Start new version, rename pp to ppp, more docs

22 files changed, 982 insertions, 166 deletions

diff --git a/.Rhistory b/.Rhistory
new file mode 100644
index 0000000..1a9e67f
--- /dev/null
+++ b/.Rhistory
@@ -0,0 +1,4 @@
+library(chents)
+?chent
+library(chents)
+?chent
diff --git a/DESCRIPTION b/DESCRIPTION
index e75912b..879bee7 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: chents
 Type: Package
 Title: Chemical Entities as R Objects
-Version: 0.3.1
-Date: 2023-11-10
+Version: 0.3.2
+Date: 2023-11-11
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
                     email = "johannes.ranke@jrwb.de"))
 Description: Utilities for dealing with chemical entities and associated
diff --git a/NAMESPACE b/NAMESPACE
index e6ced73..e56a6c6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -6,7 +6,7 @@ S3method(print,pai)
 export(chent)
 export(draw_svg.chent)
 export(pai)
-export(pp)
+export(ppp)
 importFrom(R6,R6Class)
 importFrom(grImport,PostScriptTrace)
 importFrom(grImport,grid.picture)
diff --git a/R/chent.R b/R/chent.R
index dc9be6f..fdad351 100644
--- a/R/chent.R
+++ b/R/chent.R
@@ -23,6 +23,7 @@
 #' if (!is.null(caffeine$Picture)) {
 #'   plot(caffeine)
 #' }
+
 chent <- R6Class("chent",
   public = list(
     #' @field identifier (`character(1)`)\cr
@@ -241,6 +242,7 @@ chent <- R6Class("chent",
     #' @param repo Should the file be looked for in the current working 
     #' directory, a local git repository under `~/git/chyaml`, or from
     #' the web (not implemented).
+    #' @param chyaml The filename to be looked for
     get_chyaml = function(repo = c("wd", "local", "web"),
       chyaml = paste0(URLencode(self$identifier), ".yaml"))
     {
@@ -287,8 +289,15 @@ chent <- R6Class("chent",
     },
     
     #' Add a water solubility
-    #' @param p0 The water solubility in mg/L
-    add_cwsat = function(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "") {
+    #' @param cwsat The water solubility in mg/L
+    #' @param T Temperature
+    #' @param pH The pH value
+    #' @param source An acronym specifying the source of the information
+    #' @param page The page from which the information was taken
+    #' @param remark A remark
+    add_cwsat = function(cwsat, T = NA, pH = NA,
+      source = NA, page = NA, remark = "")
+    {
       self$cwsat <- cwsat
       attr(self$cwsat, "T") <- T
       attr(self$cwsat, "pH") <- pH
@@ -299,7 +308,13 @@ chent <- R6Class("chent",
     
     #' Add a plant uptake factor
     #' @param PUF The plant uptake factor, a number between 0 and 1
-    add_PUF = function(PUF = 0, source = "focus_generic_gw_2014", page = 41, remark = "Conservative default value") {
+    #' @param source An acronym specifying the source of the information
+    #' @param page The page from which the information was taken
+    #' @param remark A remark
+    add_PUF = function(PUF = 0,
+      source = "focus_generic_gw_2014", page = 41,
+      remark = "Conservative default value")
+    {
       self$PUF <- PUF
       attr(self$PUF, "source") <- source
       attr(self$PUF, "page") <- page
@@ -326,13 +341,22 @@ chent <- R6Class("chent",
     
     #' @field transformations Data frame of observed transformations
     transformations = data.frame(study_type = character(0),
-                                 TP_identifier = character(0),
-                                 max_occurrence = numeric(0),
-                                 source = character(0),
-                                 pages = character(0),
-                                 stringsAsFactors = FALSE),
+      TP_identifier = character(0),
+      max_occurrence = numeric(0),
+      source = character(0),
+      page = character(0),
+      stringsAsFactors = FALSE),
     
     #' Add a line in the internal dataframe holding observed transformations
+    #' @param study_type A characterisation of the study type
+    #' @param TP_identifier An identifier of one of the transformation products
+    #' in `self$TPs`
+    #' @param max_occurrence The maximum observed occurrence of the 
+    #' transformation product, expressed as a fraction of the amount that would
+    #' result from stochiometric transformation
+    #' @param source An acronym specifying the source of the information
+    #' @param pages The page from which the information was taken
+    #' @param remark A remark
     add_transformation = function(study_type, TP_identifier, max_occurrence,
       remark = "", source = NA, pages = NA)
     {
@@ -344,19 +368,40 @@ chent <- R6Class("chent",
       if (is.numeric(pages)) pages <- paste(pages, collapse = ", ")
       cn <- colnames(self$transformations)
       self$transformations <- rbind(self$transformations,
-                                    data.frame(study_type = study_type,
-                                               TP_identifier = TP_identifier,
-                                               max_occurrence = max_occurrence,
-                                               remark = remark,
-                                               source = source,
-                                               pages = pages,
-                                               stringsAsFactors = FALSE))
+        data.frame(study_type = study_type,
+          TP_identifier = TP_identifier,
+          max_occurrence = max_occurrence,
+          remark = remark,
+          source = source,
+          page = page,
+          stringsAsFactors = FALSE))
     },
     
     #' @field soil_degradation Dataframe of modelling DT50 values
     soil_degradation = NULL,
     
     #' Add a line in the internal dataframe holding modelling DT50 values
+    #' @param soils Names of the soils
+    #' @param DT50_mod The modelling DT50 in the sense of regulatory pesticide
+    #' fate modelling
+    #' @param DT50_mod_ref The normalised modelling DT50 in the sense of
+    #' regulatory pesticide fate modelling
+    #' @param type The soil type
+    #' @param country The country (mainly for field studies)
+    #' @param pH_orig The pH stated in the study
+    #' @param pH_medium The medium in which this pH was measured
+    #' @param pH_H2O The pH extrapolated to pure water
+    #' @param perc_OC The percentage of organic carbon in the soil
+    #' @param temperature The temperature during the study in degrees Celsius
+    #' @param moisture The moisture during the study
+    #' @param category Is it a laboratory ('lab') or field study ('field')
+    #' @param formulation Name of the formulation applied, if it was not 
+    #' the technical active ingredient
+    #' @param model The degradation model used for deriving `DT50_mod`
+    #' @param chi2 The relative error as defined in FOCUS kinetics
+    #' @param source An acronym specifying the source of the information
+    #' @param page The page from which the information was taken
+    #' @param remark A remark
     add_soil_degradation = function(soils, DT50_mod, DT50_mod_ref,
       type = NA, country = NA,
       pH_orig = NA, pH_medium = NA, pH_H2O = NA,
@@ -396,7 +441,13 @@ chent <- R6Class("chent",
     #' @field soil_ff Dataframe of formation fractions
     soil_ff = NULL,
     
