diff options
| -rw-r--r-- | ChangeLog | 6 | ||||
| -rw-r--r-- | DESCRIPTION | 8 | ||||
| -rw-r--r-- | NAMESPACE | 1 | ||||
| -rw-r--r-- | R/GUS.R | 1 | ||||
| -rw-r--r-- | R/TOXSWA_cwa.R | 56 | ||||
| -rw-r--r-- | R/drift_data_JKI.R | 4 | ||||
| -rw-r--r-- | R/endpoint.R | 4 | ||||
| -rw-r--r-- | _pkgdown.yml | 3 | ||||
| -rw-r--r-- | docs/pkgdown.yml | 2 | ||||
| -rw-r--r-- | docs/reference/TOXSWA_cwa.html | 82 | ||||
| -rw-r--r-- | docs/reference/index.html | 19 | ||||
| -rw-r--r-- | docs/reference/pfm_degradation.html | 52 | ||||
| -rw-r--r-- | docs/reference/sawtooth-2.png | bin | 37285 -> 42340 bytes | |||
| -rw-r--r-- | docs/reference/sawtooth.html | 46 | ||||
| -rw-r--r-- | man/TOXSWA_cwa.Rd | 76 |
15 files changed, 225 insertions, 135 deletions
@@ -1,3 +1,9 @@ +commit df70d80d9ef13b69e58de6f47b9041b6a021025e +Author: Johannes Ranke <jranke@uni-bremen.de> +Date: 2020-07-21 15:50:21 +0200 + + Clean test.log after testing + commit 512cd50874b060d50a14d28df88018ac144cf6d3 Author: Johannes Ranke <jranke@uni-bremen.de> Date: 2020-07-07 12:36:56 +0200 diff --git a/DESCRIPTION b/DESCRIPTION index e877629..ef5c7a9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: pfm Type: Package Title: Utilities for Pesticide Fate Modelling -Version: 0.5.7 -Date: 2020-07-07 +Version: 0.5.8 +Date: 2020-07-23 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-4371-6538")) @@ -31,5 +31,5 @@ License: GPL LazyLoad: yes LazyData: yes Encoding: UTF-8 -URL: https://pkdown.jrwb.de/pfm -RoxygenNote: 7.1.0 +URL: https://pkgdown.jrwb.de/pfm +RoxygenNote: 7.1.1 @@ -46,7 +46,6 @@ export(soil_sorption) export(twa) import(graphics) import(mkin) -importFrom(R6,R6Class) importFrom(grDevices,dev.cur) importFrom(methods,is) importFrom(mkin,mkinpredict) @@ -7,7 +7,6 @@ #' @references Gustafson, David I. (1989) Groundwater ubiquity score: a simple #' method for assessing pesticide leachability. \emph{Environmental #' toxicology and chemistry} \bold{8}(4) 339–57. -#' @inheritParams endpoint #' @param DT50 Half-life of the chemical in soil. Should be a field #' half-life according to Gustafson (1989). However, leaching to the sub-soil #' can not completely be excluded in field dissipation experiments and Gustafson diff --git a/R/TOXSWA_cwa.R b/R/TOXSWA_cwa.R index 42cdd35..6521349 100644 --- a/R/TOXSWA_cwa.R +++ b/R/TOXSWA_cwa.R @@ -142,35 +142,24 @@ plot.TOXSWA_cwa <- function(x, time_column = c("datetime", "t", "t_firstjan", "t #' R6 class for holding TOXSWA water concentration data and associated statistics #' -#' An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics. -#' Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_cwa}}. +#' @description An R6 class for holding TOXSWA water concentration (cwa) data +#' and some associated statistics. like maximum moving window average +#' concentrations, and dataframes holding the events exceeding specified +#' thresholds. Usually, an instance of this class will be generated +#' by \code{\link{read.TOXSWA_cwa}}. #' -#' @docType class -#' @importFrom R6 R6Class #' @export #' @format An \code{\link{R6Class}} generator object. -#' @field filename Length one character vector. -#' @field basedir Length one character vector. +#' @field filename Length one character vector holding the filename. +#' @field basedir Length one character vector holding the directory where the file came from. +#' @field zipfile If not null, giving the path to the zip file from which the file was read. #' @field segment Length one integer, specifying for which segment the cwa data were read. +#' @field substance The TOXSWA name of the substance. #' @field cwas Dataframe holding the concentrations. #' @field events List of dataframes holding the event statistics for each threshold. #' @field windows Matrix of maximum time weighted average concentrations (TWAC_max) #' and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) #' for the requested moving window sizes in days. -#' @section Methods: -#' \describe{ -#' \item{\code{get_events(threshold, total = FALSE)}}{ -#' Populate a datataframe with event information for the specified threshold value -#' in µg/L. If \code{total = TRUE}, the total concentration including the amount -#' adsorbed to suspended matter will be used. The resulting dataframe is stored in the -#' \code{events} field of the object. -#' } -#' \item{\code{moving_windows(windows, total = FALSE)}}{ -#' Add to the \code{windows} field described above. -#' Again, if \code{total = TRUE}, the total concentration including the amount -#' adsorbed to suspended matter will be used. -#' } -#' } #' @examples #' H_sw_R1_stream <- read.TOXSWA_cwa("00003s_pa.cwa", #' basedir = "SwashProjects/project_H_sw/TOXSWA", @@ -180,7 +169,6 @@ plot.TOXSWA_cwa <- function(x, time_column = c("datetime", "t", "t_firstjan", "t #' H_sw_R1_stream$moving_windows(c(7, 21)) #' print(H_sw_R1_stream) #' @keywords data - TOXSWA_cwa <- R6Class("TOXSWA_cwa", public = list( filename = NULL, @@ -191,6 +179,15 @@ TOXSWA_cwa <- R6Class("TOXSWA_cwa", cwas = NULL, windows = NULL, events = list(), + + #' @description + #' Create a TOXSWA_cwa object from a file + #' @param filename The filename + #' @param basedir The directory to look in + #' @param zipfile Optional path to a zipfile holding the file + #' @param segment Either "last" or the number of the segment for which to read the data + #' @param substance The TOXSWA substance name (for TOXSWA 4 or higher) + #' @param total Should total concentrations be read in? If FALSE, free concentrations are read initialize = function(filename, basedir, zipfile = NULL, segment = "last", substance = "parent", total = FALSE) { self$filename <- filename @@ -327,6 +324,12 @@ TOXSWA_cwa <- R6Class("TOXSWA_cwa", } } }, + + #' @description + #' Add to the `windows` field described above. + #' @param windows Window sizes in days + #' @param total If TRUE, the total concentration including the amount adsorbed to + #' suspended matter will be used. moving_windows = function(windows, total = FALSE) { window_names = paste(windows, "days") n = length(window_names) @@ -350,6 +353,14 @@ TOXSWA_cwa <- R6Class("TOXSWA_cwa", } invisible(self) }, + + #' @description + #' Populate a datataframe with event information for the specified + #' threshold value. The resulting dataframe is stored in the `events` + #' field of the object. + #' @param thresholds Threshold values in µg/L. + #' @param total If TRUE, the total concentration including the amount adsorbed to + #' suspended matter will be used. get_events = function(thresholds, total = FALSE) { if (missing(thresholds)) { stop("You need to specify at least one threshold concentration in \u03bcg/L") @@ -397,6 +408,9 @@ TOXSWA_cwa <- R6Class("TOXSWA_cwa", } invisible(self) }, + + #' @description + #' Print a `TOXSWA_cwa` object print = function() { cat("<TOXSWA_cwa> data from file", self$filename, "segment", self$segment, "\n") print(head(self$cwas)) diff --git a/R/drift_data_JKI.R b/R/drift_data_JKI.R index e44079d..3b02f43 100644 --- a/R/drift_data_JKI.R +++ b/R/drift_data_JKI.R @@ -30,7 +30,7 @@ #' from #' http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html #' on 2015-06-11 -#' +#' #' Rautmann, D., Streloke, M and Winkler, R (2001) New basic drift values in #' the authorization procedure for plant protection products Mitt. Biol. #' Bundesanst. Land- Forstwirtsch. 383, 133-141 @@ -82,6 +82,6 @@ #' save(drift_data_JKI, file = "data/drift_data_JKI.RData") #' } #' -#' # And this is the resulting data +#' # And these are the resulting data #' drift_data_JKI NULL diff --git a/R/endpoint.R b/R/endpoint.R index 56a314b..08856f9 100644 --- a/R/endpoint.R +++ b/R/endpoint.R @@ -55,7 +55,6 @@ endpoint <- function(chent, else return(signif(aggregator(as.numeric(values)), signif)) } -#' @inheritParams endpoint #' @rdname endpoint #' @export soil_DT50 <- function(chent, aggregator = geomean, signif = 3, @@ -68,7 +67,6 @@ soil_DT50 <- function(chent, aggregator = geomean, signif = 3, return(ep) } -#' @inheritParams endpoint #' @rdname endpoint #' @export soil_Kfoc <- function(chent, aggregator = geomean, signif = 3, @@ -79,7 +77,6 @@ soil_Kfoc <- function(chent, aggregator = geomean, signif = 3, return(ep) } -#' @inheritParams endpoint #' @rdname endpoint #' @export soil_N <- function(chent, aggregator = mean, signif = 3, raw = FALSE) { @@ -89,7 +86,6 @@ soil_N <- function(chent, aggregator = mean, signif = 3, raw = FALSE) { return(ep) } -#' @inheritParams endpoint #' @rdname endpoint #' @param values The values to be returned #' @param aggregators A named vector of aggregator functions to be used diff --git a/_pkgdown.yml b/_pkgdown.yml index 71f3c65..4f12b7c 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -53,6 +53,9 @@ reference: contents: - SSLRC_mobility_classification - GUS + - title: Work with chent objects containing relevant information + contents: + - endpoint - title: Utilities contents: - get_vertex diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 077f218..8b86fe9 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 2.2.1 pkgdown: 1.5.1 pkgdown_sha: ~ articles: [] -last_built: 2020-06-17T11:36Z +last_built: 2020-07-22T15:06Z urls: reference: https://pkgdown.jrwb.de/pfm/reference article: