in case of uncompress in package dir

Yunuuuu · Nov 8, 2023 · 53671c1 · 53671c1
1 parent 2f81ec8
commit 53671c1
Show file tree

Hide file tree

Showing 19 changed files with 542 additions and 482 deletions.
diff --git a/R/class-FAERS.R b/R/class-FAERS.R
@@ -27,7 +27,10 @@
 #' @examples
 #' # ususaly we use faers() function to create a `FAERS` object
 #' # you must change `dir`, as the file included in the package is sampled
-#' data <- faers(2004, "q1", dir = system.file("extdata", package = "faers"))
+#' data <- faers(2004, "q1",
+#' dir = system.file("extdata", package = "faers"),
+#' compress_dir = tempdir()
+#' )
 #' faers_data(data)
 #' faers_year(data)
 #' faers_quarter(data)

diff --git a/R/counts.R b/R/counts.R
@@ -5,7 +5,8 @@
 #' @examples
 #' # you must change `dir`, as the files included in the package are sampled
 #' data <- faers(c(2004, 2017), c("q1", "q2"),
-#' dir = system.file("extdata", package = "faers")
+#' dir = system.file("extdata", package = "faers"),
+#' compress_dir = tempdir()
 #' )
 #' \dontrun{
 #' # you must standardize and deduplication before disproportionality analysis

diff --git a/R/dedup.R b/R/dedup.R
@@ -6,7 +6,8 @@
 #' @examples
 #' # you must change `dir`, as the files included in the package are sampled
 #' data <- faers(c(2004, 2017), c("q1", "q2"),
-#' dir = system.file("extdata", package = "faers")
+#' dir = system.file("extdata", package = "faers"),
+#' compress_dir = tempdir()
 #' )
 #' \dontrun{
 #' # we must standardize firstly

diff --git a/R/faers.R b/R/faers.R
@@ -6,7 +6,10 @@
 #' @return A [FAERSxml] or [FAERSascii] object.
 #' @examples
 #' # you must change `dir`, as the file included in the package is sampled
-#' data <- faers(2004, "q1", dir = system.file("extdata", package = "faers"))
+#' data <- faers(2004, "q1",
+#' dir = system.file("extdata", package = "faers"),
+#' compress_dir = tempdir()
+#' )
 #' @export
 faers <- function(years, quarters, format = NULL, dir = getwd(), compress_dir = dir, handle_opts = list()) {
  format <- match.arg(format, faers_file_format)

diff --git a/R/merge.R b/R/merge.R
@@ -13,7 +13,10 @@
 #' @return A [data.table][data.table::data.table] object.
 #' @examples
 #' # you must change `dir`, as the file included in the package is sampled
-#' data <- faers(2004, "q1", dir = system.file("extdata", package = "faers"))
+#' data <- faers(2004, "q1",
+#' dir = system.file("extdata", package = "faers"),
+#' compress_dir = tempdir()
+#' )
 #' faers_merge(data, "indi") # only one field is just like faers_get()
 #' faers_merge(data, c("demo", "indi"))
 #' @export

diff --git a/R/methods-utils.R b/R/methods-utils.R
@@ -26,7 +26,10 @@
 #' @return See details.
 #' @examples
 #' # you must change `dir`, as the file included in the package is sampled
-#' data <- faers(2004, "q1", dir = system.file("extdata", package = "faers"))
+#' data <- faers(2004, "q1",
+#' dir = system.file("extdata", package = "faers"),
+#' compress_dir = tempdir()
+#' )
 #' faers_get(data, "indi")
 #' data[["indi"]]
 #' data$indi

diff --git a/R/signal.R b/R/signal.R
@@ -12,7 +12,8 @@
 #' @examples
 #' # you must change `dir`, as the files included in the package are sampled
 #' data <- faers(c(2004, 2017), c("q1", "q2"),
-#' dir = system.file("extdata", package = "faers")
+#' dir = system.file("extdata", package = "faers"),
+#' compress_dir = tempdir()
 #' )
 #' \dontrun{
 #' # you must standardize and deduplication before disproportionality analysis

diff --git a/R/standardize.R b/R/standardize.R
@@ -6,7 +6,8 @@
 #' @examples
 #' #' # you must change `dir`, as the files included in the package are sampled
 #' data <- faers(c(2004, 2017), c("q1", "q2"),
-#' dir = system.file("extdata", package = "faers")
+#' dir = system.file("extdata", package = "faers"),
+#' compress_dir = tempdir()
 #' )
 #' \dontrun{
 #' # you should replace `meddra_path` with yours

diff --git a/README.html b/README.html
diff --git a/README.md b/README.md
@@ -39,9 +39,10 @@ will parse metadata in
 
 ``` r
 faers_meta()
-#> → Using FAERS metadata from cached
-#> '~/.cache/faers/metadata/faers_meta_data.rds'
-#> Snapshot time: 2023-11-05 17:10:13.921026
+#> → Reading html:
+#> <https://fis.fda.gov/extensions/FPD-QDE-FAERS/FPD-QDE-FAERS.html>
+#> → Writing FAERS metadata into cached
+#> '~/.cache/R/faers/metadata/faers_meta_data.rds'
 #> year quarter period
 #> <int> <char> <char>
 #> 1: 2023 q3 July - September
@@ -266,6 +267,9 @@ TRUE`.
 
