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\documentclass{article}
\usepackage{geometry}
\usepackage{graphicx}
\usepackage{longtable}
\usepackage{pdflscape}
\usepackage{fancyhdr}
\usepackage[iso]{isodateo}
\geometry{tmargin=2cm,bmargin=2.5cm,lmargin=2cm,rmargin=2cm}
\pagestyle{fancy}
\headheight 25pt
\begin{document}
\lhead{Data interpretation report}
\rhead{Acquisition Time: \Sexpr{attr(immunoassay.environment$l.run,"Date")} }
\rfoot{Page: \thepage}
\cfoot{Report Date: \today}
\setcounter{secnumdepth}{-1 }
<<results=hide, echo=FALSE>>=
# Load libraries
library(xtable)
library(Cairo)
# Prepare data for table
tab1 = tab2 = pfile = vector("list", immunoassay.environment$n)
for (i2 in 1:immunoassay.environment$n) {
tab = print(immunoassay.environment$l.run)
tab1[[i2]] = tab[,c("Type", paste(c("MFI","CTS","conc","pred"), immunoassay.environment$l.analytes[i2],
sep="."))]
tab1[[i2]]$fitted = NA
tab1[[i2]]$fitted[tab1[[i2]]$Type=="Standard"] = immunoassay.environment$fits[[i2]]$data$use
tab = project.means(immunoassay.environment$l.run)
tab2[[i2]] = tab[,c("SPL", "Type", paste(c("MFI","CTS","conc","pred"),
immunoassay.environment$l.analytes[i2], sep="."), paste("pred", immunoassay.environment$l.analytes[i2], "cv", sep="."))]
tab2[[i2]]$prec = (1- (tab[,paste("conc", immunoassay.environment$l.analytes[i2], sep=".")] /
tab[,paste("pred", immunoassay.environment$l.analytes[i2], sep=".")])) *100
# Set file name
i3 = gsub("_", "-", attr(immunoassay.environment$l.run, "file"), fixed=T)
pfile[[i2]] = paste("pdf/", i3, "-", i2,".pdf", sep="")
# Make the plot
CairoPDF(file=paste(immunoassay.environment$path, "/Tex/", pfile[[i2]], sep=""), width=14, height=11)
par(mfrow=c(2,2))
plot(immunoassay.environment$fits[[i2]])
plot(immunoassay.environment$fits[[i2]], type="resid", bg="#bbccaa99")
plot(immunoassay.environment$l.run, analyte=i2, type="cv")
plot(immunoassay.environment$l.run, analyte=i2, type="accuracy")
dev.off()
}
@
<<results=tex, echo=FALSE>>=
for (i2 in 1:immunoassay.environment$n) {
# Header & footer
cat("\\begin{center}\n", sep="")
cat(" \\section{\\LARGE{Plate: ", i3, "}}\n", sep="")
cat(" \\section{\\large{Analyte: ", attr(immunoassay.environment$l.run, "Analytes")[i2], "}}\n", sep="")
cat("\\end{center}\n", sep="")
cat("\n\\lfoot{Analyte: ", attr(immunoassay.environment$l.run, "Analytes")[i2], " }\n\n", sep="")
# Run information
cat("\\begin{minipage}{0.55\\textwidth}\\footnotesize\n", sep="")
cat(" \\begin{flushleft}\n", sep="")
cat(" \\emph{Platform: }\n ", attr(immunoassay.environment$l.run,"Assay")[1], "\\\\ \n", sep="")
cat(" \\emph{Instrument S/N: }\n ", attr(immunoassay.environment$l.run,"Assay")[2], "\\\\ \n", sep="")
cat(" \\emph{Operator: }\n ", attr(immunoassay.environment$l.run,"Operator"), "\\\\ \n", sep="")
cat(" \\end{flushleft}\n", sep="")
cat("\\end{minipage}\n", sep="")
cat("\\begin{minipage}{0.37\\textwidth}\\footnotesize\n", sep="")
