From 53671c1c4777c3da22af2321fb5f041c738f928c Mon Sep 17 00:00:00 2001 From: yun Date: Wed, 8 Nov 2023 14:33:53 +0800 Subject: [PATCH] in case of uncompress in package dir --- R/class-FAERS.R | 5 +- R/counts.R | 3 +- R/dedup.R | 3 +- R/faers.R | 5 +- R/merge.R | 5 +- R/methods-utils.R | 5 +- R/signal.R | 3 +- R/standardize.R | 3 +- README.html | 920 +++++++++++++------------- README.md | 32 +- man/FAERS-class.Rd | 5 +- man/FAERS-methods.Rd | 5 +- man/faers.Rd | 5 +- man/faers_counts.Rd | 3 +- man/faers_dedup.Rd | 3 +- man/faers_merge.Rd | 5 +- man/faers_phv_signal.Rd | 3 +- man/faers_standardize.Rd | 3 +- vignettes/FAERS-Pharmacovigilance.Rmd | 8 +- 19 files changed, 542 insertions(+), 482 deletions(-) diff --git a/R/class-FAERS.R b/R/class-FAERS.R index f498472..71a5d72 100644 --- 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 index 12dc41c..54fdc7f 100644 --- 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 index 55be34e..9f6652a 100644 --- 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 index 75b1167..fd1c1b5 100644 --- 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 index 9ed4309..d1ccfe8 100644 --- 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 index 9c39b01..8d3ab95 100644 --- 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 index 900798e..cfa06a2 100644 --- 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 index 67e6d3b..46bba46 100644 --- 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 index 5593190..5791cce 100644 --- a/README.html +++ b/README.html @@ -619,445 +619,449 @@

Pharmacovigilance Analysis using

check metadata of FAERS

This will return a data.table reporting years, period, quarter, and file urls and file sizes. By default, this will use the cached file in rappdirs::user_cache_dir("faers"). If it doesn’t exist, the internal will parse metadata in https://fis.fda.gov/extensions/FPD-QDE-FAERS/FPD-QDE-FAERS.html

