diff --git a/DESCRIPTION b/DESCRIPTION
index 7665b96..2994cb9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: faers
Title: R interface for FDA Adverse Event Reporting System
-Version: 1.1.4
+Version: 1.1.5
Authors@R:
c(
person("Yun", "Peng", , "yunyunp96@163.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2801-3332")),
diff --git a/NEWS.md b/NEWS.md
index d710661..fd7a838 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,9 @@
# faers 0.99.0
* Initial Bioconductor submission.
+
+# faers 1.1.4
+
+* fix error when download failed
+
+* meddra augment additional argument `primary_soc` to help save the full meddra data
diff --git a/R/meddra.R b/R/meddra.R
index 0f39f85..b6fd0ec 100644
--- a/R/meddra.R
+++ b/R/meddra.R
@@ -28,10 +28,12 @@ NULL
#' @param path A string, define the path of MedDRA directory.
#' @param add_smq A bool, indicates whether Standardised MedDRA Queries (SMQ)
#' should be added. If `TRUE`, "smq_content.asc", and "smq_list.asc" must exist.
+#' @param primary_soc A bool, indicates whether keep primary soc only.
#' @export
#' @rdname MedDRA-class
-meddra <- function(path, add_smq = FALSE) {
- hierarchy <- meddra_load_hierarchy(path, primary_soc = FALSE)
+meddra <- function(path, add_smq = FALSE, primary_soc = FALSE) {
+ assert_bool(primary_soc)
+ hierarchy <- meddra_load_hierarchy(path, primary_soc = primary_soc)
version <- meddra_load_version(path)
if (add_smq) {
smq_data <- meddra_load_smq(path)
diff --git a/R/period.R b/R/period.R
index 42c25ee..2db4ec6 100644
--- a/R/period.R
+++ b/R/period.R
@@ -18,7 +18,7 @@ faers_before_period <- function(years, quarters, y, q, inclusive = TRUE) {
if (!rlang::is_string(q, string = faers_file_quarters)) {
cli::cli_abort("{.arg q} must be a string in {.val {faers_file_quarters}}")
}
- assert_bool(inclusive, 1L)
+ assert_bool(inclusive)
do.call(
is_before_period,
c(periods, list(y = y, q = q, inclusive = inclusive))
diff --git a/R/standardize.R b/R/standardize.R
index 3c5520e..2f8ad93 100644
--- a/R/standardize.R
+++ b/R/standardize.R
@@ -28,7 +28,7 @@ methods::setMethod("faers_standardize", "FAERSascii", function(object, meddra_pa
# standardize PT terms
# for indi
assert_string(meddra_path)
- meddra_data <- meddra(meddra_path, add_smq = add_smq)
+ meddra_data <- meddra(meddra_path, add_smq = add_smq, primary_soc = TRUE)
# https://stackoverflow.com/questions/70181149/is-a-saved-and-loaded-data-table-with-qs-a-correct-data-table
# fix error: when load a saved FAERS object, don't change by reference
cli::cli_alert("standardize {.field Preferred Term} in indi")
diff --git a/README.html b/README.html
index e85c340..5c21bf0 100644
--- a/README.html
+++ b/README.html
@@ -893,224 +893,224 @@
#> ✔ Removing '/home/yun/.cache/R/faers/faers/metadata' successfully
faers_meta(internal = TRUE)
#> → Using internal FAERS metadata
-#> Snapshot time: 2023-11-08 13:06:35.726011
+#> Snapshot time: 2024-07-24 01:26:02.219535
#> 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
+#> 1: 2024 q1 January - March
+#> 2: 2023 q4 October - December
+#> 3: 2023 q3 July - September
+#> 4: 2023 q2 April - June
+#> 5: 2023 q1 January - March
+#> 6: 2022 q4 October - December
+#> 7: 2022 q3 July - September
+#> 8: 2022 q2 April - June
+#> 9: 2022 q1 January - March
+#> 10: 2021 q4 October - December
+#> 11: 2021 q3 July - September
+#> 12: 2021 q2 April - June
+#> 13: 2021 q1 January - March
+#> 14: 2020 q4 October - December
+#> 15: 2020 q3 July - September
+#> 16: 2020 q2 April - June
+#> 17: 2020 q1 January - March
+#> 18: 2019 q4 October - December
+#> 19: 2019 q3 July - September
+#> 20: 2019 q2 April - June
+#> 21: 2019 q1 January - March
+#> 22: 2018 q4 October - December
+#> 23: 2018 q3 July - September
+#> 24: 2018 q2 April - June
+#> 25: 2018 q1 January - March
+#> 26: 2017 q4 October - December
+#> 27: 2017 q3 July - September
+#> 28: 2017 q2 April - June
+#> 29: 2017 q1 January - March
+#> 30: 2016 q4 October - December
+#> 31: 2016 q3 July - September
+#> 32: 2016 q2 April - June
+#> 33: 2016 q1 January - March
+#> 34: 2015 q4 October - December
