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PKbioanalysis overview

Omar Elashkar

library(PKbioanalysis)

Plate generation, reusing and managing plates

plate <- generate_96() 
plot(plate)
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 96 rows containing missing values or values outside the scale range
#> (`geom_text()`).

Calibration study examples

plate <- generate_96("Calibration study") |> 
    add_cs_curve(c(1, 3, 5, 10, 20, 50, 100, 200, 500)) |>
    add_DB() |> 
    add_DB() |>
    add_blank() |>   # CS0IS1
    add_suitability(conc = 20) |>
    add_qcs(2, 200 ,400, qc_serial = FALSE) |> 
    add_DB() |> 
    add_blank(analyte = TRUE, IS = FALSE) |> # CS1IS0
    add_cs_curve(c(1, 3, 5, 10, 20, 50, 100, 200, 500)) |>
    add_qcs(lqc_conc = 2, mqc_conc =  180 , hqc_conc = 400) 

plot(plate)
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 48 rows containing missing values or values outside the scale range
#> (`geom_text()`).

plot(plate, color = "TYPE")
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 48 rows containing missing values or values outside the scale range
#> (`geom_text()`).

plate <- register_plate(plate)
plot(plate)
plate <- generate_96() |> 
    add_suitability(conc = 10) |>
    make_calibration_study(
        plate_std = c(1, 3, 5, 10, 20, 50, 100, 200, 500), 
        lqc_conc = 2, 
        mqc_conc = 40,
        hqc_conc = 100, 
        n_qc = 4, 
        qc_serial = TRUE, 
        n_CS0IS0 = 2,
        n_CS1IS0 = 2,
        n_CS0IS1 = 2)
plot(plate, color = "TYPE")
plot(plate, color  = "conc")
plate <- register_plate(plate)
plate_app()

Adding samples

plate <- generate_96() |> add_samples(1:20)

plot(plate)
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 76 rows containing missing values or values outside the scale range
#> (`geom_text()`).

Adding samples manually or from external spreadsheet

plate <- generate_96()

plate <- plate |> 
    add_samples("sample1") |> 
    add_samples("sample2") |>
    add_samples("sample3")

plot(plate)
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 93 rows containing missing values or values outside the scale range
#> (`geom_text()`).

Define samples by attributes

data(Indometh)
plate <- generate_96() |> 
    add_samples(samples = Indometh$Subject, 
                time = Indometh$time)
plot(plate, color = "time")
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 30 rows containing missing values or values outside the scale range
#> (`geom_text()`).

plot(plate, color = "samples")
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 30 rows containing missing values or values outside the scale range
#> (`geom_text()`).

Automated crossover

plate <- generate_96() |> 
    # add_samples_c(c("subject1", "subject2"), time = c(0, 10, 30, 60, 120), factor = "Male") |>
    add_samples_c("subject1", time = c(0, 10, 30, 60, 120), 
                  factor = "Male") |>
    add_samples_c("subject2", time =   c(0, 10, 30, 120), 
                  factor = "Female") 

plot(plate, color = "time")
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 87 rows containing missing values or values outside the scale range
#> (`geom_text()`).

plot(plate, color = "samples")
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 87 rows containing missing values or values outside the scale range
#> (`geom_text()`).

plot(plate, color = "factor")
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 87 rows containing missing values or values outside the scale range
#> (`geom_text()`).

plot(plate, color = "conc")
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 87 rows containing missing values or values outside the scale range
#> (`geom_text()`).

Food Effect Example

plate <- generate_96() |> 
    add_samples_c(1:4, time = c(0, 10, 30, 60, 120), 
         factor = c("Fed", "Fast"))
plot(plate, color = "time")
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 56 rows containing missing values or values outside the scale range
#> (`geom_text()`).

plot(plate, color = "samples")
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 56 rows containing missing values or values outside the scale range
#> (`geom_text()`).

plot(plate, color = "factor")
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 56 rows containing missing values or values outside the scale range
#> (`geom_text()`).

plot(plate, color = "conc")
#> Plate not registered. To register, use register_plate()
#> Warning: Removed 56 rows containing missing values or values outside the scale range
#> (`geom_text()`).

Metabolic study (Multiple plates)

plates <- make_metabolic_study(
    cmpd = c("NE", "DA", "5HT", "HVA", 
             "DOPAC", "MHPG", "5HIAA", "VMA"),
    time_points = c(0, 5, 10, 15, 30, 45, 60, 90, 120),
    n_NAD = 3, 
    n_noNAD = 2
)
length(plates)
#> [1] 7
plot(plates[[1]], color = "samples", label_size = 9)
#> Plate not registered. To register, use register_plate()

plot(plates[[2]], color = "samples", label_size = 9)
#> Plate not registered. To register, use register_plate()

plot(plates[[3]], color = "samples", label_size = 9)
#> Plate not registered. To register, use register_plate()

plot(plates[[4]], color = "samples", label_size = 9)
#> Plate not registered. To register, use register_plate()

plot(plates[[5]], color = "samples", label_size = 9)
#> Plate not registered. To register, use register_plate()

plot(plates[[6]], color = "samples", label_size = 9)
#> Plate not registered. To register, use register_plate()

register_plate(plates)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.