Residue processing for depth profiles over time

14 files changed, 627 insertions, 427 deletions

diff --git a/ChangeLog b/ChangeLog
index 579b8bb..0ce369b 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,9 @@
+commit a2ca8be6f5593f0afd833ea73b62149055ee84f9
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2019-10-10 14:56:35 +0200
+
+    Do not mess with zero values at time zero
+
 commit a071d46f698397a6c8247e19eceb0fcd5f139056
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Date:   2019-10-10 12:25:42 +0200
diff --git a/DESCRIPTION b/DESCRIPTION
index 39e174b..af046d1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: pfm
 Type: Package
 Title: Utilities for Pesticide Fate Modelling
 Version: 0.5.7
-Date: 2019-10-10
+Date: 2019-10-15
 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de",
                   role = c("aut", "cre", "cph"),
                   comment = c(ORCID = "0000-0003-4371-6538"))
diff --git a/NAMESPACE b/NAMESPACE
index 8eb6863..fffadd7 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -36,8 +36,8 @@ export(perc_runoff_reduction_exposit)
 export(pfm_degradation)
 export(read.TOXSWA_cwa)
 export(sawtooth)
-export(set_nd)
-export(set_nd_focus)
+export(set_nd_nq)
+export(set_nd_nq_focus)
 export(soil_DT50)
 export(soil_Kfoc)
 export(soil_N)
diff --git a/R/set_nd.R b/R/set_nd.R
deleted file mode 100644
index a9f3df4..0000000
--- a/R/set_nd.R
+++ /dev/null
@@ -1,118 +0,0 @@
-#' Set non-detects in residue series without replicates
-#'
-#' Sets non-detects directly before or directly after detects to NA. Values between
-#' lod and loq are set to their mean value if an loq is specified.
-#' If 'time_zero' is set to TRUE, the residue series is assumed to start with time
-#' zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the
-#' set_nd_focus variant, this is zero, otherwise this argument has NA as default
-#' value.
-#' If stopping after the first non-detection is requested, as in in the FOCUS
-#' variant of the function, an loq has to be specified in order to decide
-#' if any later detections are above the loq.
-#'
-#' @param r A character vector of sequential residues without replicates, with
-#' non-detects specified as 'nd' and unquantified values above the limit of
-#' detection specified as 'nq', otherwise coercible to numeric
-#' @param lod Limit of detection (numeric)
-#' @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 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,
-#'   18 December 2014, p. 251
-#' @describeIn set_nd Set non-detects in residues series
-#' @export
-#' @examples
-#' # FOCUS (2014) p. 75/76 and 131/132
-#' parent_1 <- c(.12, .09, .05, .03, "nd", "nd", "nd", "nd", "nd", "nd")
-#' set_nd(parent_1, 0.02)
-#' parent_2 <- c(.12, .09, .05, .03, "nd", "nd", .03, "nd", "nd", "nd")
-#' set_nd(parent_2, 0.02)
-#' set_nd_focus(parent_2, 0.02, loq = 0.05)
-#' parent_3 <- c(.12, .09, .05, .03, "nd", "nd", .06, "nd", "nd", "nd")
-#' set_nd(parent_3, 0.02)
-#' set_nd_focus(parent_3, 0.02, loq = 0.05)
-#' metabolite <- c("nd", "nd", "nd", 0.03, 0.06, 0.10, 0.11, 0.10, 0.09, 0.05, 0.03, "nd", "nd")
-#' set_nd(metabolite, 0.02)
-set_nd <- function(r, lod, loq = NA,
-  time_zero = TRUE, time_zero_nd_value = NA, stop_after_first_nondetect = FALSE)
-{
-
-  if (stop_after_first_nondetect & is.na(loq)) {
-    stop("You need to specify an loq to decide if the curve should be cut off after the first non-detect")
-  }
-
-  result <- r
-
-  # Handle nq values
-  if (!missing(loq)) {
-    nq = 0.5 * (lod + loq)
-    result[r == "nq"] <- nq
-  } else {
-    if (any(r == "nq", na.rm = TRUE)) stop("You need to specify lod and loq")
-  }
-
-  #  Handle nd values
-  if (time_zero) {
-    if (r[1] %in% c("nd")) {
-      residues_present = FALSE
-      result[1] <- time_zero_nd_value
-    } else {
-      residues_present = TRUE
-    }
-    start_i <- 2
-  } else {
-    residues_present <- if (r[1] == "nd") FALSE else TRUE
-    start_i <- 1
-  }
-
-  for (i in start_i:length(r)) {
-
-    # residues_in_next
-    if (i < length(r)) {
-      next_value <- r[i + 1]
-      if (is.na(next_value) || next_value == "nd") residues_in_next = FALSE
-      else residues_in_next = TRUE
-    } else {
-      residues_in_next = FALSE
-    }
-
-    if (is.na(r[i])) {
-      residues_present <- FALSE
-      result[i] <- NA
-    } else {
-      if (r[i] == "nd") {
-        if (residues_present | residues_in_next) {
-          result[i] <- 0.5 * lod
-        } else {
-          result[i] <- NA
-        }
-
-        if (stop_after_first_nondetect) {
-          if (residues_present & !residues_in_next) {
-            remaining <- (i + 1):length(r)
-            if (!any(suppressWarnings(as.numeric(r[remaining])) > loq, na.rm = TRUE)) {
-              result[remaining] <- NA
-              return(as.numeric(result))
-            }
-          }
-        }
-        if (!residues_in_next) residues_present <- FALSE
-        else residues_present <- TRUE
-      } else {
-        residues_present <- TRUE
-      }
-    }
-  }
-  return(as.numeric(result))
-}
-
-#' @describeIn set_nd Set non-detects in residues series according to FOCUS rules
-#' @export
-set_nd_focus <- function(r, lod, loq = NA, time_zero = TRUE) {
-  result <- set_nd(r, lod, loq = loq, time_zero = time_zero,
-    time_zero_nd_value = 0, stop_after_first_nondetect = TRUE)
-  return(result)
-}
diff --git a/R/set_nd_nq.R b/R/set_nd_nq.R
new file mode 100644
index 0000000..a372879
--- /dev/null
+++ b/R/set_nd_nq.R
@@ -0,0 +1,164 @@
+#' Set non-detects and unquantified values in residue series without replicates
+
+#' This function automates replacing unquantified values in residue time and
+#' depth series. For time series, the function performs part of the residue
+#' processing proposed in the FOCUS kinetics guidance for parent compounds
+#' and metabolites. For two-dimensional residue series over time and depth,
+#' it automates the proposal of Boesten et al (2015).
+
+#' @param res_raw Character vector of a residue time series, or matrix of
+#' residue values with rows representing depth profiles for a specific sampling
+#' time, and columns representing time series of residues at the same depth.
+#' Values below the limit of detection (lod) have to be coded as "nd", values
+#' between the limit of detection and the limit of quantification, if any, have
+#' to be coded as "nq". Samples not analysed have to be coded as "na". All