+#> 35: 2015 q3 July - September
+#> 36: 2015 q2 April - June
+#> 37: 2015 q1 January - March
+#> 38: 2014 q4 October - December
+#> 39: 2014 q3 July - September
+#> 40: 2014 q2 April - June
+#> 41: 2014 q1 January - March
+#> 42: 2013 q4 October - December
+#> 43: 2013 q3 July - September
+#> 44: 2013 q2 April - June
+#> 45: 2013 q1 January - March
+#> 46: 2012 q4 October - December
+#> 47: 2012 q3 July - September
+#> 48: 2012 q2 April - June
+#> 49: 2012 q1 January - March
+#> 50: 2011 q4 October - December
+#> 51: 2011 q3 July - September
+#> 52: 2011 q2 April - June
+#> 53: 2011 q1 January - March
+#> 54: 2010 q4 October - December
+#> 55: 2010 q3 July - September
+#> 56: 2010 q2 April - June
+#> 57: 2010 q1 January - March
+#> 58: 2009 q4 October - December
+#> 59: 2009 q3 July - September
+#> 60: 2009 q2 April - June
+#> 61: 2009 q1 January - March
+#> 62: 2008 q4 October - December
+#> 63: 2008 q3 July - September
+#> 64: 2008 q2 April - June
+#> 65: 2008 q1 January - March
+#> 66: 2007 q4 October - December
+#> 67: 2007 q3 July - September
+#> 68: 2007 q2 April - June
+#> 69: 2007 q1 January - March
+#> 70: 2006 q4 October - December
#> 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
+#> 1: https://fis.fda.gov/content/Exports/faers_ascii_2024q1.zip 63.1MB
+#> 2: https://fis.fda.gov/content/Exports/faers_ascii_2023Q4.zip 69.1MB
+#> 3: https://fis.fda.gov/content/Exports/faers_ascii_2023Q3.zip 60.1MB
+#> 4: https://fis.fda.gov/content/Exports/faers_ascii_2023q2.zip 64.5MB
+#> 5: https://fis.fda.gov/content/Exports/faers_ascii_2023q1.zip 64.3MB
+#> 6: https://fis.fda.gov/content/Exports/faers_ascii_2022Q4.zip 69MB
+#> 7: https://fis.fda.gov/content/Exports/faers_ascii_2022Q3.zip 63.2MB
+#> 8: https://fis.fda.gov/content/Exports/faers_ascii_2022q2.zip 63MB
+#> 9: https://fis.fda.gov/content/Exports/faers_ascii_2022q1.zip 64.7MB
+#> 10: https://fis.fda.gov/content/Exports/faers_ascii_2021Q4.zip 59MB
+#> 11: https://fis.fda.gov/content/Exports/faers_ascii_2021Q3.zip 70MB
+#> 12: https://fis.fda.gov/content/Exports/faers_ascii_2021Q2.zip 66MB
+#> 13: https://fis.fda.gov/content/Exports/faers_ascii_2021Q1.zip 69MB
+#> 14: https://fis.fda.gov/content/Exports/faers_ascii_2020Q4.zip 71MB
+#> 15: https://fis.fda.gov/content/Exports/faers_ascii_2020Q3.zip 64MB
+#> 16: https://fis.fda.gov/content/Exports/faers_ascii_2020Q2.zip 66MB
+#> 17: https://fis.fda.gov/content/Exports/faers_ascii_2020Q1.zip 65MB
+#> 18: https://fis.fda.gov/content/Exports/faers_ascii_2019Q4.zip 60MB
+#> 19: https://fis.fda.gov/content/Exports/faers_ascii_2019Q3.zip 62MB
+#> 20: https://fis.fda.gov/content/Exports/faers_ascii_2019Q2.zip 62MB
+#> 21: https://fis.fda.gov/content/Exports/faers_ascii_2019Q1.zip 56MB
+#> 22: https://fis.fda.gov/content/Exports/faers_ascii_2018q4.zip 60MB
+#> 23: https://fis.fda.gov/content/Exports/faers_ascii_2018q3.zip 60MB
+#> 24: https://fis.fda.gov/content/Exports/faers_ascii_2018q2.zip 60MB
+#> 25: https://fis.fda.gov/content/Exports/faers_ascii_2018q1.zip 52MB
+#> 26: https://fis.fda.gov/content/Exports/faers_ascii_2017q4.zip 41MB
+#> 27: https://fis.fda.gov/content/Exports/faers_ascii_2017q3.zip 48MB
+#> 28: https://fis.fda.gov/content/Exports/faers_ascii_2017q2.zip 46MB
+#> 29: https://fis.fda.gov/content/Exports/faers_ascii_2017q1.zip 48MB
+#> 30: https://fis.fda.gov/content/Exports/faers_ascii_2016q4.zip 44MB
+#> 31: https://fis.fda.gov/content/Exports/faers_ascii_2016q3.zip 46MB
+#> 32: https://fis.fda.gov/content/Exports/faers_ascii_2016q2.zip 44MB
+#> 33: https://fis.fda.gov/content/Exports/faers_ascii_2016q1.zip 46MB
+#> 34: https://fis.fda.gov/content/Exports/faers_ascii_2015q4.zip 42MB
+#> 35: https://fis.fda.gov/content/Exports/faers_ascii_2015q3.zip 47MB
+#> 36: https://fis.fda.gov/content/Exports/faers_ascii_2015q2.zip 38MB
+#> 37: https://fis.fda.gov/content/Exports/faers_ascii_2015q1.zip 39MB
+#> 38: https://fis.fda.gov/content/Exports/faers_ascii_2014q4.zip 28MB
+#> 39: https://fis.fda.gov/content/Exports/faers_ascii_2014q3.zip 28MB
+#> 40: https://fis.fda.gov/content/Exports/faers_ascii_2014q2.zip 25MB