-    add_soil_ff = function(target, soils, ff = 1, remark = "", source, page = NA) {
+    # Add one or more formation fractions for degradation in soil
+    #' @param target The identifier(s) of the transformation product
+    #' @param soils The soil name(s) in which the transformation was observed
+    #' @param ff The formation fraction(s)
+    add_soil_ff = function(target, soils, ff = 1,
+      remark = "", source, page = NA)
+    {
       new_soil_ff = data.frame(
         target = target,
         target = target,
@@ -416,12 +467,19 @@ chent <- R6Class("chent",
     #' @field soil_sorption Dataframe of soil sorption data
     soil_sorption = NULL,
     
+    #' Add soil sorption data
+    #' @param Kf The sorption constant in L/kg, either linear (then `N` is 1) 
+    #' or according to Freundlich
+    #' @param Kfoc The constant from above, normalised to soil organic carbon
+    #' @param N The Freundlich exponent
+    #' @param perc_clay The percentage of clay in the soil
+    #' @param CEC The cation exchange capacity
     add_soil_sorption = function(soils, Kf, Kfoc, N,
-                                 type = NA,
-                                 pH_orig = NA, pH_medium = NA,
-                                 pH_H2O = NA,
-                                 perc_OC = NA, perc_clay = NA, CEC = NA,
-                                 remark = "", source, page = NA) {
+      type = NA, pH_orig = NA, pH_medium = NA,
+      pH_H2O = NA,
+      perc_OC = NA, perc_clay = NA, CEC = NA,
+      remark = "", source, page = NA)
+    {
       new_soil_sorption = data.frame(
         soils = soils,
         Kf = Kf, Kfoc = Kfoc, N = N,
@@ -441,6 +499,10 @@ chent <- R6Class("chent",
       }
     },
     
+    #' Write a PDF image of the structure
+    #' @param file The file to write to 
+    #' @param dir The directory to write the file to
+    #' @param template A template expressed as SMILES to use in RDKit
     pdf = function(file = paste0(self$identifier, ".pdf"),
         dir = "structures/pdf", template = NULL) {
       if (!dir.exists(dir)) {
@@ -462,8 +524,12 @@ chent <- R6Class("chent",
       m_line <- suppressWarnings(grep("MediaBox", head, value = TRUE))
       self$pdf_height <- as.numeric(gsub("/MediaBox \\[.* (.*)\\]", "\\1", m_line))
     },
-    png = function(file = paste0(self$identifier, ".png"), dir = "structures/png",
-                   antialias = 'gray') {
+    
+    #' Write a PNG image of the structure
+    #' @param antialias Passed to [png][grDevices::png]
+    png = function(file = paste0(self$identifier, ".png"),
+      dir = "structures/png", antialias = 'gray')
+    {
       if (!dir.exists(dir)) {
         message("Directory '", dir, "' does not exist")
         message("Trying to create directory '", dir, "'")
@@ -475,7 +541,12 @@ chent <- R6Class("chent",
       plot(self)
       dev.off()
     },
-    emf = function(file = paste0(self$identifier, ".emf"), dir = "structures/emf") {
+    
+    #' Write an EMF image of the structure using [emf][devEMF::emf]
+    #' @param file The file to write to
+    emf = function(file = paste0(self$identifier, ".emf"),
+      dir = "structures/emf")
+    {
       if (!requireNamespace("devEMF")) {
         stop("You need to have the devEMF package installed for this function")
       }
@@ -521,8 +592,8 @@ print.chent = function(x, ...) {
 #' @param subdir The path to which the file should be written
 #' @export
 draw_svg.chent = function(x, width = 300, height = 150,
-                          filename = paste0(names(x$identifier), ".svg"),
-                          subdir = "svg") {
+   filename = paste0(names(x$identifier), ".svg"),
+   subdir = "svg") {
   if (!rdkit_available) {
     stop("RDkit is not available via reticulate")
   } else {
@@ -560,8 +631,6 @@ plot.chent = function(x, ...) {
 #' @importFrom R6 R6Class
 #' @export
 #' @format An \code{\link{R6Class}} generator object
-#' @field iso ISO common name according to ISO 1750 as retreived from pesticidecompendium.bcpc.org
-#' @field bcpc List of information retrieved from pesticidecompendium.bcpc.org
 #' @examples
 #' # On Travis, we get a certificate validation error,
 #' # likely because the system (xenial) is so old,
@@ -575,18 +644,35 @@ plot.chent = function(x, ...) {
 #' }
 #'
 #' }
+
 pai <- R6Class("pai",
   inherit = chent,
-  public <- list(
+  public = list(
+    
+    #' @field iso ISO common name of the active ingredient according to ISO 1750
     iso = NULL,
+    
+    #' @field bcpc Information retrieved from the BCPC compendium available online
+    #' at <pesticidecompendium.bcpc.org>
     bcpc = NULL,
+    
+    #' Creates a new instance of this [R6][R6::R6Class] class.
+    #'
+    #' @description This class is derived from [chent]. It makes it easy
+    #' to create a [chent] from the ISO common name of a pesticide active
+    #' ingredient, and additionally stores the ISO name as well as
+    #' the complete result of querying the BCPC compendium using
+    #' [bcpc_query][webchem::bcpc_query].
+    #' 
+    #' @param iso The ISO common name to be used in the query of the 
+    #' BCPC compendium
+    #'
+    #' @param identifier Alternative identifier used for querying pubchem
     initialize = function(iso, identifier = iso,
-                          smiles = NULL,
-                          inchikey = NULL,
-                          bcpc = TRUE,
-                          pubchem = TRUE, pubchem_from = 'auto',
-                          rdkit = TRUE, template = NULL,
-                          chyaml = TRUE)
+      smiles = NULL, inchikey = NULL, bcpc = TRUE,
+      pubchem = TRUE, pubchem_from = 'auto',
+      rdkit = TRUE, template = NULL,
+      chyaml = TRUE)
     {
 
       if (!is.null(inchikey)) {
@@ -631,10 +717,9 @@ pai <- R6Class("pai",
       }
 
       super$initialize(identifier = identifier,
-                       smiles = smiles, 
-                       inchikey = self$inchikey,
-                       pubchem = pubchem, pubchem_from = pubchem_from,
-                       rdkit = rdkit, template = template, chyaml = chyaml)
+        smiles = smiles, inchikey = self$inchikey,
+        pubchem = pubchem, pubchem_from = pubchem_from,
+        rdkit = rdkit, template = template, chyaml = chyaml)
 
       invisible(self)
     }
@@ -659,30 +744,47 @@ print.pai = function(x, ...) {
   }
 }
 
