1 files changed, 0 insertions, 108 deletions
diff --git a/R/endpoints.R b/R/endpoints.R
deleted file mode 100644
index c9a6a51..0000000
--- a/R/endpoints.R
+++ /dev/null
@@ -1,108 +0,0 @@
-endpoints <- function(fit, pseudoDT50 = FALSE) {
-  # Calculate dissipation times DT50 and DT90 and, if necessary, formation
-  # fractions and SFORB eigenvalues from optimised parameters
-  ep <- list()
-  obs_vars <- fit$obs_vars
-  parms.all <- fit$bparms.ode
-  ep$distimes <- data.frame(DT50 = rep(NA, length(obs_vars)), 
-			    DT90 = rep(NA, length(obs_vars)), 
-    row.names = obs_vars)
-  ep$ff <- vector()
-  ep$SFORB <- vector()
-  for (obs_var in obs_vars) {
-    type = names(fit$mkinmod$map[[obs_var]])[1]  
-
-    # Get formation fractions if directly fitted, and calculate remaining fraction to sink
-    f_names = grep(paste("f", obs_var, sep = "_"), names(parms.all), value=TRUE)
-    f_values = parms.all[f_names]
-    f_to_sink = 1 - sum(f_values)
-    names(f_to_sink) = ifelse(type == "SFORB", 
-                            paste(obs_var, "free", "sink", sep = "_"), 
-                            paste(obs_var, "sink", sep = "_"))
-    for (f_name in f_names) {
-      ep$ff[[sub("f_", "", sub("_to_", "_", f_name))]] = f_values[[f_name]]
-    }
-    ep$ff = append(ep$ff, f_to_sink)
-
-    # Get the rest
-    if (type == "SFO") {
-      k_names = grep(paste("k", obs_var, sep="_"), names(parms.all), value=TRUE)
-      k_tot = sum(parms.all[k_names])
-      DT50 = log(2)/k_tot
-      DT90 = log(10)/k_tot
-      for (k_name in k_names)
-      {
-        ep$ff[[sub("k_", "", k_name)]] = parms.all[[k_name]] / k_tot
-      }
-    }
-    if (type == "FOMC") {
-      alpha = parms.all["alpha"]
-      beta = parms.all["beta"]
-      DT50 = beta * (2^(1/alpha) - 1)
-      DT90 = beta * (10^(1/alpha) - 1)
-    }
-    if (type == "DFOP") {
-      k1 = parms.all["k1"]
-      k2 = parms.all["k2"]
-      g = parms.all["g"]
-      f <- function(t, x) {
-        fraction <- g * exp( - k1 * t) + (1 - g) * exp( - k2 * t)
-        (fraction - (1 - x/100))^2
-      }
-      DTmax <- 1000
-      DT50.o <- optimize(f, c(0.001, DTmax), x=50)$minimum
-      DT50 = ifelse(DTmax - DT50.o < 0.1, NA, DT50.o)
-      DT90.o <- optimize(f, c(0.001, DTmax), x=90)$minimum
-      DT90 = ifelse(DTmax - DT90.o < 0.1, NA, DT90.o)
-    }
-    if (type == "HS") {
-      k1 = parms.all["k1"]
-      k2 = parms.all["k2"]
-      tb = parms.all["tb"]
-      DTx <- function(x) {
-        DTx.a <- (log(100/(100 - x)))/k1
-        DTx.b <- tb + (log(100/(100 - x)) - k1 * tb)/k2
-        if (DTx.a < tb) DTx <- DTx.a
-        else DTx <- DTx.b
-        return(DTx)
-      }
-      DT50 <- DTx(50)
-      DT90 <- DTx(90)
-    }
-    if (type == "SFORB") {
-      # FOCUS kinetics (2006), p. 60 f
-      k_out_names = grep(paste("k", obs_var, "free", sep="_"), names(parms.all), value=TRUE)
-      k_out_names = setdiff(k_out_names, paste("k", obs_var, "free", "bound", sep="_"))
-      k_1output = sum(parms.all[k_out_names])
-      k_12 = parms.all[paste("k", obs_var, "free", "bound", sep="_")]
-      k_21 = parms.all[paste("k", obs_var, "bound", "free", sep="_")]
-
-      sqrt_exp = sqrt(1/4 * (k_12 + k_21 + k_1output)^2 + k_12 * k_21 - (k_12 + k_1output) * k_21)
-      b1 = 0.5 * (k_12 + k_21 + k_1output) + sqrt_exp
-      b2 = 0.5 * (k_12 + k_21 + k_1output) - sqrt_exp
-
-      SFORB_fraction = function(t) {
-        ((k_12 + k_21 - b1)/(b2 - b1)) * exp(-b1 * t) +
-        ((k_12 + k_21 - b2)/(b1 - b2)) * exp(-b2 * t)
-      }
-      f_50 <- function(t) (SFORB_fraction(t) - 0.5)^2
-      max_DT <- 1000
-      DT50.o <- optimize(f_50, c(0.01, max_DT))$minimum
-      if (abs(DT50.o - max_DT) < 0.01) DT50 = NA else DT50 = DT50.o
-      f_90 <- function(t) (SFORB_fraction(t) - 0.1)^2
-      DT90.o <- optimize(f_90, c(0.01, max_DT))$minimum
-      if (abs(DT90.o - max_DT) < 0.01) DT90 = NA else DT90 = DT90.o
-
-      for (k_out_name in k_out_names)
-      {
-        ep$ff[[sub("k_", "", k_out_name)]] = parms.all[[k_out_name]] / k_1output
-      }
-
-      # Return the eigenvalues for comparison with DFOP rate constants
-      ep$SFORB[[paste(obs_var, "b1", sep="_")]] = b1
-      ep$SFORB[[paste(obs_var, "b2", sep="_")]] = b2
-    }
-    ep$distimes[obs_var, ] = c(DT50, DT90)
-  }
-  return(ep)
-}