https://pkgdown.jrwb.de/pfm/articles diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html index 9f9e3c3..16dc5db 100644 --- a/docs/reference/TOXSWA_cwa.html +++ b/docs/reference/TOXSWA_cwa.html @@ -40,8 +40,11 @@ <meta property="og:title" content="R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa" /> -<meta property="og:description" content="An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics. -Usually, an instance of this class will be generated by read.TOXSWA_cwa." /> +<meta property="og:description" content="An R6 class for holding TOXSWA water concentration (cwa) data +and some associated statistics. like maximum moving window average +concentrations, and dataframes holding the events exceeding specified +thresholds. Usually, an instance of this class will be generated +by read.TOXSWA_cwa." /> @@ -110,8 +113,11 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." /> </div> <div class="ref-description"> - <p>An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics. -Usually, an instance of this class will be generated by <code><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></code>.</p> + <p>An R6 class for holding TOXSWA water concentration (cwa) data +and some associated statistics. like maximum moving window average +concentrations, and dataframes holding the events exceeding specified +thresholds. Usually, an instance of this class will be generated +by <code><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></code>.</p> </div> @@ -119,30 +125,19 @@ Usually, an instance of this class will be generated by <code><a href='read.TOXS <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>An <code>R6Class</code> generator object.</p> - <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2> - - - -<dl'> - <dt><code>get_events(threshold, total = FALSE)</code></dt><dd><p>Populate a datataframe with event information for the specified threshold value - in µg/L. If <code>total = TRUE</code>, the total concentration including the amount - adsorbed to suspended matter will be used. The resulting dataframe is stored in the - <code>events</code> field of the object.</p></dd> - <dt><code>moving_windows(windows, total = FALSE)</code></dt><dd><p>Add to the <code>windows</code> field described above. - Again, if <code>total = TRUE</code>, the total concentration including the amount - adsorbed to suspended matter will be used.</p></dd> - -</dl> - <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2> <p><div class="r6-fields"></p><dl'> -<dt><code>filename</code></dt><dd><p>Length one character vector.</p></dd> +<dt><code>filename</code></dt><dd><p>Length one character vector holding the filename.</p></dd> -<dt><code>basedir</code></dt><dd><p>Length one character vector.</p></dd> +<dt><code>basedir</code></dt><dd><p>Length one character vector holding the directory where the file came from.</p></dd> + +<dt><code>zipfile</code></dt><dd><p>If not null, giving the path to the zip file from which the file was read.</p></dd> <dt><code>segment</code></dt><dd><p>Length one integer, specifying for which segment the cwa data were read.</p></dd> +<dt><code>substance</code></dt><dd><p>The TOXSWA name of the substance.</p></dd> + <dt><code>cwas</code></dt><dd><p>Dataframe holding the concentrations.</p></dd> <dt><code>events</code></dt><dd><p>List of dataframes holding the event statistics for each threshold.</p></dd> @@ -166,8 +161,7 @@ for the requested moving window sizes in days.</p></dd> </ul> <p><hr> <a id="method-new"></a></p><h3>Method <code>new()</code></h3> - -<h3>Usage</h3> +<p>Create a TOXSWA_cwa object from a file</p><h3>Usage</h3> <p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>new</span>( <span class='no'>filename</span>, <span class='no'>basedir</span>, @@ -177,22 +171,52 @@ for the requested moving window sizes in days.</p></dd> <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span> )</pre><p></div></p> +<h3>Arguments</h3> +<p><div class="arguments"></p><dl'> +<dt><code>filename</code></dt><dd><p>The filename</p></dd> + +<dt><code>basedir</code></dt><dd><p>The directory to look in</p></dd> + +<dt><code>zipfile</code></dt><dd><p>Optional path to a zipfile holding the file</p></dd> + +<dt><code>segment</code></dt><dd><p>Either "last" or the number of the segment for which to read the data</p></dd> + +<dt><code>substance</code></dt><dd><p>The TOXSWA substance name (for TOXSWA 4 or higher)</p></dd> + +<dt><code>total</code></dt><dd><p>Should total concentrations be read in? If FALSE, free concentrations are read</p></dd> + +</dl><p></div></p> <p><hr> <a id="method-moving_windows"></a></p><h3>Method <code>moving_windows()</code></h3> - -<h3>Usage</h3> +<p>Add to the `windows` field described above.