-#' R6 class for holding a product with at least one active ingredient
+#' @title R6 class for a plant protection product with at least one active ingredient
 #'
-#' An R6 class for holding information about a product with at least one active ingredient
+#' @description Contains basic information about the active ingredients in the
+#' product
 #'
 #' @docType class
 #' @importFrom R6 R6Class
 #' @export
 #' @format An \code{\link{R6Class}} generator object.
-#' @field name The name of the product
-#' @field ais A list of active ingredients
-#' @field concentrations The concentration of the ais
-#' @field concentration_units Defaults to g/L
-#' @keywords data
-
-pp <- R6Class("pp",
-  public <- list(
+
+ppp <- R6Class("ppp",
+  public = list(
+    
+    #' @field name The name of the product
     name = NULL,
+    
+    #' @field ais A list of active ingredients
     ais = list(),
+    
+    #' @field concentrations The concentration of the ais
     concentrations = NULL,
+    
+    #' @field concentration_units Defaults to g/L
     concentration_units = NULL,
+    
+    #' @field density The density of the product
     density = NULL,
+    
+    #' @field density_units Defaults to g/L
     density_units = "g/L",
+    
+    #' Creates a new instance of this [R6][R6::R6Class] class.
+    #' 
+    #' @field ... Identifiers of the active ingredients
+    #' @field concentrations Concentrations of the active ingredients
+    #' @field concentration_units Defaults to g/L
+    #' @field density The density
+    #' @field density_units Defaults to g/L
     initialize = function(name, ..., concentrations, concentration_units = "g/L",
-                          density = 1000, density_units = "g/L") {
+      density = 1000, density_units = "g/L")
+    {
       self$name <- name
       self$ais <- list(...)
       self$concentrations <- concentrations
@@ -691,6 +793,8 @@ pp <- R6Class("pp",
       names(self$concentrations) <- names(self$ais)
       self$concentration_units <- concentration_units
     },
+    
+    #' Printing method
     print = function() {
       cat("<pp> named", self$name, "\n")
     }
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 2d8ddc3..f099651 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -12,4 +12,4 @@ reference:
       - print.chent
       - pai
       - print.pai
-      - pp
+      - ppp
diff --git a/docs/404.html b/docs/404.html
index eb79a5d..26a509c 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -32,7 +32,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.2</span>
       </span>
     </div>
 
diff --git a/docs/authors.html b/docs/authors.html
index 0c3b654..1e764a7 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.2</span>
       </span>
     </div>
 
@@ -60,13 +60,13 @@
 
     <p>Ranke J (2023).
 <em>chents: Chemical Entities as R Objects</em>.
-R package version 0.3.1, <a href="https://github.com/jranke/chents" class="external-link">https://github.com/jranke/chents</a>. 
+R package version 0.3.2, <a href="https://github.com/jranke/chents" class="external-link">https://github.com/jranke/chents</a>. 
 </p>
     <pre>@Manual{,
   title = {chents: Chemical Entities as R Objects},
   author = {Johannes Ranke},
   year = {2023},
-  note = {R package version 0.3.1},
+  note = {R package version 0.3.2},
   url = {https://github.com/jranke/chents},
 }</pre>
 
diff --git a/docs/index.html b/docs/index.html
index f241bb6..313ff06 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -37,7 +37,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.2</span>
       </span>
     </div>
 
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index dd7c4f0..eb77ea1 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.1
 pkgdown: 2.0.7
 pkgdown_sha: ~
 articles: {}
-last_built: 2023-11-10T17:41Z
+last_built: 2023-11-11T07:23Z
 
diff --git a/docs/reference/chent.html b/docs/reference/chent.html
index a6b8dde..48ccf3f 100644
--- a/docs/reference/chent.html
+++ b/docs/reference/chent.html
@@ -19,7 +19,7 @@ generated using RDKit if RDKit and its python bindings are installed."><!-- math
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.2</span>
       </span>
     </div>
 
@@ -126,15 +126,18 @@ List of information retrieved from PubChem</p></dd>
 
 
 <dt><code>TPs</code></dt>
-<dd><p>List of transformation products as chent objects</p></dd>
+<dd><p>List of transformation products as chent objects
+Add a transformation product to the internal list</p></dd>
 
 
 <dt><code>transformations</code></dt>
-<dd><p>Data frame of observed transformations</p></dd>
+<dd><p>Data frame of observed transformations
+Add a line in the internal dataframe holding observed transformations</p></dd>
 
 
 <dt><code>soil_degradation</code></dt>
-<dd><p>Dataframe of modelling DT50 values</p></dd>
+<dd><p>Dataframe of modelling DT50 values
+Add a line in the internal dataframe holding modelling DT50 values</p></dd>
 
 
 <dt><code>soil_ff</code></dt>
@@ -142,7 +145,8 @@ List of information retrieved from PubChem</p></dd>
 
 
 <dt><code>soil_sorption</code></dt>
-<dd><p>Dataframe of soil sorption data</p></dd>
+<dd><p>Dataframe of soil sorption data
+Add soil sorption data</p></dd>
 
 
 </dl><p></p></div>
@@ -262,7 +266,8 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <div class="section">
 <h4 id="arguments-2">Arguments<a class="anchor" aria-label="anchor" href="#arguments-2"></a></h4>
 <p></p><div class="arguments"><dl><dt><code>pubchem_cid</code></dt>
-<dd><p>CID</p></dd>
+<dd><p>CID
+Get chemical information from RDKit if available</p></dd>
 
