The FDA Adverse Event Reporting System (FAERS) stands as a database dedicated to the monitoring of post-marketing drug safety and exercises a notable influence over FDA safety guidance documents, including the modification of drug labels. The quantity of cases stored within FAERS has experienced an exponential surge due to the refinement of submission techniques and adherence to standardized data protocols, making it a pivotal asset for the realm of regulatory science. While FAERS has predominantly focused on safety signal detection, the faers package acts as the intermediary, seamlessly bridging the gap between the FAERS database and the programming language R. Moreover, the faers package provides a unified methodology for the seamless execution of pharmacovigilance analysis, facilitating the integration of genetic tools in R. With an ultimate ambition towards precision medicine, it aspires to scrutinize the vast expanse of the human genome, revealing drug pathways that may be intricately tied to potentially functional, population-differentiated polymorphisms.
You can install the development version of faers from GitHub with:
if (!requireNamespace("pak")) {
- install.packages("pak",
- repos = sprintf(
- "https://r-lib.github.io/p/pak/devel/%s/%s/%s",
- .Platform$pkgType, R.Version()$os, R.Version()$arch
- )
- )
-}
-pak::pkg_install("Yunuuuu/faers")To install from Bioconductor, use the following code:
+if (!requireNamespace("BiocManager", quietly = TRUE)) {
+ install.packages("BiocManager")
+}
+BiocManager::install("faers")You can install the development version of faers from GitHub with:
if (!requireNamespace("pak")) {
+ install.packages("pak",
+ repos = sprintf(
+ "https://r-lib.github.io/p/pak/devel/%s/%s/%s",
+ .Platform$pkgType, R.Version()$os, R.Version()$arch
+ )
+ )
+}
+pak::pkg_install("Yunuuuu/faers")FAERS is a database for the spontaneous reporting of adverse events and medication errors involving human drugs and therapeutic biological products. This package accelarate the process of Pharmacovigilance Analysis using FAERS.
-library(faers)library(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()
-#> → Reading html:
-#> <https://fis.fda.gov/extensions/FPD-QDE-FAERS/FPD-QDE-FAERS.html>
-#> → Writing FAERS metadata into cache file
-#> '~/.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. However, this copy will only be used if the cached file on your computer cannot be found as the cached file on your computer should be more up-to-date than this metadata copy.
faers_clearcache("metadata")
-#> ✔ Removing '~/.cache/R/faers/metadata' successfully
-faers_meta(internal = TRUE)
-#> → Using internal FAERS metadata
-#> Snapshot time: 2023-11-08 13:06:35.726011
+faers_meta()
+#> → Reading html:
+#> <https://fis.fda.gov/extensions/FPD-QDE-FAERS/FPD-QDE-FAERS.html>
+#> → Writing FAERS metadata into cache file
+#> '~/.cache/R/faers/metadata/faers_meta_data.rds'
#> year quarter period
#> <int> <char> <char>
#> 1: 2023 q3 July - September
@@ -1063,7 +859,230 @@ Check metadata of FAERS
#> 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
+An metadata copy was associated with the package, just set internal = TRUE. However, this copy will only be used if the cached file on your computer cannot be found as the cached file on your computer should be more up-to-date than this metadata copy.
+faers_clearcache("metadata")
+#> ✔ Removing '~/.cache/R/faers/metadata' successfully
+faers_meta(internal = TRUE)
+#> → Using internal FAERS metadata
+#> Snapshot time: 2023-11-08 13:06:35.726011
+#> 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 ]
+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:
demo: demographic and administrative informationDownload and Parse q
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.)
Some variables has been added into specific field. See ?faers_parse for details.
-# # you must change `dir`, as the file included in the package is sampled
-data1 <- faers(2004, "q1",
- dir = system.file("extdata", package = "faers"),
- compress_dir = tempdir()
-)
-#> Finding 1 file already downloaded: 'aers_ascii_2004q1.zip'
-data1
-#> FAERS data from 1 Quarterly ascii file
-#> Total reports: 100 (with duplicates)
+# # you must change `dir`, as the file included in the package is sampled
+data1 <- faers(2004, "q1",
+ dir = system.file("extdata", package = "faers"),
+ compress_dir = tempdir()
+)
+#> Finding 1 file already downloaded: 'aers_ascii_2004q1.zip'
+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"),
- 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)
+data2 <- faers(c(2004, 2017), c("q1", "q2"),
+ 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)
You can use faers_get() to get specific field data, a data.table will be returned.