</p><h3>Usage</h3> <p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>moving_windows</span>(<span class='no'>windows</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre><p></div></p> +<h3>Arguments</h3> +<p><div class="arguments"></p><dl'> +<dt><code>windows</code></dt><dd><p>Window sizes in days</p></dd> + +<dt><code>total</code></dt><dd><p>If TRUE, the total concentration including the amount adsorbed to +suspended matter will be used.</p></dd> + +</dl><p></div></p> <p><hr> <a id="method-get_events"></a></p><h3>Method <code>get_events()</code></h3> - -<h3>Usage</h3> +<p>Populate a datataframe with event information for the specified +threshold value. The resulting dataframe is stored in the `events` +field of the object.</p><h3>Usage</h3> <p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>get_events</span>(<span class='no'>thresholds</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre><p></div></p> +<h3>Arguments</h3> +<p><div class="arguments"></p><dl'> +<dt><code>thresholds</code></dt><dd><p>Threshold values in µg/L.</p></dd> + +<dt><code>total</code></dt><dd><p>If TRUE, the total concentration including the amount adsorbed to +suspended matter will be used.</p></dd> + +</dl><p></div></p> <p><hr> <a id="method-print"></a></p><h3>Method <code><a href='https://rdrr.io/r/base/print.html'>print()</a></code></h3> - -<h3>Usage</h3> +<p>Print a `TOXSWA_cwa` object</p><h3>Usage</h3> <p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>()</pre><p></div></p> <p><hr> diff --git a/docs/reference/index.html b/docs/reference/index.html index 944f1f2..186390e 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -393,6 +393,25 @@ water concentrations</p></td> </tbody><tbody> <tr> <th colspan="2"> + <h2 id="section-work-with-chent-objects-containing-relevant-information" class="hasAnchor"><a href="#section-work-with-chent-objects-containing-relevant-information" class="anchor"></a>Work with chent objects containing relevant information</h2> + <p class="section-desc"></p> + </th> + </tr> + + + </tbody><tbody> + + + <tr> + + <td> + <p><code><a href="endpoint.html">endpoint()</a></code> <code><a href="endpoint.html">soil_DT50()</a></code> <code><a href="endpoint.html">soil_Kfoc()</a></code> <code><a href="endpoint.html">soil_N()</a></code> <code><a href="endpoint.html">soil_sorption()</a></code> </p> + </td> + <td><p>Retrieve endpoint information from the chyaml field of a chent object</p></td> + </tr> + </tbody><tbody> + <tr> + <th colspan="2"> <h2 id="section-utilities" class="hasAnchor"><a href="#section-utilities" class="anchor"></a>Utilities</h2> <p class="section-desc"></p> </th> diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html index d2e62f6..8d06107 100644 --- a/docs/reference/pfm_degradation.html +++ b/docs/reference/pfm_degradation.html @@ -10,23 +10,27 @@ <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> <!-- Bootstrap --> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> + +<!-- bootstrap-toc --> +<link rel="stylesheet" href="../bootstrap-toc.css"> +<script src="../bootstrap-toc.js"></script> <!-- Font Awesome icons --> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" /> <!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script> <!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> @@ -37,7 +41,6 @@ <meta property="og:title" content="Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation" /> <meta property="og:description" content="Calculate a time course of relative concentrations based on an mkinmod model" /> -<meta name="twitter:card" content="summary" /> @@ -55,7 +58,7 @@ </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -112,7 +115,7 @@ <pre class="usage"><span class='fu'>pfm_degradation</span>( <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>, - <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span>(<span class='fl'>2</span>)/<span class='no'>DT50</span>), + <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span>(<span class='fl'>2</span>)/<span class='no'>DT50</span>), <span class='kw'>years</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>step_days</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='no'>years</span> * <span class='fl'>365</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='no'>step_days</span>) @@ -152,22 +155,17 @@ is calculated (SFO model).