+#> 41: https://fis.fda.gov/content/Exports/faers_ascii_2014q1.zip 30MB
+#> 42: https://fis.fda.gov/content/Exports/faers_ascii_2013q4.zip 26MB
+#> 43: https://fis.fda.gov/content/Exports/faers_ascii_2013q3.zip 22MB
+#> 44: https://fis.fda.gov/content/Exports/faers_ascii_2013q2.zip 21MB
+#> 45: https://fis.fda.gov/content/Exports/faers_ascii_2013q1.zip 25MB
+#> 46: https://fis.fda.gov/content/Exports/faers_ascii_2012q4.zip 28MB
+#> 47: https://fis.fda.gov/content/Exports/aers_ascii_2012q3.zip 16MB
+#> 48: https://fis.fda.gov/content/Exports/aers_ascii_2012q2.zip 25MB
+#> 49: https://fis.fda.gov/content/Exports/aers_ascii_2012q1.zip 26MB
+#> 50: https://fis.fda.gov/content/Exports/aers_ascii_2011q4.zip 23MB
+#> 51: https://fis.fda.gov/content/Exports/aers_ascii_2011q3.zip 23MB
+#> 52: https://fis.fda.gov/content/Exports/aers_ascii_2011q2.zip 23MB
+#> 53: https://fis.fda.gov/content/Exports/aers_ascii_2011q1.zip 21MB
+#> 54: https://fis.fda.gov/content/Exports/aers_ascii_2010q4.zip 20MB
+#> 55: https://fis.fda.gov/content/Exports/aers_ascii_2010q3.zip 22MB
+#> 56: https://fis.fda.gov/content/Exports/aers_ascii_2010q2.zip 17MB
+#> 57: https://fis.fda.gov/content/Exports/aers_ascii_2010q1.zip 16MB
+#> 58: https://fis.fda.gov/content/Exports/aers_ascii_2009q4.zip 16MB
+#> 59: https://fis.fda.gov/content/Exports/aers_ascii_2009q3.zip 16MB
+#> 60: https://fis.fda.gov/content/Exports/aers_ascii_2009q2.zip 14MB
+#> 61: https://fis.fda.gov/content/Exports/aers_ascii_2009q1.zip 13MB
+#> 62: https://fis.fda.gov/content/Exports/aers_ascii_2008q4.zip 13MB
+#> 63: https://fis.fda.gov/content/Exports/aers_ascii_2008q3.zip 13MB
+#> 64: https://fis.fda.gov/content/Exports/aers_ascii_2008q2.zip 12MB
+#> 65: https://fis.fda.gov/content/Exports/aers_ascii_2008q1.zip 12MB
+#> 66: https://fis.fda.gov/content/Exports/aers_ascii_2007q4.zip 12MB
+#> 67: https://fis.fda.gov/content/Exports/aers_ascii_2007q3.zip 9.9MB
+#> 68: https://fis.fda.gov/content/Exports/aers_ascii_2007q2.zip 9.5MB
+#> 69: https://fis.fda.gov/content/Exports/aers_ascii_2007q1.zip 9.6MB
+#> 70: https://fis.fda.gov/content/Exports/aers_ascii_2006q4.zip 9.1MB
#> 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 ]
Download and
Parse quarterly data files from FAERS
The FAERS Quarterly Data files contain raw data extracted from the
@@ -1268,123 +1268,124 @@
Standardize and
faers_meddra(data)
#> Hierarchy data for MedDRA (version 26.1)
faers_meddra(data, use = "hierarchy")
-#> llt_code
-#> <int>
-#> 1: 10000001
-#> 2: 10000002
-#> 3: 10000003
-#> 4: 10000004
-#> 5: 10000005
-#> ---
-#> 87588: 10089903
-#> 87589: 10089904
-#> 87590: 10089905
-#> 87591: 10089906
-#> 87592: 10089907
-#> llt_name
-#> <char>
-#> 1: "Ventilation" pneumonitis
-#> 2: 11-beta-hydroxylase deficiency
-#> 3: 11-oxysteroid activity incr
-#> 4: 11-oxysteroid activity increased
-#> 5: 17 ketosteroids urine
-#> ---
-#> 87588: Unintentional exposure to product
-#> 87589: Unintentional exposure to product by child
-#> 87590: Smouldering systemic mastocytosis
-#> 87591: Systemic mastocytosis with an associated haematological neoplasm
-#> 87592: Smouldering myeloma
-#> pt_code pt_name hlt_code
-#> <int> <char> <int>
-#> 1: 10081988 Hypersensitivity pneumonitis 10024972
-#> 2: 10000002 11-beta-hydroxylase deficiency 10021608
-#> 3: 10033315 Oxycorticosteroids increased 10001339
-#> 4: 10033315 Oxycorticosteroids increased 10001339
-#> 5: 10000005 17 ketosteroids urine 10038589
-#> ---
-#> 87588: 10073317 Accidental exposure to product 10073316
-#> 87589: 10073318 Accidental exposure to product by child 10073316
-#> 87590: 10089905 Smouldering systemic mastocytosis 10018845
-#> 87591: 10089805 Advanced systemic mastocytosis 10018845
-#> 87592: 10035226 Plasma cell myeloma 10074470
-#> hlt_name
-#> <char>
-#> 1: Lower respiratory tract inflammatory and immunologic conditions
-#> 2: Inborn errors of steroid synthesis
-#> 3: Adrenal cortex tests
-#> 4: Adrenal cortex tests
-#> 5: Reproductive hormone analyses
-#> ---
-#> 87588: Accidental exposures to product