cat(" \\begin{flushright}\n", sep="")
cat(" \\emph{Standards \\& Controls Lot \\#: }\n ", gsub("_", "-", attr(immunoassay.environment$l.run,"Kit")[1], fixed=T), "\\\\ \n", sep="")
cat(" \\emph{Background MFI: }\n ", attr(immunoassay.environment$l.run,"Background")[i2], "\\\\ \n", sep="")
cat(" \\end{flushright}\n", sep="")
cat("\\end{minipage}\n", sep="")
cat("\n\\vspace{0.2cm}\n\n", sep="")
# Fit information
cat("\\begin{minipage}{0.55\\textwidth}\\footnotesize\n", sep="")
cat(" \\begin{flushleft}\n", sep="")
cat(" \\emph{Fit $R^2 = $}\n ", round(check(immunoassay.environment$fits[[i2]])$r.squared,4), "\\\\ \n", sep="")
cat(" \\emph{$S_{y|x} = $}\n ", round(check(immunoassay.environment$fits[[i2]])$Syx,4), "\\\\ \n", sep="")
cat(" \\emph{Residual deviance = }\n ", round(check(immunoassay.environment$fits[[i2]])$sigma,2), "\\\\ \n", sep="")
cat(" \\end{flushleft}\n", sep="")
cat(" \\end{minipage}\n", sep="")
cat("\\begin{minipage}{0.37\\textwidth}\\footnotesize\n", sep="")
cat(" \\begin{flushright}\n", sep="")
cat(" \\emph{Fit type: }\n ", paste(immunoassay.environment$fits[[i2]]$model[1], ".",
immunoassay.environment$fits[[i2]]$model[2], " with ", immunoassay.environment$fits[[i2]]$model[3],
" weights.", sep=""), "\\\\ \n", sep="")
cat(" \\emph{Mean Calibrator Inaccuracy [\\%]: }\n ", round(check(immunoassay.environment$fits[[i2]])$St.error[2],1), "\\\\ \n", sep="")
cat(" \\emph{Mean QC Inaccuracy [\\%]: }\n ", round(check(immunoassay.environment$fits[[i2]])$QC.error[2],1), "\\\\ \n", sep="")
cat(" \\end{flushright}\n", sep="")
cat("\\end{minipage}\n\n", sep="")
# Add plot
cat("\\begin{center}\n", sep="")
cat(" \\includegraphics[width=1.01\\textwidth]{\"", substr(pfile[[i2]], 0, nchar(pfile[[i2]])-4), "\"}\n", sep="")
cat("\\end{center}\n\n", sep="")
# Print the table of means - standards
cat("\\begin{center}\\footnotesize \r\n Table of means: Standards \r\n \\begin{longtable}{p{1.5cm}r *{6}{c}} \r\n", sep="")
cat("\\hline \r\n SPL & Type & MFI & Counts & Expected & Measured & Precision & Inaccuracy \\\\ \r\n", sep="")
cat("\\hline \r\n \\endhead \r\n \\hline \r\n \\endfoot \r\n\n \\hline \\hline \r\n \\endlastfoot \r\n", sep="")
print(xtable(tab2[[i2]][tab2[[i2]]$Type=="Standard",]), include.rownames=F, include.colnames=F, hline.after=NULL, only.contents=T)
cat("\r\n \\hline \r\n", "Mean & & & & & & ", round(mean(abs(tab2[[i2]][tab2[[i2]]$Type=="Standard", 7]), na.rm=T),2), " & ",
round(mean(abs(tab2[[i2]][tab2[[i2]]$Type=="Standard", 8]), na.rm=T),2), " \\\\"," \r\n", sep="")
cat("\r\n \\end{longtable} \r\n \\end{center}", "\r\n", "\\newpage", "\r\n", sep="")
cat("\r\n", "\r\n", sep="")
# Print the table of means - QCs
if (nrow(tab2[[i2]][tab2[[i2]]$Type=="QC",])>0) {
cat("\\begin{center}\\footnotesize \r\n Table of means: QCs \r\n \\begin{longtable}{p{1.5cm}r *{6}{c}} \r\n", sep="")
