Update docs, use run.sh on travis

3 files changed, 89 insertions, 89 deletions

diff --git a/man/chent.Rd b/man/chent.Rd
index d94452e..15fbc54 100644
--- a/man/chent.Rd
+++ b/man/chent.Rd
@@ -69,28 +69,28 @@ if (!is.null(caffeine$Picture)) {
 \section{Methods}{
 \subsection{Public methods}{
 \itemize{
-\item \href{#method-new}{\code{chent$new()}}
-\item \href{#method-try_pubchem}{\code{chent$try_pubchem()}}
-\item \href{#method-get_pubchem}{\code{chent$get_pubchem()}}
-\item \href{#method-get_rdkit}{\code{chent$get_rdkit()}}
-\item \href{#method-get_chyaml}{\code{chent$get_chyaml()}}
-\item \href{#method-add_p0}{\code{chent$add_p0()}}
-\item \href{#method-add_cwsat}{\code{chent$add_cwsat()}}
-\item \href{#method-add_PUF}{\code{chent$add_PUF()}}
-\item \href{#method-add_TP}{\code{chent$add_TP()}}
-\item \href{#method-add_transformation}{\code{chent$add_transformation()}}
-\item \href{#method-add_soil_degradation}{\code{chent$add_soil_degradation()}}
-\item \href{#method-add_soil_ff}{\code{chent$add_soil_ff()}}
-\item \href{#method-add_soil_sorption}{\code{chent$add_soil_sorption()}}
-\item \href{#method-pdf}{\code{chent$pdf()}}
-\item \href{#method-png}{\code{chent$png()}}
-\item \href{#method-emf}{\code{chent$emf()}}
-\item \href{#method-clone}{\code{chent$clone()}}
+\item \href{#method-chent-new}{\code{chent$new()}}
+\item \href{#method-chent-try_pubchem}{\code{chent$try_pubchem()}}
+\item \href{#method-chent-get_pubchem}{\code{chent$get_pubchem()}}
+\item \href{#method-chent-get_rdkit}{\code{chent$get_rdkit()}}
+\item \href{#method-chent-get_chyaml}{\code{chent$get_chyaml()}}
+\item \href{#method-chent-add_p0}{\code{chent$add_p0()}}
+\item \href{#method-chent-add_cwsat}{\code{chent$add_cwsat()}}
+\item \href{#method-chent-add_PUF}{\code{chent$add_PUF()}}
+\item \href{#method-chent-add_TP}{\code{chent$add_TP()}}
+\item \href{#method-chent-add_transformation}{\code{chent$add_transformation()}}
+\item \href{#method-chent-add_soil_degradation}{\code{chent$add_soil_degradation()}}
+\item \href{#method-chent-add_soil_ff}{\code{chent$add_soil_ff()}}
+\item \href{#method-chent-add_soil_sorption}{\code{chent$add_soil_sorption()}}
+\item \href{#method-chent-pdf}{\code{chent$pdf()}}
+\item \href{#method-chent-png}{\code{chent$png()}}
+\item \href{#method-chent-emf}{\code{chent$emf()}}
+\item \href{#method-chent-clone}{\code{chent$clone()}}
 }
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-new"></a>}}
-\if{latex}{\out{\hypertarget{method-new}{}}}
+\if{html}{\out{<a id="method-chent-new"></a>}}
+\if{latex}{\out{\hypertarget{method-chent-new}{}}}
 \subsection{Method \code{new()}}{
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{chent$new(
@@ -109,8 +109,8 @@ if (!is.null(caffeine$Picture)) {
 
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-try_pubchem"></a>}}
-\if{latex}{\out{\hypertarget{method-try_pubchem}{}}}
+\if{html}{\out{<a id="method-chent-try_pubchem"></a>}}
+\if{latex}{\out{\hypertarget{method-chent-try_pubchem}{}}}
 \subsection{Method \code{try_pubchem()}}{
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{chent$try_pubchem(query, from = "name")}\if{html}{\out{</div>}}
@@ -118,8 +118,8 @@ if (!is.null(caffeine$Picture)) {
 
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-get_pubchem"></a>}}
-\if{latex}{\out{\hypertarget{method-get_pubchem}{}}}
+\if{html}{\out{<a id="method-chent-get_pubchem"></a>}}
+\if{latex}{\out{\hypertarget{method-chent-get_pubchem}{}}}
 \subsection{Method \code{get_pubchem()}}{
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{chent$get_pubchem(pubchem_cid)}\if{html}{\out{</div>}}
@@ -127,8 +127,8 @@ if (!is.null(caffeine$Picture)) {
 