-#> 87589: Accidental exposures to product
-#> 87590: Haematologic neoplasms NEC
-#> 87591: Haematologic neoplasms NEC
-#> 87592: Plasma cell myelomas
-#> hlgt_code
-#> <int>
-#> 1: 10024967
-#> 2: 10027424
-#> 3: 10014706
-#> 4: 10014706
-#> 5: 10014706
-#> ---
-#> 87588: 10079145
-#> 87589: 10079145
-#> 87590: 10018865
-#> 87591: 10018865
-#> 87592: 10035227
-#> hlgt_name
-#> <char>
-#> 1: Lower respiratory tract disorders (excl obstruction and infection)
-#> 2: Metabolic and nutritional disorders congenital
-#> 3: Endocrine investigations (incl sex hormones)
-#> 4: Endocrine investigations (incl sex hormones)
-#> 5: Endocrine investigations (incl sex hormones)
-#> ---
-#> 87588: Medication errors and other product use errors and issues
-#> 87589: Medication errors and other product use errors and issues
-#> 87590: Haematopoietic neoplasms (excl leukaemias and lymphomas)
-#> 87591: Haematopoietic neoplasms (excl leukaemias and lymphomas)
-#> 87592: Plasma cell neoplasms
-#> soc_code
-#> <int>
-#> 1: 10038738
-#> 2: 10010331
-#> 3: 10022891
-#> 4: 10022891
-#> 5: 10022891
-#> ---
-#> 87588: 10022117
-#> 87589: 10022117
-#> 87590: 10029104
-#> 87591: 10029104
-#> 87592: 10029104
-#> soc_name
-#> <char>
-#> 1: Respiratory, thoracic and mediastinal disorders
-#> 2: Congenital, familial and genetic disorders
-#> 3: Investigations
-#> 4: Investigations
-#> 5: Investigations
-#> ---
-#> 87588: Injury, poisoning and procedural complications
-#> 87589: Injury, poisoning and procedural complications
-#> 87590: Neoplasms benign, malignant and unspecified (incl cysts and polyps)
-#> 87591: Neoplasms benign, malignant and unspecified (incl cysts and polyps)
-#> 87592: Neoplasms benign, malignant and unspecified (incl cysts and polyps)
-#> soc_abbrev primary_soc_fg
-#> <char> <char>
-#> 1: Resp Y
-#> 2: Cong Y
-#> 3: Inv Y
-#> 4: Inv Y
-#> 5: Inv Y
-#> ---
-#> 87588: Inj&P Y
-#> 87589: Inj&P Y
-#> 87590: Neopl Y
-#> 87591: Neopl Y
-#> 87592: Neopl Y
The internal will include a meddra_hierarchy_idx column
that represents the index of the MedDRA hierarchy data in the
indi and reac field when standardized.
@@ -1661,8 +1662,8 @@
Pharmacovigilance analysis
grepl(insulin_pattern, ActiveIngredient, ignore.case = TRUE)
]
#> → Using Drugs@FDA data from cached
-#> '/home/yun/.cache/R/faers/faers/fdadrugs/fda_drugs_data_2024-07-02.zip'
-#> Snapshot date: 2024-07-02
+#> '/home/yun/.cache/R/faers/faers/fdadrugs/fda_drugs_data_2024-07-24.zip'
+#> Snapshot date: 2024-07-24
#> Warning: One or more parsing issues, call `problems()` on your data frame for details,
#> e.g.:
#> dat <- vroom(...)
@@ -1960,7 +1961,7 @@ sessionInfo
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
-#> [1] faers_1.1.2
+#> [1] faers_1.1.5
#>
#> loaded via a namespace (and not attached):
#> [1] generics_0.1.3 utf8_1.2.4 xml2_1.3.6
diff --git a/README.md b/README.md
index e3de436..76dd566 100644
--- a/README.md
+++ b/README.md
@@ -314,224 +314,224 @@ faers_clearcache("metadata")
``` r
faers_meta(internal = TRUE)
#> → Using internal FAERS metadata
-#> Snapshot time: 2023-11-08 13:06:35.726011
+#> Snapshot time: 2024-07-24 01:26:02.219535
#> year quarter period
#>
-#> 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
+#> 1: 2024 q1 January - March
+#> 2: 2023 q4 October - December
+#> 3: 2023 q3 July - September
+#> 4: 2023 q2 April - June
+#> 5: 2023 q1 January - March
+#> 6: 2022 q4 October - December
+#> 7: 2022 q3 July - September
+#> 8: 2022 q2 April - June
+#> 9: 2022 q1 January - March
+#> 10: 2021 q4 October - December
+#> 11: 2021 q3 July - September
+#> 12: 2021 q2 April - June
+#> 13: 2021 q1 January - March
+#> 14: 2020 q4 October - December
+#> 15: 2020 q3 July - September
+#> 16: 2020 q2 April - June
+#> 17: 2020 q1 January - March
+#> 18: 2019 q4 October - December
+#> 19: 2019 q3 July - September
+#> 20: 2019 q2 April - June
+#> 21: 2019 q1 January - March
+#> 22: 2018 q4 October - December
+#> 23: 2018 q3 July - September
+#> 24: 2018 q2 April - June
+#> 25: 2018 q1 January - March
+#> 26: 2017 q4 October - December
+#> 27: 2017 q3 July - September
