pla: Parallel Line Assays

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Parallel Line Assays: Completely randomized design, Randomized Block design, and Latin squares design. Balanced data are fitted as described in the Ph.Eur. In the presence of missing values complete data analysis can be performed (with computation of Fieller's confidence intervals for the estimated potency), or imputation of values can be applied. The package contains a script such that a pdf-document with a report of an analysis of an assay can be produced from an input file with data of the assay. Here no knowledge of R is needed by the user.

Author
Jens Henrik Badsberg
Date of publication
2015-09-09 21:19:32
Maintainer
Jens Henrik Badsberg <pla2015@badsberg.eu>
License
GPL (>= 2)
Version
0.2

View on CRAN

Man pages

AgarDiffusionAssay
Antibiotic agar diffusion assay using a rectangular tray
assayTable2frame
Expand table to matrix of measurements by variables - for...
Corticotrophin
An assay of corticotrophin by subcutaneous injection in rats
data2assayFrame
Check dataframe for pla.fit
Diphteria
Diphteria vaccine - Intradermal challenge
Erythromycin
Erythromycin - Assay 1
Erythropoietin
Erythropoietin rDNA - Normocythaemic assay in mice
FactorIX
Factor IX - Coagulation
Fiellers
Fiellers confidence interval
HeparinSodium
Heparin Sodium - European Pharmacopoeia (1997), 2.7.5
HepatitisB
An in-vitro assay of three hepatitis B vaccines against a...
HepatitisBvaccine
Hepatitis B vaccine
HumanHepatitis
Human Hepatitis A immunoglobulin - Elisa
IPV
Inactivated poliomyelitis vaccine - Type 3
jitterSteps
Compute a perturbed version of the dose-variable
Nystatin
Nystatin: Antibiotic agar diffusion assay
pheur325
Potency with confidence intervals
pla
Create a parallel line assay model
pla.fit
Estimation in parallel line models, with listing of results
pla-package
Parallel Line Assays
pla.plots
Make plots for parallel line models
plotSamples
Scatter plot for parallel line models
potency
Return or compute potency
readAssayTable
Read a .txt file with responses of an assay
Turbidimetric
Antibiotic turbidimetric assay
Vancomycin
Antibiotic agar diffusion assay on 6 plates
Work/reduceDimension
Reduce the number of dimensions by one

