Small improvements, see NEWS.md

In the README, improve the scaling of the graphs

1 files changed, 32 insertions, 22 deletions

diff --git a/README.md b/README.md
index 1bea80d..bbf4ae9 100644
--- a/README.md
+++ b/README.md
@@ -10,8 +10,11 @@ status](https://jranke.r-universe.dev/badges/chents)](https://jranke.r-universe.
 [![Code
 coverage](https://img.shields.io/badge/coverage-jrwb.de-blue.svg)](https://pkgdown.jrwb.de/chents/coverage/coverage.html)
 
-The R package **chents** provides some utilities for working with
-chemical entities in R.
+When working with data on chemical substances, we often need a reliable
+link between the data and the chemical identity of the substances. The R
+package **chents** provides a way to define and check the identity of
+chemically defined substances (“chemical entities”) and to collect
+related information.
 
 When first defining a chemical entity, some chemical information is
 retrieved from the [PubChem](https://pubchem.ncbi.nlm.nih.gov/) website
@@ -20,8 +23,8 @@ using the [webchem](https://docs.ropensci.org/webchem/) package.
 ``` r
 library(chents)
 caffeine <- chent$new("caffeine")
-#> Querying PubChem ...
-#> Trying to get chemical information from RDKit using PubChem SMILES
+#> Querying PubChem for name caffeine ...
+#> Get chemical information from RDKit using PubChem SMILES
 #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C
 ```
 
@@ -47,7 +50,7 @@ print(caffeine)
 #>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"
 #>  [5] "Methyltheobromine"       "Theine"                 
 #>  [7] "Thein"                   "Cafeina"                
-#>  [9] "Koffein"                 "Mateina"
+#>  [9] "Caffein"                 "Cafipel"
 ```
 
 There is a very simple plotting method for the chemical structure.
@@ -58,41 +61,46 @@ plot(caffeine)
 
 ![](man/figures/README-unnamed-chunk-4-1.png)<!-- -->
 
-Additional information can be (but is rarely ever) read from a local
-.yaml file. This information can be leveraged e.g. by the
-[PEC_soil](https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html) function
-of the ‘pfm’ package.
-
 If you have a so-called ISO common name of a pesticide active
 ingredient, you can use the ‘pai’ class derived from the ‘chent’ class,
 which starts with querying the [BCPC
 compendium](http://www.bcpcpesticidecompendium.org/) first.
 
 ``` r
-lambda <- pai$new("lambda-cyhalothrin")
-#> Querying BCPC for lambda-cyhalothrin ...
-#> Querying PubChem ...
-#> Trying to get chemical information from RDKit using PubChem SMILES
-#> CC1([C@@H]([C@@H]1C(=O)O[C@@H](C#N)C2=CC(=CC=C2)OC3=CC=CC=C3)/C=C(/C(F)(F)F)\Cl)C
-#> RDKit mw is 449.856
-#> mw is 449.8
-plot(lambda)
+delta <- pai$new("deltamethrin")
+#> Querying BCPC for deltamethrin ...
+#> Querying PubChem for inchikey OWZREIFADZCYQD-NSHGMRRFSA-N ...
+#> Get chemical information from RDKit using PubChem SMILES
+#> CC1([C@H]([C@H]1C(=O)O[C@H](C#N)C2=CC(=CC=C2)OC3=CC=CC=C3)C=C(Br)Br)C
+plot(delta)
 ```
 
 ![](man/figures/README-unnamed-chunk-5-1.png)<!-- -->
 
+Additional information can be read from a local .yaml file. This
+information can be leveraged e.g. by the
+[PEC_soil](https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html) function
+of the ‘pfm’ package. However, this functionality is to be superseded by
+a dedicated package, defining data for the environmental risk assessment
+on chemicals, in particular on active ingredients of plant protection
+products.
+
 ## Installation
 
 You can conveniently install chents from the repository kindly made
 available by the R-Universe project:
 
-    install.packages("chents",
-      repos = c("https://jranke.r-universe.dev", "https://cran.r-project.org"))
+``` r
+install.packages("chents",
+  repos = c("https://jranke.r-universe.dev", "https://cran.r-project.org"))
+```
 
 In order to profit from the chemoinformatics, you need to install RDKit
 and its python bindings. On a Debian type Linux distribution, just use
 
-    sudo apt install python3-rdkit
+``` sh
+sudo apt install python3-rdkit
+```
 
 If you use this package on Windows or MacOS, I would be happy to include
 installation instructions here if you share them with me, e.g. via a
@@ -105,4 +113,6 @@ your global or project specific `.Rprofile` file to tell the
 `reticulate` package to use the system Python version that will find the
 RDKit installed in the system location.
 
-    Sys.setenv(RETICULATE_PYTHON="/usr/bin/python3")
+``` r
+Sys.setenv(RETICULATE_PYTHON="/usr/bin/python3")
+```