LtdSamplingSummary-class: Class "LtdSamplingSummary"

In FFD: Freedom from Disease

Description

Contains the parameters and the data necessery for a survey to substantiate freedom from disease using "limited sampling". Additionally to the survey parameters: design prevalence (=prevalence of the disease under the null hypothesis), overall significance level (=1-confidence), intra-herd prevalence, sensitivity of the diagnostic test, cost per tested animal and cost per tested herd, the object contains the mean herd sensitivity, the number of herds to be tested, the mean overall number of animals to be tested and the expected costs for a range of possible sample limits (= fixed number of animals to test per herd).

Objects from the Class

Objects can be created by calls of the form new("LtdSamplingSummary", ...).

Slots

surveyData:

Object of class "SurveyData". Containing the necessary survey parameters.

sampleSizeLtdVec:

Object of class "numeric". Pre-fixed number of animals to be tested per holding, irrespective of the herd size. If a herd contains fewer animals the entire herd is tested (vector).

meanHerdSensVec:

Object of class "numeric" with values between 0 and 1. Mean herd sensitivity in the population (vector).

meanHerdSensPerRGMx:

Object of class "matrix" with values between 0 and 1. Mean herd sensitivity of each risk group [columns] and sample limit [rows] (if population is stratified by risk groups).

nHerdsVec:

Object of class "numeric". Number of herds to be tested according to the herd sensitivity meanHerdSensitivity (vector).

nHerdsPerRiskGroupMx:

Object of class "matrix". Number of herds to be tested per risk group [columns] and sample limit [rows] (if population is stratified by risk groups).

nSampleFixVec:

Object of class "numeric". Numeric vector containing some NAs (optional argument). For risk groups for which the sample size is fixed it specifies the sample size. For the risk groups for which the sample size was computed it was set to NA (order of the risk groups is the same as in survey.Data@riskValueData).

probVec:

Object of class "numeric". Contains the sample probabilities for those risk groups for which the sample size was computed (=NA entries in nSampleFixVec).

nAnimalsMeanVec:

Object of class "numeric". Expected total number of animals to be tested in the survey (vector).

expectedCostVec:

Object of class "numeric". Expected costs of the survey (vector).

Methods

HTML

signature(x = "LtdSamplingSummary"): Creates an html file containing the summary data and the diagnostic plots. Title, file name, output directory, css-file, etc. can additionally be specified using the parameters, filename, outdir, CSSFile, Title, as well as all the other parameters of the R2HTML-function HTMLInitFile.

plot

signature(x = "LtdSamplingSummary"): Create plots of 1) the mean herd sensitivity, 2) the number of herds to be tested, 3) the expected total number of animals to be tested, 4) the expected total cost of the survey plotted against the vector of sample limits.

show

signature(object = "LtdSamplingSummary"): Display structure of the class and content of the slots.

summary

signature(object = "LtdSamplingSummary"): Display structure of the class and a summary of the content of the slots.

Note

No notes yet.

Author(s)

Ian Kopacka <[e-mail]>

See Also

The slot surveyData contains an object of the class SurveyData.

Examples

## Show the structure of the class:
showClass("LtdSamplingSummary")
## Create an object:
data(sheepData)
mySurvey <- surveyData(nAnimalVec = sheepData$nSheep, 
    populationData = sheepData, designPrevalence = 0.002, 
    alpha = 0.05, intraHerdPrevalence = 0.13,
    diagSensitivity = 0.9, costHerd = 30, costAnimal = 7.1)
myLtdSamplingSummary <- ltdSamplingSummary(survey.Data = mySurvey, 
    sampleSizeLtdMax = 7)
## Display results:
summary(myLtdSamplingSummary)
plot(myLtdSamplingSummary)
## Write results to an html-file:
## Not run: 
target <- HTMLInitFile(getwd(), filename = "LtdSampling")
HTML(myLtdSamplingSummary)
HTMLEndFile()
## End(Not run)

FFD documentation built on Dec. 21, 2020, 3:02 p.m.