 ``` r
 faers_meta(internal = TRUE)
+#> → Using FAERS metadata from cached
+#> '~/.cache/R/faers/metadata/faers_meta_data.rds'
+#> Snapshot time: 2023-11-08 14:33:01.032028
 #> year quarter period
 #> <int> <char> <char>
 #> 1: 2023 q3 July - September
@@ -510,8 +514,12 @@ in the following process.)
 
 ``` r
 # # you must change `dir`, as the file included in the package is sampled
-data1 <- faers(2004, "q1", dir = system.file("extdata", package = "faers"))
+data1 <- faers(2004, "q1",
+ dir = system.file("extdata", package = "faers"),
+ compress_dir = tempdir()
+)
 #> Finding 1 file already downloaded: 'aers_ascii_2004q1.zip'
+#> → Nothing to do since only one <FAERS> data provided
 data1
 #> FAERS data from 1 Quarterly ascii file
 #> Total reports: 100 (with duplicates)
@@ -522,11 +530,12 @@ the `faers_combine()` function is judiciously employed.
 
 ``` r
 data2 <- faers(c(2004, 2017), c("q1", "q2"),
- dir = system.file("extdata", package = "faers")
+ dir = system.file("extdata", package = "faers"),
+ compress_dir = tempdir()
 )
 #> Finding 2 files already downloaded: 'aers_ascii_2004q1.zip' and
 #> 'faers_ascii_2017q2.zip'
-#> → Combining all 2 FAERS Quarterly ascii Data files
+#> → Combining all 2 <FAERS> Datas
 data2
 #> FAERS data from 2 Quarterly ascii files
 #> Total reports: 200 (with duplicates)
@@ -597,8 +606,11 @@ sessionInfo()
 #> [1] faers_0.99.0
 #> 
 #> loaded via a namespace (and not attached):
-#> [1] compiler_4.3.1 fastmap_1.1.1 cli_3.6.1 tools_4.3.1 
-#> [5] htmltools_0.5.5 rstudioapi_0.15.0 rappdirs_0.3.3 yaml_2.3.7 
-#> [9] rmarkdown_2.23 data.table_1.14.9 knitr_1.43 xfun_0.39 
-#> [13] digest_0.6.33 rlang_1.1.1 evaluate_0.21
+#> [1] digest_0.6.33 R6_2.5.1 fastmap_1.1.1 rvest_1.0.3 
+#> [5] xfun_0.39 magrittr_2.0.3 rappdirs_0.3.3 glue_1.6.2 
+#> [9] stringr_1.5.0 knitr_1.43 htmltools_0.5.5 rmarkdown_2.23 
+#> [13] lifecycle_1.0.3 xml2_1.3.5 cli_3.6.1 vctrs_0.6.3 
+#> [17] data.table_1.14.9 compiler_4.3.1 httr_1.4.6 rstudioapi_0.15.0
+#> [21] tools_4.3.1 curl_5.0.1 evaluate_0.21 yaml_2.3.7 
+#> [25] rlang_1.1.1 stringi_1.7.12 selectr_0.4-2
 ```
diff --git a/man/FAERS-class.Rd b/man/FAERS-class.Rd
diff --git a/man/FAERS-methods.Rd b/man/FAERS-methods.Rd
diff --git a/man/faers.Rd b/man/faers.Rd
diff --git a/man/faers_counts.Rd b/man/faers_counts.Rd
diff --git a/man/faers_dedup.Rd b/man/faers_dedup.Rd
diff --git a/man/faers_merge.Rd b/man/faers_merge.Rd
diff --git a/man/faers_phv_signal.Rd b/man/faers_phv_signal.Rd
diff --git a/man/faers_standardize.Rd b/man/faers_standardize.Rd
diff --git a/vignettes/FAERS-Pharmacovigilance.Rmd b/vignettes/FAERS-Pharmacovigilance.Rmd
@@ -87,15 +87,19 @@ in the following process.)
 
 ```{r}
 # # you must change `dir`, as the file included in the package is sampled
-data1 <- faers(2004, "q1", dir = system.file("extdata", package = "faers"))
+data1 <- faers(2004, "q1",
+ dir = system.file("extdata", package = "faers"),
+ compress_dir = tempdir()
+)
 data1
 ```
 
 Furthermore, in cases where multiple quarterly data files are requisite, the
 `faers_combine()` function is judiciously employed. 
 ```{r}
 data2 <- faers(c(2004, 2017), c("q1", "q2"),
- dir = system.file("extdata", package = "faers")
+ dir = system.file("extdata", package = "faers"),
+ compress_dir = tempdir()
 )
 data2
 ```