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-get_rdkit"></a>}}
-\if{latex}{\out{\hypertarget{method-get_rdkit}{}}}
+\if{html}{\out{<a id="method-chent-get_rdkit"></a>}}
+\if{latex}{\out{\hypertarget{method-chent-get_rdkit}{}}}
 \subsection{Method \code{get_rdkit()}}{
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{chent$get_rdkit(template = NULL)}\if{html}{\out{</div>}}
@@ -136,8 +136,8 @@ if (!is.null(caffeine$Picture)) {
 
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-get_chyaml"></a>}}
-\if{latex}{\out{\hypertarget{method-get_chyaml}{}}}
+\if{html}{\out{<a id="method-chent-get_chyaml"></a>}}
+\if{latex}{\out{\hypertarget{method-chent-get_chyaml}{}}}
 \subsection{Method \code{get_chyaml()}}{
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{chent$get_chyaml(
@@ -148,8 +148,8 @@ if (!is.null(caffeine$Picture)) {
 
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_p0"></a>}}
-\if{latex}{\out{\hypertarget{method-add_p0}{}}}
+\if{html}{\out{<a id="method-chent-add_p0"></a>}}
+\if{latex}{\out{\hypertarget{method-chent-add_p0}{}}}
 \subsection{Method \code{add_p0()}}{
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{chent$add_p0(p0, T = NA, source = NA, page = NA, remark = "")}\if{html}{\out{</div>}}
@@ -157,8 +157,8 @@ if (!is.null(caffeine$Picture)) {
 
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_cwsat"></a>}}
-\if{latex}{\out{\hypertarget{method-add_cwsat}{}}}
+\if{html}{\out{<a id="method-chent-add_cwsat"></a>}}
+\if{latex}{\out{\hypertarget{method-chent-add_cwsat}{}}}
 \subsection{Method \code{add_cwsat()}}{
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "")}\if{html}{\out{</div>}}
@@ -166,8 +166,8 @@ if (!is.null(caffeine$Picture)) {
 
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_PUF"></a>}}
-\if{latex}{\out{\hypertarget{method-add_PUF}{}}}
+\if{html}{\out{<a id="method-chent-add_PUF"></a>}}
+\if{latex}{\out{\hypertarget{method-chent-add_PUF}{}}}
 \subsection{Method \code{add_PUF()}}{
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{chent$add_PUF(
@@ -180,8 +180,8 @@ if (!is.null(caffeine$Picture)) {
 
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_TP"></a>}}
-\if{latex}{\out{\hypertarget{method-add_TP}{}}}
+\if{html}{\out{<a id="method-chent-add_TP"></a>}}
+\if{latex}{\out{\hypertarget{method-chent-add_TP}{}}}
 \subsection{Method \code{add_TP()}}{
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{chent$add_TP(x, smiles = NULL, pubchem = FALSE)}\if{html}{\out{</div>}}
@@ -189,8 +189,8 @@ if (!is.null(caffeine$Picture)) {
 
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_transformation"></a>}}
-\if{latex}{\out{\hypertarget{method-add_transformation}{}}}
+\if{html}{\out{<a id="method-chent-add_transformation"></a>}}
+\if{latex}{\out{\hypertarget{method-chent-add_transformation}{}}}
 \subsection{Method \code{add_transformation()}}{
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{chent$add_transformation(
@@ -205,8 +205,8 @@ if (!is.null(caffeine$Picture)) {
 
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_soil_degradation"></a>}}
-\if{latex}{\out{\hypertarget{method-add_soil_degradation}{}}}
+\if{html}{\out{<a id="method-chent-add_soil_degradation"></a>}}
+\if{latex}{\out{\hypertarget{method-chent-add_soil_degradation}{}}}
 \subsection{Method \code{add_soil_degradation()}}{
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{chent$add_soil_degradation(
@@ -233,8 +233,8 @@ if (!is.null(caffeine$Picture)) {
 
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_soil_ff"></a>}}
-\if{latex}{\out{\hypertarget{method-add_soil_ff}{}}}
+\if{html}{\out{<a id="method-chent-add_soil_ff"></a>}}
+\if{latex}{\out{\hypertarget{method-chent-add_soil_ff}{}}}
 \subsection{Method \code{add_soil_ff()}}{
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{chent$add_soil_ff(target, soils, ff = 1, remark = "", source, page = NA)}\if{html}{\out{</div>}}
@@ -242,8 +242,8 @@ if (!is.null(caffeine$Picture)) {
 
