fix tests and NEW [skipci]

NEWS.md

@@ -13,37 +13,46 @@
 * `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)
+   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`.
 
 ## Other Breaking Changes
-* The argument `cancer_types` in `extr_iris`  was removed. The database returns
+* 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 type
+   tox assessments types.
 *  `extr_casrn_from_cid` lost the argument `stop_at_warning`. To be consistent
-   with other functions now it warns and returns data.frame with NA if no 
+   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`.
 
 ## 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), 
+  (#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`
+     `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`.
-* Cache ...........
-* More general function for extr_pubchem_section_
-* added checks check_na_warn, with_r_sandbox, search_and_match
+* 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
 
-*Breaking change*: note that now `extr_tox`.,
 
 # extractox 0.1.0
 

R/cache.R

@@ -11,6 +11,7 @@
 #' @details The cache directory is determined using [tools::R_user_dir()] with the `cache` subdirectory
 #' for the `extractox` package. If the directory does not exist, it is created automatically.
 #' The function will overwrite any existing file with the same name.
+#' @keywords internal
 #' @noRd
 save_to_cache <- function(dat, file_name, verbose = FALSE) {
   # Sys.getenv("R_USER_CACHE_DIR")
@@ -55,6 +56,7 @@ save_to_cache <- function(dat, file_name, verbose = FALSE) {
 #' @return The R object read from the cache, or NULL if the file does not exist.
 #' @details The cache directory is determined using [tools::R_user_dir()] with the `cache` subdirectory
 #' for the `extractox` package. If the file does not exist, a message is printed if verbose is TRUE.
+#' @keywords internal
 #' @noRd
 read_from_cache <- function(file_name, verbose = FALSE) {
 

R/extr_ice.R

@@ -20,7 +20,7 @@
 #' @export
 #' @examples
 #' \donttest{
-#' extr_ice(c("50-00-0"))
+#' extr_ice(casrn = c("50-00-0"))
 #' }
 extr_ice <- function(casrn,
                      assays = NULL,

R/extr_iris.R

@@ -12,7 +12,7 @@
 #' @export
 #' @examples
 #' \donttest{
-#' extr_iris(c("1332-21-4", "50-00-0"))
+#' extr_iris(casrn = c("1332-21-4", "50-00-0"))
 #' }
 extr_iris <- function(casrn = NULL, verbose = TRUE) {
   cancer_types <- c("non_cancer", "cancer")

R/extr_monograph.R

@@ -1,8 +1,10 @@
 #' Retrieve WHO IARC Monograph Information
 #'
-#' This function retrieves information regarding Monographs from the World Health
+#' This function returns information regarding Monographs from the World Health
 #' Organization (WHO) International Agency for Research on Cancer (IARC)  based on
-#' CAS Registry Number or Name of the chemical.
+#' CAS Registry Number or Name of the chemical. Note that the data is not fetched
+#' dynamically from the website, but has retrieved and  copy hasbeen saved as
+#' internal data in the package.
 #'
 #' @param search_type A character string specifying the type of search to
 #'   perform. Valid options are "cas_rn" (CAS Registry Number) and "name"

R/extr_pprtv.R

@@ -2,8 +2,8 @@
 #'
 #' Extracts data for specified identifiers (CASRN or chemical names) from the EPA's
 #' Provisional Peer-Reviewed Toxicity Values (PPRTVs) database. The function
-#'   retrieves and processes data, with options to use cached files or force a
-#'   fresh download.
+#' retrieves and processes data, with options to use cached files or force a
+#' fresh download.
 #'
 #' @param ids Character vector of identifiers to search (e.g., CASRN or chemical
 #'   names).
@@ -13,7 +13,6 @@
 #'   partial match search for the chemical name. NOTE: Since partial mached is
 #'   use, multiple seraches might match the same chemical, therefore chemical ids
 #'   might not be  uniques.
-#'
 #' @param verbose Logical indicating whether to display progress messages.
 #'   Default is TRUE.
 #' @param force Logical indicating whether to force a fresh download of the