 
 </dl><p></p></div>
@@ -276,6 +281,15 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_rdkit</span><span class="op">(</span>template <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-3">Arguments<a class="anchor" aria-label="anchor" href="#arguments-3"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>template</code></dt>
+<dd><p>Optional template specified as a SMILES code
+Obtain information from a YAML file</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-get_chyaml"></a><div class="section">
 <h3 id="method-get-chyaml-">Method <code>get_chyaml()</code><a class="anchor" aria-label="anchor" href="#method-get-chyaml-"></a></h3>
@@ -288,6 +302,21 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-4">Arguments<a class="anchor" aria-label="anchor" href="#arguments-4"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>repo</code></dt>
+<dd><p>Should the file be looked for in the current working
+directory, a local git repository under <code>~/git/chyaml</code>, or from
+the web (not implemented).</p></dd>
+
+
+<dt><code>chyaml</code></dt>
+<dd><p>The filename to be looked for
+Add a vapour pressure</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-add_p0"></a><div class="section">
 <h3 id="method-add-p-">Method <code>add_p0()</code><a class="anchor" aria-label="anchor" href="#method-add-p-"></a></h3>
@@ -297,6 +326,31 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_p0</span><span class="op">(</span><span class="va">p0</span>, T <span class="op">=</span> <span class="cn">NA</span>, source <span class="op">=</span> <span class="cn">NA</span>, page <span class="op">=</span> <span class="cn">NA</span>, remark <span class="op">=</span> <span class="st">""</span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-5">Arguments<a class="anchor" aria-label="anchor" href="#arguments-5"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>p0</code></dt>
+<dd><p>The vapour pressure in Pa</p></dd>
+
+
+<dt><code>T</code></dt>
+<dd><p>Temperature</p></dd>
+
+
+<dt><code>source</code></dt>
+<dd><p>An acronym specifying the source of the information</p></dd>
+
+
+<dt><code>page</code></dt>
+<dd><p>The page from which the information was taken</p></dd>
+
+
+<dt><code>remark</code></dt>
+<dd><p>A remark
+Add a water solubility</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-add_cwsat"></a><div class="section">
 <h3 id="method-add-cwsat-">Method <code>add_cwsat()</code><a class="anchor" aria-label="anchor" href="#method-add-cwsat-"></a></h3>
@@ -306,6 +360,35 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_cwsat</span><span class="op">(</span><span class="va">cwsat</span>, T <span class="op">=</span> <span class="cn">NA</span>, pH <span class="op">=</span> <span class="cn">NA</span>, source <span class="op">=</span> <span class="cn">NA</span>, page <span class="op">=</span> <span class="cn">NA</span>, remark <span class="op">=</span> <span class="st">""</span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-6">Arguments<a class="anchor" aria-label="anchor" href="#arguments-6"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>cwsat</code></dt>
+<dd><p>The water solubility in mg/L</p></dd>
+
+
+<dt><code>T</code></dt>
+<dd><p>Temperature</p></dd>
+
+
+<dt><code>pH</code></dt>
+<dd><p>The pH value</p></dd>
+
+
+<dt><code>source</code></dt>
+<dd><p>An acronym specifying the source of the information</p></dd>
+
+
+<dt><code>page</code></dt>
+<dd><p>The page from which the information was taken</p></dd>
+
+
+<dt><code>remark</code></dt>
+<dd><p>A remark
+Add a plant uptake factor</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-add_PUF"></a><div class="section">
 <h3 id="method-add-puf-">Method <code>add_PUF()</code><a class="anchor" aria-label="anchor" href="#method-add-puf-"></a></h3>
@@ -320,6 +403,26 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-7">Arguments<a class="anchor" aria-label="anchor" href="#arguments-7"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>PUF</code></dt>
+<dd><p>The plant uptake factor, a number between 0 and 1</p></dd>
+
+
+<dt><code>source</code></dt>
+<dd><p>An acronym specifying the source of the information</p></dd>
+
+
+<dt><code>page</code></dt>
+<dd><p>The page from which the information was taken</p></dd>
+
+
+<dt><code>remark</code></dt>
+<dd><p>A remark</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-add_TP"></a><div class="section">
 <h3 id="method-add-tp-">Method <code>add_TP()</code><a class="anchor" aria-label="anchor" href="#method-add-tp-"></a></h3>
@@ -329,6 +432,22 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_TP</span><span class="op">(</span><span class="va">x</span>, smiles <span class="op">=</span> <span class="cn">NULL</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-8">Arguments<a class="anchor" aria-label="anchor" href="#arguments-8"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>x</code></dt>
+<dd><p>A chent object, or an identifier to generate a chent object</p></dd>
+
+
+<dt><code>smiles</code></dt>
+<dd><p>A SMILES code for defining a chent object</p></dd>
+
+
+<dt><code>pubchem</code></dt>
+<dd><p>Should chemical information be obtained from PubChem?</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-add_transformation"></a><div class="section">
 <h3 id="method-add-transformation-">Method <code>add_transformation()</code><a class="anchor" aria-label="anchor" href="#method-add-transformation-"></a></h3>
@@ -345,6 +464,37 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-9">Arguments<a class="anchor" aria-label="anchor" href="#arguments-9"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>study_type</code></dt>
+<dd><p>A characterisation of the study type</p></dd>
+
+
+<dt><code>TP_identifier</code></dt>
+<dd><p>An identifier of one of the transformation products
+in <code>self$TPs</code></p></dd>
+
+
+<dt><code>max_occurrence</code></dt>
+<dd><p>The maximum observed occurrence of the
+transformation product, expressed as a fraction of the amount that would
+result from stochiometric transformation</p></dd>
+
+
+<dt><code>remark</code></dt>
+<dd><p>A remark</p></dd>
+
+
+<dt><code>source</code></dt>
+<dd><p>An acronym specifying the source of the information</p></dd>
+
+
+<dt><code>pages</code></dt>
+<dd><p>The page from which the information was taken</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-add_soil_degradation"></a><div class="section">
 <h3 id="method-add-soil-degradation-">Method <code>add_soil_degradation()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-degradation-"></a></h3>
@@ -373,6 +523,85 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-10">Arguments<a class="anchor" aria-label="anchor" href="#arguments-10"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>soils</code></dt>
+<dd><p>Names of the soils</p></dd>
+
+
+<dt><code>DT50_mod</code></dt>
+<dd><p>The modelling DT50 in the sense of regulatory pesticide
+fate modelling</p></dd>
+
+
+<dt><code>DT50_mod_ref</code></dt>
+<dd><p>The normalised modelling DT50 in the sense of
+regulatory pesticide fate modelling</p></dd>
+
+
+<dt><code>type</code></dt>
+<dd><p>The soil type</p></dd>
+
+
+<dt><code>country</code></dt>
+<dd><p>The country (mainly for field studies)</p></dd>
+
+
+<dt><code>pH_orig</code></dt>
+<dd><p>The pH stated in the study</p></dd>
+
+
+<dt><code>pH_medium</code></dt>
+<dd><p>The medium in which this pH was measured</p></dd>
+
+
+<dt><code>pH_H2O</code></dt>
+<dd><p>The pH extrapolated to pure water</p></dd>
+
+
+<dt><code>perc_OC</code></dt>
+<dd><p>The percentage of organic carbon in the soil</p></dd>
+
+
+<dt><code>temperature</code></dt>
+<dd><p>The temperature during the study in degrees Celsius</p></dd>
+
+
+<dt><code>moisture</code></dt>
+<dd><p>The moisture during the study</p></dd>
+
+
+<dt><code>category</code></dt>
+<dd><p>Is it a laboratory ('lab') or field study ('field')</p></dd>
+
+
+<dt><code>formulation</code></dt>
+<dd><p>Name of the formulation applied, if it was not
+the technical active ingredient</p></dd>
+
+
+<dt><code>model</code></dt>
+<dd><p>The degradation model used for deriving <code>DT50_mod</code></p></dd>
+
+
+<dt><code>chi2</code></dt>
+<dd><p>The relative error as defined in FOCUS kinetics</p></dd>
+
+
+<dt><code>remark</code></dt>
+<dd><p>A remark</p></dd>
+
+
+<dt><code>source</code></dt>
+<dd><p>An acronym specifying the source of the information</p></dd>
+
+
+<dt><code>page</code></dt>
+<dd><p>The page from which the information was taken</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-add_soil_ff"></a><div class="section">
 <h3 id="method-add-soil-ff-">Method <code>add_soil_ff()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-ff-"></a></h3>
@@ -382,6 +611,22 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_soil_ff</span><span class="op">(</span><span class="va">target</span>, <span class="va">soils</span>, ff <span class="op">=</span> <span class="fl">1</span>, remark <span class="op">=</span> <span class="st">""</span>, <span class="va">source</span>, page <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-11">Arguments<a class="anchor" aria-label="anchor" href="#arguments-11"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>target</code></dt>
+<dd><p>The identifier(s) of the transformation product</p></dd>
+
+
+<dt><code>soils</code></dt>
+<dd><p>The soil name(s) in which the transformation was observed</p></dd>
+
+
+<dt><code>ff</code></dt>
+<dd><p>The formation fraction(s)</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-add_soil_sorption"></a><div class="section">
 <h3 id="method-add-soil-sorption-">Method <code>add_soil_sorption()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-sorption-"></a></h3>
@@ -406,6 +651,32 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-12">Arguments<a class="anchor" aria-label="anchor" href="#arguments-12"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>Kf</code></dt>
+<dd><p>The sorption constant in L/kg, either linear (then <code>N</code> is 1)
+or according to Freundlich</p></dd>
+
+
+<dt><code>Kfoc</code></dt>
+<dd><p>The constant from above, normalised to soil organic carbon</p></dd>
+
+
+<dt><code>N</code></dt>
+<dd><p>The Freundlich exponent</p></dd>
+
+
+<dt><code>perc_clay</code></dt>
+<dd><p>The percentage of clay in the soil</p></dd>
+
+
+<dt><code>CEC</code></dt>
+<dd><p>The cation exchange capacity
+Write a PDF image of the structure</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-pdf"></a><div class="section">
 <h3 id="method-pdf-">Method <code><a href="https://rdrr.io/r/grDevices/pdf.html" class="external-link">pdf()</a></code><a class="anchor" aria-label="anchor" href="#method-pdf-"></a></h3>
@@ -419,6 +690,23 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-13">Arguments<a class="anchor" aria-label="anchor" href="#arguments-13"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>file</code></dt>
+<dd><p>The file to write to</p></dd>
+
+
+<dt><code>dir</code></dt>
+<dd><p>The directory to write the file to</p></dd>
+
+
+<dt><code>template</code></dt>
+<dd><p>A template expressed as SMILES to use in RDKit
+Write a PNG image of the structure</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-png"></a><div class="section">
 <h3 id="method-png-">Method <code><a href="https://rdrr.io/r/grDevices/png.html" class="external-link">png()</a></code><a class="anchor" aria-label="anchor" href="#method-png-"></a></h3>
@@ -432,6 +720,15 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-14">Arguments<a class="anchor" aria-label="anchor" href="#arguments-14"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>antialias</code></dt>
+<dd><p>Passed to <a href="https://rdrr.io/r/grDevices/png.html" class="external-link">png</a>
+Write an EMF image of the structure using <a href="https://rdrr.io/pkg/devEMF/man/emf.html" class="external-link">emf</a></p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-emf"></a><div class="section">
 <h3 id="method-emf-">Method <code>emf()</code><a class="anchor" aria-label="anchor" href="#method-emf-"></a></h3>
@@ -441,6 +738,14 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">emf</span><span class="op">(</span>file <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">self</span><span class="op">$</span><span class="va">identifier</span>, <span class="st">".emf"</span><span class="op">)</span>, dir <span class="op">=</span> <span class="st">"structures/emf"</span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments-15">Arguments<a class="anchor" aria-label="anchor" href="#arguments-15"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>file</code></dt>
+<dd><p>The file to write to</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-chent-clone"></a><div class="section">
 <h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3>
@@ -450,7 +755,7 @@ Get chemical information from PubChem for a known PubChem CID</p></dd>
 </div>
 