faers_meta()
-#> → Using FAERS metadata from cached
-#>   '~/.cache/faers/metadata/faers_meta_data.rds'
-#>   Snapshot time: 2023-11-05 17:10:13.921026
-#>      year quarter             period
-#>     <int>  <char>             <char>
-#>  1:  2023      q3   July - September
-#>  2:  2023      q2       April - June
-#>  3:  2023      q1    January - March
-#>  4:  2022      q4 October - December
-#>  5:  2022      q3   July - September
-#>  6:  2022      q2       April - June
-#>  7:  2022      q1    January - March
-#>  8:  2021      q4 October - December
-#>  9:  2021      q3   July - September
-#> 10:  2021      q2       April - June
-#> 11:  2021      q1    January - March
-#> 12:  2020      q4 October - December
-#> 13:  2020      q3   July - September
-#> 14:  2020      q2       April - June
-#> 15:  2020      q1    January - March
-#> 16:  2019      q4 October - December
-#> 17:  2019      q3   July - September
-#> 18:  2019      q2       April - June
-#> 19:  2019      q1    January - March
-#> 20:  2018      q4 October - December
-#> 21:  2018      q3   July - September
-#> 22:  2018      q2       April - June
-#> 23:  2018      q1    January - March
-#> 24:  2017      q4 October - December
-#> 25:  2017      q3   July - September
-#> 26:  2017      q2       April - June
-#> 27:  2017      q1    January - March
-#> 28:  2016      q4 October - December
-#> 29:  2016      q3   July - September
-#> 30:  2016      q2       April - June
-#> 31:  2016      q1    January - March
-#> 32:  2015      q4 October - December
-#> 33:  2015      q3   July - September
-#> 34:  2015      q2       April - June
-#> 35:  2015      q1    January - March
-#> 36:  2014      q4 October - December
-#> 37:  2014      q3   July - September
-#> 38:  2014      q2       April - June
-#> 39:  2014      q1    January - March
-#> 40:  2013      q4 October - December
-#> 41:  2013      q3   July - September
-#> 42:  2013      q2       April - June
-#> 43:  2013      q1    January - March
-#> 44:  2012      q4 October - December
-#> 45:  2012      q3   July - September
-#> 46:  2012      q2       April - June
-#> 47:  2012      q1    January - March
-#> 48:  2011      q4 October - December
-#> 49:  2011      q3   July - September
-#> 50:  2011      q2       April - June
-#> 51:  2011      q1    January - March
-#> 52:  2010      q4 October - December
-#> 53:  2010      q3   July - September
-#> 54:  2010      q2       April - June
-#> 55:  2010      q1    January - March
-#> 56:  2009      q4 October - December
-#> 57:  2009      q3   July - September
-#> 58:  2009      q2       April - June
-#> 59:  2009      q1    January - March
-#> 60:  2008      q4 October - December
-#> 61:  2008      q3   July - September
-#> 62:  2008      q2       April - June
-#> 63:  2008      q1    January - March
-#> 64:  2007      q4 October - December
-#> 65:  2007      q3   July - September
-#> 66:  2007      q2       April - June
-#> 67:  2007      q1    January - March
-#> 68:  2006      q4 October - December
-#> 69:  2006      q3   July - September
-#> 70:  2006      q2       April - June
-#>                                                     ascii_urls ascii_file_size
-#>                                                         <char>          <char>
-#>  1: https://fis.fda.gov/content/Exports/faers_ascii_2023Q3.zip          60.1MB
-#>  2: https://fis.fda.gov/content/Exports/faers_ascii_2023q2.zip          64.5MB
-#>  3: https://fis.fda.gov/content/Exports/faers_ascii_2023q1.zip          64.3MB
-#>  4: https://fis.fda.gov/content/Exports/faers_ascii_2022Q4.zip            69MB
-#>  5: https://fis.fda.gov/content/Exports/faers_ascii_2022Q3.zip          63.2MB
-#>  6: https://fis.fda.gov/content/Exports/faers_ascii_2022q2.zip            63MB
-#>  7: https://fis.fda.gov/content/Exports/faers_ascii_2022q1.zip          64.7MB
-#>  8: https://fis.fda.gov/content/Exports/faers_ascii_2021Q4.zip            59MB
-#>  9: https://fis.fda.gov/content/Exports/faers_ascii_2021Q3.zip            70MB
-#> 10: https://fis.fda.gov/content/Exports/faers_ascii_2021Q2.zip            66MB
-#> 11: https://fis.fda.gov/content/Exports/faers_ascii_2021Q1.zip            69MB
-#> 12: https://fis.fda.gov/content/Exports/faers_ascii_2020Q4.zip            71MB
-#> 13: https://fis.fda.gov/content/Exports/faers_ascii_2020Q3.zip            64MB
-#> 14: https://fis.fda.gov/content/Exports/faers_ascii_2020Q2.zip            66MB
-#> 15: https://fis.fda.gov/content/Exports/faers_ascii_2020Q1.zip            65MB
-#> 16: https://fis.fda.gov/content/Exports/faers_ascii_2019Q4.zip            60MB
-#> 17: https://fis.fda.gov/content/Exports/faers_ascii_2019Q3.zip            62MB
-#> 18: https://fis.fda.gov/content/Exports/faers_ascii_2019Q2.zip            62MB
-#> 19: https://fis.fda.gov/content/Exports/faers_ascii_2019Q1.zip            56MB
-#> 20: https://fis.fda.gov/content/Exports/faers_ascii_2018q4.zip            60MB
-#> 21: https://fis.fda.gov/content/Exports/faers_ascii_2018q3.zip            60MB
-#> 22: https://fis.fda.gov/content/Exports/faers_ascii_2018q2.zip            60MB
-#> 23: https://fis.fda.gov/content/Exports/faers_ascii_2018q1.zip            52MB
-#> 24: https://fis.fda.gov/content/Exports/faers_ascii_2017q4.zip            41MB
-#> 25: https://fis.fda.gov/content/Exports/faers_ascii_2017q3.zip            48MB
-#> 26: https://fis.fda.gov/content/Exports/faers_ascii_2017q2.zip            46MB
-#> 27: https://fis.fda.gov/content/Exports/faers_ascii_2017q1.zip            48MB
-#> 28: https://fis.fda.gov/content/Exports/faers_ascii_2016q4.zip            44MB
-#> 29: https://fis.fda.gov/content/Exports/faers_ascii_2016q3.zip            46MB
-#> 30: https://fis.fda.gov/content/Exports/faers_ascii_2016q2.zip            44MB
-#> 31: https://fis.fda.gov/content/Exports/faers_ascii_2016q1.zip            46MB
-#> 32: https://fis.fda.gov/content/Exports/faers_ascii_2015q4.zip            42MB
-#> 33: https://fis.fda.gov/content/Exports/faers_ascii_2015q3.zip            47MB
-#> 34: https://fis.fda.gov/content/Exports/faers_ascii_2015q2.zip            38MB
-#> 35: https://fis.fda.gov/content/Exports/faers_ascii_2015q1.zip            39MB
-#> 36: https://fis.fda.gov/content/Exports/faers_ascii_2014q4.zip            28MB
-#> 37: https://fis.fda.gov/content/Exports/faers_ascii_2014q3.zip            28MB
-#> 38: https://fis.fda.gov/content/Exports/faers_ascii_2014q2.zip            25MB
-#> 39: https://fis.fda.gov/content/Exports/faers_ascii_2014q1.zip            30MB
-#> 40: https://fis.fda.gov/content/Exports/faers_ascii_2013q4.zip            26MB
-#> 41: https://fis.fda.gov/content/Exports/faers_ascii_2013q3.zip            22MB
-#> 42: https://fis.fda.gov/content/Exports/faers_ascii_2013q2.zip            21MB