+#' values that are not "na", "nd" or "nq" have to be coercible to numeric
+#' @param lod Limit of detection (numeric)
+#' @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_presence Do we assume that residues occur at time zero?
+#' This only affects samples from the first sampling time that have been
+#' reported as "nd" (not detected).
+#' @references Boesten, J. J. T. I., van der Linden, A. M. A., Beltman, W. H.
+#' J. and Pol, J. W. (2015). Leaching of plant protection products and their
+#' transformation products; Proposals for improving the assessment of leaching
+#' to groundwater in the Netherlands — Version 2. Alterra report 2630, Alterra
+#' Wageningen UR (University & Research centre)
+#' @references FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation
+#'   Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1,
+#'   18 December 2014, p. 251
+#' @return A numeric vector, if a vector was supplied, or a numeric matrix otherwise
+#' @export
+#' @examples
+#' # FOCUS (2014) p. 75/76 and 131/132
+#' parent_1 <- c(.12, .09, .05, .03, "nd", "nd", "nd", "nd", "nd", "nd")
+#' set_nd_nq(parent_1, 0.02)
+#' parent_2 <- c(.12, .09, .05, .03, "nd", "nd", .03, "nd", "nd", "nd")
+#' set_nd_nq(parent_2, 0.02)
+#' set_nd_nq_focus(parent_2, 0.02, loq = 0.05)
+#' parent_3 <- c(.12, .09, .05, .03, "nd", "nd", .06, "nd", "nd", "nd")
+#' set_nd_nq(parent_3, 0.02)
+#' set_nd_nq_focus(parent_3, 0.02, loq = 0.05)
+#' metabolite <- c("nd", "nd", "nd", 0.03, 0.06, 0.10, 0.11, 0.10, 0.09, 0.05, 0.03, "nd", "nd")
+#' set_nd_nq(metabolite, 0.02)
+#' set_nd_nq_focus(metabolite, 0.02, 0.05)
+#' #
+#' # Boesten et al. (2015), p. 57/58
+#' table_8 <- matrix(
+#'   c(10, 10, rep("nd", 4),
+#'     10, 10, rep("nq", 2), rep("nd", 2),
+#'     10, 10, 10, "nq", "nd", "nd",
+#'     "nq", 10, "nq", rep("nd", 3),
+#'     "nd", "nq", "nq", rep("nd", 3),
+#'     rep("nd", 6), rep("nd", 6)),
+#'   ncol = 6, byrow = TRUE)
+#' set_nd_nq(table_8, 0.5, 1.5, time_zero_presence = TRUE)
+#' table_10 <- matrix(
+#'   c(10, 10, rep("nd", 4),
+#'     10, 10, rep("nd", 4),
+#'     10, 10, 10, rep("nd", 3),
+#'     "nd", 10, rep("nd", 4),
+#'     rep("nd", 18)),
+#'   ncol = 6, byrow = TRUE)
+#' set_nd_nq(table_10, 0.5, time_zero_presence = TRUE)
+set_nd_nq <- function(res_raw, lod, loq = NA, time_zero_presence = FALSE) {
+  if (!is.character(res_raw)) {
+    stop("Please supply a vector or a matrix of character values")
+  }
+  if (is.vector(res_raw)) {
+    was_vector <- TRUE
+    res_raw <- as.matrix(res_raw)
+  } else {
+    was_vector <- FALSE
+    if (!is.matrix(res_raw)) {
+      stop("Please supply a vector or a matrix of character values")
+    }
+  }
+  nq <- 0.5 * (loq + lod)
+  nda <- 0.5 * lod # not detected but adjacent to detection
+  res_raw[res_raw == "nq"] <- nq
+
+  if (!time_zero_presence) {
+    for (j in 1:ncol(res_raw)) {
+      if (res_raw[1, j] == "nd") res_raw[1, j] <- "na"
+    }
+  }
+  res_raw[res_raw == "na"] <- NA
+
+  not_nd_na <- function(value) !(grepl("nd", value) | is.na(value))
+
+  for (i in 1:nrow(res_raw)) {
+    for (j in 1:ncol(res_raw)) {
+      if (!is.na(res_raw[i, j]) && res_raw[i, j] == "nd") {
+        if (i > 1) { # check earlier sample in same layer
+          if (not_nd_na(res_raw[i - 1, j])) res_raw[i, j] <- "nda"
+        }
+        if (i < nrow(res_raw)) { # check later sample
+          if (not_nd_na(res_raw[i + 1, j])) res_raw[i, j] <- "nda"
+        }
+        if (j > 1) { # check above sample at the same time
+          if (not_nd_na(res_raw[i, j - 1])) res_raw[i, j] <- "nda"
+        }
+        if (j < ncol(res_raw)) { # check sample below at the same time
+          if (not_nd_na(res_raw[i, j + 1])) res_raw[i, j] <- "nda"
+        }
+      }
+    }
+  }
+  res_raw[res_raw == "nda"] <- nda
+  res_raw[res_raw == "nd"] <- NA
+
+  result <- as.numeric(res_raw)
+  dim(result) <- dim(res_raw)
+  dimnames(result) <- dimnames(res_raw)
+  if (was_vector) result <- as.vector(result)
+  return(result)
+}
+
+#' @describeIn set_nd_nq Set non-detects in residue time series according to FOCUS rules
+#' @param set_first_sample_nd Should the first sample be set to "first_sample_nd_value"
+#' in case it is a non-detection?
+#' @param first_sample_nd_value Value to be used for the first sample if it is a non-detection
+#' @param ignore_below_loq_after_first_nd Should we ignore values below the LOQ after the first
+#' non-detection that occurs after the quantified values?
+#' @export
+set_nd_nq_focus <- function(res_raw, lod, loq = NA,
+  set_first_sample_nd = TRUE, first_sample_nd_value = 0,
+  ignore_below_loq_after_first_nd = TRUE)
+{
+
+  if (!is.vector(res_raw)) stop("FOCUS rules are only specified for one-dimensional time series")
+
+  if (ignore_below_loq_after_first_nd & is.na(loq)) {
+    stop("You need to specify an LOQ")
+  }
+
+  n <- length(res_raw)
+  if (ignore_below_loq_after_first_nd) {
+    for (i in 3:n) {
+      if (!res_raw[i - 2] %in% c("na", "nd")) {
+        if (res_raw[i - 1] == "nd") {
+          res_remaining <- res_raw[i:n]
+          res_remaining_unquantified <- ifelse(res_remaining == "na", TRUE,
+            ifelse(res_remaining == "nd", TRUE,
+              ifelse(res_remaining == "nq", TRUE,
+                ifelse(suppressWarnings(as.numeric(res_remaining)) < loq, TRUE, FALSE))))
+          res_remaining_numeric <- suppressWarnings(as.numeric(res_remaining))
+          res_remaining_below_loq <- ifelse(res_remaining == "nq", TRUE,
+                ifelse(!is.na(res_remaining_numeric) & res_remaining_numeric < loq, TRUE, FALSE))
+          if (all(res_remaining_unquantified)) {
+            res_raw[i:n] <- ifelse(res_remaining_below_loq, "nd", res_remaining)
+          }
+        }
+      }
+    }
+  }
+
+  result <- set_nd_nq(res_raw, lod = lod, loq = loq)
+
+  if (set_first_sample_nd) {
+    if (res_raw[1] == "nd") result[1] <- first_sample_nd_value
+  }
+
+  return(result)
+}
diff --git a/_pkgdown.yml b/_pkgdown.yml
index e12082d..b40e223 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -18,7 +18,7 @@ reference:
       - pfm_degradation
       - SFO_actual_twa
       - FOMC_actual_twa
-      - set_nd
+      - set_nd_nq
   - title: Predicted environmental concentrations in soil
     contents:
       - PEC_soil
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 455ee07..e9c7098 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -170,9 +170,14 @@
       </tr><tr>
         