+#> 28: 2017 q2 April - June
+#> 29: 2017 q1 January - March
+#> 30: 2016 q4 October - December
+#> 31: 2016 q3 July - September
+#> 32: 2016 q2 April - June
+#> 33: 2016 q1 January - March
+#> 34: 2015 q4 October - December
+#> 35: 2015 q3 July - September
+#> 36: 2015 q2 April - June
+#> 37: 2015 q1 January - March
+#> 38: 2014 q4 October - December
+#> 39: 2014 q3 July - September
+#> 40: 2014 q2 April - June
+#> 41: 2014 q1 January - March
+#> 42: 2013 q4 October - December
+#> 43: 2013 q3 July - September
+#> 44: 2013 q2 April - June
+#> 45: 2013 q1 January - March
+#> 46: 2012 q4 October - December
+#> 47: 2012 q3 July - September
+#> 48: 2012 q2 April - June
+#> 49: 2012 q1 January - March
+#> 50: 2011 q4 October - December
+#> 51: 2011 q3 July - September
+#> 52: 2011 q2 April - June
+#> 53: 2011 q1 January - March
+#> 54: 2010 q4 October - December
+#> 55: 2010 q3 July - September
+#> 56: 2010 q2 April - June
+#> 57: 2010 q1 January - March
+#> 58: 2009 q4 October - December
+#> 59: 2009 q3 July - September
+#> 60: 2009 q2 April - June
+#> 61: 2009 q1 January - March
+#> 62: 2008 q4 October - December
+#> 63: 2008 q3 July - September
+#> 64: 2008 q2 April - June
+#> 65: 2008 q1 January - March
+#> 66: 2007 q4 October - December
+#> 67: 2007 q3 July - September
+#> 68: 2007 q2 April - June
+#> 69: 2007 q1 January - March
+#> 70: 2006 q4 October - December
#> ascii_urls ascii_file_size
#>
-#> 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
+#> 1: https://fis.fda.gov/content/Exports/faers_ascii_2024q1.zip 63.1MB
+#> 2: https://fis.fda.gov/content/Exports/faers_ascii_2023Q4.zip 69.1MB
+#> 3: https://fis.fda.gov/content/Exports/faers_ascii_2023Q3.zip 60.1MB
+#> 4: https://fis.fda.gov/content/Exports/faers_ascii_2023q2.zip 64.5MB
+#> 5: https://fis.fda.gov/content/Exports/faers_ascii_2023q1.zip 64.3MB
+#> 6: https://fis.fda.gov/content/Exports/faers_ascii_2022Q4.zip 69MB
+#> 7: https://fis.fda.gov/content/Exports/faers_ascii_2022Q3.zip 63.2MB
+#> 8: https://fis.fda.gov/content/Exports/faers_ascii_2022q2.zip 63MB
+#> 9: https://fis.fda.gov/content/Exports/faers_ascii_2022q1.zip 64.7MB
+#> 10: https://fis.fda.gov/content/Exports/faers_ascii_2021Q4.zip 59MB
+#> 11: https://fis.fda.gov/content/Exports/faers_ascii_2021Q3.zip 70MB
+#> 12: https://fis.fda.gov/content/Exports/faers_ascii_2021Q2.zip 66MB
+#> 13: https://fis.fda.gov/content/Exports/faers_ascii_2021Q1.zip 69MB
+#> 14: https://fis.fda.gov/content/Exports/faers_ascii_2020Q4.zip 71MB
+#> 15: https://fis.fda.gov/content/Exports/faers_ascii_2020Q3.zip 64MB
+#> 16: https://fis.fda.gov/content/Exports/faers_ascii_2020Q2.zip 66MB
+#> 17: https://fis.fda.gov/content/Exports/faers_ascii_2020Q1.zip 65MB
+#> 18: https://fis.fda.gov/content/Exports/faers_ascii_2019Q4.zip 60MB
+#> 19: https://fis.fda.gov/content/Exports/faers_ascii_2019Q3.zip 62MB
+#> 20: https://fis.fda.gov/content/Exports/faers_ascii_2019Q2.zip 62MB
+#> 21: https://fis.fda.gov/content/Exports/faers_ascii_2019Q1.zip 56MB
+#> 22: https://fis.fda.gov/content/Exports/faers_ascii_2018q4.zip 60MB
+#> 23: https://fis.fda.gov/content/Exports/faers_ascii_2018q3.zip 60MB
+#> 24: https://fis.fda.gov/content/Exports/faers_ascii_2018q2.zip 60MB
+#> 25: https://fis.fda.gov/content/Exports/faers_ascii_2018q1.zip 52MB
+#> 26: https://fis.fda.gov/content/Exports/faers_ascii_2017q4.zip 41MB
+#> 27: https://fis.fda.gov/content/Exports/faers_ascii_2017q3.zip 48MB
+#> 28: https://fis.fda.gov/content/Exports/faers_ascii_2017q2.zip 46MB
+#> 29: https://fis.fda.gov/content/Exports/faers_ascii_2017q1.zip 48MB
+#> 30: https://fis.fda.gov/content/Exports/faers_ascii_2016q4.zip 44MB
+#> 31: https://fis.fda.gov/content/Exports/faers_ascii_2016q3.zip 46MB
+#> 32: https://fis.fda.gov/content/Exports/faers_ascii_2016q2.zip 44MB
+#> 33: https://fis.fda.gov/content/Exports/faers_ascii_2016q1.zip 46MB
+#> 34: https://fis.fda.gov/content/Exports/faers_ascii_2015q4.zip 42MB
+#> 35: https://fis.fda.gov/content/Exports/faers_ascii_2015q3.zip 47MB
+#> 36: https://fis.fda.gov/content/Exports/faers_ascii_2015q2.zip 38MB
