pla: Parallel Line Assays
Version 0.2

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.

AuthorJens Henrik Badsberg
Date of publication2015-09-09 21:19:32
MaintainerJens Henrik Badsberg <pla2015@badsberg.eu>
LicenseGPL (>= 2)
Version0.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("pla")

Getting started

Package overview

Popular man pages

Corticotrophin: An assay of corticotrophin by subcutaneous injection in rats
data2assayFrame: Check dataframe for pla.fit
Erythropoietin: Erythropoietin rDNA - Normocythaemic assay in mice
pla: Create a parallel line assay model
pla.fit: Estimation in parallel line models, with listing of results
pla-package: Parallel Line Assays
Work/reduceDimension: Reduce the number of dimensions by one
See all...

All man pages Function index File listing

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

Functions

AgarDiffusionAssay Man page
Corticotrophin Man page
Diphteria Man page
Erythromycin Man page
Erythropoietin Man page
FactorIX Man page
Fiellers Man page Source code
HeparinSodium Man page
HepatitisB Man page
HepatitisBvaccine Man page
HumanHepatitis Man page
IPV Man page
Nystatin Man page
Turbidimetric Man page
Vancomycin Man page
anova,ANY-method Man page
anova,pla-method Man page
anova,plaFit-method Man page
anova-methods Man page
apermAssay Source code
as.array,assayFrame-method Man page
as.array,assayTable-method Man page
as.array,data.frame-method Man page
as.data.frame,assayFrame-method Man page
as.data.frame,assayTable-method Man page
as.data.frame,pla-method Man page
as.table,assayFrame-method Man page
as.table,assayTable-method Man page
assayData-class Man page
assayFrame-class Man page
assayModel-class Man page
assayTable-class Man page
assayTable2frame Man page Source code
checkPlaFrame Source code
classFactor Source code
coef,ANY-method Man page
coef,pla-method Man page
coef,plaFit-method Man page
coef-methods Man page
confint,ANY-method Man page
confint,pla-method Man page
confint,plaFit-method Man page
confint-methods Man page
countBlocks Source code
countFactorLevels Source code
countRun Source code
data2assayFrame Man page Source code
extractAlpha Source code
findArrayDescription Source code
fit Man page Source code
fitted,ANY-method Man page
fitted,pla-method Man page
fitted,plaFit-method Man page
fitted-methods Man page
jitterSteps Man page Source code
lm.influence,ANY-method Man page
lm.influence,pla-method Man page
lm.influence,plaFit-method Man page
lm.influence-methods Man page
mputeCRD Source code
mputeLatinSquare Source code
mputeRBD Source code
mputeRBDframe Source code
multiplyByFactor Source code
nsertTable Source code
nvalidBlockDesign Source code
nvalidLatinSquare Source code
patchDescription Source code
pheur325 Man page Source code
pla Man page Source code
pla-class Man page
pla-package Man page
pla.fit Man page Source code
pla.plots Man page Source code
plaCRD Man page Source code
plaCRD-class Man page
plaFit-class Man page
plaLSD Man page Source code
plaLSD-class Man page
plaRBD Man page Source code
plaRBD-class Man page
plot,ANY-method Man page
plot,pla-method Man page
plot,plaFit-method Man page
plot-methods Man page
plotMoreSamples Man page Source code
plotSamples Man page Source code
plotTwoSamples Man page Source code
potency Man page Source code
predict,ANY-method Man page
predict,pla-method Man page
predict,plaFit-method Man page
predict-methods Man page
print,ANY-method Man page
print,assayFrame-method Man page
print,assayTable-method Man page
print,pla-method Man page
print,plaFit-method Man page
print-methods Man page
readAssayTable Man page Source code
reduceDimension Man page Source code
reduceDimensionSub Source code
residuals,ANY-method Man page
residuals,pla-method Man page
residuals,plaFit-method Man page
residuals-methods Man page
s.digits Source code
s.llower Source code
s.lower Source code
s.upper Source code
s.uupper Source code
show,assayFrame-method Man page
show,assayTable-method Man page
string2design Source code
summary,ANY-method Man page
summary,pla-method Man page
summary,plaFit-method Man page
summary-methods Man page
transposeTable Source code
vcov,ANY-method Man page
vcov,pla-method Man page
vcov,plaFit-method Man page
vcov-methods Man page