         <td>
-          <p><code><a href="set_nd.html">set_nd()</a></code> <code><a href="set_nd.html">set_nd_focus()</a></code> </p>
-        </td>
-        <td><p>Set non-detects in residue series without replicates</p></td>
+          <p><code><a href="set_nd_nq.html">set_nd_nq()</a></code> <code><a href="set_nd_nq.html">set_nd_nq_focus()</a></code> </p>
+        </td>
+        <td><p>Set non-detects and unquantified values in residue series without replicates
+This function automates replacing unquantified values in residue time and
+depth series. For time series, the function performs part of the residue
+processing proposed in the FOCUS kinetics guidance for parent compounds
+and metabolites. For two-dimensional residue series over time and depth,
+it automates the proposal of Boesten et al (2015).</p></td>
       </tr>
     </tbody><tbody>
       <tr>
diff --git a/docs/reference/set_nd.html b/docs/reference/set_nd.html
deleted file mode 100644
index 7b0e779..0000000
--- a/docs/reference/set_nd.html
+++ /dev/null
@@ -1,222 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
-<!DOCTYPE html>
-<html lang="en">
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<title>Set non-detects in residue series without replicates — set_nd • pfm</title>
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-<meta property="og:title" content="Set non-detects in residue series without replicates — set_nd" />
-
-<meta property="og:description" content="Sets non-detects directly before or directly after detects to NA. Values between
-lod and loq are set to their mean value if an loq is specified.
-If 'time_zero' is set to TRUE, the residue series is assumed to start with time
-zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the
-set_nd_focus variant, this is zero, otherwise this argument has NA as default
-value.
-If stopping after the first non-detection is requested, as in in the FOCUS
-variant of the function, an loq has to be specified in order to decide
-if any later detections are above the loq." />
-<meta name="twitter:card" content="summary" />
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-    <div class="page-header">
-    <h1>Set non-detects in residue series without replicates</h1>
-    
-    <div class="hidden name"><code>set_nd.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Sets non-detects directly before or directly after detects to NA. Values between
-lod and loq are set to their mean value if an loq is specified.
-If 'time_zero' is set to TRUE, the residue series is assumed to start with time
-zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the
-set_nd_focus variant, this is zero, otherwise this argument has NA as default
-value.
-If stopping after the first non-detection is requested, as in in the FOCUS
-variant of the function, an loq has to be specified in order to decide
-if any later detections are above the loq.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>set_nd</span>(<span class='no'>r</span>, <span class='no'>lod</span>, <span class='kw'>loq</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>time_zero</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>time_zero_nd_value</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
-  <span class='kw'>stop_after_first_nondetect</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
-
-<span class='fu'>set_nd_focus</span>(<span class='no'>r</span>, <span class='no'>lod</span>, <span class='kw'>loq</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>time_zero</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>r</th>
-      <td><p>A character vector of sequential residues without replicates, with
-non-detects specified as 'nd' and unquantified values above the limit of
-detection specified as 'nq', otherwise coercible to numeric</p></td>
-    </tr>
-    <tr>
-      <th>lod</th>
-      <td><p>Limit of detection (numeric)</p></td>
-    </tr>
-    <tr>
-      <th>loq</th>
-      <td><p>Limit of quantification(numeric). Must be specified if the FOCUS rule to
-stop after the first non-detection is to be applied</p></td>
-    </tr>
-    <tr>
-      <th>time_zero</th>
-      <td><p>Is the first value in the series a time zero value?</p></td>
-    </tr>
-    <tr>
-      <th>time_zero_nd_value</th>
-      <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>
-      <td><p>Should we really stop after the first non-detection?</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="functions"><a class="anchor" href="#functions"></a>Functions</h2>
-
-    
-<ul>
-<li><p><code>set_nd</code>: Set non-detects in residues series</p></li>
-<li><p><code>set_nd_focus</code>: Set non-detects in residues series according to FOCUS rules</p></li>
-</ul>
-    
-    <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,
-  18 December 2014, p. 251</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='co'># FOCUS (2014) p. 75/76 and 131/132</span>
-<span class='no'>parent_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>.12</span>, <span class='fl'>.09</span>, <span class='fl'>.05</span>, <span class='fl'>.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>)
-<span class='fu'>set_nd</span>(<span class='no'>parent_1</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#&gt;  [1] 0.12 0.09 0.05 0.03 0.01   NA   NA   NA   NA   NA</div><div class='input'><span class='no'>parent_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>.12</span>, <span class='fl'>.09</span>, <span class='fl'>.05</span>, <span class='fl'>.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='fl'>.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>)
-<span class='fu'>set_nd</span>(<span class='no'>parent_2</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#&gt;  [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.03 0.01   NA   NA</div><div class='input'><span class='fu'>set_nd_focus</span>(<span class='no'>parent_2</span>, <span class='fl'>0.02</span>, <span class='kw'>loq</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)</div><div class='output co'>#&gt;  [1] 0.12 0.09 0.05 0.03 0.01   NA   NA   NA   NA   NA</div><div class='input'><span class='no'>parent_3</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>.12</span>, <span class='fl'>.09</span>, <span class='fl'>.05</span>, <span class='fl'>.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='fl'>.06</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>)
-<span class='fu'>set_nd</span>(<span class='no'>parent_3</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#&gt;  [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01   NA   NA</div><div class='input'><span class='fu'>set_nd_focus</span>(<span class='no'>parent_3</span>, <span class='fl'>0.02</span>, <span class='kw'>loq</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)</div><div class='output co'>#&gt;  [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01   NA   NA</div><div class='input'><span class='no'>metabolite</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='fl'>0.03</span>, <span class='fl'>0.06</span>, <span class='fl'>0.10</span>, <span class='fl'>0.11</span>, <span class='fl'>0.10</span>, <span class='fl'>0.09</span>, <span class='fl'>0.05</span>, <span class='fl'>0.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>)