-#> 43: https://fis.fda.gov/content/Exports/faers_ascii_2013q1.zip            25MB
-#> 44: https://fis.fda.gov/content/Exports/faers_ascii_2012q4.zip            28MB
-#> 45:  https://fis.fda.gov/content/Exports/aers_ascii_2012q3.zip            16MB
-#> 46:  https://fis.fda.gov/content/Exports/aers_ascii_2012q2.zip            25MB
-#> 47:  https://fis.fda.gov/content/Exports/aers_ascii_2012q1.zip            26MB
-#> 48:  https://fis.fda.gov/content/Exports/aers_ascii_2011q4.zip            23MB
-#> 49:  https://fis.fda.gov/content/Exports/aers_ascii_2011q3.zip            23MB
-#> 50:  https://fis.fda.gov/content/Exports/aers_ascii_2011q2.zip            23MB
-#> 51:  https://fis.fda.gov/content/Exports/aers_ascii_2011q1.zip            21MB
-#> 52:  https://fis.fda.gov/content/Exports/aers_ascii_2010q4.zip            20MB
-#> 53:  https://fis.fda.gov/content/Exports/aers_ascii_2010q3.zip            22MB
-#> 54:  https://fis.fda.gov/content/Exports/aers_ascii_2010q2.zip            17MB
-#> 55:  https://fis.fda.gov/content/Exports/aers_ascii_2010q1.zip            16MB
-#> 56:  https://fis.fda.gov/content/Exports/aers_ascii_2009q4.zip            16MB
-#> 57:  https://fis.fda.gov/content/Exports/aers_ascii_2009q3.zip            16MB
-#> 58:  https://fis.fda.gov/content/Exports/aers_ascii_2009q2.zip            14MB
-#> 59:  https://fis.fda.gov/content/Exports/aers_ascii_2009q1.zip            13MB
-#> 60:  https://fis.fda.gov/content/Exports/aers_ascii_2008q4.zip            13MB
-#> 61:  https://fis.fda.gov/content/Exports/aers_ascii_2008q3.zip            13MB
-#> 62:  https://fis.fda.gov/content/Exports/aers_ascii_2008q2.zip            12MB
-#> 63:  https://fis.fda.gov/content/Exports/aers_ascii_2008q1.zip            12MB
-#> 64:  https://fis.fda.gov/content/Exports/aers_ascii_2007q4.zip            12MB
-#> 65:  https://fis.fda.gov/content/Exports/aers_ascii_2007q3.zip           9.9MB
-#> 66:  https://fis.fda.gov/content/Exports/aers_ascii_2007q2.zip           9.5MB
-#> 67:  https://fis.fda.gov/content/Exports/aers_ascii_2007q1.zip           9.6MB
-#> 68:  https://fis.fda.gov/content/Exports/aers_ascii_2006q4.zip           9.1MB
-#> 69:  https://fis.fda.gov/content/Exports/aers_ascii_2006q3.zip           8.5MB
-#> 70:  https://fis.fda.gov/content/Exports/aers_ascii_2006q2.zip           9.7MB
-#>                                                     xml_urls xml_file_size
-#>                                                       <char>        <char>
-#>  1: https://fis.fda.gov/content/Exports/faers_xml_2023Q3.zip         123MB
-#>  2: https://fis.fda.gov/content/Exports/faers_xml_2023q2.zip         130MB
-#>  3: https://fis.fda.gov/content/Exports/faers_xml_2023q1.zip         133MB
-#>  4: https://fis.fda.gov/content/Exports/faers_xml_2022Q4.zip         144MB
-#>  5: https://fis.fda.gov/content/Exports/faers_xml_2022Q3.zip         132MB
-#>  6: https://fis.fda.gov/content/Exports/faers_xml_2022q2.zip         140MB
-#>  7: https://fis.fda.gov/content/Exports/faers_xml_2022q1.zip         136MB
-#>  8: https://fis.fda.gov/content/Exports/faers_xml_2021Q4.zip         123MB
-#>  9: https://fis.fda.gov/content/Exports/faers_xml_2021Q3.zip         132MB
-#> 10: https://fis.fda.gov/content/Exports/faers_xml_2021Q2.zip         123MB
-#> 11: https://fis.fda.gov/content/Exports/faers_xml_2021Q1.zip         130MB
-#> 12: https://fis.fda.gov/content/Exports/faers_xml_2020Q4.zip         131MB
-#> 13: https://fis.fda.gov/content/Exports/faers_xml_2020Q3.zip         121MB
-#> 14: https://fis.fda.gov/content/Exports/faers_xml_2020Q2.zip         123MB
-#> 15: https://fis.fda.gov/content/Exports/faers_xml_2020Q1.zip         125MB
-#> 16: https://fis.fda.gov/content/Exports/faers_xml_2019Q4.zip         113MB
-#> 17: https://fis.fda.gov/content/Exports/faers_xml_2019Q3.zip         118MB
-#> 18: https://fis.fda.gov/content/Exports/faers_xml_2019Q2.zip         118MB
-#> 19: https://fis.fda.gov/content/Exports/faers_xml_2019Q1.zip         103MB
-#> 20: https://fis.fda.gov/content/Exports/faers_xml_2018q4.zip         112MB
-#> 21: https://fis.fda.gov/content/Exports/faers_xml_2018q3.zip         112MB
-#> 22: https://fis.fda.gov/content/Exports/faers_xml_2018q2.zip         112MB
-#> 23: https://fis.fda.gov/content/Exports/faers_xml_2018q1.zip          94MB
-#> 24: https://fis.fda.gov/content/Exports/faers_xml_2017q4.zip          76MB
-#> 25: https://fis.fda.gov/content/Exports/faers_xml_2017q3.zip          91MB
-#> 26: https://fis.fda.gov/content/Exports/faers_xml_2017q2.zip          86MB
-#> 27: https://fis.fda.gov/content/Exports/faers_xml_2017q1.zip          91MB
-#> 28: https://fis.fda.gov/content/Exports/faers_xml_2016q4.zip          82MB
-#> 29: https://fis.fda.gov/content/Exports/faers_xml_2016q3.zip          87MB
-#> 30: https://fis.fda.gov/content/Exports/faers_xml_2016q2.zip          81MB
-#> 31: https://fis.fda.gov/content/Exports/faers_xml_2016q1.zip          84MB
-#> 32: https://fis.fda.gov/content/Exports/faers_xml_2015q4.zip          77MB
-#> 33: https://fis.fda.gov/content/Exports/faers_xml_2015q3.zip          88MB
-#> 34: https://fis.fda.gov/content/Exports/faers_xml_2015q2.zip          70MB
-#> 35: https://fis.fda.gov/content/Exports/faers_xml_2015q1.zip          72MB
-#> 36: https://fis.fda.gov/content/Exports/faers_xml_2014q4.zip          53MB
-#> 37: https://fis.fda.gov/content/Exports/faers_xml_2014q3.zip          54MB
-#> 38: https://fis.fda.gov/content/Exports/faers_xml_2014q2.zip          44MB
-#> 39: https://fis.fda.gov/content/Exports/faers_xml_2014q1.zip          52MB
-#> 40: https://fis.fda.gov/content/Exports/faers_xml_2013q4.zip          46MB
-#> 41: https://fis.fda.gov/content/Exports/faers_xml_2013q3.zip          40MB
-#> 42: https://fis.fda.gov/content/Exports/faers_xml_2013q2.zip          38MB
-#> 43: https://fis.fda.gov/content/Exports/faers_xml_2013q1.zip          44MB
-#> 44: https://fis.fda.gov/content/Exports/faers_xml_2012q4.zip          50MB
-#> 45: https://fis.fda.gov/content/Exports/aers_sgml_2012q3.zip          21MB
-#> 46: https://fis.fda.gov/content/Exports/aers_sgml_2012q2.zip          32MB
-#> 47: https://fis.fda.gov/content/Exports/aers_sgml_2012q1.zip          33MB
-#> 48: https://fis.fda.gov/content/Exports/aers_sgml_2011q4.zip          29MB
-#> 49: https://fis.fda.gov/content/Exports/aers_sgml_2011q3.zip          29MB
-#> 50: https://fis.fda.gov/content/Exports/aers_sgml_2011q2.zip          29MB
-#> 51: https://fis.fda.gov/content/Exports/aers_sgml_2011q1.zip          26MB
-#> 52: https://fis.fda.gov/content/Exports/aers_sgml_2010q4.zip          25MB
-#> 53: https://fis.fda.gov/content/Exports/aers_sgml_2010q3.zip          28MB
-#> 54: https://fis.fda.gov/content/Exports/aers_sgml_2010q2.zip          22MB
-#> 55: https://fis.fda.gov/content/Exports/aers_sgml_2010q1.zip          20MB
