merge dbplyr into main work-in-progress branch (#7)

* Initial implementation of dplyr verbs

* Corrected the datatype for NCBI_TAXID field

* minor corrections

* Final fixes before submitting to CRAN

Co-authored-by: Vries <[email protected]>

Author: pepijn-devries

DESCRIPTION

@@ -1,12 +1,13 @@
 Package: ECOTOXr
 Type: Package
 Title: Download and Extract Data from US EPA's ECOTOX Database
-Version: 0.1.2
-Date: TODO
+Version: 0.2.0
+Date: 2022-11-17
 Authors@R: c(person("Pepijn", "de Vries", role = c("aut", "cre", "dtc"),
-    email = "[email protected]"))
+    email = "[email protected]",
+    comment = list(ORCID = "0000-0002-7961-6646")))
 Author:
-    Pepijn de Vries [aut, cre, dtc]
+    Pepijn de Vries [aut, cre, dtc] (0000-0002-7961-6646)
 Maintainer: Pepijn de Vries <[email protected]>
 Description: The US EPA ECOTOX database is a freely available database
     with a treasure of aquatic and terrestrial ecotoxicological data.
@@ -19,17 +20,24 @@ Depends:
     RSQLite
 Imports:
     crayon,
+    dbplyr,
+    dplyr,
     httr,
+    purrr,
     rappdirs,
     readr,
+    rlang,
     rvest,
     stringr,
     tibble,
+    tidyr,
+    tidyselect,
     utils
 Suggests:
     DBI,
-    webchem,
-    testthat (>= 3.0.0)
+    standartox,
+    testthat (>= 3.0.0),
+    webchem
 URL: <https://github.com/pepijn-devries/ECOTOXr>
 BugReports: https://github.com/pepijn-devries/ECOTOXr/issues
 License: GPL (>= 3)

NAMESPACE

@@ -1,35 +1,45 @@
-# Generated by roxygen2: do not edit by hand
-
-S3method("[",cas)
-S3method("[<-",cas)
-S3method("[[",cas)
-S3method("[[<-",cas)
-S3method(as.character,cas)
-S3method(as.data.frame,cas)
-S3method(as.double,cas)
-S3method(as.integer,cas)
-S3method(as.list,cas)
-S3method(c,cas)
-S3method(format,cas)
-S3method(print,cas)
-export(as.cas)
-export(build_ecotox_sqlite)
-export(cas)
-export(check_ecotox_availability)
-export(cite_ecotox)
-export(dbConnectEcotox)
-export(dbDisconnectEcotox)
-export(download_ecotox_data)
-export(get_ecotox_info)
-export(get_ecotox_path)
-export(get_ecotox_sqlite_file)
-export(get_ecotox_url)
-export(is.cas)
-export(list_ecotox_fields)
-export(search_ecotox)
-export(search_query_ecotox)
-export(show.cas)
-importFrom(RSQLite,dbConnect)
-importFrom(RSQLite,dbDisconnect)
-importFrom(RSQLite,dbExecute)
-importFrom(RSQLite,dbWriteTable)
+# Generated by roxygen2: do not edit by hand
+
+S3method("[",cas)
+S3method("[<-",cas)
+S3method("[[",cas)
+S3method("[[<-",cas)
+S3method(as.character,cas)
+S3method(as.data.frame,cas)
+S3method(as.double,cas)
+S3method(as.integer,cas)
+S3method(as.list,cas)
+S3method(c,cas)
+S3method(format,cas)
+S3method(print,cas)
+export("%>%")
+export(as.cas)
+export(build_ecotox_sqlite)
+export(cas)
+export(check_ecotox_availability)
+export(cite_ecotox)
+export(dbConnectEcotox)
+export(dbDisconnectEcotox)
+export(download_ecotox_data)
+export(get_ecotox_info)
+export(get_ecotox_path)
+export(get_ecotox_sqlite_file)
+export(get_ecotox_url)
+export(is.cas)
+export(list_ecotox_fields)
+export(search_ecotox)
+export(search_ecotox_lazy)
+export(search_query_ecotox)
+export(show.cas)
+importFrom(RSQLite,dbConnect)
+importFrom(RSQLite,dbDisconnect)
+importFrom(RSQLite,dbExecute)
+importFrom(RSQLite,dbWriteTable)
+importFrom(dplyr,"%>%")
+importFrom(dplyr,collect)
+importFrom(dplyr,inner_join)
+importFrom(dplyr,left_join)
+importFrom(dplyr,select)
+importFrom(dplyr,sql)
+importFrom(dplyr,tbl)
+importFrom(rlang,":=")

NEWS

@@ -1,3 +1,19 @@
+ECOTOXr v0.2.0 (Release date: ***********TODO)
+=============
+
+  * Major changes:
+
+    * Modified searching routines to make advantage of
+      the sql parser and optimisers implemented in
+      the package 'dplyr'. Performance (i.e. speed) of the
+      search routines have improved considerably.
+    * Added support for handling Chemical Abstracts
+      Service (CAS) numbers.
+
+  * Several minor adjustments and corrections to code
+    and manual. These include fixes to address notes
+    from CRAN checks.
+
 ECOTOXr v0.1.1 (Release date: 2021-10-04)
 =============
 

R/ECOTOXr.r

@@ -19,7 +19,7 @@
 #' This may not always work on all machines as R does not always accept the website SSL certificate from the EPA.
 #' In those cases the zipped archive with the database files can be downloaded manually with a different (more
 #' forgiving) browser. The files from the zip archive can be extracted to a location of choice. Alternatively,
-#' the user could try to use \code{\link{download_ecotox_data(ssl_verifypeer = 0L)}} when the download URL is trusted.
+#' the user could try to use \code{\link{download_ecotox_data}(ssl_verifypeer = 0L)} when the download URL is trusted.
 #' }
 #' \item{
 #' Next, an SQLite database needs to be build from the downloaded files. This will be done automatically when