-<span class='fu'>set_nd</span>(<span class='no'>metabolite</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#&gt;  [1]   NA   NA 0.01 0.03 0.06 0.10 0.11 0.10 0.09 0.05 0.03 0.01   NA</div></pre>
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-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
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-      <li><a href="#functions">Functions</a></li>
-
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diff --git a/docs/reference/set_nd_nq.html b/docs/reference/set_nd_nq.html
new file mode 100644
index 0000000..ff751dd
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+++ b/docs/reference/set_nd_nq.html
@@ -0,0 +1,284 @@
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+
+<title>Set non-detects and unquantified values in residue series without replicates
+This function automates replacing unquantified values in residue time and
+depth series. For time series, the function performs part of the residue
+processing proposed in the FOCUS kinetics guidance for parent compounds
+and metabolites. For two-dimensional residue series over time and depth,
+it automates the proposal of Boesten et al (2015). — set_nd_nq • pfm</title>
+
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+<meta property="og:title" content="Set non-detects and unquantified values in residue series without replicates
+This function automates replacing unquantified values in residue time and
+depth series. For time series, the function performs part of the residue
+processing proposed in the FOCUS kinetics guidance for parent compounds
+and metabolites. For two-dimensional residue series over time and depth,
+it automates the proposal of Boesten et al (2015). — set_nd_nq" />
+
+<meta property="og:description" content="Set non-detects and unquantified values in residue series without replicates
+This function automates replacing unquantified values in residue time and
+depth series. For time series, the function performs part of the residue
+processing proposed in the FOCUS kinetics guidance for parent compounds
+and metabolites. For two-dimensional residue series over time and depth,
+it automates the proposal of Boesten et al (2015)." />
+<meta name="twitter:card" content="summary" />
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+
+<div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Set non-detects and unquantified values in residue series without replicates
+This function automates replacing unquantified values in residue time and
+depth series. For time series, the function performs part of the residue
+processing proposed in the FOCUS kinetics guidance for parent compounds
+and metabolites. For two-dimensional residue series over time and depth,
+it automates the proposal of Boesten et al (2015).</h1>
+    
+    <div class="hidden name"><code>set_nd_nq.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    
+    <p>Set non-detects and unquantified values in residue series without replicates
+This function automates replacing unquantified values in residue time and
+depth series. For time series, the function performs part of the residue
+processing proposed in the FOCUS kinetics guidance for parent compounds
+and metabolites. For two-dimensional residue series over time and depth,
+it automates the proposal of Boesten et al (2015).</p>
+    
+    </div>
+
+    <pre class="usage"><span class='fu'>set_nd_nq</span>(<span class='no'>res_raw</span>, <span class='no'>lod</span>, <span class='kw'>loq</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>time_zero_presence</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
+
+<span class='fu'>set_nd_nq_focus</span>(<span class='no'>res_raw</span>, <span class='no'>lod</span>, <span class='kw'>loq</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>set_first_sample_nd</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+  <span class='kw'>first_sample_nd_value</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>ignore_below_loq_after_first_nd</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+    
+    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+    <table class="ref-arguments">
+    <colgroup><col class="name" /><col class="desc" /></colgroup>
+    <tr>
+      <th>res_raw</th>
+      <td><p>Character vector of a residue time series, or matrix of
+residue values with rows representing depth profiles for a specific sampling
+time, and columns representing time series of residues at the same depth.
+Values below the limit of detection (lod) have to be coded as "nd", values
+between the limit of detection and the limit of quantification, if any, have
+to be coded as "nq". Samples not analysed have to be coded as "na". All
+values that are not "na", "nd" or "nq" have to be coercible to numeric</p></td>
+    </tr>
+    <tr>
+      <th>lod</th>
+      <td><p>Limit of detection (numeric)</p></td>
+    </tr>
+    <tr>
+      <th>loq</th>
+      <td><p>Limit of quantification(numeric). Must be specified if the FOCUS rule to
+stop after the first non-detection is to be applied</p></td>
+    </tr>
+    <tr>
+      <th>time_zero_presence</th>
+      <td><p>Do we assume that residues occur at time zero?
+This only affects samples from the first sampling time that have been
+reported as "nd" (not detected).</p></td>
+    </tr>
+    <tr>
+      <th>set_first_sample_nd</th>
+      <td><p>Should the first sample be set to "first_sample_nd_value"
+in case it is a non-detection?</p></td>
+    </tr>
+    <tr>
+      <th>first_sample_nd_value</th>
+      <td><p>Value to be used for the first sample if it is a non-detection</p></td>
+    </tr>
+    <tr>
+      <th>ignore_below_loq_after_first_nd</th>
+      <td><p>Should we ignore values below the LOQ after the first
+non-detection that occurs after the quantified values?</p></td>
+    </tr>
+    </table>
+    
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>A numeric vector, if a vector was supplied, or a numeric matrix otherwise</p>
+    
+    <h2 class="hasAnchor" id="functions"><a class="anchor" href="#functions"></a>Functions</h2>
+
+    
+<ul>
+<li><p><code>set_nd_nq_focus</code>: Set non-detects in residue time series according to FOCUS rules</p></li>
+</ul>
+    
+    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+    <p>Boesten, J. J. T. I., van der Linden, A. M. A., Beltman, W. H.
+J. and Pol, J. W. (2015). Leaching of plant protection products and their
+transformation products; Proposals for improving the assessment of leaching
+to groundwater in the Netherlands — Version 2. Alterra report 2630, Alterra
+Wageningen UR (University &amp; Research centre)</p>
+<p>FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation
+  Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1,
+  18 December 2014, p. 251</p>
+    
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'><span class='co'># FOCUS (2014) p. 75/76 and 131/132</span>
