From a071d46f698397a6c8247e19eceb0fcd5f139056 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 10 Oct 2019 12:25:42 +0200
Subject: Fix set_nd for metabolites, handle zero at time zero

---
 ChangeLog                    | 12 ++++++++++++
 R/set_nd.R                   | 10 +++++-----
 docs/reference/set_nd.html   |  4 ++--
 man/set_nd.Rd                |  4 ++--
 tests/testthat/test_set_nd.R |  2 ++
 5 files changed, 23 insertions(+), 9 deletions(-)

diff --git a/ChangeLog b/ChangeLog
index a14aa23..b0775e1 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,15 @@
+commit a5503d3e26408f7308a7bf4da617205b93d17422
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2019-10-10 09:21:46 +0200
+
+    Fix documentation for set_nd
+
+commit a5e458ecb33ae87e46b2237174a194f6252a97cf
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2019-10-10 08:53:30 +0200
+
+    Finish documentation of set_nd and test it
+
 commit 63df3871a442de4bf47e4d9de1449e7f6ed65b2f
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Date:   2019-10-09 19:17:07 +0200
diff --git a/R/set_nd.R b/R/set_nd.R
index 10c5cba..b2fb720 100644
--- a/R/set_nd.R
+++ b/R/set_nd.R
@@ -17,10 +17,10 @@
 #' @param loq Limit of quantification(numeric). Must be specified if the FOCUS rule to
 #' stop after the first non-detection is to be applied
 #' @param time_zero Is the first value in the series a time zero value?
-#' @param time_zero_nd_value Which value should we use for non-detects at time zero?
+#' @param time_zero_nd_value Which value should we use for non-detects or zero values at time zero?
 #' @param stop_after_first_nondetect Should we really stop after the first non-detection?
 #' @references FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation
-#'   Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, 
+#'   Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1,
 #'   18 December 2014, p. 251
 #' @describeIn set_nd Set non-detects in residues series
 #' @export
@@ -56,7 +56,7 @@ set_nd <- function(r, lod, loq = NA,
 
   #  Handle nd values
   if (time_zero) {
-    if (r[1] == "nd") {
+    if (r[1] %in% c("nd", 0)) {
       residues_present = FALSE
       result[1] <- time_zero_nd_value
     } else {
@@ -94,12 +94,12 @@ set_nd <- function(r, lod, loq = NA,
             return(as.numeric(result))
           }
         }
-
       }
       if (!residues_in_next) residues_present <- FALSE
       else residues_present <- TRUE
+    } else {
+      residues_present <- TRUE
     }
-
   }
   return(as.numeric(result))
 }
diff --git a/docs/reference/set_nd.html b/docs/reference/set_nd.html
index 75a8fb1..7b0e779 100644
--- a/docs/reference/set_nd.html
+++ b/docs/reference/set_nd.html
@@ -154,7 +154,7 @@ stop after the first non-detection is to be applied</p></td>
     </tr>
     <tr>
       <th>time_zero_nd_value</th>
-      <td><p>Which value should we use for non-detects at time zero?</p></td>
+      <td><p>Which value should we use for non-detects or zero values at time zero?</p></td>
     </tr>
     <tr>
       <th>stop_after_first_nondetect</th>
@@ -173,7 +173,7 @@ stop after the first non-detection is to be applied</p></td>
     <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
 
     <p>FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation
-  Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, 
+  Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1,
   18 December 2014, p. 251</p>
     
 
diff --git a/man/set_nd.Rd b/man/set_nd.Rd
index bdbc6d2..085b606 100644
--- a/man/set_nd.Rd
+++ b/man/set_nd.Rd
@@ -22,7 +22,7 @@ stop after the first non-detection is to be applied}
 
 \item{time_zero}{Is the first value in the series a time zero value?}
 
-\item{time_zero_nd_value}{Which value should we use for non-detects at time zero?}
+\item{time_zero_nd_value}{Which value should we use for non-detects or zero values at time zero?}
 
 \item{stop_after_first_nondetect}{Should we really stop after the first non-detection?}
 }
@@ -59,6 +59,6 @@ set_nd(metabolite, 0.02)
 }
 \references{
 FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation
-  Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, 
+  Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1,
   18 December 2014, p. 251
 }
diff --git a/tests/testthat/test_set_nd.R b/tests/testthat/test_set_nd.R
index 29087a8..6b73e2d 100644
--- a/tests/testthat/test_set_nd.R
+++ b/tests/testthat/test_set_nd.R
@@ -17,6 +17,8 @@ test_that("Simple residue series processed as intended", {
   expect_equal(set_nd(metabolite, 0.02, loq = 0.05),
     c(NA, NA, .01, .03, .06, .1, .11, .1, .09, .05, .03, .01, NA))
 
+  expect_equal(set_nd(c("nd", 1, 0.2, "nd"), 0.1), c(NA, 1, 0.2, 0.05))
+
 })
 
 test_that("Simple residue series are processed as in the FOCUS guidance", {
-- 
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