</p></td> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>(<span class='fu'>pfm_degradation</span>(<span class='st'>"SFO"</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>10</span>))</div><div class='output co'>#> time parent -#> 1 0 1.0000000 -#> 2 1 0.9330330 -#> 3 2 0.8705506 -#> 4 3 0.8122524 -#> 5 4 0.7578583 -#> 6 5 0.7071068</div></pre> +#> 0 0 1.0000000 +#> 1 1 0.9330330 +#> 2 2 0.8705506 +#> 3 3 0.8122524 +#> 4 4 0.7578583 +#> 5 5 0.7071068</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="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> - <p>Johannes Ranke</p> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"> + <h2 data-toc-skip>Contents</h2> + </nav> </div> </div> @@ -178,7 +176,7 @@ is calculated (SFO model).</p></td> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/sawtooth-2.png b/docs/reference/sawtooth-2.png Binary files differindex ad93165..87da954 100644 --- a/docs/reference/sawtooth-2.png +++ b/docs/reference/sawtooth-2.png diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html index 7720afc..fea24d4 100644 --- a/docs/reference/sawtooth.html +++ b/docs/reference/sawtooth.html @@ -10,23 +10,27 @@ <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> <!-- Bootstrap --> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> + +<!-- bootstrap-toc --> +<link rel="stylesheet" href="../bootstrap-toc.css"> +<script src="../bootstrap-toc.js"></script> <!-- Font Awesome icons --> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" /> <!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script> <!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> @@ -36,9 +40,8 @@ <meta property="og:title" content="Create decline time series for multiple applications — sawtooth" /> -<meta property="og:description" content="If the application pattern is specified in applications, +<meta property="og:description" content="If the application pattern is specified in applications, n and i are disregarded." /> -<meta name="twitter:card" content="summary" /> @@ -56,7 +59,7 @@ n and i are disregarded." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -107,7 +110,7 @@ n and i are disregarded." /> </div> <div class="ref-description"> - <p>If the application pattern is specified in <code>applications</code>, + <p>If the application pattern is specified in <code>applications</code>, <code>n</code> and <code>i</code> are disregarded.</p> </div> @@ -145,10 +148,10 @@ the corresponding amounts applied in the second column.</p></td> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>applications</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>14</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>3</span>)) <span class='no'>pred</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>) -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='fu'>sawtooth</span>(<span class='no'>pred</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='no'>applications</span>))</div><div class='img'><img src='sawtooth-1.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='no'>m_2</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>pred_2</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>) +<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='fu'>sawtooth</span>(<span class='no'>pred</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='no'>applications</span>))</div><div class='img'><img src='sawtooth-1.png' alt='' width='700' height='433' /></div><div class='input'> +<span class='no'>m_2</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='input'><span class='no'>pred_2</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>) <span class='no'>pred_2_saw</span> <span class='kw'><-</span> <span class='fu'>sawtooth</span>(<span class='no'>pred_2</span>, <span class='fl'>2</span>, <span class='fl'>7</span>) -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><div class='img'><img src='sawtooth-2.png' alt='' width='700' height='433' /></div><div class='input'> +<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><div class='img'><img src='sawtooth-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='max_twa.html'>max_twa</a></span>(<span class='no'>pred_2_saw</span>)</div><div class='output co'>#> $max #> parent m1 #> 0.7834480 0.8617048 @@ -162,13 +165,10 @@ the corresponding amounts applied in the second column.</p></td> #> 21.00 47.85 #> </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="#examples">Examples</a></li> - </ul> - + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"> + <h2 data-toc-skip>Contents</h2> + </nav> </div> </div> @@ -179,7 +179,7 @@ the corresponding amounts applied in the second column.