Make measurement slice

Wrap the information about a particular type of measurement, e.g., NPPCR. NB: add example! copy some from the vignette file.

Usage

make_meas_object(patho, specimen, test, quality, cause_list, sep_char = "_")

Arguments

patho

A vector of pathogen names

specimen

Specimen name

test

Test name

quality

Quality category: any of "BrS", "SS" or "GS".

cause_list

The vector of potential latent status

sep_char

a character string that separate the pathogen names and the specimen-test pair; Default to "_"

Value

A list with measurement information

• quality same as argument

• patho same as argument

• name_in_data the names used in the raw data to locate these measurements

• template a mapping from patho to cause_list. NROW = length(cause_list)+1; NCOL = length(patho). This value is crucial in model fitting to determine which measurements are informative of a particular category of latent status.

• specimen same as argument

• test same as argument

• nm_spec_test paste specimen and test together

See also

make_template()

Examples

make_meas_object(
patho = c("A","B","C","D","E","F"), 
specimen = "MBS",
test = "1",
quality = "BrS", 
cause_list = c("A","B","C","D","E"))
#> $quality
#> [1] "BrS"
#> 
#> $patho
#> [1] "A" "B" "C" "D" "E" "F"
#> 
#> $name_in_data
#> [1] "A_MBS1" "B_MBS1" "C_MBS1" "D_MBS1" "E_MBS1" "F_MBS1"
#> 
#> $template
#>      [,1] [,2] [,3] [,4] [,5] [,6]
#> [1,]    1    0    0    0    0    0
#> [2,]    0    1    0    0    0    0
#> [3,]    0    0    1    0    0    0
#> [4,]    0    0    0    1    0    0
#> [5,]    0    0    0    0    1    0
#> [6,]    0    0    0    0    0    0
#> 
#> $specimen
#> [1] "MBS"
#> 
#> $test
#> [1] "1"
#> 
#> $nm_spec_test
#> [1] "MBS1"
#>