report generation after new setup of repo; linearity XL report improved

dev/Doc_BioassayLinReport.Rmd

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+---
+output:
+  pdf_document:
+    extra_dependencies: ["float"]
+    number_sections: true
+    toc: true
+    toc_depth: 3
+header_includes:
+  -\usepackage{fancyheadr}
+  -\setlength{\headheight}{22pt}%
+  -\usepackage{lastpage}
+  -\pagestyle{fancy}
+  -\usepackage{pdflscape}
+  -\usepackage{longtable}
+  -\rhead{\includegraphics[width=.15\textwidth]{`r getwd()`/logo.png}}
+params:
+  FileName: NA
+  newTitle: NA
+  author: NA
+  REP: NA
+  REPlin: NA
+  coeffsLin: NA
+  NoP: NA
+  Assay: NA
+author: "Author: `r params$author`"
+title: |
+    | ![](logo.png){width=1in}
+    | Linear bioassay evaluation
+subtitle: |
+  `r params$FileName`
+  
+  <left> Unique time: </left> <right> `r Sys.time()`</right>
+date: "`r paste(params$NoP, params$Assay)`"
+
+---
+
+<!-- \fancyfoot[C]{\thepage\ of \pageref{LastPage}} -->
+<!-- \newpage -->
+
+<!-- \newpage -->
+
+```{r setup, include=FALSE}
+
+knitr::opts_chunk$set(echo = TRUE)
+
+library(knitr)
+library(DT)
+
+REP <- params$REP
+REPlin <- params$REPlin
+author <- params$author
+coeffsLin <- params$coeffsLin
+
+all_l <- REP$all_l
+circles <- REPlin$circles
+#ANOVAXLS <- REP$ANOVAXLS
+SuModAB <- REPlin$SuModAB
+SuModABu <- REPlin$SuModABu
+LinTests <-  REPlin$LinTests
+XLplotLin <- REPlin$pLin
+LinPotTab <- REPlin$LinPotTab
+
+XLdat2 <- REP$XLdat2
+
+LinTests1 <- LinTests[,1:3]
+ANOVAlin <- LinTests[,4:ncol(LinTests)]
+
+
+```
+
+
+# Introduction
+
+Bioassay potency estimation uses statistical methods to quantify the strength of a biological product or drug by comparing its response to that of a reference standard. Biological responses are inherently variable, affected by assay conditions, cell systems or organisms, and measurement noise. To control this variability, a linear regression approach is used to obtain reliable potency values. Three consecutive dilution steps showing the steepest slope are used for linear fitting.   
+USP<1034> recommends calculation of standard errors of ratios of the parameters using Fieller's theorem [Finney D.J. 1978] or using the "delta" method (for a discussion about the "delta" method see [Ver Hoef 2012]). The present analysis calculated the relative potency with the "delta" method. The formula of the relative potency is in the Appendix.
+
+# Raw data
+
+All data used for evaluation is shown in table 1.
+
+```{r Alll, echo=FALSE, warning=FALSE, results='asis'}
+
+kable(XLdat2, format = "markdown", caption= "Uploaded data (test and reference) ", digits=3)
+
+```
+
+The linerar regression is calculated on the readout listed in table 2.
+
+```{r Circles, echo=FALSE, warning=FALSE, results='asis'}
+
+kable(circles, format = "markdown", caption= "Concentrations and readout used for linear regression", digits=3, row.names = F)
+
+```
+
+
+
+# Results
+
+## Overall result
+
+```{r Over_all, echo=FALSE, comment=NA, warning=NA, message=NA}
+
+#browser()
+potFlag <- 0
+if (LinPotTab[1,"test_result"]==1) potFlag <- 1
+AnalysisFlag <- FALSE
+if (potFlag==1 | sum(LinTests$test_results)>0) AnalysisFlag <- TRUE
+
+colFmt <- function() {
+  
+  outputFormat <- knitr::opts_knit$get("rmarkdown.pandoc.to")
+ if(AnalysisFlag) {
+    text <- paste("\\textcolor{red}{Analysis failed}",sep="")
+  } else  {
+    text <- paste("\\textcolor{black}{Analysis succeeded}",sep="")
+  }  
+  return(text)
+}
+
+
+```
+
+`r colFmt()`
+
+
+## Plots and ANOVA
+
+Plots in Figure 1 show the restricted and unrestricted model, respectively.
+
+```{r LinPlot, echo=FALSE, warning=FALSE, fig.height=4, fig.width=6, fig.cap="Plot of models", fig.align='left'}
+
+library(cowplot)
+
+
+plot_grid(XLplotLin)
+
+
+
+```
+
+
+The relative potency can be read from tbale 3.
+
+```{r LinPotTab, echo=FALSE, warning=FALSE, results='asis'}
+
+kable(LinPotTab, format = "markdown", caption= "Potency table", digits=3)
+
+
+```
+
+
+
+
+The ANOVA of the unconstrained model is listed in table 4.
+
+```{r anovaxls, echo=FALSE, warning=FALSE, results='asis'}
+
+kable(ANOVAlin, format = "markdown", caption= "ANOVA table unrestricted", digits=3)
+
+RMSE <- sqrt(ANOVAlin[5,4])
+
+```
+
+The standard deviation of the model is `r RMSE`. 
+
+The assay suitability tests are shown in table 5.
+
+
+```{r SST_ergebn, echo=FALSE, cache=FALSE, warning=FALSE, message=FALSE, tidy=TRUE}
+
+kable(LinTests1, row.names = F, format = "markdown", caption="Assay suitability test results", digits=3)
+
+
+```
+
+
+The estimate is the p-value of the test.  
+F-tests on regression, significance of slopes, and preparation need to have a p-value <0.05 to pass.
+All other tests pass if p-value > 0.05.
+
+  0 ... test passed;
+  
+  1 ... test failed);
+
+(NOTE: F-tests are sensitive, when the residual variability of the method is small. On the other hand effects may not be detected if residual variability is high.)
+
+## Fitting results
+
+The results of the linear fitting procedure for the restricted model is listed in table 6:
+
+```{r SumCSSI, echo=FALSE, warning=FALSE, results='asis'}
+
+kable(SuModAB, format = "markdown", caption= "Restricted linear regression (CSSI)", digits=3, row.names = F)
+
+
+```
+
+CSSI: common slope, separate intercept
+
+The results of the linear fitting procedure for the unrestricted model is listed in table 7.
+
+
+```{r SumSSSI, echo=FALSE, warning=FALSE, results='asis'}
+
+kable(SuModABu, format = "markdown", caption= "Restricted linear regression (SSSI)", digits=3, row.names = F)
+
+
+```
+
+SSSI: separate slope, separate intercept
+
+
+
+
+# Appendix: Formulas
+
+## Potency of linear PLA
+
+$$
+ rel Potency = \frac{I_{ref} - I_{test}}{k}
+$$
+where: I... intercept of reference or test
+k ... common slope
+
+
+
+# Literature
+
+Finney, D.J.: (1978) Statistical Method in Biological Assay, London: Charles Griffin House, 3rd edition (pp. 80-82)
+
+Franz, V.H.: Ratios: A short guide to confidence limits and proper use. arXiv:0710.2024v1, 10 Oct 2007
+
+VerHoef, J.M.: Who invented the Delta Method? The American Statistician, 2012, 66:2, 124-127 DOI: 10.1080/00031305.2012.687494
+
+
+
+