Files in this package

pla
pla/inst
pla/inst/R.xtables
pla/inst/R.xtables/xtableValidity.R
pla/inst/R.xtables/xtablePotency.R
pla/inst/R.xtables/xtableLabels.R
pla/inst/R.xtables/xtableTable.R
pla/inst/R.xtables/xtableAnova.R
pla/inst/R.xtables/xtablesAssay.R
pla/inst/R.xtables/fun.R
pla/inst/R.xtables/xtabularAssay.R
pla/inst/R.xtables/xtableLatinSquare.R
pla/inst/R.xtables/xtables.R
pla/inst/R.xtables/xtableModel.R
pla/inst/R.xtables/xtableParameters.R
pla/inst/R.xtables/xtableHead.R
pla/inst/R.xtables/xtableTableCS.R
pla/inst/scripts
pla/inst/scripts/Makefile
pla/inst/scripts/DejaVu.csh
pla/inst/scripts/DejaVu.bat
pla/inst/scripts/data
pla/inst/scripts/data/Assay500000.txt
pla/inst/scripts/data/Assay000002.txt
pla/inst/scripts/data/Assay100100.txt
pla/inst/scripts/data/Assay757500.txt
pla/inst/scripts/data/Assay252500.txt
pla/inst/scripts/data/AssayTable.txt
pla/inst/scripts/data/Assay3.txt
pla/inst/scripts/data/Assay505050.txt
pla/inst/scripts/data/Assay2.txt
pla/inst/scripts/data/Assay1.txt
pla/inst/scripts/data/Assay000800.txt
pla/inst/scripts/data/Assay010010.txt
pla/inst/scripts/data/Assay505000.txt
pla/inst/scripts/data/Assay000600.txt
pla/inst/scripts/R
pla/inst/scripts/R/xtables.bak.R
pla/inst/scripts/R/xtables.R
pla/inst/scripts/Skeleton
pla/inst/scripts/Skeleton/Skeleton.Rnw
pla/inst/scripts/Skeleton/SkeletonDesign-xtable.Rnw
pla/inst/scripts/Skeleton/Skeleton-xtable.Rnw
pla/inst/scripts/BatchSubstitute.bat
pla/inst/vignettes
pla/inst/vignettes/Makefile
pla/inst/vignettes/PhEur
pla/inst/vignettes/PhEur/CorticotrophinST-xtable.Rnw
pla/inst/vignettes/PhEur/AntibioticAgarDiffusionAssay-xtable.Rnw
pla/inst/vignettes/PhEur/HepatitisB-byOrder-W-xtable.Rnw
pla/inst/vignettes/PhEur/Makefile
pla/inst/vignettes/PhEur/Corticotrophin.Rnw
pla/inst/vignettes/PhEur/Agar-xtable.Rnw
pla/inst/vignettes/PhEur/AntibioticAgarDiffusionAssay.Rnw
pla/inst/vignettes/PhEur/CorticotrophinST.Rnw
pla/inst/vignettes/PhEur/Agar-impute-xtable.Rnw
pla/inst/vignettes/PhEur/data
pla/inst/vignettes/PhEur/data/HepatitisB_Error.txt
pla/inst/vignettes/PhEur/data/HepatitisB.txt
pla/inst/vignettes/PhEur/data/AntibioticAgarDiffusionAssay.txt
pla/inst/vignettes/PhEur/data/HepatitisB_byOrder.txt
pla/inst/vignettes/PhEur/data/AntibioticTurbidimetric.txt
pla/inst/vignettes/PhEur/data/CorticotrophinST.txt
pla/inst/vignettes/PhEur/data/HepatitisB_Error.wrong.txt
pla/inst/vignettes/PhEur/data/HepatitisB.B.txt
pla/inst/vignettes/PhEur/data/Agar-invalid.txt
pla/inst/vignettes/PhEur/data/HepatitisB_flop.txt
pla/inst/vignettes/PhEur/data/Agar.txt
pla/inst/vignettes/PhEur/data/Corticotrophin.txt
pla/inst/vignettes/PhEur/data/HepatitisB_Missing.txt
pla/inst/vignettes/PhEur/data/Agar-missing.txt
pla/inst/vignettes/PhEur/data/HepatitisB_byLabel.txt
pla/inst/vignettes/PhEur/AntibioticTurbidimetric.Rnw
pla/inst/vignettes/PhEur/R
pla/inst/vignettes/PhEur/R/xtables.R
pla/inst/vignettes/PhEur/AntibioticTurbidimetric-xtable.Rnw
pla/inst/vignettes/PhEur/HepatitisB-xtable.Rnw
pla/inst/vignettes/PhEur/HepatitisB_Missing.Rnw
pla/inst/vignettes/PhEur/HepatitisB-B-xtable.Rnw
