  m012 <- 90; y01 <- 15; N01 <- 1500;
m021 <- 41; m022 <- 200; y02 <-  9; N02 <- 2500;
data <- c(z11, z12, z21, z22, m011, m012, m021, m022, y01, y02)

fullMLE(data, N1, N2, N01, N02)
margMLE(data, N1, N2, N01, N02)





## End(Not run)

Compute the marginal MLE confidence interval for the phi

Description

Compute the marginal MLE confidence interval of the ratio of two Poisson rates in a two-sample Poisson rate problem with misclassified data given fallible and infallible datasets.

Usage

margMLECI(data, N1, N2, N01, N02, conf.level = 0.95, l = 1e-10, u = 1e+10)

Arguments

data

the vector of counts of the fallible data (z11, z12, z21, z22) followed by the infallible data (m011, m012, m021, m022, y01, y02)
N1

the opportunity size of group 1 for the fallible data
N2

the opportunity size of group 2 for the fallible data
N01

the opportunity size of group 1 for the infallible data
N02

the opportunity size of group 2 for the infallible data
conf.level

confidence level of the interval
l

the lower end of the range of possible phi's (for optim)
u

the upper end of the range of possible phi's (for optim)

Value

a named vector containing the lower and upper bounds of the confidence interval

Examples

## Not run: 

# small example
z11 <- 34; z12 <- 35; N1 <- 10;
z21 <- 22; z22 <- 31; N2 <- 10;
m011 <- 9; m012 <- 1; y01 <- 3; N01 <- 3;
m021 <- 8; m022 <- 8; y02 <- 2; N02 <- 3;
data <- c(z11, z12, z21, z22, m011, m012, m021, m022, y01, y02)

waldCI(data, N1, N2, N01, N02)
margMLECI(data, N1, N2, N01, N02)
profMLECI(data, N1, N2, N01, N02)
approxMargMLECI(data, N1, N2, N01, N02)


# big example :
z11 <- 477; z12 <- 1025; N1 <- 16186;
z21 <- 255; z22 <- 1450; N2 <- 18811;
m011 <- 38;  m012 <- 90; y01 <- 15; N01 <- 1500;
m021 <- 41; m022 <- 200; y02 <-  9; N02 <- 2500;
data <- c(z11, z12, z21, z22, m011, m012, m021, m022, y01, y02)

waldCI(data, N1, N2, N01, N02)
margMLECI(data, N1, N2, N01, N02)
profMLECI(data, N1, N2, N01, N02)
approxMargMLECI(data, N1, N2, N01, N02)




## End(Not run)

poisDoubleSamp : Confidence intervals with Poisson double sampling

Description

Functions to create confidence intervals for ratios of Poisson rates under misclassification using double sampling.

Compute the profile MLE CI of phi

Description

Compute the profile MLE confidence interval of the ratio of two Poisson rates in a two-sample Poisson rate problem with misclassified data given fallible and infallible datasets. This uses a C++ implemention of the EM algorithm.

Usage

profMLECI(data, N1, N2, N01, N02, conf.level = 0.95, l = 0.001, u = 1000,
  tol = 1e-10)

Arguments

data

the vector of counts of the fallible data (z11, z12, z21, z22) followed by the infallible data (m011, m012, m021, m022, y01, y02)
N1

the opportunity size of group 1 for the fallible data
N2

the opportunity size of group 2 for the fallible data
N01

the opportunity size of group 1 for the infallible data
N02

the opportunity size of group 2 for the infallible data
conf.level

confidence level of the interval
l

the lower end of the range of possible phi's (for optim)
u

the upper end of the range of possible phi's (for optim)
tol

tolerance used in the EM algorithm to declare convergence

Value

a named vector containing the marginal mle of phi

Examples

## Not run: 

# small example
z11 <- 34; z12 <- 35; N1 <- 10;
z21 <- 22; z22 <- 31; N2 <- 10;
m011 <- 9; m012 <- 1; y01 <- 3; N01 <- 3;
m021 <- 8; m022 <- 8; y02 <- 2; N02 <- 3;
data <- c(z11, z12, z21, z22, m011, m012, m021, m022, y01, y02)

waldCI(data, N1, N2, N01, N02)
margMLECI(data, N1, N2, N01, N02)
profMLECI(data, N1, N2, N01, N02)
approxMargMLECI(data, N1, N2, N01, N02)


# big example :
z11 <- 477; z12 <- 1025; N1 <- 16186;
z21 <- 255; z22 <- 1450; N2 <- 18811;
m011 <- 38;  m012 <- 90; y01 <- 15; N01 <- 1500;
m021 <- 41; m022 <- 200; y02 <-  9; N02 <- 2500;
data <- c(z11, z12, z21, z22, m011, m012, m021, m022, y01, y02)

waldCI(data, N1, N2, N01, N02)
margMLECI(data, N1, N2, N01, N02)
profMLECI(data, N1, N2, N01, N02)
approxMargMLECI(data, N1, N2, N01, N02)




## End(Not run)

Compute the Wald confidence interval

Description

Compute the Wald confidence interval of a two-sample Poisson rate with misclassified data given fallible and infallible datasets.

Usage

waldCI(data, N1, N2, N01, N02, conf.level = 0.95)

Arguments

data

the vector of counts of the fallible data (z11, z12, z21, z22) followed by the infallible data (m011, m012, m021, m022, y01, y02)
N1

the opportunity size of group 1 for the fallible data
N2

the opportunity size of group 2 for the fallible data
N01

the opportunity size of group 1 for the infallible data
N02

the opportunity size of group 2 for the infallible data
conf.level

confidence level of the interval

Value

a named vector containing the lower and upper bounds of the confidence interval

Examples

## Not run: 

# small example
z11 <- 34; z12 <- 35; N1 <- 10;
z21 <- 22; z22 <- 31; N2 <- 10;
m011 <- 9; m012 <- 1; y01 <- 3; N01 <- 3;
m021 <- 8; m022 <- 8; y02 <- 2; N02 <- 3;
data <- c(z11, z12, z21, z22, m011, m012, m021, m022, y01, y02)

waldCI(data, N1, N2, N01, N02)
margMLECI(data, N1, N2, N01, N02)
profMLECI(data, N1, N2, N01, N02)
approxMargMLECI(data, N1, N2, N01, N02)


# big example :
z11 <- 477; z12 <- 1025; N1 <- 16186;
z21 <- 255; z22 <- 1450; N2 <- 18811;
m011 <- 38;  m012 <- 90; y01 <- 15; N01 <- 1500;
m021 <- 41; m022 <- 200; y02 <-  9; N02 <- 2500;
data <- c(z11, z12, z21, z22, m011, m012, m021, m022, y01, y02)

waldCI(data, N1, N2, N01, N02)
margMLECI(data, N1, N2, N01, N02)
profMLECI(data, N1, N2, N01, N02)
approxMargMLECI(data, N1, N2, N01, N02)



## End(Not run)