diff --git a/Doc_BioassayReport.Rmd b/Doc_BioassayReport.Rmd index 95bcdc7..c1c9bdf 100644 --- a/Doc_BioassayReport.Rmd +++ b/Doc_BioassayReport.Rmd @@ -365,7 +365,6 @@ The results of the non-linear fitting procedure for the unrestricted model (8 pa kable(UnRPLAausw, format = "markdown", caption= "UNrestricted 4PL evaluation", digits=3, row.names = F) - ``` diff --git a/TestInhibitor.numbers b/TestInhibitor.numbers new file mode 100644 index 0000000..d8864ea Binary files /dev/null and b/TestInhibitor.numbers differ diff --git a/TestInhibitor.xlsx b/TestInhibitor.xlsx new file mode 100644 index 0000000..5ea26ae Binary files /dev/null and b/TestInhibitor.xlsx differ diff --git a/Tests3Plates.xlsx b/Tests3Plates.xlsx new file mode 100644 index 0000000..f7849dd Binary files /dev/null and b/Tests3Plates.xlsx differ diff --git a/Testsdfac0.2b1.xlsx b/Testsdfac0.2b1.xlsx new file mode 100644 index 0000000..25a3b69 Binary files /dev/null and b/Testsdfac0.2b1.xlsx differ diff --git a/Testsdfac0.2b_3.xlsx b/Testsdfac0.2b_3.xlsx new file mode 100644 index 0000000..89a17f1 Binary files /dev/null and b/Testsdfac0.2b_3.xlsx differ diff --git a/Testsdfac0.2b_3Dil12.xlsx b/Testsdfac0.2b_3Dil12.xlsx new file mode 100644 index 0000000..4f35aa2 Binary files /dev/null and b/Testsdfac0.2b_3Dil12.xlsx differ diff --git a/server.R b/server.R index bc90a60..ff3da6b 100644 --- a/server.R +++ b/server.R @@ -448,10 +448,10 @@ ANOVAlintests <- function(ro_new, circles, Lim, PureErrFlag) { "F-test on R^2 A","F_test on R^2 B", "F-test on slope A","F-test on slope B", "F-test on non-parallelism","F-test on preparation"), - test_results = c(ifelse(p_F_regr<0.05,0,1),ifelse(p_F_nonlin<0.05,0,1), - ifelse(pFR2_A<0.05,0,1),ifelse(pFR2_B<0.05,0,1), + test_results = c(ifelse(p_F_regr<0.05,0,1),ifelse(p_F_nonlin<0.05,1,0), + ifelse(pFR2_A<0.05,1,0),ifelse(pFR2_B<0.05,1,0), ifelse(p_F_slope_A<0.05,0,1),ifelse(p_F_slope_B<0.05,0,1), - ifelse(p_F_nonp<0.05,0,1),ifelse(p_F_prep<0.05,0,1)), + ifelse(p_F_nonp<0.05,1,0),ifelse(p_F_prep<0.05,0,1)), estimate = c(p_F_regr, p_F_nonlin,pFR2_A,pFR2_B,p_F_slope_A, p_F_slope_B,p_F_nonp,p_F_prep), Source = c("Treatment","Preparation","Regression","Non-parallelism", @@ -571,7 +571,7 @@ pot4plFUNC <- function(ro_new, PureErrFlag) { potU_est_log <- exp(confintd(mu_log, "r", method="asymptotic")) colnames(pot_est_log) <- c("estimate","lowerCI2","upperCI") colnames(potU_est_log) <- c("estimate","lowerCI2","upperCI") - + #browser() su_mr_log <- summary(mr_log) Dat$RMSE_Rlog <- su_mr_log$sigma su_mu_log <- summary(mu_log) @@ -800,7 +800,7 @@ tests_FUNC <- function(ro_new, Lim, PureErrFlag) { test_lowA <- test_d; test_uppA <- test_a #browser() res_tab <- data.frame(test= c("F-test on sign. of regression*", - "EQ test on significance of lower asymptotes", + "EQ test on lower asymptotes difference", "EQ test ratio of lower asymptotes", "EQ test ratio of Hill slopes", "EQ test ratio of upper asymptotes", @@ -834,7 +834,7 @@ ANOVA4plUnresfunc <- function(ro_new, sigmoid) { all_l$Conc <- exp(all_l$log_dose) all_l$readout[all_l$readout < 0] <- 0.01 - pot <- drm(readout ~ Conc, isSample, data=all_l2, fct=LL.4(names=c("b","d","a","c")), + pot <- drm(readout ~ Conc, isSample, data=all_l, fct=LL.4(names=c("b","d","a","c")), pmodels=data.frame(1,1,1,isSample)) potU <- drm(readout ~ Conc, isSample, data=all_l, fct=LL.4(names=c("b","d","a","c")), pmodels=data.frame(isSample, isSample,isSample,isSample)) @@ -962,7 +962,7 @@ function(input,output, session) { #browser() cnSheets <- Dat$sheets cnSheets2 <- c("please choose", cnSheets) - selectInput(inputId = "sheet", label="Select a sheet:",choices = cnSheets2) + selectInput(inputId = "sheet", label="Select a sheet:",choices = cnSheets) } }) observeEvent(input$sign_out, { @@ -976,7 +976,7 @@ function(input,output, session) { if (!is.null(input$iFile)) { if (!is.null(input$sheet)) { if (input$sheet != "please choose") { - + #browser() XLdat <- Dat$wb[input$sheet][[1]] if (is.null(XLdat)) XLdat <- Dat$wb[Dat$sheets[1]][[1]] @@ -1095,7 +1095,7 @@ function(input,output, session) { observe({ pot_est3 <- data.frame(pot_est*100) MaxPl <- max(input$upperPot, pot_est3$upperCI) - MinPl <- max(input$lowerPot, pot_est3$lowerCI) + MinPl <- min(input$lowerPot, pot_est3$lowerCI) MaxPl_ <- MaxPl*1.1 MinPl_ <- MinPl*0.9 @@ -1787,12 +1787,13 @@ function(input,output, session) { #### output 4PL ANOVA tests --- output$ANOVA <- DT::renderDataTable({ sigmoid <- sigmoid() - tab <- ANOVA4plUnresfunc(sim2(),sigmid) - dat <- datatable(df[,1:3], + tab <- ANOVA4plUnresfunc(sim2(),sigmoid) + #browser() + dat <- datatable(tab, options=list( dom="t",rownames=F - )) %>% formatStyle("p.value", target="row", - backgroundColor = styleEqual(c("p.value"), + )) %>% formatStyle("p_value", target="row", + backgroundColor = styleEqual(c("p_value"), c("lightgrey"))) }) diff --git a/ui.R b/ui.R index b6737bf..f5632f9 100644 --- a/ui.R +++ b/ui.R @@ -236,9 +236,9 @@ function(req) { sliderInput("sdfac","Variability as % of lower to upper asymptote", max=10, value=3, min=0.1, step=0.1), checkboxInput("heterosked","heteroskedastic noise", FALSE), sliderInput("potencydiff","potency of test (%)", max=200, min=50, value=100, step=1), - sliderInput("outlL","outlier in lower asymptote", min=0, max=1.5, value=0, step=1), - sliderInput("outlM","outlier in mid part", min=0, max=1.5,value=0, step=1), - sliderInput("outlU","outlier in upper asymptote", min=0, max=1.5,value=0, step=1) + sliderInput("outlL","outlier in lower asymptote", min=0, max=1.5, value=0, step=0.1), + sliderInput("outlM","outlier in mid part", min=0, max=1.5,value=0, step=0.1), + sliderInput("outlU","outlier in upper asymptote", min=0, max=1.5,value=0, step=0.1) ), column(1, tags$table(id="dose-table", @@ -258,7 +258,7 @@ function(req) { )), column(4, "4 PL ANOVA unrestricted", - DT::renderDataTable("ANOVA"), + DT::dataTableOutput("ANOVA"), h5("Please note that for the CIs of rel. potency the RSS of the restricted model is used"), h5("RSS ... 'Residual error' in the SumSquares column"), h5("MSE ... 'Residual error' in the MSs column"),