 <div class="section">
-<h4 id="arguments-3">Arguments<a class="anchor" aria-label="anchor" href="#arguments-3"></a></h4>
+<h4 id="arguments-16">Arguments<a class="anchor" aria-label="anchor" href="#arguments-16"></a></h4>
 <p></p><div class="arguments"><dl><dt><code>deep</code></dt>
 <dd><p>Whether to make a deep clone.</p></dd>
 
diff --git a/docs/reference/draw_svg.chent.html b/docs/reference/draw_svg.chent.html
index cae8c0b..a95748e 100644
--- a/docs/reference/draw_svg.chent.html
+++ b/docs/reference/draw_svg.chent.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index d9eb797..6bc6df8 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.2</span>
       </span>
     </div>
 
@@ -72,9 +72,9 @@
         </td>
         <td><p>Printing method for pai objects (pesticidal active ingredients)</p></td>
       </tr><tr><td>
-          <p><code><a href="pp.html">pp</a></code> </p>
+          <p><code><a href="ppp.html">ppp</a></code> </p>
         </td>
-        <td><p>R6 class for holding a product with at least one active ingredient</p></td>
+        <td><p>R6 class for a plant protection product with at least one active ingredient</p></td>
       </tr></tbody></table></div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/reference/pai.html b/docs/reference/pai.html
index 636007f..d8811d0 100644
--- a/docs/reference/pai.html
+++ b/docs/reference/pai.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>An R6 class for pesticidal active ingredients and associated data — pai • chents</title><!-- jquery --><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/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><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/5.12.1/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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><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"><script src="../pkgdown.js"></script><meta property="og:title" content="An R6 class for pesticidal active ingredients and associated data — pai"><meta property="og:description" content="The class is initialised with an identifier which is generally an ISO common name.
-Additional chemical information is retrieved from the internet if available."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>An R6 class for pesticidal active ingredients and associated data — pai • chents</title><!-- jquery --><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/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><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/5.12.1/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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><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"><script src="../pkgdown.js"></script><meta property="og:title" content="An R6 class for pesticidal active ingredients and associated data — pai"><meta property="og:description" content="An R6 class for pesticidal active ingredients and associated data
+An R6 class for pesticidal active ingredients and associated data"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
@@ -18,7 +18,7 @@ Additional chemical information is retrieved from the internet if available."><!
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.2</span>
       </span>
     </div>
 
@@ -47,8 +47,8 @@ Additional chemical information is retrieved from the internet if available."><!
     </div>
 
     <div class="ref-description">
-    <p>The class is initialised with an identifier which is generally an ISO common name.
-Additional chemical information is retrieved from the internet if available.</p>
+    <p>An R6 class for pesticidal active ingredients and associated data</p>
+<p>An R6 class for pesticidal active ingredients and associated data</p>
     </div>
 
 
@@ -56,6 +56,11 @@ Additional chemical information is retrieved from the internet if available.</p>
     <h2>Format</h2>
     <p>An <code>R6Class</code> generator object</p>
     </div>
+    <div id="details">
+    <h2>Details</h2>
+    <p>The class is initialised with an identifier which is generally an ISO common name.
+Additional chemical information is retrieved from the internet if available.</p>
+    </div>
     <div id="super-class">
     <h2>Super class</h2>
     <p><code><a href="chent.html">chents::chent</a></code> -&gt; <code>pai</code></p>
@@ -63,11 +68,13 @@ Additional chemical information is retrieved from the internet if available.</p>
     <div id="public-fields">
     <h2>Public fields</h2>
     <p></p><div class="r6-fields"><dl><dt><code>iso</code></dt>
-<dd><p>ISO common name according to ISO 1750 as retreived from pesticidecompendium.bcpc.org</p></dd>
+<dd><p>ISO common name of the active ingredient according to ISO 1750</p></dd>
 