pla/inst/vignettes/PhEur/HepatitisB-byLabel-W-xtable.Rnw
pla/inst/vignettes/PhEur/Agar-invalid-xtable.Rnw
pla/inst/vignettes/PhEur/HepatitisB-byLabel-xtable.Rnw
pla/inst/vignettes/PhEur/Corticotrophin-xtable.Rnw
pla/inst/vignettes/PhEur/Corticotrophin-select-ST-xtable.Rnw
pla/inst/vignettes/PhEur/HepatitisB_Error.Rnw
pla/inst/vignettes/PhEur/HepatitisB_Missing-xtable.Rnw
pla/inst/vignettes/PhEur/HepatitisB-byOrder-xtable.Rnw
pla/inst/vignettes/PhEur/Agar-missing-xtable.Rnw
pla/inst/vignettes/PhEur/Corticotrophin-select-ST.Rnw
pla/inst/vignettes/PhEur/HepatitisB.Rnw
pla/inst/vignettes/CombiStat
pla/inst/vignettes/CombiStat/Diphteria-xtable.Rnw
pla/inst/vignettes/CombiStat/Makefile
pla/inst/vignettes/CombiStat/FactorIX.Rnw
pla/inst/vignettes/CombiStat/IPV_CompleteData-xtable.Rnw
pla/inst/vignettes/CombiStat/Diphteria-byLabel-xtable.Rnw
pla/inst/vignettes/CombiStat/Erythropoietin-xtable.Rnw
pla/inst/vignettes/CombiStat/Diphteria.Rnw
pla/inst/vignettes/CombiStat/FactorIX-xtable.Rnw
pla/inst/vignettes/CombiStat/Erythromycin.Rnw
pla/inst/vignettes/CombiStat/HeparinSodium.Rnw
pla/inst/vignettes/CombiStat/InactivatedPoliomyelitisVaccine-xtable.Rnw
pla/inst/vignettes/CombiStat/HumanHepatitisAimmunoglobulin-xtable.Rnw
pla/inst/vignettes/CombiStat/data
pla/inst/vignettes/CombiStat/data/Diphteria_byLabel.txt
pla/inst/vignettes/CombiStat/data/HumanHepatitis.txt
pla/inst/vignettes/CombiStat/data/IPV_Error.txt
pla/inst/vignettes/CombiStat/data/Diphteria.txt
pla/inst/vignettes/CombiStat/data/HepatitisBvaccine.txt
pla/inst/vignettes/CombiStat/data/Erythropoietin.txt
pla/inst/vignettes/CombiStat/data/Erythromycin.txt
pla/inst/vignettes/CombiStat/data/HeparinSodium_Error.txt
pla/inst/vignettes/CombiStat/data/IPV.txt
pla/inst/vignettes/CombiStat/data/FactorIX-T.txt
pla/inst/vignettes/CombiStat/data/HeparinSodium.txt
pla/inst/vignettes/CombiStat/data/IPV_CompleteData.txt
pla/inst/vignettes/CombiStat/data/IPV_Imputed.txt
pla/inst/vignettes/CombiStat/data/FactorIX.txt
pla/inst/vignettes/CombiStat/data/Nystatin.txt
pla/inst/vignettes/CombiStat/R
pla/inst/vignettes/CombiStat/R/xtables.R
pla/inst/vignettes/CombiStat/HeparinSodium_Error.Rnw
pla/inst/vignettes/CombiStat/IPV_Imputed.Rnw
pla/inst/vignettes/CombiStat/Nystatin-xtable.Rnw
pla/inst/vignettes/CombiStat/IPV_Imputed-xtable.Rnw
pla/inst/vignettes/CombiStat/HumanHepatitisAimmunoglobulin.Rnw
pla/inst/vignettes/CombiStat/IPV_CompleteData.Rnw
pla/inst/vignettes/CombiStat/InactivatedPoliomyelitisVaccine.Rnw
pla/inst/vignettes/CombiStat/InactivatedPoliomyelitisVaccine_Error.Rnw
pla/inst/vignettes/CombiStat/Erythropoietin.Rnw
pla/inst/vignettes/CombiStat/HepatitisBvaccine.Rnw
pla/inst/vignettes/CombiStat/HepatitisBvaccine-xtable.Rnw
pla/inst/vignettes/CombiStat/FactorIX-t-xtable.Rnw
pla/inst/vignettes/CombiStat/Nystatin.Rnw
pla/inst/vignettes/CombiStat/Erythromycin-xtable.Rnw
pla/inst/vignettes/CombiStat/HeparinSodium-xtable.Rnw
pla/inst/vignettes/Miscellaneous
pla/inst/vignettes/Miscellaneous/Vancomycin-Impute-1-xtable.Rnw
pla/inst/vignettes/Miscellaneous/Makefile
pla/inst/vignettes/Miscellaneous/Vancomycin-CompleteData-xtable.Rnw