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_soil_sorption"></a>}}
-\if{latex}{\out{\hypertarget{method-add_soil_sorption}{}}}
+\if{html}{\out{<a id="method-chent-add_soil_sorption"></a>}}
+\if{latex}{\out{\hypertarget{method-chent-add_soil_sorption}{}}}
 \subsection{Method \code{add_soil_sorption()}}{
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{chent$add_soil_sorption(
@@ -266,8 +266,8 @@ if (!is.null(caffeine$Picture)) {
 
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-pdf"></a>}}
-\if{latex}{\out{\hypertarget{method-pdf}{}}}
+\if{html}{\out{<a id="method-chent-pdf"></a>}}
+\if{latex}{\out{\hypertarget{method-chent-pdf}{}}}
 \subsection{Method \code{pdf()}}{
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{chent$pdf(
@@ -279,8 +279,8 @@ if (!is.null(caffeine$Picture)) {
 
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-png"></a>}}
-\if{latex}{\out{\hypertarget{method-png}{}}}
+\if{html}{\out{<a id="method-chent-png"></a>}}
+\if{latex}{\out{\hypertarget{method-chent-png}{}}}
 \subsection{Method \code{png()}}{
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{chent$png(
@@ -292,8 +292,8 @@ if (!is.null(caffeine$Picture)) {
 
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-emf"></a>}}
-\if{latex}{\out{\hypertarget{method-emf}{}}}
+\if{html}{\out{<a id="method-chent-emf"></a>}}
+\if{latex}{\out{\hypertarget{method-chent-emf}{}}}
 \subsection{Method \code{emf()}}{
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{chent$emf(file = paste0(self$identifier, ".emf"), dir = "structures/emf")}\if{html}{\out{</div>}}
@@ -301,8 +301,8 @@ if (!is.null(caffeine$Picture)) {
 
