diff options
| -rw-r--r-- | R/set_nd.R | 10 | ||||
| -rw-r--r-- | docs/reference/index.html | 11 | ||||
| -rw-r--r-- | docs/reference/set_nd.html | 47 | ||||
| -rw-r--r-- | man/set_nd.Rd | 19 |
4 files changed, 26 insertions, 61 deletions
@@ -1,5 +1,5 @@ #' 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 @@ -9,7 +9,7 @@ #' 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 @@ -19,9 +19,13 @@ #' @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) p. 75, 76, 131, 132 +#' @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") diff --git a/docs/reference/index.html b/docs/reference/index.html index a704ad0..455ee07 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -172,16 +172,7 @@ <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 -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></td> + <td><p>Set non-detects in residue series without replicates</p></td> </tr> </tbody><tbody> <tr> diff --git a/docs/reference/set_nd.html b/docs/reference/set_nd.html index 32ac155..75a8fb1 100644 --- a/docs/reference/set_nd.html +++ b/docs/reference/set_nd.html @@ -6,16 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>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. — set_nd • pfm</title> +<title>Set non-detects in residue series without replicates — set_nd • pfm</title> <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> @@ -41,19 +32,9 @@ if any later detections are above the loq. — set_nd • pfm</title> -<meta property="og:title" content="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. — set_nd" /> +<meta property="og:title" content="Set non-detects in residue series without replicates — set_nd" /> -<meta property="og:description" content="Set non-detects in residue series without replicates -Sets non-detects directly before or directly after detects to NA. Values between +<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 @@ -125,24 +106,14 @@ if any later detections are above the loq." /> <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>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.</h1> + <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>Set non-detects in residue series without replicates -Sets non-detects directly before or directly after detects to NA. Values between + <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 @@ -195,16 +166,20 @@ stop after the first non-detection is to be applied</p></td> <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) p. 75, 76, 131, 132</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='no'>parent_1</span> <span class='kw'><-</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>) + <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'><-</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'>#> [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'><-</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'>#> [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'>#> [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'><-</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'>#> [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'>#> [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'><-</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>) diff --git a/man/set_nd.Rd b/man/set_nd.Rd index 8c6003c..bdbc6d2 100644 --- a/man/set_nd.Rd +++ b/man/set_nd.Rd @@ -3,16 +3,7 @@ \name{set_nd} \alias{set_nd} \alias{set_nd_focus} -\title{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.} +\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) @@ -36,7 +27,6 @@ stop after the first non-detection is to be applied} \item{stop_after_first_nondetect}{Should we really stop after the first non-detection?} } \description{ -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 @@ -49,10 +39,13 @@ 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") @@ -65,5 +58,7 @@ metabolite <- c("nd", "nd", "nd", 0.03, 0.06, 0.10, 0.11, 0.10, 0.09, 0.05, 0.03 set_nd(metabolite, 0.02) } \references{ -FOCUS (2014) p. 75, 76, 131, 132 +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 } |