+#> 37: https://fis.fda.gov/content/Exports/faers_ascii_2015q1.zip 39MB
+#> 38: https://fis.fda.gov/content/Exports/faers_ascii_2014q4.zip 28MB
+#> 39: https://fis.fda.gov/content/Exports/faers_ascii_2014q3.zip 28MB
+#> 40: https://fis.fda.gov/content/Exports/faers_ascii_2014q2.zip 25MB
+#> 41: https://fis.fda.gov/content/Exports/faers_ascii_2014q1.zip 30MB
+#> 42: https://fis.fda.gov/content/Exports/faers_ascii_2013q4.zip 26MB
+#> 43: https://fis.fda.gov/content/Exports/faers_ascii_2013q3.zip 22MB
+#> 44: https://fis.fda.gov/content/Exports/faers_ascii_2013q2.zip 21MB
+#> 45: https://fis.fda.gov/content/Exports/faers_ascii_2013q1.zip 25MB
+#> 46: https://fis.fda.gov/content/Exports/faers_ascii_2012q4.zip 28MB
+#> 47: https://fis.fda.gov/content/Exports/aers_ascii_2012q3.zip 16MB
+#> 48: https://fis.fda.gov/content/Exports/aers_ascii_2012q2.zip 25MB
+#> 49: https://fis.fda.gov/content/Exports/aers_ascii_2012q1.zip 26MB
+#> 50: https://fis.fda.gov/content/Exports/aers_ascii_2011q4.zip 23MB
+#> 51: https://fis.fda.gov/content/Exports/aers_ascii_2011q3.zip 23MB
+#> 52: https://fis.fda.gov/content/Exports/aers_ascii_2011q2.zip 23MB
+#> 53: https://fis.fda.gov/content/Exports/aers_ascii_2011q1.zip 21MB
+#> 54: https://fis.fda.gov/content/Exports/aers_ascii_2010q4.zip 20MB
+#> 55: https://fis.fda.gov/content/Exports/aers_ascii_2010q3.zip 22MB
+#> 56: https://fis.fda.gov/content/Exports/aers_ascii_2010q2.zip 17MB
+#> 57: https://fis.fda.gov/content/Exports/aers_ascii_2010q1.zip 16MB
+#> 58: https://fis.fda.gov/content/Exports/aers_ascii_2009q4.zip 16MB
+#> 59: https://fis.fda.gov/content/Exports/aers_ascii_2009q3.zip 16MB
+#> 60: https://fis.fda.gov/content/Exports/aers_ascii_2009q2.zip 14MB
+#> 61: https://fis.fda.gov/content/Exports/aers_ascii_2009q1.zip 13MB
+#> 62: https://fis.fda.gov/content/Exports/aers_ascii_2008q4.zip 13MB
+#> 63: https://fis.fda.gov/content/Exports/aers_ascii_2008q3.zip 13MB
+#> 64: https://fis.fda.gov/content/Exports/aers_ascii_2008q2.zip 12MB
+#> 65: https://fis.fda.gov/content/Exports/aers_ascii_2008q1.zip 12MB
+#> 66: https://fis.fda.gov/content/Exports/aers_ascii_2007q4.zip 12MB
+#> 67: https://fis.fda.gov/content/Exports/aers_ascii_2007q3.zip 9.9MB
+#> 68: https://fis.fda.gov/content/Exports/aers_ascii_2007q2.zip 9.5MB
+#> 69: https://fis.fda.gov/content/Exports/aers_ascii_2007q1.zip 9.6MB
+#> 70: https://fis.fda.gov/content/Exports/aers_ascii_2006q4.zip 9.1MB
#> xml_urls xml_file_size
#>
-#> 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 ]
+#> 1: https://fis.fda.gov/content/Exports/faers_xml_2024q1.zip 128MB
+#> 2: https://fis.fda.gov/content/Exports/faers_xml_2023Q4.zip 140MB
+#> 3: https://fis.fda.gov/content/Exports/faers_xml_2023Q3.zip 123MB
+#> 4: https://fis.fda.gov/content/Exports/faers_xml_2023q2.zip 130MB
+#> 5: https://fis.fda.gov/content/Exports/faers_xml_2023q1.zip 133MB
+#> 6: https://fis.fda.gov/content/Exports/faers_xml_2022Q4.zip 144MB
+#> 7: https://fis.fda.gov/content/Exports/faers_xml_2022Q3.zip 132MB
+#> 8: https://fis.fda.gov/content/Exports/faers_xml_2022q2.zip 140MB
+#> 9: https://fis.fda.gov/content/Exports/faers_xml_2022q1.zip 136MB
+#> 10: https://fis.fda.gov/content/Exports/faers_xml_2021Q4.zip 123MB
+#> 11: https://fis.fda.gov/content/Exports/faers_xml_2021Q3.zip 132MB
+#> 12: https://fis.fda.gov/content/Exports/faers_xml_2021Q2.zip 123MB
+#> 13: https://fis.fda.gov/content/Exports/faers_xml_2021Q1.zip 130MB
+#> 14: https://fis.fda.gov/content/Exports/faers_xml_2020Q4.zip 131MB
+#> 15: https://fis.fda.gov/content/Exports/faers_xml_2020Q3.zip 121MB
+#> 16: https://fis.fda.gov/content/Exports/faers_xml_2020Q2.zip 123MB
+#> 17: https://fis.fda.gov/content/Exports/faers_xml_2020Q1.zip 125MB
+#> 18: https://fis.fda.gov/content/Exports/faers_xml_2019Q4.zip 113MB
+#> 19: https://fis.fda.gov/content/Exports/faers_xml_2019Q3.zip 118MB
+#> 20: https://fis.fda.gov/content/Exports/faers_xml_2019Q2.zip 118MB
+#> 21: https://fis.fda.gov/content/Exports/faers_xml_2019Q1.zip 103MB
+#> 22: https://fis.fda.gov/content/Exports/faers_xml_2018q4.zip 112MB