pla/inst/vignettes/Miscellaneous/ToothGrowth.Rnw
pla/inst/vignettes/Miscellaneous/Vancomycin-Impute-Frame-xtable.Rnw
pla/inst/vignettes/Miscellaneous/data
pla/inst/vignettes/Miscellaneous/data/Vancomycin_outlier.txt
pla/inst/vignettes/Miscellaneous/data/Vancomycin_tabular.txt
pla/inst/vignettes/Miscellaneous/data/Vancomycin_wrong.txt
pla/inst/vignettes/Miscellaneous/data/Vancomycin_check.txt
pla/inst/vignettes/Miscellaneous/data/AssayTable.txt
pla/inst/vignettes/Miscellaneous/data/Vancomycin_frame.txt
pla/inst/vignettes/Miscellaneous/data/Vancomycin_outlier_1.txt
pla/inst/vignettes/Miscellaneous/data/Vancomycin_frame_NA.txt
pla/inst/vignettes/Miscellaneous/data/Vancomycin.txt
pla/inst/vignettes/Miscellaneous/data/Vancomycin_Error.txt
pla/inst/vignettes/Miscellaneous/R
pla/inst/vignettes/Miscellaneous/R/xtables.R
pla/inst/vignettes/Miscellaneous/Vancomycin-xtable.Rnw
pla/inst/vignettes/Miscellaneous/Vancomycin_check-xtable.Rnw
pla/inst/vignettes/Miscellaneous/Vancomycin-Impute-2-xtable.Rnw
pla/inst/vignettes/Miscellaneous/Vancomycin-tabularx.Rnw
pla/inst/vignettes/Miscellaneous/Vancomycin.Rnw
pla/inst/vignettes/Miscellaneous/ToothGrowth-xtable.Rnw
pla/inst/vignettes/Miscellaneous/Vancomycin-Impute-xtable.Rnw
pla/NAMESPACE
pla/data
pla/data/HumanHepatitis.rda
pla/data/Corticotrophin.rda
pla/data/AgarDiffusionAssay.rda
pla/data/HeparinSodium.rda
pla/data/IPV.rda
pla/data/Vancomycin.rda
pla/data/Nystatin.rda
pla/data/HepatitisBvaccine.rda
pla/data/Diphteria.rda
pla/data/Turbidimetric.rda
pla/data/FactorIX.rda
pla/data/Erythropoietin.rda
pla/data/HepatitisB.rda
pla/data/Erythromycin.rda
pla/R
pla/R/classes.R
pla/R/methodsFit.R
pla/R/plotTwoSamples.R
pla/R/imputeLatinSquares.R
pla/R/imputeCRD.R
pla/R/as.array.R
pla/R/invalidBlockDesign.R
pla/R/methodsData.R
pla/R/checkPlaFrame.R
pla/R/countFactorLevels.R
pla/R/data2assayFrame.R
pla/R/plaRBD.R
pla/R/assayTable2frame.R
pla/R/Fiellers.R
pla/R/methodsPla.R
pla/R/pla.fit.R
pla/R/readAssayTable.R
pla/R/extractAlpha.R
pla/R/multiplyByFactor.R
pla/R/jitterSteps.R
pla/R/invalidLatinSquare.R
pla/R/plaCRD.R
pla/R/findArrayDescription.R
pla/R/transposeTable.R
pla/R/plaLSD.R
pla/R/pheur325.R
pla/R/imputeRBD.R
pla/R/pla.plots.R
pla/R/apermAssay.R
pla/R/reduceDimension.R
pla/R/pla.R
pla/R/imputeRBDframe.R
pla/R/string2design.R
pla/R/potency.R
pla/R/plotSamples.R
pla/R/insertTable.R
pla/R/plotMoreSamples.R
pla/MD5
pla/DESCRIPTION
pla/man
pla/man/Work
pla/man/Work/reduceDimension.Rd
pla/man/readAssayTable.Rd
pla/man/Turbidimetric.Rd
pla/man/HeparinSodium.Rd
pla/man/assayTable2frame.Rd
pla/man/pheur325.Rd
pla/man/Erythropoietin.Rd
pla/man/Diphteria.Rd
pla/man/HepatitisB.Rd
pla/man/Erythromycin.Rd
pla/man/Corticotrophin.Rd
pla/man/pla-package.Rd
pla/man/pla.fit.Rd
pla/man/data2assayFrame.Rd
pla/man/FactorIX.Rd
pla/man/Nystatin.Rd
pla/man/potency.Rd
pla/man/AgarDiffusionAssay.Rd
pla/man/pla.Rd
pla/man/jitterSteps.Rd
pla/man/plotSamples.Rd
pla/man/Fiellers.Rd
pla/man/pla.plots.Rd
pla/man/HepatitisBvaccine.Rd
pla/man/Vancomycin.Rd
pla/man/IPV.Rd
pla/man/HumanHepatitis.Rd