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-clone"></a>}}
-\if{latex}{\out{\hypertarget{method-clone}{}}}
+\if{html}{\out{<a id="method-chent-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-chent-clone}{}}}
 \subsection{Method \code{clone()}}{
 The objects of this class are cloneable with this method.
 \subsection{Usage}{
diff --git a/man/pai.Rd b/man/pai.Rd
index cec3015..088f5b9 100644
--- a/man/pai.Rd
+++ b/man/pai.Rd
@@ -41,34 +41,34 @@ if (!is.null(atr$Picture)) {
 \section{Methods}{
 \subsection{Public methods}{
 \itemize{
-\item \href{#method-new}{\code{pai$new()}}
-\item \href{#method-clone}{\code{pai$clone()}}
-}
-}
-\if{html}{
-\out{<details ><summary>Inherited methods</summary>}
-\itemize{
-\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_PUF">}\href{../../chents/html/chent.html#method-add_PUF}{\code{chents::chent$add_PUF()}}\out{</span>}
-\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_TP">}\href{../../chents/html/chent.html#method-add_TP}{\code{chents::chent$add_TP()}}\out{</span>}
-\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_cwsat">}\href{../../chents/html/chent.html#method-add_cwsat}{\code{chents::chent$add_cwsat()}}\out{</span>}
-\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_p0">}\href{../../chents/html/chent.html#method-add_p0}{\code{chents::chent$add_p0()}}\out{</span>}
-\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_degradation">}\href{../../chents/html/chent.html#method-add_soil_degradation}{\code{chents::chent$add_soil_degradation()}}\out{</span>}
-\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_ff">}\href{../../chents/html/chent.html#method-add_soil_ff}{\code{chents::chent$add_soil_ff()}}\out{</span>}
-\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_sorption">}\href{../../chents/html/chent.html#method-add_soil_sorption}{\code{chents::chent$add_soil_sorption()}}\out{</span>}
-\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_transformation">}\href{../../chents/html/chent.html#method-add_transformation}{\code{chents::chent$add_transformation()}}\out{</span>}
-\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="emf">}\href{../../chents/html/chent.html#method-emf}{\code{chents::chent$emf()}}\out{</span>}
-\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_chyaml">}\href{../../chents/html/chent.html#method-get_chyaml}{\code{chents::chent$get_chyaml()}}\out{</span>}
-\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_pubchem">}\href{../../chents/html/chent.html#method-get_pubchem}{\code{chents::chent$get_pubchem()}}\out{</span>}
-\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_rdkit">}\href{../../chents/html/chent.html#method-get_rdkit}{\code{chents::chent$get_rdkit()}}\out{</span>}
-\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="pdf">}\href{../../chents/html/chent.html#method-pdf}{\code{chents::chent$pdf()}}\out{</span>}
-\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="png">}\href{../../chents/html/chent.html#method-png}{\code{chents::chent$png()}}\out{</span>}
-\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="try_pubchem">}\href{../../chents/html/chent.html#method-try_pubchem}{\code{chents::chent$try_pubchem()}}\out{</span>}
-}
-\out{</details>}
-}
+\item \href{#method-pai-new}{\code{pai$new()}}
+\item \href{#method-pai-clone}{\code{pai$clone()}}
+}
+}
+\if{html}{\out{
+<details><summary>Inherited methods</summary>
+<ul>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_PUF"><a href='../../chents/html/chent.html#method-chent-add_PUF'><code>chents::chent$add_PUF()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_TP"><a href='../../chents/html/chent.html#method-chent-add_TP'><code>chents::chent$add_TP()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_cwsat"><a href='../../chents/html/chent.html#method-chent-add_cwsat'><code>chents::chent$add_cwsat()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_p0"><a href='../../chents/html/chent.html#method-chent-add_p0'><code>chents::chent$add_p0()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_degradation"><a href='../../chents/html/chent.html#method-chent-add_soil_degradation'><code>chents::chent$add_soil_degradation()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_ff"><a href='../../chents/html/chent.html#method-chent-add_soil_ff'><code>chents::chent$add_soil_ff()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_sorption"><a href='../../chents/html/chent.html#method-chent-add_soil_sorption'><code>chents::chent$add_soil_sorption()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_transformation"><a href='../../chents/html/chent.html#method-chent-add_transformation'><code>chents::chent$add_transformation()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="emf"><a href='../../chents/html/chent.html#method-chent-emf'><code>chents::chent$emf()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_chyaml"><a href='../../chents/html/chent.html#method-chent-get_chyaml'><code>chents::chent$get_chyaml()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_pubchem"><a href='../../chents/html/chent.html#method-chent-get_pubchem'><code>chents::chent$get_pubchem()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_rdkit"><a href='../../chents/html/chent.html#method-chent-get_rdkit'><code>chents::chent$get_rdkit()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="pdf"><a href='../../chents/html/chent.html#method-chent-pdf'><code>chents::chent$pdf()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="png"><a href='../../chents/html/chent.html#method-chent-png'><code>chents::chent$png()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="try_pubchem"><a href='../../chents/html/chent.html#method-chent-try_pubchem'><code>chents::chent$try_pubchem()</code></a></span></li>
+</ul>
+</details>
+}}
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-new"></a>}}
-\if{latex}{\out{\hypertarget{method-new}{}}}
+\if{html}{\out{<a id="method-pai-new"></a>}}
+\if{latex}{\out{\hypertarget{method-pai-new}{}}}
 \subsection{Method \code{new()}}{
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{pai$new(
@@ -89,8 +89,8 @@ if (!is.null(atr$Picture)) {
 
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-clone"></a>}}
-\if{latex}{\out{\hypertarget{method-clone}{}}}
+\if{html}{\out{<a id="method-pai-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-pai-clone}{}}}
 \subsection{Method \code{clone()}}{
 The objects of this class are cloneable with this method.
 \subsection{Usage}{
diff --git a/man/pp.Rd b/man/pp.Rd
index cd950df..363f9ba 100644
--- a/man/pp.Rd
+++ b/man/pp.Rd
@@ -27,14 +27,14 @@ An R6 class for holding information about a product with at least one active ing
 \section{Methods}{
 \subsection{Public methods}{
 \itemize{
-\item \href{#method-new}{\code{pp$new()}}
-\item \href{#method-print}{\code{pp$print()}}
-\item \href{#method-clone}{\code{pp$clone()}}
+\item \href{#method-pp-new}{\code{pp$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-new"></a>}}
-\if{latex}{\out{\hypertarget{method-new}{}}}
+\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(
@@ -49,8 +49,8 @@ An R6 class for holding information about a product with at least one active ing
 
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-print"></a>}}
-\if{latex}{\out{\hypertarget{method-print}{}}}
+\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>}}
@@ -58,8 +58,8 @@ An R6 class for holding information about a product with at least one active ing
 
 }
 \if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-clone"></a>}}
-\if{latex}{\out{\hypertarget{method-clone}{}}}
+\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}{