From 4a918da6d5f971335b74b0fc83cb08f5c3163f95 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 21 Jul 2017 14:42:14 +0200
Subject: Rename twa to max_twa_parent, update docs

---
 R/max_twa_parent.R | 65 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 R/twa.R            | 65 ------------------------------------------------------
 2 files changed, 65 insertions(+), 65 deletions(-)
 create mode 100644 R/max_twa_parent.R
 delete mode 100644 R/twa.R

(limited to 'R')

diff --git a/R/max_twa_parent.R b/R/max_twa_parent.R
new file mode 100644
index 00000000..8d8b77f8
--- /dev/null
+++ b/R/max_twa_parent.R
@@ -0,0 +1,65 @@
+# Copyright (C) 2016,2017 Johannes Ranke
+# Contact: jranke@uni-bremen.de
+
+# This file is part of the R package mkin
+
+# mkin is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+# details.
+
+# You should have received a copy of the GNU General Public License along with
+# this program. If not, see <http://www.gnu.org/licenses/>
+
+max_twa_parent <- function(fit, windows) {
+  parms.all <- c(fit$bparms.optim, fit$bparms.fixed)
+  obs_vars <- fit$obs_vars
+  if (length(obs_vars) > 1) {
+    warning("Calculation of maximum time weighted average concentrations is",
+            "currently only implemented for the parent compound using",
+            "analytical solutions")
+  }
+  obs_var <- obs_vars[1]
+  spec = fit$mkinmod$spec
+  type = spec[[1]]$type
+
+  M0 <- parms.all[paste0(obs_var, "_0")]
+
+  if (type == "SFO") {
+    k_name <- paste0("k_", obs_var)
+    if (fit$mkinmod$use_of_ff == "min") {
+      k_name <- paste0(k_name, "_sink")
+    }
+    k <- parms.all[k_name]
+    twafunc <- function(t) {
+      M0 * (1 - exp(- k * t)) / (k * t)
+    }
+  }
+  if (type == "FOMC") {
+    alpha <- parms.all["alpha"]
+    beta <- parms.all["beta"]
+    twafunc <- function(t) {
+      M0 * (beta)/(t * (1 - alpha)) * ((t/beta + 1)^(1 - alpha) - 1)
+    }
+  }
+  if (type == "DFOP") {
+    k1 <- parms.all["k1"]
+    k2 <- parms.all["k2"]
+    g <- parms.all["g"]
+    twafunc <- function(t) {
+      M0/t * ((g/k1) * (1 - exp(- k1 * t)) + ((1 - g)/k2) * (1 - exp(- k2 * t)))
+    }
+  }
+  if (type %in% c("HS", "IORE", "SFORB")) {
+    stop("Calculation of maximum time weighted average concentrations is currently ",
+         "not implemented for the ", type, " model.")
+  }
+  res <- twafunc(windows)
+  names(res) <- windows
+  return(res)
+}
diff --git a/R/twa.R b/R/twa.R
deleted file mode 100644
index e8894b0b..00000000
--- a/R/twa.R
+++ /dev/null
@@ -1,65 +0,0 @@
-# Copyright (C) 2016 Johannes Ranke
-# Contact: jranke@uni-bremen.de
-
-# This file is part of the R package mkin
-
-# mkin is free software: you can redistribute it and/or modify it under the
-# terms of the GNU General Public License as published by the Free Software
-# Foundation, either version 3 of the License, or (at your option) any later
-# version.
-
-# This program is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
-# details.
-
-# You should have received a copy of the GNU General Public License along with
-# this program. If not, see <http://www.gnu.org/licenses/>
-
-twa <- function(fit, windows) {
-  parms.all <- c(fit$bparms.optim, fit$bparms.fixed)
-  obs_vars <- fit$obs_vars
-  if (length(obs_vars) > 1) {
-    warning("Calculation of maximum time weighted average concentrations is",
-            "currently only implemented for the parent compound using",
-            "analytical solutions")
-  }
-  obs_var <- obs_vars[1]
-  spec = fit$mkinmod$spec
-  type = spec[[1]]$type
-
-  M0 <- parms.all[paste0(obs_var, "_0")]
-
-  if (type == "SFO") {
-    k_name <- paste0("k_", obs_var)
-    if (fit$mkinmod$use_of_ff == "min") {
-      k_name <- paste0(k_name, "_sink")
-    }
-    k <- parms.all[k_name]
-    twafunc <- function(t) {
-      M0 * (1 - exp(- k * t)) / (k * t)
-    }
-  }
-  if (type == "FOMC") {
-    alpha <- parms.all["alpha"]
-    beta <- parms.all["beta"]
-    twafunc <- function(t) {
-      M0 * (beta)/(t * (1 - alpha)) * ((t/beta + 1)^(1 - alpha) - 1)
-    }
-  }
-  if (type == "DFOP") {
-    k1 <- parms.all["k1"]
-    k2 <- parms.all["k2"]
-    g <- parms.all["g"]
-    twafunc <- function(t) {
-      M0/t * ((g/k1) * (1 - exp(- k1 * t)) + ((1 - g)/k2) * (1 - exp(- k2 * t)))
-    }
-  }
-  if (type %in% c("HS", "IORE", "SFORB")) {
-    stop("Calculation of maximum time weighted average concentrations is currently ",
-         "not implemented for the ", type, " model.")
-  }
-  res <- twafunc(windows)
-  names(res) <- windows
-  return(res)
-}
-- 
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