 
 <dt><code>bcpc</code></dt>
-<dd><p>List of information retrieved from pesticidecompendium.bcpc.org</p></dd>
+<dd><p>Information retrieved from the BCPC compendium available online
+at &lt;pesticidecompendium.bcpc.org&gt;
+Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p></dd>
 
 
 </dl><p></p></div>
@@ -97,8 +104,11 @@ Additional chemical information is retrieved from the internet if available.</p>
 <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="try_pubchem"><a href="chent.html#method-try_pubchem"><code>chents::chent$try_pubchem()</code></a></span></li>
 </ul></details></p><hr><a id="method-pai-new"></a><div class="section">
 <h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3>
-
-<div class="section">
+<p>This class is derived from <a href="chent.html">chent</a>. It makes it easy
+to create a <a href="chent.html">chent</a> from the ISO common name of a pesticide active
+ingredient, and additionally stores the ISO name as well as
+the complete result of querying the BCPC compendium using
+<a href="https://docs.ropensci.org/webchem/reference/bcpc_query.html" class="external-link">bcpc_query</a>.</p><div class="section">
 <h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4>
 <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/pai.html">pai</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span>
 <span>  <span class="va">iso</span>,</span>
@@ -114,6 +124,19 @@ Additional chemical information is retrieved from the internet if available.</p>
 <span><span class="op">)</span></span></code></pre></div><p></p></div>
 </div>
 
+<div class="section">
+<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>iso</code></dt>
+<dd><p>The ISO common name to be used in the query of the
+BCPC compendium</p></dd>
+
+
+<dt><code>identifier</code></dt>
+<dd><p>Alternative identifier used for querying pubchem</p></dd>
+
+
+</dl><p></p></div>
+</div>
 
 </div><p></p><hr><a id="method-pai-clone"></a><div class="section">
 <h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3>
@@ -123,7 +146,7 @@ Additional chemical information is retrieved from the internet if available.</p>
 </div>
 
 <div class="section">
-<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4>
+<h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4>
 <p></p><div class="arguments"><dl><dt><code>deep</code></dt>
 <dd><p>Whether to make a deep clone.</p></dd>
 
diff --git a/docs/reference/plot.chent.html b/docs/reference/plot.chent.html
index 470ce79..26d8445 100644
--- a/docs/reference/plot.chent.html
+++ b/docs/reference/plot.chent.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/ppp.html b/docs/reference/ppp.html
new file mode 100644
index 0000000..7a9b861
--- /dev/null
+++ b/docs/reference/ppp.html
@@ -0,0 +1,194 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>R6 class for a plant protection product with at least one active ingredient — ppp • chents</title><!-- jquery --><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/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><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/5.12.1/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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><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"><script src="../pkgdown.js"></script><meta property="og:title" content="R6 class for a plant protection product with at least one active ingredient — ppp"><meta property="og:description" content="Contains basic information about the active ingredients in the
+product"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
+
+    <div class="container template-reference-topic">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">chents</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.2</span>
+      </span>
+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav"><li>
+  <a href="../reference/index.html">Reference</a>
+</li>
+      </ul><ul class="nav navbar-nav navbar-right"><li>
+  <a href="https://github.com/jranke/chents/" class="external-link">
+    <span class="fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header><div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>R6 class for a plant protection product with at least one active ingredient</h1>
+    <small class="dont-index">Source: <a href="https://github.com/jranke/chents/blob/HEAD/R/chent.R" class="external-link"><code>R/chent.R</code></a></small>
+    <div class="hidden name"><code>ppp.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Contains basic information about the active ingredients in the
+product</p>
+    </div>
+
+
+    <div id="format">
+    <h2>Format</h2>
+    <p>An <code>R6Class</code> generator object.</p>
+    </div>
+    <div id="public-fields">
+    <h2>Public fields</h2>
+    <p></p><div class="r6-fields"><dl><dt><code>name</code></dt>
+<dd><p>The name of the product</p></dd>
+
+
+<dt><code>ais</code></dt>
+<dd><p>A list of active ingredients</p></dd>
+
+
+<dt><code>concentrations</code></dt>
+<dd><p>The concentration of the ais</p></dd>
+
+
+<dt><code>concentration_units</code></dt>
+<dd><p>Defaults to g/L</p></dd>
+
+
+<dt><code>density</code></dt>
+<dd><p>The density of the product</p></dd>
+
+
+<dt><code>density_units</code></dt>
+<dd><p>Defaults to g/L
+Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p></dd>
+
+
+<dt><code>...</code></dt>
+<dd><p>Identifiers of the active ingredients</p></dd>
+
+
+<dt><code>concentrations</code></dt>
+<dd><p>Concentrations of the active ingredients</p></dd>
+
+
+<dt><code>concentration_units</code></dt>
+<dd><p>Defaults to g/L</p></dd>
+
+
+<dt><code>density</code></dt>
+<dd><p>The density</p></dd>
+
+
+<dt><code>density_units</code></dt>
+<dd><p>Defaults to g/L
+Printing method</p></dd>
+
+
+</dl><p></p></div>
+    </div>
+    <div id="active-bindings">
+    <h2>Active bindings</h2>
+    <p></p><div class="r6-active-bindings"><dl><dt><code>...</code></dt>
+<dd><p>Identifiers of the active ingredients</p></dd>
+
+
+</dl><p></p></div>
+    </div>
+    <div id="methods">
+    <h2>Methods</h2>
+    
+<div class="section">
+<h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
+
+<ul><li><p><a href="#method-ppp-new"><code>ppp$new()</code></a></p></li>
+<li><p><a href="#method-ppp-print"><code>ppp$print()</code></a></p></li>
+<li><p><a href="#method-ppp-clone"><code>ppp$clone()</code></a></p></li>
+</ul></div><p></p><hr><a id="method-ppp-new"></a><div class="section">
+<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3>
+
+<div class="section">
+<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/ppp.html">ppp</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span>
+<span>  <span class="va">name</span>,</span>
+<span>  <span class="va">...</span>,</span>
+<span>  <span class="va">concentrations</span>,</span>
+<span>  concentration_units <span class="op">=</span> <span class="st">"g/L"</span>,</span>
+<span>  density <span class="op">=</span> <span class="fl">1000</span>,</span>
+<span>  density_units <span class="op">=</span> <span class="st">"g/L"</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</div><p></p><hr><a id="method-ppp-print"></a><div class="section">
+<h3 id="method-print-">Method <code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code><a class="anchor" aria-label="anchor" href="#method-print-"></a></h3>
+
+<div class="section">
+<h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">ppp</span><span class="op">$</span><span class="fu">print</span><span class="op">(</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</div><p></p><hr><a id="method-ppp-clone"></a><div class="section">
+<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3>
+<p>The objects of this class are cloneable with this method.</p><div class="section">
+<h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">ppp</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+<div class="section">
+<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>deep</code></dt>
+<dd><p>Whether to make a deep clone.</p></dd>
+
+
+</dl><p></p></div>
+</div>
+
+</div>
+
+    </div>
+
+  </div>
+  <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>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
+
+      </footer></div>
+
+  
+
+
+  
+
+  </body></html>
+
diff --git a/docs/reference/print.chent.html b/docs/reference/print.chent.html
index 08497dd..da3ba4f 100644
--- a/docs/reference/print.chent.html
+++ b/docs/reference/print.chent.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/print.pai.html b/docs/reference/print.pai.html
index 3faa5f7..5a08066 100644
--- a/docs/reference/print.pai.html
+++ b/docs/reference/print.pai.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.2</span>
       </span>
     </div>
 
