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

R/Global.R

@@ -280,14 +280,14 @@ plot_f <- function(dat, TransFlag = F) { # sigmoid,det_sig,
   s_mr <- MODLS[[1]]
   a <- s_mr$coefficients["a", 1]
   b <- s_mr$coefficients["b", 1]
-  cs <- s_mr$coefficients["cs", 1]
+  c <- s_mr$coefficients["cs", 1]
   d <- s_mr$coefficients["d", 1]
   r <- s_mr$coefficients["r", 1]
 
   log_dose <- unique(all_l$log_dose)
   seq_x <- seq(min(log_dose), max(log_dose), 0.1)
-  SAMPLE <- a + (d - a) / (1 + exp(b * ((cs - r) - seq_x)))
-  REF <- a + (d - a) / (1 + exp(b * ((cs) - seq_x)))
+  SAMPLE <- a + (d - a) / (1 + exp(b * ((c - r) - seq_x)))
+  REF <- a + (d - a) / (1 + exp(b * (c - seq_x)))
 
   s_mu <- MODLS[[2]]
 
@@ -310,16 +310,16 @@ plot_f <- function(dat, TransFlag = F) { # sigmoid,det_sig,
   all_l2$readout[all_l2$readout < 0] <- 0.01
   all_l2$readouttrans <- log(all_l2$readout)
   slopeEC50 <- b * (d - a) / 4
-  Intercept <- a + (d - a) / 2 - b * (d - a) / 4 * cs
+  Intercept <- a + (d - a) / 2 - b * (d - a) / 4 * c
   # browser()
-  Xbendl3 <- cs - (1.5434 / b)
-  Xbendu3 <- cs + (1.5434 / b)
-  XbendlT <- cs - r - (1.5434 / b)
-  XbenduT <- cs - r + (1.5434 / b)
-  XasymplS <- cs - (3 / b)
-  XasympuS <- cs + (3 / b)
-  XasymplT <- cs - r - (3 / b)
-  XasympuT <- cs - r + (3 / b)
+  Xbendl3 <- c - (1.5434 / b)
+  Xbendu3 <- c + (1.5434 / b)
+  XbendlT <- c - r - (1.5434 / b)
+  XbenduT <- c - r + (1.5434 / b)
+  XasymplS <- c - (3 / b)
+  XasympuS <- c + (3 / b)
+  XasymplT <- c - r - (3 / b)
+  XasympuT <- c - r + (3 / b)
   bendpoints <- c(
     bendREF_lower = round(Xbendl3, 3), bendREF_upper = round(Xbendu3, 3),
     bendSAMPLE_lower = round(XbendlT, 3), bendSAMPLE_upper = round(XbenduT, 3),
@@ -362,7 +362,7 @@ plot_f <- function(dat, TransFlag = F) { # sigmoid,det_sig,
     geom_vline(xintercept = c(XbendlT, XbenduT), col = "#C2173F", linetype = 2) +
     geom_vline(xintercept = c(XasymplS, XasympuS), col = "#4545BABB", linetype = 3) +
     geom_vline(xintercept = c(XasymplT, XasympuT), col = "#C2173FBB", linetype = 3) +
-    annotate("text", x = cs, y = a + (d - a) / 2, label = "0", size = 5) +
+    annotate("text", x = c, y = a + (d - a) / 2, label = "0", size = 5) +
     geom_abline(slope = slopeEC50, intercept = Intercept) +
     theme(legend.position = "none")
   Dat$p2 <- p2
@@ -419,16 +419,8 @@ plot_f <- function(dat, TransFlag = F) { # sigmoid,det_sig,
   cte <- Sum_u$coefficients["cs", 1] - Sum_u$coefficients["r", 1]
   dst <- Sum_u$coefficients["ds", 1]
   dte <- Sum_u$coefficients["dt", 1]
-  # } else {
-  #   ast <- det_sig[5]
-  #   ate <- det_sig[6]
-  #   bst <- det_sig[1]
-  #   bte <- det_sig[2]
-  #   cst <- det_sig[7]
-  #   cte <- det_sig[8]
-  #   dst <- det_sig[3]
-  #   dte <- det_sig[4]
-  # }
+ 
+  
   REFu <- ast + (dst - ast) / (1 + exp(bst * (cst - seq_x)))
   SAMPLEu <- ate + (dte - ate) / (1 + exp(bte * (cte - seq_x)))
   pl_df2 <- cbind(seq_x, SAMPLEu, REFu)
@@ -877,7 +869,7 @@ ANOVAlintests <- function(ro_new, circles, Lim, PureErrFlag) {
 #'
 #' PlotLinPLA_FUNC(circle, sigmoid, all_l2, pl_df, indS, indT)
 PlotLinPLA_FUNC <- function(circle, sigmoid, all_l2, pl_df, indS, indT) {
-  # browser()
+   #browser()
   mLin <- gsl_nls(readout ~ (intS + r) * isSample + intS * isRef + k * log_dose,
     data = circle,
     start = list(intS = 0, k = 1, r = 0),