-#> 56: https://fis.fda.gov/content/Exports/aers_sgml_2009q4.zip          20MB
-#> 57: https://fis.fda.gov/content/Exports/aers_sgml_2009q3.zip          19MB
-#> 58: https://fis.fda.gov/content/Exports/aers_sgml_2009q2.zip          18MB
-#> 59: https://fis.fda.gov/content/Exports/aers_sgml_2009q1.zip          16MB
-#> 60: https://fis.fda.gov/content/Exports/aers_sgml_2008q4.zip          16MB
-#> 61: https://fis.fda.gov/content/Exports/aers_sgml_2008q3.zip          16MB
-#> 62: https://fis.fda.gov/content/Exports/aers_sgml_2008q2.zip          16MB
-#> 63: https://fis.fda.gov/content/Exports/aers_sgml_2008q1.zip          15MB
-#> 64: https://fis.fda.gov/content/Exports/aers_sgml_2007q4.zip          14MB
-#> 65: https://fis.fda.gov/content/Exports/aers_sgml_2007q3.zip          13MB
-#> 66: https://fis.fda.gov/content/Exports/aers_sgml_2007q2.zip          12MB
-#> 67: https://fis.fda.gov/content/Exports/aers_sgml_2007q1.zip          12MB
-#> 68: https://fis.fda.gov/content/Exports/aers_sgml_2006q4.zip          12MB
-#> 69: https://fis.fda.gov/content/Exports/aers_sgml_2006q3.zip          11MB
-#> 70: https://fis.fda.gov/content/Exports/aers_sgml_2006q2.zip          13MB
-#>  [ reached getOption("max.print") -- omitted 10 rows ]
+#> → 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 +#> 2: 2023 q2 April - June +#> 3: 2023 q1 January - March +#> 4: 2022 q4 October - December +#> 5: 2022 q3 July - September +#> 6: 2022 q2 April - June +#> 7: 2022 q1 January - March +#> 8: 2021 q4 October - December +#> 9: 2021 q3 July - September +#> 10: 2021 q2 April - June +#> 11: 2021 q1 January - March +#> 12: 2020 q4 October - December +#> 13: 2020 q3 July - September +#> 14: 2020 q2 April - June +#> 15: 2020 q1 January - March +#> 16: 2019 q4 October - December +#> 17: 2019 q3 July - September +#> 18: 2019 q2 April - June +#> 19: 2019 q1 January - March +#> 20: 2018 q4 October - December +#> 21: 2018 q3 July - September +#> 22: 2018 q2 April - June +#> 23: 2018 q1 January - March +#> 24: 2017 q4 October - December +#> 25: 2017 q3 July - September +#> 26: 2017 q2 April - June +#> 27: 2017 q1 January - March +#> 28: 2016 q4 October - December +#> 29: 2016 q3 July - September +#> 30: 2016 q2 April - June +#> 31: 2016 q1 January - March +#> 32: 2015 q4 October - December +#> 33: 2015 q3 July - September +#> 34: 2015 q2 April - June +#> 35: 2015 q1 January - March +#> 36: 2014 q4 October - December +#> 37: 2014 q3 July - September +#> 38: 2014 q2 April - June +#> 39: 2014 q1 January - March +#> 40: 2013 q4 October - December +#> 41: 2013 q3 July - September +#> 42: 2013 q2 April - June +#> 43: 2013 q1 January - March +#> 44: 2012 q4 October - December +#> 45: 2012 q3 July - September +#> 46: 2012 q2 April - June +#> 47: 2012 q1 January - March +#> 48: 2011 q4 October - December +#> 49: 2011 q3 July - September +#> 50: 2011 q2 April - June +#> 51: 2011 q1 January - March +#> 52: 2010 q4 October - December +#> 53: 2010 q3 July - September +#> 54: 2010 q2 April - June +#> 55: 2010 q1 January - March +#> 56: 2009 q4 October - December +#> 57: 2009 q3 July - September +#> 58: 2009 q2 April - June +#> 59: 2009 q1 January - March +#> 60: 2008 q4 October - December +#> 61: 2008 q3 July - September +#> 62: 2008 q2 April - June +#> 63: 2008 q1 January - March +#> 64: 2007 q4 October - December +#> 65: 2007 q3 July - September +#> 66: 2007 q2 April - June +#> 67: 2007 q1 January - March +#> 68: 2006 q4 October - December +#> 69: 2006 q3 July - September +#> 70: 2006 q2 April - June +#> ascii_urls ascii_file_size +#> <char> <char> +#> 1: https://fis.fda.gov/content/Exports/faers_ascii_2023Q3.zip 60.1MB +#> 2: https://fis.fda.gov/content/Exports/faers_ascii_2023q2.zip 64.5MB +#> 3: https://fis.fda.gov/content/Exports/faers_ascii_2023q1.zip 64.3MB +#> 4: https://fis.fda.gov/content/Exports/faers_ascii_2022Q4.zip 69MB +#> 5: https://fis.fda.gov/content/Exports/faers_ascii_2022Q3.zip 63.2MB +#> 6: https://fis.fda.gov/content/Exports/faers_ascii_2022q2.zip 63MB +#> 7: https://fis.fda.gov/content/Exports/faers_ascii_2022q1.zip 64.7MB +#> 8: https://fis.fda.gov/content/Exports/faers_ascii_2021Q4.zip 59MB +#> 9: https://fis.fda.gov/content/Exports/faers_ascii_2021Q3.zip 70MB +#> 10: https://fis.fda.gov/content/Exports/faers_ascii_2021Q2.zip 66MB +#> 11: https://fis.fda.gov/content/Exports/faers_ascii_2021Q1.zip 69MB +#> 12: https://fis.fda.gov/content/Exports/faers_ascii_2020Q4.zip 71MB +#> 13: https://fis.fda.gov/content/Exports/faers_ascii_2020Q3.zip 64MB +#> 14: https://fis.fda.gov/content/Exports/faers_ascii_2020Q2.zip 66MB +#> 15: https://fis.fda.gov/content/Exports/faers_ascii_2020Q1.zip 65MB +#> 16: https://fis.fda.gov/content/Exports/faers_ascii_2019Q4.zip 60MB +#> 17: https://fis.fda.gov/content/Exports/faers_ascii_2019Q3.zip 62MB +#> 18: https://fis.fda.gov/content/Exports/faers_ascii_2019Q2.zip 62MB +#> 19: https://fis.fda.gov/content/Exports/faers_ascii_2019Q1.zip 56MB +#> 20: https://fis.fda.gov/content/Exports/faers_ascii_2018q4.zip 60MB +#> 21: https://fis.fda.gov/content/Exports/faers_ascii_2018q3.zip 60MB +#> 22: https://fis.fda.gov/content/Exports/faers_ascii_2018q2.zip 60MB +#> 23: https://fis.fda.gov/content/Exports/faers_ascii_2018q1.zip 52MB +#> 24: https://fis.fda.gov/content/Exports/faers_ascii_2017q4.zip 41MB +#> 25: https://fis.fda.gov/content/Exports/faers_ascii_2017q3.zip 48MB +#> 26: https://fis.fda.gov/content/Exports/faers_ascii_2017q2.zip 46MB +#> 27: https://fis.fda.gov/content/Exports/faers_ascii_2017q1.zip 48MB +#> 28: https://fis.fda.gov/content/Exports/faers_ascii_2016q4.zip 44MB +#> 29: https://fis.fda.gov/content/Exports/faers_ascii_2016q3.zip 46MB +#> 30: https://fis.fda.gov/content/Exports/faers_ascii_2016q2.zip 44MB +#> 31: https://fis.fda.gov/content/Exports/faers_ascii_2016q1.zip 46MB +#> 32: https://fis.fda.gov/content/Exports/faers_ascii_2015q4.zip 42MB +#> 33: https://fis.fda.gov/content/Exports/faers_ascii_2015q3.zip 47MB +#> 34: https://fis.fda.gov/content/Exports/faers_ascii_2015q2.zip 38MB +#> 35: https://fis.fda.gov/content/Exports/faers_ascii_2015q1.zip 39MB +#> 36: https://fis.fda.gov/content/Exports/faers_ascii_2014q4.zip 28MB +#> 37: https://fis.fda.gov/content/Exports/faers_ascii_2014q3.zip 28MB +#> 38: https://fis.fda.gov/content/Exports/faers_ascii_2014q2.zip 25MB +#> 39: https://fis.fda.gov/content/Exports/faers_ascii_2014q1.zip 30MB +#> 40: https://fis.fda.gov/content/Exports/faers_ascii_2013q4.zip 26MB +#> 41: https://fis.fda.gov/content/Exports/faers_ascii_2013q3.zip 22MB +#> 42: https://fis.fda.gov/content/Exports/faers_ascii_2013q2.zip 21MB +#> 43: https://fis.fda.gov/content/Exports/faers_ascii_2013q1.zip 25MB +#> 44: https://fis.fda.gov/content/Exports/faers_ascii_2012q4.zip 28MB +#> 45: https://fis.fda.gov/content/Exports/aers_ascii_2012q3.zip 16MB +#> 46: https://fis.fda.gov/content/Exports/aers_ascii_2012q2.zip 25MB +#> 47: https://fis.fda.gov/content/Exports/aers_ascii_2012q1.zip 26MB +#> 48: https://fis.fda.gov/content/Exports/aers_ascii_2011q4.zip 23MB +#> 49: https://fis.fda.gov/content/Exports/aers_ascii_2011q3.zip 23MB +#> 50: https://fis.fda.gov/content/Exports/aers_ascii_2011q2.zip 23MB +#> 51: https://fis.fda.gov/content/Exports/aers_ascii_2011q1.zip 21MB +#> 52: https://fis.fda.gov/content/Exports/aers_ascii_2010q4.zip 20MB +#> 53: https://fis.fda.gov/content/Exports/aers_ascii_2010q3.zip 22MB +#> 54: https://fis.fda.gov/content/Exports/aers_ascii_2010q2.zip 17MB +#> 55: https://fis.fda.gov/content/Exports/aers_ascii_2010q1.zip 16MB +#> 56: https://fis.fda.gov/content/Exports/aers_ascii_2009q4.zip 16MB +#> 57: https://fis.fda.gov/content/Exports/aers_ascii_2009q3.zip 16MB +#> 58: https://fis.fda.gov/content/Exports/aers_ascii_2009q2.zip 14MB +#> 59: https://fis.fda.gov/content/Exports/aers_ascii_2009q1.zip 13MB +#> 60: https://fis.fda.gov/content/Exports/aers_ascii_2008q4.zip 13MB +#> 61: https://fis.fda.gov/content/Exports/aers_ascii_2008q3.zip 13MB +#> 62: https://fis.fda.gov/content/Exports/aers_ascii_2008q2.zip 12MB +#> 63: https://fis.fda.gov/content/Exports/aers_ascii_2008q1.zip 12MB +#> 64: https://fis.fda.gov/content/Exports/aers_ascii_2007q4.zip 12MB +#> 65: https://fis.fda.gov/content/Exports/aers_ascii_2007q3.zip 9.9MB +#> 66: https://fis.fda.gov/content/Exports/aers_ascii_2007q2.zip 9.5MB +#> 67: https://fis.fda.gov/content/Exports/aers_ascii_2007q1.zip 9.6MB +#> 68: https://fis.fda.gov/content/Exports/aers_ascii_2006q4.zip 9.1MB +#> 69: https://fis.fda.gov/content/Exports/aers_ascii_2006q3.zip 8.5MB +#> 70: https://fis.fda.gov/content/Exports/aers_ascii_2006q2.zip 9.7MB +#> xml_urls xml_file_size +#> <char> <char> +#> 1: https://fis.fda.gov/content/Exports/faers_xml_2023Q3.zip 123MB +#> 2: https://fis.fda.gov/content/Exports/faers_xml_2023q2.zip 130MB +#> 3: https://fis.fda.gov/content/Exports/faers_xml_2023q1.zip 133MB +#> 4: https://fis.fda.gov/content/Exports/faers_xml_2022Q4.zip 144MB +#> 5: https://fis.fda.gov/content/Exports/faers_xml_2022Q3.zip 132MB +#> 6: https://fis.fda.gov/content/Exports/faers_xml_2022q2.zip 140MB +#> 7: https://fis.fda.gov/content/Exports/faers_xml_2022q1.zip 136MB +#> 8: https://fis.fda.gov/content/Exports/faers_xml_2021Q4.zip 123MB +#> 9: https://fis.fda.gov/content/Exports/faers_xml_2021Q3.zip 132MB +#> 10: https://fis.fda.gov/content/Exports/faers_xml_2021Q2.zip 123MB +#> 11: https://fis.fda.gov/content/Exports/faers_xml_2021Q1.zip 130MB +#> 12: https://fis.fda.gov/content/Exports/faers_xml_2020Q4.zip 131MB +#> 13: https://fis.fda.gov/content/Exports/faers_xml_2020Q3.zip 121MB +#> 14: https://fis.fda.gov/content/Exports/faers_xml_2020Q2.zip 123MB +#> 15: https://fis.fda.gov/content/Exports/faers_xml_2020Q1.zip 125MB +#> 16: https://fis.fda.gov/content/Exports/faers_xml_2019Q4.zip 113MB +#> 17: https://fis.fda.gov/content/Exports/faers_xml_2019Q3.zip 118MB +#> 18: https://fis.fda.gov/content/Exports/faers_xml_2019Q2.zip 118MB +#> 19: https://fis.fda.gov/content/Exports/faers_xml_2019Q1.zip 103MB +#> 20: https://fis.fda.gov/content/Exports/faers_xml_2018q4.zip 112MB +#> 21: https://fis.fda.gov/content/Exports/faers_xml_2018q3.zip 112MB +#> 22: https://fis.fda.gov/content/Exports/faers_xml_2018q2.zip 112MB +#> 23: https://fis.fda.gov/content/Exports/faers_xml_2018q1.zip 94MB +#> 24: https://fis.fda.gov/content/Exports/faers_xml_2017q4.zip 76MB +#> 25: https://fis.fda.gov/content/Exports/faers_xml_2017q3.zip 91MB +#> 26: https://fis.fda.gov/content/Exports/faers_xml_2017q2.zip 86MB +#> 27: https://fis.fda.gov/content/Exports/faers_xml_2017q1.zip 91MB +#> 28: https://fis.fda.gov/content/Exports/faers_xml_2016q4.zip 82MB +#> 29: https://fis.fda.gov/content/Exports/faers_xml_2016q3.zip 87MB +#> 30: https://fis.fda.gov/content/Exports/faers_xml_2016q2.zip 81MB +#> 31: https://fis.fda.gov/content/Exports/faers_xml_2016q1.zip 84MB +#> 32: https://fis.fda.gov/content/Exports/faers_xml_2015q4.zip 77MB +#> 33: https://fis.fda.gov/content/Exports/faers_xml_2015q3.zip 88MB +#> 34: https://fis.fda.gov/content/Exports/faers_xml_2015q2.zip 70MB +#> 35: https://fis.fda.gov/content/Exports/faers_xml_2015q1.zip 72MB +#> 36: https://fis.fda.gov/content/Exports/faers_xml_2014q4.zip 53MB +#> 37: https://fis.fda.gov/content/Exports/faers_xml_2014q3.zip 54MB +#> 38: https://fis.fda.gov/content/Exports/faers_xml_2014q2.zip 44MB +#> 39: https://fis.fda.gov/content/Exports/faers_xml_2014q1.zip 52MB +#> 40: https://fis.fda.gov/content/Exports/faers_xml_2013q4.zip 46MB +#> 41: https://fis.fda.gov/content/Exports/faers_xml_2013q3.zip 40MB +#> 42: https://fis.fda.gov/content/Exports/faers_xml_2013q2.zip 38MB +#> 43: https://fis.fda.gov/content/Exports/faers_xml_2013q1.zip 44MB +#> 44: https://fis.fda.gov/content/Exports/faers_xml_2012q4.zip 50MB +#> 45: https://fis.fda.gov/content/Exports/aers_sgml_2012q3.zip 21MB +#> 46: https://fis.fda.gov/content/Exports/aers_sgml_2012q2.zip 32MB +#> 47: https://fis.fda.gov/content/Exports/aers_sgml_2012q1.zip 33MB +#> 48: https://fis.fda.gov/content/Exports/aers_sgml_2011q4.zip 29MB +#> 49: https://fis.fda.gov/content/Exports/aers_sgml_2011q3.zip 29MB +#> 50: https://fis.fda.gov/content/Exports/aers_sgml_2011q2.zip 29MB +#> 51: https://fis.fda.gov/content/Exports/aers_sgml_2011q1.zip 26MB +#> 52: https://fis.fda.gov/content/Exports/aers_sgml_2010q4.zip 25MB +#> 53: https://fis.fda.gov/content/Exports/aers_sgml_2010q3.zip 28MB +#> 54: https://fis.fda.gov/content/Exports/aers_sgml_2010q2.zip 22MB +#> 55: https://fis.fda.gov/content/Exports/aers_sgml_2010q1.zip 20MB +#> 56: https://fis.fda.gov/content/Exports/aers_sgml_2009q4.zip 20MB +#> 57: https://fis.fda.gov/content/Exports/aers_sgml_2009q3.zip 19MB +#> 58: https://fis.fda.gov/content/Exports/aers_sgml_2009q2.zip 18MB +#> 59: https://fis.fda.gov/content/Exports/aers_sgml_2009q1.zip 16MB +#> 60: https://fis.fda.gov/content/Exports/aers_sgml_2008q4.zip 16MB +#> 61: https://fis.fda.gov/content/Exports/aers_sgml_2008q3.zip 16MB +#> 62: https://fis.fda.gov/content/Exports/aers_sgml_2008q2.zip 16MB +#> 63: https://fis.fda.gov/content/Exports/aers_sgml_2008q1.zip 15MB +#> 64: https://fis.fda.gov/content/Exports/aers_sgml_2007q4.zip 14MB +#> 65: https://fis.fda.gov/content/Exports/aers_sgml_2007q3.zip 13MB +#> 66: https://fis.fda.gov/content/Exports/aers_sgml_2007q2.zip 12MB +#> 67: https://fis.fda.gov/content/Exports/aers_sgml_2007q1.zip 12MB +#> 68: https://fis.fda.gov/content/Exports/aers_sgml_2006q4.zip 12MB +#> 69: https://fis.fda.gov/content/Exports/aers_sgml_2006q3.zip 11MB +#> 70: https://fis.fda.gov/content/Exports/aers_sgml_2006q2.zip 13MB +#> [ reached getOption("max.print") -- omitted 10 rows ]