Files

inst
inst/R.xtables
inst/R.xtables/xtableValidity.R
inst/R.xtables/xtablePotency.R
inst/R.xtables/xtableLabels.R
inst/R.xtables/xtableTable.R
inst/R.xtables/xtableAnova.R
inst/R.xtables/xtablesAssay.R
inst/R.xtables/fun.R
inst/R.xtables/xtabularAssay.R
inst/R.xtables/xtableLatinSquare.R
inst/R.xtables/xtables.R
inst/R.xtables/xtableModel.R
inst/R.xtables/xtableParameters.R
inst/R.xtables/xtableHead.R
inst/R.xtables/xtableTableCS.R
inst/scripts
inst/scripts/Makefile
inst/scripts/DejaVu.csh
inst/scripts/DejaVu.bat
inst/scripts/data
inst/scripts/data/Assay500000.txt
inst/scripts/data/Assay000002.txt
inst/scripts/data/Assay100100.txt
inst/scripts/data/Assay757500.txt
inst/scripts/data/Assay252500.txt
inst/scripts/data/AssayTable.txt
inst/scripts/data/Assay3.txt
inst/scripts/data/Assay505050.txt
inst/scripts/data/Assay2.txt
inst/scripts/data/Assay1.txt
inst/scripts/data/Assay000800.txt
inst/scripts/data/Assay010010.txt
inst/scripts/data/Assay505000.txt
inst/scripts/data/Assay000600.txt
inst/scripts/R
inst/scripts/R/xtables.bak.R
inst/scripts/R/xtables.R
inst/scripts/Skeleton
inst/scripts/Skeleton/Skeleton.Rnw
inst/scripts/Skeleton/SkeletonDesign-xtable.Rnw
inst/scripts/Skeleton/Skeleton-xtable.Rnw
inst/scripts/BatchSubstitute.bat
inst/vignettes
inst/vignettes/Makefile
inst/vignettes/PhEur
inst/vignettes/PhEur/CorticotrophinST-xtable.Rnw
inst/vignettes/PhEur/AntibioticAgarDiffusionAssay-xtable.Rnw
inst/vignettes/PhEur/HepatitisB-byOrder-W-xtable.Rnw
inst/vignettes/PhEur/Makefile
inst/vignettes/PhEur/Corticotrophin.Rnw
inst/vignettes/PhEur/Agar-xtable.Rnw
inst/vignettes/PhEur/AntibioticAgarDiffusionAssay.Rnw
inst/vignettes/PhEur/CorticotrophinST.Rnw
inst/vignettes/PhEur/Agar-impute-xtable.Rnw
inst/vignettes/PhEur/data
inst/vignettes/PhEur/data/HepatitisB_Error.txt
inst/vignettes/PhEur/data/HepatitisB.txt
inst/vignettes/PhEur/data/AntibioticAgarDiffusionAssay.txt
inst/vignettes/PhEur/data/HepatitisB_byOrder.txt
inst/vignettes/PhEur/data/AntibioticTurbidimetric.txt
inst/vignettes/PhEur/data/CorticotrophinST.txt
inst/vignettes/PhEur/data/HepatitisB_Error.wrong.txt
inst/vignettes/PhEur/data/HepatitisB.B.txt
inst/vignettes/PhEur/data/Agar-invalid.txt
inst/vignettes/PhEur/data/HepatitisB_flop.txt
inst/vignettes/PhEur/data/Agar.txt
inst/vignettes/PhEur/data/Corticotrophin.txt
inst/vignettes/PhEur/data/HepatitisB_Missing.txt
inst/vignettes/PhEur/data/Agar-missing.txt
inst/vignettes/PhEur/data/HepatitisB_byLabel.txt
inst/vignettes/PhEur/AntibioticTurbidimetric.Rnw
inst/vignettes/PhEur/R
inst/vignettes/PhEur/R/xtables.R
inst/vignettes/PhEur/AntibioticTurbidimetric-xtable.Rnw
inst/vignettes/PhEur/HepatitisB-xtable.Rnw
inst/vignettes/PhEur/HepatitisB_Missing.Rnw
inst/vignettes/PhEur/HepatitisB-B-xtable.Rnw
inst/vignettes/PhEur/HepatitisB-byLabel-W-xtable.Rnw
