docs: NEWS

NEWS.md

@@ -1,57 +1,48 @@
-
-# extractox 0.2.0 (dev)
+# extractox 0.2.0
 
 ## Bug Fixes
-* Fixed `extr_iris` extracts the correct number of chemicals with no repetition 
-   (#15}.
-* Fixed `extr_comtox` works when a single `download_items` different than 
-   `DTXCID` is selected (#17).
-* Fixed `extr_casrn_from_cid`: when no results function was faling.
+* Fixed `extr_iris` extracting the correct number of chemicals without 
+  repetition (#15).
+* Fixed `extr_comtox` working when a single `download_items` different from 
+  `DTXCID` is selected (#17).
+* Fixed `extr_casrn_from_cid` failure when no results are found.
 
 ## New Features
-* `extr_ice_assay_names` retrieves ice assay names (#16).
-* `extr_monograph` checks if a substance is listed in WHO IARC monograph and 
-   returns the details of it (#19).
-* `extr_pprtv` extracts information from EPA Provisional Peer-Reviewed Toxicity Values 
-   database (#20). Since the all file of chemicals need to be dowloaded, the
-   functions `save_to_cache` and `load_from_cache`, have been introduced to
-   avoid re-downloading the file at each function call. See argument `force`.
+* Added `extr_ice_assay_names` to retrieve ICE assay names (#16).
+* Added `extr_monograph` to check if a substance is listed in WHO IARC 
+  monograph and return its details (#19).
+* Added `extr_pprtv` to extract information from the EPA Provisional 
+  Peer-Reviewed Toxicity Values database (#20). Introduced `save_to_cache` 
+  and `load_from_cache` functions to avoid re-downloading the file each time. 
+  See `force` argument.
 
 ## Other Breaking Changes
-* The argument `cancer_types` in `extr_iris` has been removed. The database returns
-   a dataframe with different columns depending on the request args, and implementing
-   a way around that is much more tedious than just filter the resulting dataframe
-   after. Plus it's unlikely that someone wouldn't want to know other non-cancer
-   tox assessments types.
-*  `extr_casrn_from_cid` lost the argument `stop_at_warning`. To be consistent
-   with other functions now it warns and returns a data.frame with NA if no 
-   ids are found.
-*  `extr_tox`  returns a longer list of dataframes, the outputs of `extr_monograph` and
-   `extr_pprtv`.
+* Removed `cancer_types` argument from `extr_iris`. Database returns a 
+  dataframe with different columns based on `request` arguments.
+* Removed `stop_at_warning` argument from `extr_casrn_from_cid`. Now warns 
+  and returns a dataframe with NA if no IDs are found.
+* `extr_tox` now returns a longer list of dataframes, including the outputs 
+  of `extr_monograph` and `extr_pprtv`.
 
 ## Enhancements and Fixes
-* All the `extr_` functions have gained a `verbose` argument (#18).
-* All the `extr_` functions now behave similarly when ids are not founds 
-  (#30, #31, #32, #33, #34, #35): 
-
-   - for all the functions but `extr_comptox`, a  column `query` reports the ids searched. 
-     For `extr_comptox` that info  can be found in the the element `main_sheet` of
-     the result. Note that for `extr_ice` given the nature of the request
-     the `query` values contains all the ids found (not single id).
-   - now the results  contains rows with NAs values for all columns except
-     `query`.
-   - Note that `exptr_pprtv` and `extr_monograph` use the internal function
-      `save_and_match` to output results that have NAs for missing ids.
-
-* All unit tests have been improved and extended.
-* Fixed `extr_comptox` now outputs a list of dataframes with "clean" names.
-* Fixed `extr_ctd` names: column `pub_med_ids` or `pub_med_i_ds` are now `pubmed_ids`.
-* Enhancement: An internal function `extr_pubchem_section_` is used to fetch 
-   both FEMA and GHS to avoid repeated code.
-* Enhancement: The internal function `check_na_warn` has been introduced to generate
-   warnings for missing ids.
-* Enhancement: `with_extr_sandbox` has been created to handle cache for CRAN
-   examples
+* Added `verbose` argument to all `extr_` functions (#18).
+* Unified behavior across all `extr_` functions when chemicals are not found 
+  (#30-#35):
+   - For all functions except `extr_comptox`, a `query` column reports the IDs 
+     searched. In `extr_comptox`, this info is in the `main_sheet` element. For 
+     `extr_ice`, `query` values contain all IDs found.
+   - Results now contain rows with NA values for all columns except `query`.
+   - `extr_pprtv` and `extr_monograph` use `save_and_match` to output results 
+     with NA for missing IDs.
+* Improved and extended all unit tests.
+* `extr_comptox` now outputs a list of dataframes with clean names.
+* Fixed `extr_ctd` column names: `pub_med_ids` or `pub_med_i_ds` are now 
+  `pubmed_ids`.
+* Introduced `extr_pubchem_section_` internal function to fetch FEMA and GHS 
+  info, avoiding repeated code.
+* Introduced `check_na_warn` internal function to generate warnings for 
+  missing IDs.
+* Created `with_extr_sandbox` to handle cache for CRAN examples.
 
 
 # extractox 0.1.0

README.Rmd

@@ -18,7 +18,7 @@ knitr::opts_chunk$set(
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/c1au6i0/extractox/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/c1au6i0/extractox/actions/workflows/R-CMD-check.yaml)
 [![CRAN status](https://www.r-pkg.org/badges/version/extractox)](https://CRAN.R-project.org/package=extractox)
-[![DEV version](https://img.shields.io/badge/devel%20version-0.1.9001-blue.svg)](https://github.com/c1au6i0/extractox)
+[![DEV version](https://img.shields.io/badge/devel%20version-0.1.9003-blue.svg)](https://github.com/c1au6i0/extractox)
 <!-- badges: end -->
 
 `extractox` is a comprehensive R package designed to simplify querying various chemical, toxicological, and biological databases such as the Comparative Toxicogenomics Database (CTP) of the  MDI Biological Laboratory and NC State University, the Integrated Chemical Environment (ICE) of the National Toxicology Program (NTP), the Integrated Risk Information System (IRIS) of the Environmental Protection Agency (EPA), the CompTox Chemicals Dashboard Resource Hub (CompTox) of EPA, and PubChem of the National Center for Biotechnology Information/National Institures Of Health (NCBI, NIH). The package facilitates interaction with APIs, providing curated and user-friendly outputs.
@@ -130,7 +130,7 @@ A series of functions that rely on the `webchem` package are used to extract che
 The function `extr_chem_info` retrieves chemical information of IUPAC-named chemicals. A warning is displayed if the chemical is not found.
 
 ```{r}
-chem_info <- extr_chem_info(IUPAC_names = c("Formaldehyde", "Aflatoxin B1"))
+chem_info <- extr_chem_info(iupac_names = c("Formaldehyde", "Aflatoxin B1"))
 names(chem_info)
 ```
 
@@ -191,6 +191,10 @@ Tetramers are computationally generated information units that interrelate four
 
 `extr_tetramer` extract info related to tetramers from CTD.
 
+```{r echo=FALSE}
+Sys.sleep(3)
+```
+
 ```{r}
 tetramer_data <- extr_tetramer(
   chem = c("50-00-0", "ethanol"),