testassay: Hypothesis testing procedure for assay validation for...

In sachsmc/testassay: A Hypothesis Testing Framework for Validating an Assay for Precision

Description

Does an m:n:q procedure for assay validation for precision. Returns an object of class 'assaytest'. There is are predict and print methods for that class.

Usage

testassay(x, m, n, q = 0.9, model = "normal", constant = "SD", data = NULL)

Arguments

x	The vector of assay values
m	The vector of values indicating sample membership
n	The vector of values indicating replicate membership
q	The confidence level, typically 0.8 or 0.9
model	String specifying the distribution for the assay values. Valid values are "normal" or "lognormal"
constant	String specifying whether the standard deviation is assumed to be constant over the levels ("SD") or the coefficient of variation is assumed constant over the levels ("CV"). The values "sd", "var", or "variance" may be used for "SD", and "cv" may be used for "CV".
data	Data frame or environment in which to look for x

Details

The m:n:q procedure uses m different samples that have different levels of the true value with n replicates for each sample. The output is a 100q percent upper limit of the bound on the precision parameter when the true values within the range of values for the m samples all follow either a a constant coefficient of variation model or a constant standard deviation model (same as a constant variance model) (see constant argument).

For example, if the 4:4:90 percent procedure using a normal model with a constant variance model returns a bound on the standard deviation (the Umax element of the assaytest class) of 7.9 then under the assumptions we have 90 percent confidence that the true SD is less than 7.9.

The predict method gives effective standard deviation intervals (i.e., 68.27 pct CIs) for the expected response from subsequent observed values from the assay.

Value

An object of class "assaytest", which is a list of components including a data frame of the relevant statistics calculated on x. Print, summary, predict, and plot methods are available. The list has the following components

• sumtabTable summarizing the experiment, includes mean values, SD or CV estimates, and upper confidence limits on those.

• UmaxThe maximum of the upper limits on the SD or CV, used in the effective SD interval calculation

• nThe number of samples per level

• mThe number of levels

• qThe confidence level

• modelThe assumed model

• constantThe parameter assumed to be constant (either 'SD' or 'CV').

• alphaThe alpha level, calculated as (1 - q)^(1 / m)

• xThe data vector supplied by the user

References

Fay, MP, Sachs, MC, and Miura, K (2016). A Hypothesis Testing Framework for Validating and Assay for Precision (unpublished manuscript).

Examples

# reproduce Table 3 of Fay, Sachs and Miura
I<- gia$parasite=="3D7" & gia$meanAAgia<80
treD7.test<-testassay(x=gia, m=sample, n=assay, q=.9,
  data=subset(gia, parasite=="3D7" & meanAAgia<80))
treD7.test
# get estimated effective standard deviation intervals (68.27 percent CIs)
# for observed values 21.4 and 65.9
# using results from testassay
predict(treD7.test,c(21.4,65.9))

sachsmc/testassay documentation built on June 15, 2020, 12:33 p.m.