+#> 23: https://fis.fda.gov/content/Exports/faers_xml_2018q3.zip 112MB
+#> 24: https://fis.fda.gov/content/Exports/faers_xml_2018q2.zip 112MB
+#> 25: https://fis.fda.gov/content/Exports/faers_xml_2018q1.zip 94MB
+#> 26: https://fis.fda.gov/content/Exports/faers_xml_2017q4.zip 76MB
+#> 27: https://fis.fda.gov/content/Exports/faers_xml_2017q3.zip 91MB
+#> 28: https://fis.fda.gov/content/Exports/faers_xml_2017q2.zip 86MB
+#> 29: https://fis.fda.gov/content/Exports/faers_xml_2017q1.zip 91MB
+#> 30: https://fis.fda.gov/content/Exports/faers_xml_2016q4.zip 82MB
+#> 31: https://fis.fda.gov/content/Exports/faers_xml_2016q3.zip 87MB
+#> 32: https://fis.fda.gov/content/Exports/faers_xml_2016q2.zip 81MB
+#> 33: https://fis.fda.gov/content/Exports/faers_xml_2016q1.zip 84MB
+#> 34: https://fis.fda.gov/content/Exports/faers_xml_2015q4.zip 77MB
+#> 35: https://fis.fda.gov/content/Exports/faers_xml_2015q3.zip 88MB
+#> 36: https://fis.fda.gov/content/Exports/faers_xml_2015q2.zip 70MB
+#> 37: https://fis.fda.gov/content/Exports/faers_xml_2015q1.zip 72MB
+#> 38: https://fis.fda.gov/content/Exports/faers_xml_2014q4.zip 53MB
+#> 39: https://fis.fda.gov/content/Exports/faers_xml_2014q3.zip 54MB
+#> 40: https://fis.fda.gov/content/Exports/faers_xml_2014q2.zip 44MB
+#> 41: https://fis.fda.gov/content/Exports/faers_xml_2014q1.zip 52MB
+#> 42: https://fis.fda.gov/content/Exports/faers_xml_2013q4.zip 46MB
+#> 43: https://fis.fda.gov/content/Exports/faers_xml_2013q3.zip 40MB
+#> 44: https://fis.fda.gov/content/Exports/faers_xml_2013q2.zip 38MB
+#> 45: https://fis.fda.gov/content/Exports/faers_xml_2013q1.zip 44MB
+#> 46: https://fis.fda.gov/content/Exports/faers_xml_2012q4.zip 50MB
+#> 47: https://fis.fda.gov/content/Exports/aers_sgml_2012q3.zip 21MB
+#> 48: https://fis.fda.gov/content/Exports/aers_sgml_2012q2.zip 32MB
+#> 49: https://fis.fda.gov/content/Exports/aers_sgml_2012q1.zip 33MB
+#> 50: https://fis.fda.gov/content/Exports/aers_sgml_2011q4.zip 29MB
+#> 51: https://fis.fda.gov/content/Exports/aers_sgml_2011q3.zip 29MB
+#> 52: https://fis.fda.gov/content/Exports/aers_sgml_2011q2.zip 29MB
+#> 53: https://fis.fda.gov/content/Exports/aers_sgml_2011q1.zip 26MB
+#> 54: https://fis.fda.gov/content/Exports/aers_sgml_2010q4.zip 25MB
+#> 55: https://fis.fda.gov/content/Exports/aers_sgml_2010q3.zip 28MB
+#> 56: https://fis.fda.gov/content/Exports/aers_sgml_2010q2.zip 22MB
+#> 57: https://fis.fda.gov/content/Exports/aers_sgml_2010q1.zip 20MB
+#> 58: https://fis.fda.gov/content/Exports/aers_sgml_2009q4.zip 20MB
+#> 59: https://fis.fda.gov/content/Exports/aers_sgml_2009q3.zip 19MB
+#> 60: https://fis.fda.gov/content/Exports/aers_sgml_2009q2.zip 18MB
+#> 61: https://fis.fda.gov/content/Exports/aers_sgml_2009q1.zip 16MB
+#> 62: https://fis.fda.gov/content/Exports/aers_sgml_2008q4.zip 16MB
+#> 63: https://fis.fda.gov/content/Exports/aers_sgml_2008q3.zip 16MB
+#> 64: https://fis.fda.gov/content/Exports/aers_sgml_2008q2.zip 16MB
+#> 65: https://fis.fda.gov/content/Exports/aers_sgml_2008q1.zip 15MB
+#> 66: https://fis.fda.gov/content/Exports/aers_sgml_2007q4.zip 14MB
+#> 67: https://fis.fda.gov/content/Exports/aers_sgml_2007q3.zip 13MB
+#> 68: https://fis.fda.gov/content/Exports/aers_sgml_2007q2.zip 12MB
+#> 69: https://fis.fda.gov/content/Exports/aers_sgml_2007q1.zip 12MB
+#> 70: https://fis.fda.gov/content/Exports/aers_sgml_2006q4.zip 12MB
+#> [ reached getOption("max.print") -- omitted 12 rows ]
```
### Download and Parse quarterly data files from FAERS
@@ -717,6 +717,7 @@ faers_meddra(data)
``` r
faers_meddra(data, use = "hierarchy")
+#> Index:
#> llt_code
#>
#> 1: 10000001
@@ -1125,8 +1126,8 @@ fda_insulin <- fda_drugs()[
grepl(insulin_pattern, ActiveIngredient, ignore.case = TRUE)
]
#> → Using Drugs@FDA data from cached
-#> '/home/yun/.cache/R/faers/faers/fdadrugs/fda_drugs_data_2024-07-02.zip'
-#> Snapshot date: 2024-07-02
+#> '/home/yun/.cache/R/faers/faers/fdadrugs/fda_drugs_data_2024-07-24.zip'
+#> Snapshot date: 2024-07-24
#> Warning: One or more parsing issues, call `problems()` on your data frame for details,
#> e.g.:
#> dat <- vroom(...)