cat("\\hline \r\n SPL & Type & MFI & Counts & Expected & Measured & Precision & Inaccuracy \\\\ \r\n", sep="")
cat("\\hline \r\n \\endhead \r\n \\hline \r\n \\endfoot \r\n\n \\hline \\hline \r\n \\endlastfoot \r\n", sep="")
print(xtable(tab2[[i2]][tab2[[i2]]$Type=="QC",]), include.rownames=F, include.colnames=F, hline.after=NULL, only.contents=T)
cat("\r\n \\hline \r\n", "Mean & & & & & & ", round(mean(abs(tab2[[i2]][tab2[[i2]]$Type=="QC", 7]), na.rm=T),2), " & ",
round(mean(abs(tab2[[i2]][tab2[[i2]]$Type=="QC", 8]), na.rm=T),2), " \\\\"," \r\n", sep="")
cat("\r\n \\end{longtable} \r\n \\end{center}", "\r\n", sep="")
cat("\r\n", "\r\n", sep="")
}
# Print the table of means - Pools
cat("\\begin{center}\\footnotesize \r\n Table of means: Pools \r\n \\begin{longtable}{p{1.5cm}r *{6}{c}} \r\n", sep="")
cat("\\hline \r\n SPL & Type & MFI & Counts & Expected & Measured & Precision \\\\ \r\n", sep="")
cat("\\hline \r\n \\endhead \r\n \\hline \r\n \\endfoot \r\n\n \\hline \\hline \r\n \\endlastfoot \r\n", sep="")
print(xtable(tab2[[i2]][tab2[[i2]]$Type=="Pool", 1:7]), include.rownames=F, include.colnames=F, hline.after=NULL, only.contents=T)
cat("\r\n \\hline \r\n", "Mean & & & & & & ", round(mean(abs(tab2[[i2]][tab2[[i2]]$Type=="Pool", 7]), na.rm=T),2), " \\\\"," \r\n", sep="")
cat("\r\n \\end{longtable} \r\n \\end{center}", "\r\n", sep="")
cat("\r\n", "\r\n", sep="")
# Print the table of means - Samples
cat("\\begin{center}\\footnotesize \r\n Table of means: Samples \r\n \\begin{longtable}{p{2.5cm}r *{6}{c}} \r\n", sep="")
cat("\\hline \r\n SPL & Type & MFI & Counts & Expected & Measured & Precision \\\\ \r\n", sep="")
cat("\\hline \r\n \\endhead \r\n \\hline \r\n \\endfoot \r\n\n \\hline \\hline \r\n \\endlastfoot \r\n", sep="")
print(xtable(tab2[[i2]][tab2[[i2]]$Type %in% c("Sample","Retest"), 1:7]), include.rownames=F,
include.colnames=F, hline.after=NULL, only.contents=T)
cat("\r\n \\hline \r\n", "Mean & & & & & & ", round(mean(abs(tab2[[i2]][tab2[[i2]]$Type %in% c("Sample",
"Retest"), 7]), na.rm=T),2), " \\\\"," \r\n", sep="")
cat("\r\n \\end{longtable} \r\n \\end{center}", "\r\n", sep="")
cat("\r\n", "\r\n", sep="")
# Print the table of duplicates - all samples
cat("\\begin{center}\\footnotesize \r\n Table of duplicate results \r\n \\begin{longtable}{p{4.0cm}r *{6}{c}} \r\n", sep="")
cat("\\hline \r\n SPL & Type & MFI & Counts & Expected & Measured & Used \\\\ \r\n", sep="")
cat("\\hline \r\n \\endhead \r\n \\hline \r\n \\endfoot \r\n\n \\hline \\hline \r\n \\endlastfoot \r\n", sep="")
print(xtable(tab1[[i2]]), include.colnames=F, hline.after=NULL, only.contents=T)
cat("\r\n \\end{longtable} \r\n \\end{center}", "\r\n", "\\newpage", "\r\n", sep="")
cat("\r\n", "\r\n", sep="")
if (i2<immunoassay.environment$n) cat("\n \\newpage \n\n", sep="")
}
rm(tab,tab1,tab2, i2, i3, pfile)
@
\end{document}
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