An metadata copy was associated with the package, just set internal = TRUE.

faers_meta(internal = TRUE)
-#>      year quarter             period
-#>     <int>  <char>             <char>
-#>  1:  2023      q3   July - September
-#>  2:  2023      q2       April - June
-#>  3:  2023      q1    January - March
-#>  4:  2022      q4 October - December
-#>  5:  2022      q3   July - September
-#>  6:  2022      q2       April - June
-#>  7:  2022      q1    January - March
-#>  8:  2021      q4 October - December
-#>  9:  2021      q3   July - September
-#> 10:  2021      q2       April - June
-#> 11:  2021      q1    January - March
-#> 12:  2020      q4 October - December
-#> 13:  2020      q3   July - September
-#> 14:  2020      q2       April - June
-#> 15:  2020      q1    January - March
-#> 16:  2019      q4 October - December
-#> 17:  2019      q3   July - September
-#> 18:  2019      q2       April - June
-#> 19:  2019      q1    January - March
-#> 20:  2018      q4 October - December
-#> 21:  2018      q3   July - September
-#> 22:  2018      q2       April - June
-#> 23:  2018      q1    January - March
-#> 24:  2017      q4 October - December
-#> 25:  2017      q3   July - September
-#> 26:  2017      q2       April - June
-#> 27:  2017      q1    January - March
-#> 28:  2016      q4 October - December
-#> 29:  2016      q3   July - September
-#> 30:  2016      q2       April - June
-#> 31:  2016      q1    January - March
-#> 32:  2015      q4 October - December
-#> 33:  2015      q3   July - September
-#> 34:  2015      q2       April - June
-#> 35:  2015      q1    January - March
-#> 36:  2014      q4 October - December
-#> 37:  2014      q3   July - September
-#> 38:  2014      q2       April - June
-#> 39:  2014      q1    January - March
-#> 40:  2013      q4 October - December
-#> 41:  2013      q3   July - September
-#> 42:  2013      q2       April - June
-#> 43:  2013      q1    January - March
-#> 44:  2012      q4 October - December
-#> 45:  2012      q3   July - September
-#> 46:  2012      q2       April - June
-#> 47:  2012      q1    January - March
-#> 48:  2011      q4 October - December
-#> 49:  2011      q3   July - September
-#> 50:  2011      q2       April - June
-#> 51:  2011      q1    January - March
-#> 52:  2010      q4 October - December
-#> 53:  2010      q3   July - September
-#> 54:  2010      q2       April - June
-#> 55:  2010      q1    January - March
-#> 56:  2009      q4 October - December
-#> 57:  2009      q3   July - September
-#> 58:  2009      q2       April - June
-#> 59:  2009      q1    January - March
-#> 60:  2008      q4 October - December
-#> 61:  2008      q3   July - September
-#> 62:  2008      q2       April - June
-#> 63:  2008      q1    January - March
-#> 64:  2007      q4 October - December
-#> 65:  2007      q3   July - September
-#> 66:  2007      q2       April - June
-#> 67:  2007      q1    January - March
-#> 68:  2006      q4 October - December
-#> 69:  2006      q3   July - September
-#> 70:  2006      q2       April - June
-#>                                                     ascii_urls ascii_file_size
-#>                                                         <char>          <char>
-#>  1: https://fis.fda.gov/content/Exports/faers_ascii_2023Q3.zip          60.1MB
-#>  2: https://fis.fda.gov/content/Exports/faers_ascii_2023q2.zip          64.5MB
-#>  3: https://fis.fda.gov/content/Exports/faers_ascii_2023q1.zip          64.3MB
-#>  4: https://fis.fda.gov/content/Exports/faers_ascii_2022Q4.zip            69MB
-#>  5: https://fis.fda.gov/content/Exports/faers_ascii_2022Q3.zip          63.2MB
-#>  6: https://fis.fda.gov/content/Exports/faers_ascii_2022q2.zip            63MB
-#>  7: https://fis.fda.gov/content/Exports/faers_ascii_2022q1.zip          64.7MB
-#>  8: https://fis.fda.gov/content/Exports/faers_ascii_2021Q4.zip            59MB
-#>  9: https://fis.fda.gov/content/Exports/faers_ascii_2021Q3.zip            70MB
-#> 10: https://fis.fda.gov/content/Exports/faers_ascii_2021Q2.zip            66MB
-#> 11: https://fis.fda.gov/content/Exports/faers_ascii_2021Q1.zip            69MB
-#> 12: https://fis.fda.gov/content/Exports/faers_ascii_2020Q4.zip            71MB
-#> 13: https://fis.fda.gov/content/Exports/faers_ascii_2020Q3.zip            64MB
-#> 14: https://fis.fda.gov/content/Exports/faers_ascii_2020Q2.zip            66MB
-#> 15: https://fis.fda.gov/content/Exports/faers_ascii_2020Q1.zip            65MB
-#> 16: https://fis.fda.gov/content/Exports/faers_ascii_2019Q4.zip            60MB
-#> 17: https://fis.fda.gov/content/Exports/faers_ascii_2019Q3.zip            62MB
-#> 18: https://fis.fda.gov/content/Exports/faers_ascii_2019Q2.zip            62MB
-#> 19: https://fis.fda.gov/content/Exports/faers_ascii_2019Q1.zip            56MB
-#> 20: https://fis.fda.gov/content/Exports/faers_ascii_2018q4.zip            60MB
-#> 21: https://fis.fda.gov/content/Exports/faers_ascii_2018q3.zip            60MB
-#> 22: https://fis.fda.gov/content/Exports/faers_ascii_2018q2.zip            60MB
-#> 23: https://fis.fda.gov/content/Exports/faers_ascii_2018q1.zip            52MB
-#> 24: https://fis.fda.gov/content/Exports/faers_ascii_2017q4.zip            41MB
-#> 25: https://fis.fda.gov/content/Exports/faers_ascii_2017q3.zip            48MB
-#> 26: https://fis.fda.gov/content/Exports/faers_ascii_2017q2.zip            46MB
-#> 27: https://fis.fda.gov/content/Exports/faers_ascii_2017q1.zip            48MB
-#> 28: https://fis.fda.gov/content/Exports/faers_ascii_2016q4.zip            44MB
-#> 29: https://fis.fda.gov/content/Exports/faers_ascii_2016q3.zip            46MB
-#> 30: https://fis.fda.gov/content/Exports/faers_ascii_2016q2.zip            44MB
-#> 31: https://fis.fda.gov/content/Exports/faers_ascii_2016q1.zip            46MB
-#> 32: https://fis.fda.gov/content/Exports/faers_ascii_2015q4.zip            42MB
-#> 33: https://fis.fda.gov/content/Exports/faers_ascii_2015q3.zip            47MB
-#> 34: https://fis.fda.gov/content/Exports/faers_ascii_2015q2.zip            38MB
-#> 35: https://fis.fda.gov/content/Exports/faers_ascii_2015q1.zip            39MB
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-#> 59:  https://fis.fda.gov/content/Exports/aers_ascii_2009q1.zip            13MB
-#> 60:  https://fis.fda.gov/content/Exports/aers_ascii_2008q4.zip            13MB
-#> 61:  https://fis.fda.gov/content/Exports/aers_ascii_2008q3.zip            13MB
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-#> 63:  https://fis.fda.gov/content/Exports/aers_ascii_2008q1.zip            12MB
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-#> 65:  https://fis.fda.gov/content/Exports/aers_ascii_2007q3.zip           9.9MB
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-#>                                                     xml_urls xml_file_size
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-#> 18: https://fis.fda.gov/content/Exports/faers_xml_2019Q2.zip         118MB
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+#> → 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 +#> 2: 2023 q2 April - June +#> 3: 2023 q1 January - March +#> 4: 2022 q4 October - December +#> 5: 2022 q3 July - September +#> 6: 2022 q2 April - June +#> 7: 2022 q1 January - March +#> 8: 2021 q4 October - December +#> 9: 2021 q3 July - September +#> 10: 2021 q2 April - June +#> 11: 2021 q1 January - March +#> 12: 2020 q4 October - December +#> 13: 2020 q3 July - September +#> 14: 2020 q2 April - June +#> 15: 2020 q1 January - March +#> 16: 2019 q4 October - December +#> 17: 2019 q3 July - September +#> 18: 2019 q2 April - June +#> 19: 2019 q1 January - March +#> 20: 2018 q4 October - December +#> 21: 2018 q3 July - September +#> 22: 2018 q2 April - June +#> 23: 2018 q1 January - March +#> 24: 2017 q4 October - December +#> 25: 2017 q3 July - September +#> 26: 2017 q2 April - June +#> 27: 2017 q1 January - March +#> 28: 2016 q4 October - December +#> 29: 2016 q3 July - September +#> 30: 2016 q2 April - June +#> 31: 2016 q1 January - March +#> 32: 2015 q4 October - December +#> 33: 2015 q3 July - September +#> 34: 2015 q2 April - June +#> 35: 2015 q1 January - March +#> 36: 2014 q4 October - December +#> 37: 2014 q3 July - September +#> 38: 2014 q2 April - June +#> 39: 2014 q1 January - March +#> 40: 2013 q4 October - December +#> 41: 2013 q3 July - September +#> 42: 2013 q2 April - June +#> 43: 2013 q1 January - March +#> 44: 2012 q4 October - December +#> 45: 2012 q3 July - September +#> 46: 2012 q2 April - June +#> 47: 2012 q1 January - March +#> 48: 2011 q4 October - December +#> 49: 2011 q3 July - September +#> 50: 2011 q2 April - June +#> 51: 2011 q1 January - March +#> 52: 2010 q4 October - December +#> 53: 2010 q3 July - September +#> 54: 2010 q2 April - June +#> 55: 2010 q1 January - March +#> 56: 2009 q4 October - December +#> 57: 2009 q3 July - September +#> 58: 2009 q2 April - June +#> 59: 2009 q1 January - March +#> 60: 2008 q4 October - December +#> 61: 2008 q3 July - September +#> 62: 2008 q2 April - June +#> 63: 2008 q1 January - March +#> 64: 2007 q4 October - December +#> 65: 2007 q3 July - September +#> 66: 2007 q2 April - June +#> 67: 2007 q1 January - March +#> 68: 2006 q4 October - December +#> 69: 2006 q3 July - September +#> 70: 2006 q2 April - June +#> ascii_urls ascii_file_size +#> <char> <char> +#> 1: https://fis.fda.gov/content/Exports/faers_ascii_2023Q3.zip 60.1MB +#> 2: https://fis.fda.gov/content/Exports/faers_ascii_2023q2.zip 64.5MB +#> 3: https://fis.fda.gov/content/Exports/faers_ascii_2023q1.zip 64.3MB +#> 4: https://fis.fda.gov/content/Exports/faers_ascii_2022Q4.zip 69MB +#> 5: https://fis.fda.gov/content/Exports/faers_ascii_2022Q3.zip 63.2MB +#> 6: https://fis.fda.gov/content/Exports/faers_ascii_2022q2.zip 63MB +#> 7: https://fis.fda.gov/content/Exports/faers_ascii_2022q1.zip 64.7MB +#> 8: https://fis.fda.gov/content/Exports/faers_ascii_2021Q4.zip 59MB +#> 9: https://fis.fda.gov/content/Exports/faers_ascii_2021Q3.zip 70MB +#> 10: https://fis.fda.gov/content/Exports/faers_ascii_2021Q2.zip 66MB +#> 11: https://fis.fda.gov/content/Exports/faers_ascii_2021Q1.zip 69MB +#> 12: https://fis.fda.gov/content/Exports/faers_ascii_2020Q4.zip 71MB +#> 13: https://fis.fda.gov/content/Exports/faers_ascii_2020Q3.zip 64MB +#> 14: https://fis.fda.gov/content/Exports/faers_ascii_2020Q2.zip 66MB +#> 15: https://fis.fda.gov/content/Exports/faers_ascii_2020Q1.zip 65MB +#> 16: https://fis.fda.gov/content/Exports/faers_ascii_2019Q4.zip 60MB +#> 17: https://fis.fda.gov/content/Exports/faers_ascii_2019Q3.zip 62MB +#> 18: https://fis.fda.gov/content/Exports/faers_ascii_2019Q2.zip 62MB +#> 19: https://fis.fda.gov/content/Exports/faers_ascii_2019Q1.zip 56MB +#> 20: https://fis.fda.gov/content/Exports/faers_ascii_2018q4.zip 60MB +#> 21: https://fis.fda.gov/content/Exports/faers_ascii_2018q3.zip 60MB +#> 22: https://fis.fda.gov/content/Exports/faers_ascii_2018q2.zip 60MB +#> 23: https://fis.fda.gov/content/Exports/faers_ascii_2018q1.zip 52MB +#> 24: https://fis.fda.gov/content/Exports/faers_ascii_2017q4.zip 41MB +#> 25: https://fis.fda.gov/content/Exports/faers_ascii_2017q3.zip 48MB +#> 26: https://fis.fda.gov/content/Exports/faers_ascii_2017q2.zip 46MB +#> 27: https://fis.fda.gov/content/Exports/faers_ascii_2017q1.zip 48MB +#> 28: https://fis.fda.gov/content/Exports/faers_ascii_2016q4.zip 44MB +#> 29: https://fis.fda.gov/content/Exports/faers_ascii_2016q3.zip 46MB +#> 30: https://fis.fda.gov/content/Exports/faers_ascii_2016q2.zip 44MB +#> 31: https://fis.fda.gov/content/Exports/faers_ascii_2016q1.zip 46MB +#> 32: https://fis.fda.gov/content/Exports/faers_ascii_2015q4.zip 42MB +#> 33: https://fis.fda.gov/content/Exports/faers_ascii_2015q3.zip 47MB +#> 34: https://fis.fda.gov/content/Exports/faers_ascii_2015q2.zip 38MB +#> 35: https://fis.fda.gov/content/Exports/faers_ascii_2015q1.zip 39MB +#> 36: https://fis.fda.gov/content/Exports/faers_ascii_2014q4.zip 28MB +#> 37: https://fis.fda.gov/content/Exports/faers_ascii_2014q3.zip 28MB +#> 38: https://fis.fda.gov/content/Exports/faers_ascii_2014q2.zip 25MB +#> 39: https://fis.fda.gov/content/Exports/faers_ascii_2014q1.zip 30MB +#> 40: https://fis.fda.gov/content/Exports/faers_ascii_2013q4.zip 26MB +#> 41: https://fis.fda.gov/content/Exports/faers_ascii_2013q3.zip 22MB +#> 42: https://fis.fda.gov/content/Exports/faers_ascii_2013q2.zip 21MB +#> 43: https://fis.fda.gov/content/Exports/faers_ascii_2013q1.zip 25MB +#> 44: https://fis.fda.gov/content/Exports/faers_ascii_2012q4.zip 28MB +#> 45: https://fis.fda.gov/content/Exports/aers_ascii_2012q3.zip 16MB +#> 46: https://fis.fda.gov/content/Exports/aers_ascii_2012q2.zip 25MB +#> 47: https://fis.fda.gov/content/Exports/aers_ascii_2012q1.zip 26MB +#> 48: https://fis.fda.gov/content/Exports/aers_ascii_2011q4.zip 23MB +#> 49: https://fis.fda.gov/content/Exports/aers_ascii_2011q3.zip 23MB +#> 50: https://fis.fda.gov/content/Exports/aers_ascii_2011q2.zip 23MB +#> 51: https://fis.fda.gov/content/Exports/aers_ascii_2011q1.zip 21MB +#> 52: https://fis.fda.gov/content/Exports/aers_ascii_2010q4.zip 20MB +#> 53: https://fis.fda.gov/content/Exports/aers_ascii_2010q3.zip 22MB +#> 54: https://fis.fda.gov/content/Exports/aers_ascii_2010q2.zip 17MB +#> 55: https://fis.fda.gov/content/Exports/aers_ascii_2010q1.zip 16MB +#> 56: https://fis.fda.gov/content/Exports/aers_ascii_2009q4.zip 16MB +#> 57: https://fis.fda.gov/content/Exports/aers_ascii_2009q3.zip 16MB +#> 58: https://fis.fda.gov/content/Exports/aers_ascii_2009q2.zip 14MB +#> 59: https://fis.fda.gov/content/Exports/aers_ascii_2009q1.zip 13MB +#> 60: https://fis.fda.gov/content/Exports/aers_ascii_2008q4.zip 13MB +#> 61: https://fis.fda.gov/content/Exports/aers_ascii_2008q3.zip 13MB +#> 62: https://fis.fda.gov/content/Exports/aers_ascii_2008q2.zip 12MB +#> 63: https://fis.fda.gov/content/Exports/aers_ascii_2008q1.zip 12MB +#> 64: https://fis.fda.gov/content/Exports/aers_ascii_2007q4.zip 12MB +#> 65: https://fis.fda.gov/content/Exports/aers_ascii_2007q3.zip 9.9MB +#> 66: https://fis.fda.gov/content/Exports/aers_ascii_2007q2.zip 9.5MB +#> 67: https://fis.fda.gov/content/Exports/aers_ascii_2007q1.zip 9.6MB +#> 68: https://fis.fda.gov/content/Exports/aers_ascii_2006q4.zip 9.1MB +#> 69: https://fis.fda.gov/content/Exports/aers_ascii_2006q3.zip 8.5MB +#> 70: https://fis.fda.gov/content/Exports/aers_ascii_2006q2.zip 9.7MB +#> xml_urls xml_file_size +#> <char> <char> +#> 1: https://fis.fda.gov/content/Exports/faers_xml_2023Q3.zip 123MB +#> 2: https://fis.fda.gov/content/Exports/faers_xml_2023q2.zip 130MB +#> 3: https://fis.fda.gov/content/Exports/faers_xml_2023q1.zip 133MB +#> 4: https://fis.fda.gov/content/Exports/faers_xml_2022Q4.zip 144MB +#> 5: https://fis.fda.gov/content/Exports/faers_xml_2022Q3.zip 132MB +#> 6: https://fis.fda.gov/content/Exports/faers_xml_2022q2.zip 140MB +#> 7: https://fis.fda.gov/content/Exports/faers_xml_2022q1.zip 136MB +#> 8: https://fis.fda.gov/content/Exports/faers_xml_2021Q4.zip 123MB +#> 9: https://fis.fda.gov/content/Exports/faers_xml_2021Q3.zip 132MB +#> 10: https://fis.fda.gov/content/Exports/faers_xml_2021Q2.zip 123MB +#> 11: https://fis.fda.gov/content/Exports/faers_xml_2021Q1.zip 130MB +#> 12: https://fis.fda.gov/content/Exports/faers_xml_2020Q4.zip 131MB +#> 13: https://fis.fda.gov/content/Exports/faers_xml_2020Q3.zip 121MB +#> 14: https://fis.fda.gov/content/Exports/faers_xml_2020Q2.zip 123MB +#> 15: https://fis.fda.gov/content/Exports/faers_xml_2020Q1.zip 125MB +#> 16: https://fis.fda.gov/content/Exports/faers_xml_2019Q4.zip 113MB +#> 17: https://fis.fda.gov/content/Exports/faers_xml_2019Q3.zip 118MB +#> 18: https://fis.fda.gov/content/Exports/faers_xml_2019Q2.zip 118MB +#> 19: https://fis.fda.gov/content/Exports/faers_xml_2019Q1.zip 103MB +#> 20: https://fis.fda.gov/content/Exports/faers_xml_2018q4.zip 112MB +#> 21: https://fis.fda.gov/content/Exports/faers_xml_2018q3.zip 112MB +#> 22: https://fis.fda.gov/content/Exports/faers_xml_2018q2.zip 112MB +#> 23: https://fis.fda.gov/content/Exports/faers_xml_2018q1.zip 94MB +#> 24: https://fis.fda.gov/content/Exports/faers_xml_2017q4.zip 76MB +#> 25: https://fis.fda.gov/content/Exports/faers_xml_2017q3.zip 91MB +#> 26: https://fis.fda.gov/content/Exports/faers_xml_2017q2.zip 86MB +#> 27: https://fis.fda.gov/content/Exports/faers_xml_2017q1.zip 91MB +#> 28: https://fis.fda.gov/content/Exports/faers_xml_2016q4.zip 82MB +#> 29: https://fis.fda.gov/content/Exports/faers_xml_2016q3.zip 87MB +#> 30: https://fis.fda.gov/content/Exports/faers_xml_2016q2.zip 81MB +#> 31: https://fis.fda.gov/content/Exports/faers_xml_2016q1.zip 84MB +#> 32: https://fis.fda.gov/content/Exports/faers_xml_2015q4.zip 77MB +#> 33: https://fis.fda.gov/content/Exports/faers_xml_2015q3.zip 88MB +#> 34: 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download and parse quarterly data files from FAERS