+<span class='no'>parent_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>.12</span>, <span class='fl'>.09</span>, <span class='fl'>.05</span>, <span class='fl'>.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>)
+<span class='fu'>set_nd_nq</span>(<span class='no'>parent_1</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#&gt;  [1] 0.12 0.09 0.05 0.03 0.01   NA   NA   NA   NA   NA</div><div class='input'><span class='no'>parent_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>.12</span>, <span class='fl'>.09</span>, <span class='fl'>.05</span>, <span class='fl'>.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='fl'>.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>)
+<span class='fu'>set_nd_nq</span>(<span class='no'>parent_2</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#&gt;  [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.03 0.01   NA   NA</div><div class='input'><span class='fu'>set_nd_nq_focus</span>(<span class='no'>parent_2</span>, <span class='fl'>0.02</span>, <span class='kw'>loq</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)</div><div class='output co'>#&gt;  [1] 0.12 0.09 0.05 0.03 0.01   NA   NA   NA   NA   NA</div><div class='input'><span class='no'>parent_3</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>.12</span>, <span class='fl'>.09</span>, <span class='fl'>.05</span>, <span class='fl'>.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='fl'>.06</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>)
+<span class='fu'>set_nd_nq</span>(<span class='no'>parent_3</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#&gt;  [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01   NA   NA</div><div class='input'><span class='fu'>set_nd_nq_focus</span>(<span class='no'>parent_3</span>, <span class='fl'>0.02</span>, <span class='kw'>loq</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)</div><div class='output co'>#&gt;  [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01   NA   NA</div><div class='input'><span class='no'>metabolite</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>, <span class='fl'>0.03</span>, <span class='fl'>0.06</span>, <span class='fl'>0.10</span>, <span class='fl'>0.11</span>, <span class='fl'>0.10</span>, <span class='fl'>0.09</span>, <span class='fl'>0.05</span>, <span class='fl'>0.03</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>)
+<span class='fu'>set_nd_nq</span>(<span class='no'>metabolite</span>, <span class='fl'>0.02</span>)</div><div class='output co'>#&gt;  [1]   NA   NA 0.01 0.03 0.06 0.10 0.11 0.10 0.09 0.05 0.03 0.01   NA</div><div class='input'><span class='fu'>set_nd_nq_focus</span>(<span class='no'>metabolite</span>, <span class='fl'>0.02</span>, <span class='fl'>0.05</span>)</div><div class='output co'>#&gt;  [1] 0.00   NA 0.01 0.03 0.06 0.10 0.11 0.10 0.09 0.05 0.03 0.01   NA</div><div class='input'><span class='co'>#</span>
+<span class='co'># Boesten et al. (2015), p. 57/58</span>
+<span class='no'>table_8</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(
+  <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>10</span>, <span class='fl'>10</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>4</span>),
+    <span class='fl'>10</span>, <span class='fl'>10</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nq"</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>2</span>),
+    <span class='fl'>10</span>, <span class='fl'>10</span>, <span class='fl'>10</span>, <span class='st'>"nq"</span>, <span class='st'>"nd"</span>, <span class='st'>"nd"</span>,
+    <span class='st'>"nq"</span>, <span class='fl'>10</span>, <span class='st'>"nq"</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>3</span>),
+    <span class='st'>"nd"</span>, <span class='st'>"nq"</span>, <span class='st'>"nq"</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>3</span>),
+    <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>6</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>6</span>)),
+  <span class='kw'>ncol</span> <span class='kw'>=</span> <span class='fl'>6</span>, <span class='kw'>byrow</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>set_nd_nq</span>(<span class='no'>table_8</span>, <span class='fl'>0.5</span>, <span class='fl'>1.5</span>, <span class='kw'>time_zero_presence</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt;       [,1]  [,2]  [,3] [,4] [,5] [,6]
+#&gt; [1,] 10.00 10.00  0.25 0.25   NA   NA
+#&gt; [2,] 10.00 10.00  1.00 1.00 0.25   NA
+#&gt; [3,] 10.00 10.00 10.00 1.00 0.25   NA
+#&gt; [4,]  1.00 10.00  1.00 0.25   NA   NA
+#&gt; [5,]  0.25  1.00  1.00 0.25   NA   NA
+#&gt; [6,]    NA  0.25  0.25   NA   NA   NA
+#&gt; [7,]    NA    NA    NA   NA   NA   NA</div><div class='input'><span class='no'>table_10</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(
+  <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>10</span>, <span class='fl'>10</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>4</span>),
+    <span class='fl'>10</span>, <span class='fl'>10</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>4</span>),
+    <span class='fl'>10</span>, <span class='fl'>10</span>, <span class='fl'>10</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>3</span>),
+    <span class='st'>"nd"</span>, <span class='fl'>10</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>4</span>),
+    <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"nd"</span>, <span class='fl'>18</span>)),
+  <span class='kw'>ncol</span> <span class='kw'>=</span> <span class='fl'>6</span>, <span class='kw'>byrow</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>set_nd_nq</span>(<span class='no'>table_10</span>, <span class='fl'>0.5</span>, <span class='kw'>time_zero_presence</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt;       [,1]  [,2]  [,3] [,4] [,5] [,6]
+#&gt; [1,] 10.00 10.00  0.25   NA   NA   NA
+#&gt; [2,] 10.00 10.00  0.25   NA   NA   NA
+#&gt; [3,] 10.00 10.00 10.00 0.25   NA   NA
+#&gt; [4,]  0.25 10.00  0.25   NA   NA   NA
+#&gt; [5,]    NA  0.25    NA   NA   NA   NA
+#&gt; [6,]    NA    NA    NA   NA   NA   NA
+#&gt; [7,]    NA    NA    NA   NA   NA   NA</div></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+    <h2>Contents</h2>
+    <ul class="nav nav-pills nav-stacked">
+      <li><a href="#arguments">Arguments</a></li>
+      
+      <li><a href="#value">Value</a></li>
+
+      <li><a href="#functions">Functions</a></li>
+
+      <li><a href="#references">References</a></li>
+      
+      <li><a href="#examples">Examples</a></li>
+    </ul>
+
+  </div>
+</div>
+
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+      </footer>
+   </div>
+
+  
+
+
+  </body>
+</html>
+
+
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 79d9b14..b619e4d 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -100,7 +100,7 @@
     <loc>https://pkgdown.jrwb.de/pfm/reference/sawtooth.html</loc>
   </url>
   <url>
-    <loc>https://pkgdown.jrwb.de/pfm/reference/set_nd.html</loc>
+    <loc>https://pkgdown.jrwb.de/pfm/reference/set_nd_nq.html</loc>
   </url>
   <url>