inst/vignettes/PhEur/Agar-invalid-xtable.Rnw
inst/vignettes/PhEur/HepatitisB-byLabel-xtable.Rnw
inst/vignettes/PhEur/Corticotrophin-xtable.Rnw
inst/vignettes/PhEur/Corticotrophin-select-ST-xtable.Rnw
inst/vignettes/PhEur/HepatitisB_Error.Rnw
inst/vignettes/PhEur/HepatitisB_Missing-xtable.Rnw
inst/vignettes/PhEur/HepatitisB-byOrder-xtable.Rnw
inst/vignettes/PhEur/Agar-missing-xtable.Rnw
inst/vignettes/PhEur/Corticotrophin-select-ST.Rnw
inst/vignettes/PhEur/HepatitisB.Rnw
inst/vignettes/CombiStat
inst/vignettes/CombiStat/Diphteria-xtable.Rnw
inst/vignettes/CombiStat/Makefile
inst/vignettes/CombiStat/FactorIX.Rnw
inst/vignettes/CombiStat/IPV_CompleteData-xtable.Rnw
inst/vignettes/CombiStat/Diphteria-byLabel-xtable.Rnw
inst/vignettes/CombiStat/Erythropoietin-xtable.Rnw
inst/vignettes/CombiStat/Diphteria.Rnw
inst/vignettes/CombiStat/FactorIX-xtable.Rnw
inst/vignettes/CombiStat/Erythromycin.Rnw
inst/vignettes/CombiStat/HeparinSodium.Rnw
inst/vignettes/CombiStat/InactivatedPoliomyelitisVaccine-xtable.Rnw
inst/vignettes/CombiStat/HumanHepatitisAimmunoglobulin-xtable.Rnw
inst/vignettes/CombiStat/data
inst/vignettes/CombiStat/data/Diphteria_byLabel.txt
inst/vignettes/CombiStat/data/HumanHepatitis.txt
inst/vignettes/CombiStat/data/IPV_Error.txt
inst/vignettes/CombiStat/data/Diphteria.txt
inst/vignettes/CombiStat/data/HepatitisBvaccine.txt
inst/vignettes/CombiStat/data/Erythropoietin.txt
inst/vignettes/CombiStat/data/Erythromycin.txt
inst/vignettes/CombiStat/data/HeparinSodium_Error.txt
inst/vignettes/CombiStat/data/IPV.txt
inst/vignettes/CombiStat/data/FactorIX-T.txt
inst/vignettes/CombiStat/data/HeparinSodium.txt
inst/vignettes/CombiStat/data/IPV_CompleteData.txt
inst/vignettes/CombiStat/data/IPV_Imputed.txt
inst/vignettes/CombiStat/data/FactorIX.txt
inst/vignettes/CombiStat/data/Nystatin.txt
inst/vignettes/CombiStat/R
inst/vignettes/CombiStat/R/xtables.R
inst/vignettes/CombiStat/HeparinSodium_Error.Rnw
inst/vignettes/CombiStat/IPV_Imputed.Rnw
inst/vignettes/CombiStat/Nystatin-xtable.Rnw
inst/vignettes/CombiStat/IPV_Imputed-xtable.Rnw
inst/vignettes/CombiStat/HumanHepatitisAimmunoglobulin.Rnw
inst/vignettes/CombiStat/IPV_CompleteData.Rnw
inst/vignettes/CombiStat/InactivatedPoliomyelitisVaccine.Rnw
inst/vignettes/CombiStat/InactivatedPoliomyelitisVaccine_Error.Rnw
inst/vignettes/CombiStat/Erythropoietin.Rnw
inst/vignettes/CombiStat/HepatitisBvaccine.Rnw
inst/vignettes/CombiStat/HepatitisBvaccine-xtable.Rnw
inst/vignettes/CombiStat/FactorIX-t-xtable.Rnw
inst/vignettes/CombiStat/Nystatin.Rnw
inst/vignettes/CombiStat/Erythromycin-xtable.Rnw
inst/vignettes/CombiStat/HeparinSodium-xtable.Rnw
inst/vignettes/Miscellaneous
inst/vignettes/Miscellaneous/Vancomycin-Impute-1-xtable.Rnw
inst/vignettes/Miscellaneous/Makefile