</p></td> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/man/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd index 6a95a0b..3daa1d0 100644 --- a/man/TOXSWA_cwa.Rd +++ b/man/TOXSWA_cwa.Rd @@ -1,6 +1,5 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/TOXSWA_cwa.R -\docType{class} \name{TOXSWA_cwa} \alias{TOXSWA_cwa} \title{R6 class for holding TOXSWA water concentration data and associated statistics} @@ -8,26 +7,12 @@ An \code{\link{R6Class}} generator object. } \description{ -An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics. -Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_cwa}}. +An R6 class for holding TOXSWA water concentration (cwa) data +and some associated statistics. like maximum moving window average +concentrations, and dataframes holding the events exceeding specified +thresholds. Usually, an instance of this class will be generated +by \code{\link{read.TOXSWA_cwa}}. } -\section{Methods}{ - -\describe{ - \item{\code{get_events(threshold, total = FALSE)}}{ - Populate a datataframe with event information for the specified threshold value - in µg/L. If \code{total = TRUE}, the total concentration including the amount - adsorbed to suspended matter will be used. The resulting dataframe is stored in the - \code{events} field of the object. - } - \item{\code{moving_windows(windows, total = FALSE)}}{ - Add to the \code{windows} field described above. - Again, if \code{total = TRUE}, the total concentration including the amount - adsorbed to suspended matter will be used. - } -} -} - \examples{ H_sw_R1_stream <- read.TOXSWA_cwa("00003s_pa.cwa", basedir = "SwashProjects/project_H_sw/TOXSWA", @@ -41,12 +26,16 @@ print(H_sw_R1_stream) \section{Public fields}{ \if{html}{\out{<div class="r6-fields">}} \describe{ -\item{\code{filename}}{Length one character vector.} +\item{\code{filename}}{Length one character vector holding the filename.} + +\item{\code{basedir}}{Length one character vector holding the directory where the file came from.} -\item{\code{basedir}}{Length one character vector.} +\item{\code{zipfile}}{If not null, giving the path to the zip file from which the file was read.} \item{\code{segment}}{Length one integer, specifying for which segment the cwa data were read.} +\item{\code{substance}}{The TOXSWA name of the substance.} + \item{\code{cwas}}{Dataframe holding the concentrations.} \item{\code{events}}{List of dataframes holding the event statistics for each threshold.} @@ -71,6 +60,7 @@ for the requested moving window sizes in days.} \if{html}{\out{<a id="method-new"></a>}} \if{latex}{\out{\hypertarget{method-new}{}}} \subsection{Method \code{new()}}{ +Create a TOXSWA_cwa object from a file \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$new( filename, @@ -82,29 +72,71 @@ for the requested moving window sizes in days.} )}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{filename}}{The filename} + +\item{\code{basedir}}{The directory to look in} + +\item{\code{zipfile}}{Optional path to a zipfile holding the file} + +\item{\code{segment}}{Either "last" or the number of the segment for which to read the data} + +\item{\code{substance}}{The TOXSWA substance name (for TOXSWA 4 or higher)} + +\item{\code{total}}{Should total concentrations be read in? If FALSE, free concentrations are read} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-moving_windows"></a>}} \if{latex}{\out{\hypertarget{method-moving_windows}{}}} \subsection{Method \code{moving_windows()}}{ +Add to the `windows` field described above. \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$moving_windows(windows, total = FALSE)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{windows}}{Window sizes in days} + +\item{\code{total}}{If TRUE, the total concentration including the amount adsorbed to +suspended matter will be used.} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-get_events"></a>}} \if{latex}{\out{\hypertarget{method-get_events}{}}} \subsection{Method \code{get_events()}}{ +Populate a datataframe with event information for the specified +threshold value. The resulting dataframe is stored in the `events` +field of the object. \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$get_events(thresholds, total = FALSE)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{thresholds}}{Threshold values in µg/L.} + +\item{\code{total}}{If TRUE, the total concentration including the amount adsorbed to +suspended matter will be used.} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-print"></a>}} \if{latex}{\out{\hypertarget{method-print}{}}} \subsection{Method \code{print()}}{ +Print a `TOXSWA_cwa` object \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$print()}\if{html}{\out{</div>}} } |