     <loc>https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html</loc>
diff --git a/man/set_nd.Rd b/man/set_nd.Rd
deleted file mode 100644
index cef2705..0000000
--- a/man/set_nd.Rd
+++ /dev/null
@@ -1,64 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/set_nd.R
-\name{set_nd}
-\alias{set_nd}
-\alias{set_nd_focus}
-\title{Set non-detects in residue series without replicates}
-\usage{
-set_nd(r, lod, loq = NA, time_zero = TRUE, time_zero_nd_value = NA,
-  stop_after_first_nondetect = FALSE)
-
-set_nd_focus(r, lod, loq = NA, time_zero = TRUE)
-}
-\arguments{
-\item{r}{A character vector of sequential residues without replicates, with
-non-detects specified as 'nd' and unquantified values above the limit of
-detection specified as 'nq', otherwise coercible to numeric}
-
-\item{lod}{Limit of detection (numeric)}
-
-\item{loq}{Limit of quantification(numeric). Must be specified if the FOCUS rule to
-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{stop_after_first_nondetect}{Should we really stop after the first non-detection?}
-}
-\description{
-Sets non-detects directly before or directly after detects to NA. Values between
-lod and loq are set to their mean value if an loq is specified.
-If 'time_zero' is set to TRUE, the residue series is assumed to start with time
-zero, and non-detects at time zero are set to 'time_zero_nd_value'. For the
-set_nd_focus variant, this is zero, otherwise this argument has NA as default
-value.
-If stopping after the first non-detection is requested, as in in the FOCUS
-variant of the function, an loq has to be specified in order to decide
-if any later detections are above the loq.
-}
-\section{Functions}{
-\itemize{
-\item \code{set_nd}: Set non-detects in residues series
-
-\item \code{set_nd_focus}: Set non-detects in residues series according to FOCUS rules
-}}
-
-\examples{
-# FOCUS (2014) p. 75/76 and 131/132
-parent_1 <- c(.12, .09, .05, .03, "nd", "nd", "nd", "nd", "nd", "nd")
-set_nd(parent_1, 0.02)
-parent_2 <- c(.12, .09, .05, .03, "nd", "nd", .03, "nd", "nd", "nd")
-set_nd(parent_2, 0.02)
-set_nd_focus(parent_2, 0.02, loq = 0.05)
-parent_3 <- c(.12, .09, .05, .03, "nd", "nd", .06, "nd", "nd", "nd")
-set_nd(parent_3, 0.02)
-set_nd_focus(parent_3, 0.02, loq = 0.05)
-metabolite <- c("nd", "nd", "nd", 0.03, 0.06, 0.10, 0.11, 0.10, 0.09, 0.05, 0.03, "nd", "nd")
-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,
-  18 December 2014, p. 251
-}
diff --git a/man/set_nd_nq.Rd b/man/set_nd_nq.Rd
new file mode 100644
index 0000000..b2da429
--- /dev/null
+++ b/man/set_nd_nq.Rd
@@ -0,0 +1,103 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/set_nd_nq.R
+\name{set_nd_nq}
+\alias{set_nd_nq}
+\alias{set_nd_nq_focus}
+\title{Set non-detects and unquantified values in residue series without replicates
+This function automates replacing unquantified values in residue time and
+depth series. For time series, the function performs part of the residue
+processing proposed in the FOCUS kinetics guidance for parent compounds
+and metabolites. For two-dimensional residue series over time and depth,
+it automates the proposal of Boesten et al (2015).}
+\usage{
+set_nd_nq(res_raw, lod, loq = NA, time_zero_presence = FALSE)
+
+set_nd_nq_focus(res_raw, lod, loq = NA, set_first_sample_nd = TRUE,
+  first_sample_nd_value = 0, ignore_below_loq_after_first_nd = TRUE)
+}
+\arguments{
+\item{res_raw}{Character vector of a residue time series, or matrix of
+residue values with rows representing depth profiles for a specific sampling
+time, and columns representing time series of residues at the same depth.
+Values below the limit of detection (lod) have to be coded as "nd", values
+between the limit of detection and the limit of quantification, if any, have
+to be coded as "nq". Samples not analysed have to be coded as "na". All
+values that are not "na", "nd" or "nq" have to be coercible to numeric}
+
+\item{lod}{Limit of detection (numeric)}
+
+\item{loq}{Limit of quantification(numeric). Must be specified if the FOCUS rule to
+stop after the first non-detection is to be applied}
+
+\item{time_zero_presence}{Do we assume that residues occur at time zero?
+This only affects samples from the first sampling time that have been
+reported as "nd" (not detected).}
+
+\item{set_first_sample_nd}{Should the first sample be set to "first_sample_nd_value"
+in case it is a non-detection?}
+
+\item{first_sample_nd_value}{Value to be used for the first sample if it is a non-detection}
+
+\item{ignore_below_loq_after_first_nd}{Should we ignore values below the LOQ after the first
+non-detection that occurs after the quantified values?}
+}
+\value{
+A numeric vector, if a vector was supplied, or a numeric matrix otherwise
+}
+\description{
+Set non-detects and unquantified values in residue series without replicates
+This function automates replacing unquantified values in residue time and
+depth series. For time series, the function performs part of the residue
+processing proposed in the FOCUS kinetics guidance for parent compounds
+and metabolites. For two-dimensional residue series over time and depth,
+it automates the proposal of Boesten et al (2015).
+}
+\section{Functions}{
+\itemize{
+\item \code{set_nd_nq_focus}: Set non-detects in residue time series according to FOCUS rules
+}}
+
+\examples{
+# FOCUS (2014) p. 75/76 and 131/132
+parent_1 <- c(.12, .09, .05, .03, "nd", "nd", "nd", "nd", "nd", "nd")
+set_nd_nq(parent_1, 0.02)
+parent_2 <- c(.12, .09, .05, .03, "nd", "nd", .03, "nd", "nd", "nd")
+set_nd_nq(parent_2, 0.02)
+set_nd_nq_focus(parent_2, 0.02, loq = 0.05)
+parent_3 <- c(.12, .09, .05, .03, "nd", "nd", .06, "nd", "nd", "nd")
+set_nd_nq(parent_3, 0.02)
+set_nd_nq_focus(parent_3, 0.02, loq = 0.05)
+metabolite <- c("nd", "nd", "nd", 0.03, 0.06, 0.10, 0.11, 0.10, 0.09, 0.05, 0.03, "nd", "nd")
+set_nd_nq(metabolite, 0.02)
+set_nd_nq_focus(metabolite, 0.02, 0.05)
+#
+# Boesten et al. (2015), p. 57/58
+table_8 <- matrix(
+  c(10, 10, rep("nd", 4),
+    10, 10, rep("nq", 2), rep("nd", 2),
+    10, 10, 10, "nq", "nd", "nd",
+    "nq", 10, "nq", rep("nd", 3),
+    "nd", "nq", "nq", rep("nd", 3),
+    rep("nd", 6), rep("nd", 6)),
+  ncol = 6, byrow = TRUE)
+set_nd_nq(table_8, 0.5, 1.5, time_zero_presence = TRUE)
+table_10 <- matrix(
+  c(10, 10, rep("nd", 4),
+    10, 10, rep("nd", 4),
+    10, 10, 10, rep("nd", 3),
+    "nd", 10, rep("nd", 4),
+    rep("nd", 18)),
+  ncol = 6, byrow = TRUE)
+set_nd_nq(table_10, 0.5, time_zero_presence = TRUE)
+}
+\references{
+Boesten, J. J. T. I., van der Linden, A. M. A., Beltman, W. H.
+J. and Pol, J. W. (2015). Leaching of plant protection products and their
+transformation products; Proposals for improving the assessment of leaching
+to groundwater in the Netherlands — Version 2. Alterra report 2630, Alterra
+Wageningen UR (University & Research centre)
+
+FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation
+  Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1,
+  18 December 2014, p. 251
+}
diff --git a/test.log b/test.log
index 06512a8..741e868 100644
--- a/test.log
+++ b/test.log
@@ -5,11 +5,11 @@ Testing pfm
 ✔ |  OK F W S | Context
 