inst/vignettes/Miscellaneous/Vancomycin-CompleteData-xtable.Rnw
inst/vignettes/Miscellaneous/ToothGrowth.Rnw
inst/vignettes/Miscellaneous/Vancomycin-Impute-Frame-xtable.Rnw
inst/vignettes/Miscellaneous/data
inst/vignettes/Miscellaneous/data/Vancomycin_outlier.txt
inst/vignettes/Miscellaneous/data/Vancomycin_tabular.txt
inst/vignettes/Miscellaneous/data/Vancomycin_wrong.txt
inst/vignettes/Miscellaneous/data/Vancomycin_check.txt
inst/vignettes/Miscellaneous/data/AssayTable.txt
inst/vignettes/Miscellaneous/data/Vancomycin_frame.txt
inst/vignettes/Miscellaneous/data/Vancomycin_outlier_1.txt
inst/vignettes/Miscellaneous/data/Vancomycin_frame_NA.txt
inst/vignettes/Miscellaneous/data/Vancomycin.txt
inst/vignettes/Miscellaneous/data/Vancomycin_Error.txt
inst/vignettes/Miscellaneous/R
inst/vignettes/Miscellaneous/R/xtables.R
inst/vignettes/Miscellaneous/Vancomycin-xtable.Rnw
inst/vignettes/Miscellaneous/Vancomycin_check-xtable.Rnw
inst/vignettes/Miscellaneous/Vancomycin-Impute-2-xtable.Rnw
inst/vignettes/Miscellaneous/Vancomycin-tabularx.Rnw
inst/vignettes/Miscellaneous/Vancomycin.Rnw
inst/vignettes/Miscellaneous/ToothGrowth-xtable.Rnw
inst/vignettes/Miscellaneous/Vancomycin-Impute-xtable.Rnw
NAMESPACE
data
data/HumanHepatitis.rda
data/Corticotrophin.rda
data/AgarDiffusionAssay.rda
data/HeparinSodium.rda
data/IPV.rda
data/Vancomycin.rda
data/Nystatin.rda
data/HepatitisBvaccine.rda
data/Diphteria.rda
data/Turbidimetric.rda
data/FactorIX.rda
data/Erythropoietin.rda
data/HepatitisB.rda
data/Erythromycin.rda
R
R/classes.R
R/methodsFit.R
R/plotTwoSamples.R
R/imputeLatinSquares.R
R/imputeCRD.R
R/as.array.R
R/invalidBlockDesign.R
R/methodsData.R
R/checkPlaFrame.R
R/countFactorLevels.R
R/data2assayFrame.R
R/plaRBD.R
R/assayTable2frame.R
R/Fiellers.R
R/methodsPla.R
R/pla.fit.R
R/readAssayTable.R
R/extractAlpha.R
R/multiplyByFactor.R
R/jitterSteps.R
R/invalidLatinSquare.R
R/plaCRD.R
R/findArrayDescription.R
R/transposeTable.R
R/plaLSD.R
R/pheur325.R
R/imputeRBD.R
R/pla.plots.R
R/apermAssay.R
R/reduceDimension.R
R/pla.R
R/imputeRBDframe.R
R/string2design.R
R/potency.R
R/plotSamples.R
R/insertTable.R
R/plotMoreSamples.R
MD5
DESCRIPTION
man
man/Work
man/Work/reduceDimension.Rd
man/readAssayTable.Rd
man/Turbidimetric.Rd
man/HeparinSodium.Rd
man/assayTable2frame.Rd
man/pheur325.Rd
man/Erythropoietin.Rd
man/Diphteria.Rd
man/HepatitisB.Rd
man/Erythromycin.Rd
man/Corticotrophin.Rd
man/pla-package.Rd
man/pla.fit.Rd
man/data2assayFrame.Rd
man/FactorIX.Rd
man/Nystatin.Rd
man/potency.Rd
man/AgarDiffusionAssay.Rd
man/pla.Rd
man/jitterSteps.Rd
man/plotSamples.Rd
man/Fiellers.Rd
man/pla.plots.Rd
man/HepatitisBvaccine.Rd
man/Vancomycin.Rd
man/IPV.Rd
man/HumanHepatitis.Rd
pla documentation built on May 20, 2017, 12:44 a.m.

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