@@ -1444,7 +1445,7 @@ sessionInfo()
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
-#> [1] faers_1.1.2
+#> [1] faers_1.1.5
#>
#> loaded via a namespace (and not attached):
#> [1] generics_0.1.3 utf8_1.2.4 xml2_1.3.6
diff --git a/inst/extdata/faers_meta_data.rds b/inst/extdata/faers_meta_data.rds
index 0d8d94e..3c3df72 100644
Binary files a/inst/extdata/faers_meta_data.rds and b/inst/extdata/faers_meta_data.rds differ
diff --git a/inst/extdata/standardized_data.rds b/inst/extdata/standardized_data.rds
index 0c44d09..6a2e3bb 100644
Binary files a/inst/extdata/standardized_data.rds and b/inst/extdata/standardized_data.rds differ
diff --git a/man/MedDRA-class.Rd b/man/MedDRA-class.Rd
index f17b454..f1e4338 100644
--- a/man/MedDRA-class.Rd
+++ b/man/MedDRA-class.Rd
@@ -14,7 +14,7 @@
\alias{meddra_version,MedDRA-method}
\title{MedDRA class}
\usage{
-meddra(path, add_smq = FALSE)
+meddra(path, add_smq = FALSE, primary_soc = FALSE)
\S4method{show}{MedDRA}(object)
@@ -36,6 +36,8 @@ meddra_version(object, ...)
\item{add_smq}{A bool, indicates whether Standardised MedDRA Queries (SMQ)
should be added. If \code{TRUE}, "smq_content.asc", and "smq_list.asc" must exist.}
+\item{primary_soc}{A bool, indicates whether keep primary soc only.}
+
\item{object}{A \code{MedDRA} object.}
\item{...}{Other arguments passed to specific methods.}
diff --git a/tests/testthat/test_meddra.R b/tests/testthat/test_meddra.R
index 2e321e7..94ce560 100644
--- a/tests/testthat/test_meddra.R
+++ b/tests/testthat/test_meddra.R
@@ -8,19 +8,26 @@ testthat::test_that("meddra works well", {
testthat::expect_true(rlang::is_string(meddra_load_version(path), "26.1"))
testthat::expect_s3_class(data <- meddra_load_hierarchy(path), "data.table")
testthat::expect_true(all(data$primary_soc_fg == "Y"))
+ testthat::expect_true(anyDuplicated(data$llt_code) == 0L)
testthat::expect_s3_class(data <- meddra_load_smq(path), "data.table")
# meddra() works well
- testthat::expect_s4_class(data <- meddra(path), "MedDRA")
+ testthat::expect_s4_class(
+ data <- meddra(path, primary_soc = TRUE), "MedDRA"
+ )
testthat::expect_true(rlang::is_string(meddra_version(data), "26.1"))
testthat::expect_s3_class(hierarchy <- meddra_hierarchy(data), "data.table")
testthat::expect_null(hierarchy$smq_code)
+ testthat::expect_true(all(hierarchy$primary_soc_fg == "Y"))
+ testthat::expect_true(anyDuplicated(hierarchy$llt_code) == 0L)
testthat::expect_null(meddra_smq(data))
# meddra() with add_smq = TRUE, works well
- testthat::expect_s4_class(data <- meddra(path, TRUE), "MedDRA")
+ testthat::expect_s4_class(data <- meddra(path, TRUE, TRUE), "MedDRA")
testthat::expect_true(rlang::is_string(meddra_version(data), "26.1"))
testthat::expect_s3_class(hierarchy <- meddra_hierarchy(data), "data.table")
testthat::expect_true(any(!is.na(hierarchy$smq_code)))
+ testthat::expect_true(all(hierarchy$primary_soc_fg == "Y"))
+ testthat::expect_true(anyDuplicated(hierarchy$llt_code) == 0L)
testthat::expect_s3_class(meddra_smq(data), "data.table")
})