⠏ |   0       | Exposit calculations
✔ |   7       | Exposit calculations
 
⠏ |   0       | Geometric mean calculation
✔ |   6       | Geometric mean calculation
-
⠏ |   0       | Check max_twa for parent mkinfit models against analytical solutions
⠋ |   1       | Check max_twa for parent mkinfit models against analytical solutions
✔ |   1       | Check max_twa for parent mkinfit models against analytical solutions [1.9 s]
+
⠏ |   0       | Check max_twa for parent mkinfit models against analytical solutions
⠋ |   1       | Check max_twa for parent mkinfit models against analytical solutions
✔ |   1       | Check max_twa for parent mkinfit models against analytical solutions [1.0 s]
 
⠏ |   0       | Simple PEC sediment calculations
✔ |   1       | Simple PEC sediment calculations
 
⠏ |   0       | Simple PEC soil calculations
⠙ |   2       | Simple PEC soil calculations
✔ |  17       | Simple PEC soil calculations [0.2 s]
 
⠏ |   0       | Simple PEC surface water calculations with drift entry
✔ |   2       | Simple PEC surface water calculations with drift entry
-
⠏ |   0       | Processing of residue series
✔ |   8       | Processing of residue series
+
⠏ |   0       | Processing of residue series
✔ |  11       | Processing of residue series
 