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 986ccf3..63ab18d 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -28,6 +28,9 @@
     <loc>/reference/pp.html</loc>
   </url>
   <url>
+    <loc>/reference/ppp.html</loc>
+  </url>
+  <url>
     <loc>/reference/print.chent.html</loc>
   </url>
   <url>
diff --git a/man/chent.Rd b/man/chent.Rd
index e069938..686d6c7 100644
--- a/man/chent.Rd
+++ b/man/chent.Rd
@@ -73,7 +73,8 @@ Add a line in the internal dataframe holding modelling DT50 values}
 
 \item{\code{soil_ff}}{Dataframe of formation fractions}
 
-\item{\code{soil_sorption}}{Dataframe of soil sorption data}
+\item{\code{soil_sorption}}{Dataframe of soil sorption data
+Add soil sorption data}
 }
 \if{html}{\out{</div>}}
 }
@@ -214,7 +215,9 @@ Obtain information from a YAML file}
 \describe{
 \item{\code{repo}}{Should the file be looked for in the current working
 directory, a local git repository under \verb{~/git/chyaml}, or from
-the web (not implemented).
+the web (not implemented).}
+
+\item{\code{chyaml}}{The filename to be looked for
 Add a vapour pressure}
 }
 \if{html}{\out{</div>}}
@@ -256,7 +259,17 @@ Add a water solubility}
 \subsection{Arguments}{
 \if{html}{\out{<div class="arguments">}}
 \describe{
-\item{\code{p0}}{The water solubility in mg/L
+\item{\code{cwsat}}{The water solubility in mg/L}
+
+\item{\code{T}}{Temperature}
+
+\item{\code{pH}}{The pH value}
+
+\item{\code{source}}{An acronym specifying the source of the information}
+
+\item{\code{page}}{The page from which the information was taken}
+
+\item{\code{remark}}{A remark
 Add a plant uptake factor}
 }
 \if{html}{\out{</div>}}
@@ -279,6 +292,12 @@ Add a plant uptake factor}
 \if{html}{\out{<div class="arguments">}}
 \describe{
 \item{\code{PUF}}{The plant uptake factor, a number between 0 and 1}
+
+\item{\code{source}}{An acronym specifying the source of the information}
+
+\item{\code{page}}{The page from which the information was taken}
+
+\item{\code{remark}}{A remark}
 }
 \if{html}{\out{</div>}}
 }
@@ -318,6 +337,26 @@ Add a plant uptake factor}
 )}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{study_type}}{A characterisation of the study type}
+
+\item{\code{TP_identifier}}{An identifier of one of the transformation products
+in \code{self$TPs}}
+
+\item{\code{max_occurrence}}{The maximum observed occurrence of the
+transformation product, expressed as a fraction of the amount that would
+result from stochiometric transformation}
+
+\item{\code{remark}}{A remark}
+
+\item{\code{source}}{An acronym specifying the source of the information}
+
+\item{\code{pages}}{The page from which the information was taken}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-add_soil_degradation"></a>}}
@@ -346,6 +385,50 @@ Add a plant uptake factor}
 )}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{soils}}{Names of the soils}
+
+\item{\code{DT50_mod}}{The modelling DT50 in the sense of regulatory pesticide
+fate modelling}
+
+\item{\code{DT50_mod_ref}}{The normalised modelling DT50 in the sense of
+regulatory pesticide fate modelling}
+
+\item{\code{type}}{The soil type}
+
+\item{\code{country}}{The country (mainly for field studies)}
+
+\item{\code{pH_orig}}{The pH stated in the study}
+
+\item{\code{pH_medium}}{The medium in which this pH was measured}
+
+\item{\code{pH_H2O}}{The pH extrapolated to pure water}
+
+\item{\code{perc_OC}}{The percentage of organic carbon in the soil}
+
+\item{\code{temperature}}{The temperature during the study in degrees Celsius}
+
+\item{\code{moisture}}{The moisture during the study}
+
+\item{\code{category}}{Is it a laboratory ('lab') or field study ('field')}
+
+\item{\code{formulation}}{Name of the formulation applied, if it was not
+the technical active ingredient}
+
+\item{\code{model}}{The degradation model used for deriving \code{DT50_mod}}
+
+\item{\code{chi2}}{The relative error as defined in FOCUS kinetics}
+
+\item{\code{remark}}{A remark}
+
+\item{\code{source}}{An acronym specifying the source of the information}
+
+\item{\code{page}}{The page from which the information was taken}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-add_soil_ff"></a>}}
@@ -355,6 +438,17 @@ Add a plant uptake factor}
 \if{html}{\out{<div class="r">}}\preformatted{chent$add_soil_ff(target, soils, ff = 1, remark = "", source, page = NA)}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{target}}{The identifier(s) of the transformation product}
+
+\item{\code{soils}}{The soil name(s) in which the transformation was observed}
+
+\item{\code{ff}}{The formation fraction(s)}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-add_soil_sorption"></a>}}
@@ -379,6 +473,23 @@ Add a plant uptake factor}
 )}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{Kf}}{The sorption constant in L/kg, either linear (then \code{N} is 1)
+or according to Freundlich}
+
+\item{\code{Kfoc}}{The constant from above, normalised to soil organic carbon}
+
+\item{\code{N}}{The Freundlich exponent}
+
+\item{\code{perc_clay}}{The percentage of clay in the soil}
+
+\item{\code{CEC}}{The cation exchange capacity
+Write a PDF image of the structure}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-pdf"></a>}}
@@ -392,6 +503,18 @@ Add a plant uptake factor}
 )}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{file}}{The file to write to}
+
+\item{\code{dir}}{The directory to write the file to}
+
+\item{\code{template}}{A template expressed as SMILES to use in RDKit
+Write a PNG image of the structure}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-png"></a>}}
@@ -405,6 +528,14 @@ Add a plant uptake factor}
 )}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{antialias}}{Passed to \link[grDevices:png]{png}
+Write an EMF image of the structure using \link[devEMF:emf]{emf}}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-emf"></a>}}
@@ -414,6 +545,13 @@ Add a plant uptake factor}
 \if{html}{\out{<div class="r">}}\preformatted{chent$emf(file = paste0(self$identifier, ".emf"), dir = "structures/emf")}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{file}}{The file to write to}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-clone"></a>}}
diff --git a/man/pai.Rd b/man/pai.Rd
index d966a9e..f133c5a 100644
--- a/man/pai.Rd
+++ b/man/pai.Rd
@@ -8,6 +8,11 @@
 An \code{\link{R6Class}} generator object
 }
 \description{
+An R6 class for pesticidal active ingredients and associated data
+
+An R6 class for pesticidal active ingredients and associated data
+}
+\details{
 The class is initialised with an identifier which is generally an ISO common name.
 Additional chemical information is retrieved from the internet if available.
 }
@@ -31,9 +36,11 @@ if (!is.null(atr$Picture)) {
 \section{Public fields}{
 \if{html}{\out{<div class="r6-fields">}}
 \describe{
-\item{\code{iso}}{ISO common name according to ISO 1750 as retreived from pesticidecompendium.bcpc.org}
+\item{\code{iso}}{ISO common name of the active ingredient according to ISO 1750}
 
