adding new RSCABS, MQJT related functions

README.Rmd

@@ -31,6 +31,8 @@ Some of the functions are adapted from archived packages or single functions of
 
 This package is open source, and any contributions or improvements, especially on the documentation side,  are welcome. 
 
+*Please note that the documentation website for this package is currently under development. Some articles are still placeholders, and many more are on the way. However, the ongoing development of the website does not impact the usage of this R package. *
+
 ## Installation
 
 You can install the development version of drcHelper from [GitHub](https://github.com/) with:
@@ -51,85 +53,69 @@ pak::pak("Bayer-Group/drcHelper")
 
 ## Data Overview
 
-```{r message=FALSE,warning=FALSE}
-library(drcHelper)
-library(drc)
-library(dplyr)
-library(purrr)
-library(ggplot2)
-theme_set(theme_bw())
-sum1 <- oecd201 %>% group_by(Time,Treatment) %>% summarise(Yield_mean=mean(Yield),Yield_sd=sd(Yield),GrowthRate_mean=mean(GrowthRate),GrowthRate_sd=sd(GrowthRate))
-sum0 <- sum1%>%filter(Treatment=="Control")%>%rename(Yield0=Yield_mean,GrowthRate0=GrowthRate_mean)%>%dplyr::select(c(Time,Yield0,GrowthRate0))
-# sum0
-sumtab <- left_join(sum1%>%filter(Time>0),sum0) %>% mutate(Yield_Inhibition=(Yield0-Yield_mean)/Yield0*100,GrowthRate_Inhibition=(GrowthRate0-GrowthRate_mean)/GrowthRate0*100) %>% dplyr::select(c(Time,Treatment,Yield_mean,Yield_sd,Yield_Inhibition,GrowthRate_mean,GrowthRate_sd,GrowthRate_Inhibition))
-```
+## Preliminary Summary
 
 
-```{r}
-sumtab%>%dplyr::select(c(Yield_mean,Yield_sd,Yield_Inhibition))%>%filter(Time==72)%>%knitr::kable(.,digits = 2,caption="<center><strong>Yield Summary at Time 72h<strong><center>",escape = FALSE)##%>% kableExtra::kable_styling(bootstrap_options = "striped")##%>%kableExtra::kable_classic_2()
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  warning = FALSE,
+  message = FALSE
+)
+library(tidyverse)
 ```
 
 
-```{r}
-sumtab%>%dplyr::select(c(GrowthRate_mean,GrowthRate_sd,GrowthRate_Inhibition))%>%filter(Time==72)%>%knitr::kable(.,digits = 2,caption="<center><strong>Growth Rate Summary at Time 72h<strong><center>",escape = FALSE)##%>%kableExtra::kable_classic()
+```{r setup}
+library(drcHelper)
+
 ```
 
-## Model Fitting and Comparison For Yield
+```{r}
+data("dat_medium")
+dat_medium <- dat_medium %>% mutate(Treatment=factor(Dose,levels=unique(Dose))) 
+dat_medium$Response[dat_medium$Response < 0] <- 0
+prelimPlot3(dat_medium)
+prelimSummary(dat_medium) %>% knitr::kable(.,digits = 3)
+```
 
-```{r warning=FALSE,message=FALSE}
-datTn<- subset(oecd201,Time==72)
+## Fitting multiple models and rank them.
 
-mod <- drm(Yield~Concentration,data=datTn,fct=LL.3())
-fctList <- list(LL2.3(),W2.3(),W1.3(),EXD.3(),EXD.2(),LN.3(),W2.4(),LL.4(),LL2.4())
-plot(mod,type="all")
+```{r}
+mod <- drm(Response~Dose,data=dat_medium,fct=LL.3())
+fctList <- list(LN.4(),LL.4(),W1.3(),LL2.2())
+# plot(mod,type="all")
 res <- mselect.plus(mod,fctList = fctList )
 modList <- res$modList
-edResTab <- mselect.ED(modList = modList,respLev = c(10,20,50),trend=datTn$Trend_Yield[1])
-plot.edList(edResTab)
-resComp <- drcCompare(modRes = res,trend="Decrease")
-```
-Note that by default settings, the fitted models did not converge except for the LL.3 model. 
+res$Comparison
 
-```{r}
-knitr::kable(edResTab[1:3,],caption = "14 day TSL Yield",digits = 3)
+drcCompare(modRes=res)
 ```
 
+
 ```{r}
-knitr::kable(resComp[1,],caption = "14 day TSL Yield, Model Comparison",digits = 3)
+library(purrr)
+edResTab <- mselect.ED(modList = modList,respLev = c(10,20,50),trend="Decrease",CI="inv")
+edResTab
 ```
 
-```{r fig.cap="Yield Model Fits"}
-plot.modList(modList,scale="logx")
-
-```
 
-```{r}
-plot.modList(modList[c(1,2,3,4)],scale="logx",npts=40)
-p <-plot.modList(modList[c(1)],scale="logx",npts=80)+theme(legend.position = "none")+ggtitle("14 day Total Shoot Length, \n3-parameter type II Weibull Model Fit")
-addECxCI(p=p,object=modList[[1]],EDres=NULL,trend="Decrease",endpoint="EC", respLev=c(10,20,50),
-                     textAjust.x=0.01,textAjust.y=1,useObsCtr=FALSE,d0=NULL,textsize = 4,lineheight = 1,xmin=0.012)+ylab("Total Shoot Length [cm]") + xlab("Concentration [µg a.s./L]")
-## ggsave("TSL_14d_Yield.png")
-```
+## Plot multiple models together
 
 ```{r}
-resED <- t(edResTab[1:3, c(2,4,5,6)])
-colnames(resED) <- paste("EC", c(10,20,50))
-knitr::kable(resED,caption = "Total Shoot Length Growth Yield at 14 day",digits = 3)
+p <- plot.modList(modList[1:3])
+p
 ```
 
-```{r}
 
-mod <-modList[[1]]
-edres <- ED.plus(mod,c(5,10,20,50),trend="Decrease")
-pander::pander(as.data.frame(edres))
+## Adding ECx and ECx CI's to the plots
 
+```{r}
+## addECxCI(p)
 ```
 
 
-```{r}
-modsum <- summary(mod)
-pander::pander(coef(modsum))
-```
 
 
 ## ToDo