⠏ |   0       | Actual and time weighted average concentrations for SFO kinetics
✔ |   1       | Actual and time weighted average concentrations for SFO kinetics
 
⠏ |   0       | FOCUS Step 1 calculations
⠹ |   3       | FOCUS Step 1 calculations
✔ |   9       | FOCUS Step 1 calculations [0.1 s]
 
⠏ |   0       | FOCUS Steps 12 input files
✔ |   8       | FOCUS Steps 12 input files
@@ -17,9 +17,9 @@ Testing pfm
 
⠏ |   0       | UK drainage PEC calculations
✔ |  12       | UK drainage PEC calculations
 
 ══ Results ═════════════════════════════════════════════════════════════════════════════════════════
-Duration: 8.0 s
+Duration: 7.0 s
 
-OK:       79
+OK:       82
 Failed:   0
 Warnings: 0
 Skipped:  0
diff --git a/tests/testthat/test_set_nd.R b/tests/testthat/test_set_nd.R
index 6b73e2d..232e7c6 100644
--- a/tests/testthat/test_set_nd.R
+++ b/tests/testthat/test_set_nd.R
@@ -1,4 +1,5 @@
 context("Processing of residue series")
+
 # FOCUS (2014) page 76 (parent) and page 132 (metabolite)
 
 parent_1 <- c(.12, .09, .05, .03, "nd", "nd", "nd", "nd", "nd", "nd")
@@ -6,39 +7,80 @@ parent_2 <- c(.12, .09, .05, .03, "nd", "nd", .03, "nd", "nd", "nd")
 parent_3 <- c(.12, .09, .05, .03, "nd", "nd", .06, "nd", "nd", "nd")
 metabolite <- c("nd", "nd", "nd", 0.03, 0.06, 0.10, 0.11, 0.10, 0.09, 0.05, 0.03, "nd", "nd")
 
-test_that("Simple residue series processed as intended", {
+test_that("Simple residue series are processed as intended", {
 
-  expect_equal(set_nd(parent_1, 0.02),
+  expect_equal(set_nd_nq(parent_1, 0.02),
     c(.12, .09, .05, .03, .01, rep(NA, 5)))
 
-  expect_equal(set_nd(parent_2, 0.02, loq = 0.05),
+  expect_equal(set_nd_nq(parent_2, 0.02, loq = 0.05),
     c(.12, .09, .05, .03, .01, .01, .03, .01, NA, NA))
 
-  expect_equal(set_nd(metabolite, 0.02, loq = 0.05),
+  expect_equal(set_nd_nq(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))
+  expect_equal(set_nd_nq(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", {
 
   # Parent 1
-  expect_error(set_nd_focus(parent_1, 0.02),
-    "You need to specify an loq")
-  expect_equal(set_nd_focus(parent_1, 0.02, 0.05),
+  expect_error(set_nd_nq_focus(parent_1, 0.02),
+    "You need to specify an LOQ")
+  expect_equal(set_nd_nq_focus(parent_1, 0.02, 0.05),
     c(.12, .09, .05, .03, .01, rep(NA, 5)))
 
   # Parent 2
-  expect_equal(set_nd_focus(parent_2, 0.02, loq = 0.05),
+  expect_equal(set_nd_nq_focus(parent_2, 0.02, loq = 0.05),
     c(.12, .09, .05, .03, .01, rep(NA, 5)))
 
   # Parent 3
-  expect_equal(set_nd_focus(parent_3, 0.02, loq = 0.05),
+  expect_equal(set_nd_nq_focus(parent_3, 0.02, loq = 0.05),
     c(.12, .09, .05, .03, .01, .01, .06, .01, NA, NA))
 
   # Metabolite
-  expect_equal(set_nd_focus(metabolite, 0.02, loq = 0.05),
+  expect_equal(set_nd_nq_focus(metabolite, 0.02, loq = 0.05),
     c(0, NA, .01, .03, .06, .1, .11, .1, .09, .05, .03, .01, NA))
 
 })
+
+test_that("Examples Boesten et al. (2015, p. 57/58) are correctly processed", {
+  table_8 <- matrix(
+    c(10, 10, rep("nd", 4),
+      10, 10, rep("nq", 2), rep("nd", 2),
+      10, 10, 10, "nq", "nd", "nd",
+      "nq", 10, "nq", rep("nd", 3),
+      "nd", "nq", "nq", rep("nd", 3),
+      rep("nd", 6), rep("nd", 6)),
+    ncol = 6, byrow = TRUE)
+  table_8_processed <- set_nd_nq(table_8, 0.5, 1.5, time_zero_presence = TRUE)
+  table_9 <- matrix(
+    c(10, 10, 0.25, 0.25, NA, NA,
+      10, 10, 1, 1, 0.25, NA,
+      10, 10, 10, 1, 0.25, NA,
+      1, 10, 1, 0.25, NA, NA,
+      0.25, 1, 1, 0.25, NA, NA,
+      NA, 0.25, 0.25, NA, NA, NA,
+      rep(NA, 6)),
+    ncol = 6, byrow = TRUE)
+  expect_equal(table_8_processed, table_9)
+
+  table_10 <- matrix(
+    c(10, 10, rep("nd", 4),
+      10, 10, rep("nd", 4),
+      10, 10, 10, rep("nd", 3),
+      "nd", 10, rep("nd", 4),
+      rep("nd", 18)),
+    ncol = 6, byrow = TRUE)
+  table_10_processed <- set_nd_nq(table_10, 0.5, time_zero_presence = TRUE)
+  table_11 <- matrix(
+    c(10, 10, 0.25, rep(NA, 3),
+      10, 10, 0.25, rep(NA, 3),
+      10, 10, 10, 0.25, NA, NA,
+      0.25, 10, 0.25, rep(NA, 3),
+      NA, 0.25, rep(NA, 4),
+      rep(NA, 12)),
+    ncol = 6, byrow = TRUE)
+  expect_equal(table_10_processed, table_11)
+})