-\item{\code{bcpc}}{List of information retrieved from pesticidecompendium.bcpc.org}
+\item{\code{bcpc}}{Information retrieved from the BCPC compendium available online
+at <pesticidecompendium.bcpc.org>
+Creates a new instance of this \link[R6:R6Class]{R6} class.}
 }
 \if{html}{\out{</div>}}
 }
@@ -69,6 +76,11 @@ if (!is.null(atr$Picture)) {
 \if{html}{\out{<a id="method-pai-new"></a>}}
 \if{latex}{\out{\hypertarget{method-pai-new}{}}}
 \subsection{Method \code{new()}}{
+This class is derived from \link{chent}. It makes it easy
+to create a \link{chent} from the ISO common name of a pesticide active
+ingredient, and additionally stores the ISO name as well as
+the complete result of querying the BCPC compendium using
+\link[webchem:bcpc_query]{bcpc_query}.
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{pai$new(
   iso,
@@ -84,6 +96,16 @@ if (!is.null(atr$Picture)) {
 )}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{iso}}{The ISO common name to be used in the query of the
+BCPC compendium}
+
+\item{\code{identifier}}{Alternative identifier used for querying pubchem}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-pai-clone"></a>}}
diff --git a/man/pp.Rd b/man/pp.Rd
deleted file mode 100644
index 363f9ba..0000000
--- a/man/pp.Rd
+++ /dev/null
@@ -1,77 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/chent.R
-\docType{class}
-\name{pp}
-\alias{pp}
-\title{R6 class for holding a product with at least one active ingredient}
-\format{
-An \code{\link{R6Class}} generator object.
-}
-\description{
-An R6 class for holding information about a product with at least one active ingredient
-}
-\keyword{data}
-\section{Public fields}{
-\if{html}{\out{<div class="r6-fields">}}
-\describe{
-\item{\code{name}}{The name of the product}
-
-\item{\code{ais}}{A list of active ingredients}
-
-\item{\code{concentrations}}{The concentration of the ais}
-
-\item{\code{concentration_units}}{Defaults to g/L}
-}
-\if{html}{\out{</div>}}
-}
-\section{Methods}{
-\subsection{Public methods}{
-\itemize{
-\item \href{#method-pp-new}{\code{pp$new()}}
-\item \href{#method-pp-print}{\code{pp$print()}}
-\item \href{#method-pp-clone}{\code{pp$clone()}}
-}
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-pp-new"></a>}}
-\if{latex}{\out{\hypertarget{method-pp-new}{}}}
-\subsection{Method \code{new()}}{
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{pp$new(
-  name,
-  ...,
-  concentrations,
-  concentration_units = "g/L",
-  density = 1000,
-  density_units = "g/L"
-)}\if{html}{\out{</div>}}
-}
-
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-pp-print"></a>}}
-\if{latex}{\out{\hypertarget{method-pp-print}{}}}
-\subsection{Method \code{print()}}{
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{pp$print()}\if{html}{\out{</div>}}
-}
-
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-pp-clone"></a>}}
-\if{latex}{\out{\hypertarget{method-pp-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{pp$clone(deep = FALSE)}\if{html}{\out{</div>}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{deep}}{Whether to make a deep clone.}
-}
-\if{html}{\out{</div>}}
-}
-}
-}
diff --git a/man/ppp.Rd b/man/ppp.Rd
new file mode 100644
index 0000000..c0d35f1
--- /dev/null
+++ b/man/ppp.Rd
@@ -0,0 +1,100 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/chent.R
+\docType{class}
+\name{ppp}
+\alias{ppp}
+\title{R6 class for a plant protection product with at least one active ingredient}
+\format{
+An \code{\link{R6Class}} generator object.
+}
+\description{
+Contains basic information about the active ingredients in the
+product
+}
+\section{Public fields}{
+\if{html}{\out{<div class="r6-fields">}}
+\describe{
+\item{\code{name}}{The name of the product}
+
+\item{\code{ais}}{A list of active ingredients}
+
+\item{\code{concentrations}}{The concentration of the ais}
+
+\item{\code{concentration_units}}{Defaults to g/L}
+
+\item{\code{density}}{The density of the product}
+
+\item{\code{density_units}}{Defaults to g/L
+Creates a new instance of this \link[R6:R6Class]{R6} class.}
+
+\item{\code{...}}{Identifiers of the active ingredients}
+
+\item{\code{concentrations}}{Concentrations of the active ingredients}
+
+\item{\code{concentration_units}}{Defaults to g/L}
+
+\item{\code{density}}{The density}
+
+\item{\code{density_units}}{Defaults to g/L
+Printing method}
+}
+\if{html}{\out{</div>}}
+}
+\section{Active bindings}{
+\if{html}{\out{<div class="r6-active-bindings">}}
+\describe{
+\item{\code{...}}{Identifiers of the active ingredients}
+}
+\if{html}{\out{</div>}}
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-ppp-new}{\code{ppp$new()}}
+\item \href{#method-ppp-print}{\code{ppp$print()}}
+\item \href{#method-ppp-clone}{\code{ppp$clone()}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-ppp-new"></a>}}
+\if{latex}{\out{\hypertarget{method-ppp-new}{}}}
+\subsection{Method \code{new()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ppp$new(
+  name,
+  ...,
+  concentrations,
+  concentration_units = "g/L",
+  density = 1000,
+  density_units = "g/L"
+)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-ppp-print"></a>}}
+\if{latex}{\out{\hypertarget{method-ppp-print}{}}}
+\subsection{Method \code{print()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ppp$print()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-ppp-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-ppp-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ppp$clone(deep = FALSE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{deep}}{Whether to make a deep clone.}
+}
+\if{html}{\out{</div>}}
+}
+}
+}