The FAERS Quarterly Data files contain raw data extracted from the AERS database for the indicated time ranges. The quarterly data files, which are available in ASCII or SGML formats, include:

Generally, we can use faers() function to download and parse all quarterly data files from FAERS. Internally, the faers() function seamlessly utilizes faers_download() and faers_parse() to preprocess each quarterly data file from the FAERS repository. The default format was ascii and will return a FAERSascii object. (xml format would also be okay , but presently, the XML file receives only minimal support in the following process.)

# # you must change `dir`, as the file included in the package is sampled
-data1 <- faers(2004, "q1", dir = system.file("extdata", package = "faers"))
-#> Finding 1 file already downloaded: 'aers_ascii_2004q1.zip'
-data1
-#> FAERS data from 1 Quarterly ascii file
-#>   Total reports: 100 (with duplicates)
+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)

Furthermore, in cases where multiple quarterly data files are requisite, the faers_combine() function is judiciously employed.

data2 <- faers(c(2004, 2017), c("q1", "q2"),
-  dir = system.file("extdata", package = "faers")
-)
-#> Finding 2 files already downloaded: 'aers_ascii_2004q1.zip' and
-#> 'faers_ascii_2017q2.zip'
-#> → Combining all 2 FAERS Quarterly ascii Data files
-data2
-#> FAERS data from 2 Quarterly ascii files
-#>   Total reports: 200 (with duplicates)
+ 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> Datas +data2 +#> FAERS data from 2 Quarterly ascii files +#> Total reports: 200 (with duplicates)

standardize and De-duplication

The reac file provides the adverse drug reactions, where it includes the “P.T.” field or the “Preferred Term” level terminology from the Medical Dictionary for Regulatory Activities (MedDRA). The indi file contains the drug indications, which also uses the “P.T.” level of MedDRA as a descriptor for the drug indication. In this way, MedDRA was necessary to standardize this field and add additional informations, such as System Organ Classes.

One limitation of FAERS database is Duplicate and incomplete reports. There are many instances of duplicative reports and some reports do not contain all the necessary information. We deemed two cases to be identical if they exhibited a full concordance across drugs administered, and adverse reactions and but showed discrepancies in one or none of the following fields: gender, age, reporting country, event date, start date, and drug indications.

@@ -1124,10 +1133,13 @@

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/README.md b/README.md index 89e29ab..0e7bf4a 100644 --- 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: +#> +#> → Writing FAERS metadata into cached +#> '~/.cache/R/faers/metadata/faers_meta_data.rds' #> year quarter period #> #> 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 #> #> 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 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 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 index c0a66e1..59b6c40 100644 --- a/man/FAERS-class.Rd +++ b/man/FAERS-class.Rd @@ -114,7 +114,10 @@ performed.} \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/man/FAERS-methods.Rd b/man/FAERS-methods.Rd index e991d57..475cf25 100644 --- a/man/FAERS-methods.Rd +++ b/man/FAERS-methods.Rd @@ -110,7 +110,10 @@ better to run \link[=FAERS]{faers}. } \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/man/faers.Rd b/man/faers.Rd index 3fe75d0..b837ea5 100644 --- a/man/faers.Rd +++ b/man/faers.Rd @@ -39,5 +39,8 @@ Download and parse FAERS Quarterly Data files } \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() +) } diff --git a/man/faers_counts.Rd b/man/faers_counts.Rd index 79f5abc..b4ebd46 100644 --- a/man/faers_counts.Rd +++ b/man/faers_counts.Rd @@ -52,7 +52,8 @@ Counting the number of unique case for each event \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/man/faers_dedup.Rd b/man/faers_dedup.Rd index f5365ff..ee495a4 100644 --- a/man/faers_dedup.Rd +++ b/man/faers_dedup.Rd @@ -32,7 +32,8 @@ Tidy up FAERS Quarterly Data with duplicate records removed \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/man/faers_merge.Rd b/man/faers_merge.Rd index 2348be3..3dce988 100644 --- a/man/faers_merge.Rd +++ b/man/faers_merge.Rd @@ -54,7 +54,10 @@ be consumed to merge all fields data. } \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")) } diff --git a/man/faers_phv_signal.Rd b/man/faers_phv_signal.Rd index 3be4d5a..9b4b1f2 100644 --- a/man/faers_phv_signal.Rd +++ b/man/faers_phv_signal.Rd @@ -88,7 +88,8 @@ constructed with \code{faers_phv_table}. \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/man/faers_standardize.Rd b/man/faers_standardize.Rd index cbf2a53..dca9db3 100644 --- a/man/faers_standardize.Rd +++ b/man/faers_standardize.Rd @@ -28,7 +28,8 @@ Standardize FAERS Quarterly Data for Preferred Term and drug names \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/vignettes/FAERS-Pharmacovigilance.Rmd b/vignettes/FAERS-Pharmacovigilance.Rmd index 8157c8e..b7f3d37 100644 --- a/vignettes/FAERS-Pharmacovigilance.Rmd +++ b/vignettes/FAERS-Pharmacovigilance.Rmd @@ -87,7 +87,10 @@ 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 ``` @@ -95,7 +98,8 @@ 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 ```