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Diffstat (limited to 'README.rmd')
| -rw-r--r-- | README.rmd | 35 |
1 files changed, 21 insertions, 14 deletions
@@ -14,8 +14,12 @@ knitr::opts_chunk$set( [](https://jranke.r-universe.dev/chents) [](https://pkgdown.jrwb.de/chents/coverage/coverage.html) -The R package **chents** provides some utilities for working with chemical -entities in R. +When working with data on chemical substances, we often need a reliable link between +the data and the chemical identity of the substances. The R package **chents** +provides a way to define and check the identity of chemically defined substances +("chemical entities") and to collect related information. + + When first defining a chemical entity, some chemical information is retrieved from the [PubChem](https://pubchem.ncbi.nlm.nih.gov/) website using @@ -39,31 +43,33 @@ print(caffeine) There is a very simple plotting method for the chemical structure. -```{r fig.width = 2} +```{r fig.height = 2} plot(caffeine) ``` -Additional information can be (but is rarely ever) read from a local .yaml -file. This information can be leveraged e.g. by the -[PEC_soil](https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html) function of the -'pfm' package. - If you have a so-called ISO common name of a pesticide active ingredient, you can use the 'pai' class derived from the 'chent' class, which starts with querying the [BCPC compendium](http://www.bcpcpesticidecompendium.org/) first. -```{r fig.width = 2} -lambda <- pai$new("lambda-cyhalothrin") -plot(lambda) +```{r fig.height = 3.5} +delta <- pai$new("deltamethrin") +plot(delta) ``` +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 However, this functionality is to be superseded by a dedicated +package, defining data for the environmental risk assessment on chemicals, +in particular on active ingredients of plant protection products.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: -``` +```{r, eval = FALSE} install.packages("chents", repos = c("https://jranke.r-universe.dev", "https://cran.r-project.org")) ``` @@ -71,9 +77,10 @@ install.packages("chents", In order to profit from the chemoinformatics, you need to install RDKit and its python bindings. On a Debian type Linux distribution, just use -``` +```{sh, eval = FALSE} 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 Pull Request. @@ -85,7 +92,7 @@ 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. -``` +```{r, eval = FALSE} Sys.setenv(RETICULATE_PYTHON="/usr/bin/python3") ``` |