-faers_get(data2, "demo")
-#> year quarter primaryid caseid i_f_code foll_seq image event_dt
-#> <int> <char> <char> <char> <char> <int> <char> <int>
-#> 1: 2004 q1 4263742 4061110 I NA 4263742-7 20031115
-#> 2: 2004 q1 4264028 4064419 I NA 4264028-7 20031127
-#> 3: 2004 q1 4265584 4057482 I NA 4265584-5 20031029
-#> 4: 2004 q1 4268593 4066346 I NA 4268593-5 20031009
-#> 5: 2004 q1 4268863 4066975 I NA 4268863-0 20031228
-#> ---
-#> 196: 2017 q2 136878411 13687841 I NA <NA> 201704
-#> 197: 2017 q2 136932671 13693267 I NA <NA> 2016
-#> 198: 2017 q2 136959401 13695940 I NA <NA> NA
-#> 199: 2017 q2 136970751 13697075 I NA <NA> 20170623
-#> 200: 2017 q2 93588412 9358841 F NA <NA> 20120407
-#> mfr_dt fda_dt rept_cod mfr_num
-#> <int> <int> <char> <char>
-#> 1: 20031218 20040102 EXP DSA_23619_2003
-#> 2: 20031216 20040102 EXP GBT031201111
-#> 3: NA 20040107 DIR <NA>
-#> 4: 20031225 20040108 EXP K200301940
-#> 5: 20031230 20040108 EXP 2003UW17317
-#> ---
-#> 196: 20170616 20170626 EXP US-AMGEN-USASL2017093163
-#> 197: 20170621 20170627 EXP CA-ABBVIE-17K-028-2017994-00
-#> 198: 20170616 20170628 PER US-AMGEN-USASP2017095323
-#> 199: 20170626 20170628 EXP US-ABBVIE-17K-163-2020858-00
-#> 200: 20170518 20170522 EXP CN-PFIZER INC-2013181479
-#> mfr_sndr age age_cod sex e_sub wt wt_cod
-#> <char> <num> <char> <char> <char> <num> <char>
-#> 1: BIOVAIL PHARMACEUTICALS INC. 42 YR F N NA <NA>
-#> 2: ELI LILLY AND COMPANY 43 YR F N 71 KG
-#> 3: <NA> 44 YR F N 152 LBS
-#> 4: KING PHARMACEUTICALS, INC. 75 YR M N NA <NA>
-#> 5: ASTRAZENECA PHARMACEUTICALS 72 YR F N 109 LBS
-#> ---
-#> 196: AMGEN 64 YR M Y NA <NA>
-#> 197: ABBVIE NA <NA> F Y NA <NA>
-#> 198: AMGEN NA <NA> <NA> Y NA <NA>
-#> 199: ABBVIE 71 YR F Y NA <NA>
-#> 200: PFIZER 16 YR M Y 40 KG
-#> rept_dt occp_cod death_dt to_mfr confid v23 caseversion age_in_years
-#> <int> <char> <lgcl> <char> <char> <lgcl> <int> <num>
-#> 1: 20031231 OT NA <NA> <NA> NA 0 42
-#> 2: 20031223 MD NA <NA> <NA> NA 0 43
-#> 3: 20040106 MD NA N N NA 0 44
-#> 4: 20040107 OT NA <NA> <NA> NA 0 75
-#> 5: 20040107 <NA> NA <NA> <NA> NA 0 72
-#> ---
-#> 196: 20170625 OT NA <NA> <NA> NA 1 64
-#> 197: 20170627 CN NA <NA> <NA> NA 1 NA
-#> 198: 20170627 MD NA <NA> <NA> NA 1 NA
-#> 199: 20170628 CN NA <NA> <NA> NA 1 71
-#> 200: 20170522 OT NA <NA> <NA> NA 2 16
-#> country_code gender init_fda_dt auth_num lit_ref age_grp reporter_country
-#> <char> <char> <int> <char> <char> <char> <char>
-#> 1: <NA> F NA <NA> <NA> <NA> <NA>
-#> 2: <NA> F NA <NA> <NA> <NA> <NA>
-#> 3: <NA> F NA <NA> <NA> <NA> <NA>
-#> 4: <NA> M NA <NA> <NA> <NA> <NA>
-#> 5: <NA> F NA <NA> <NA> <NA> <NA>
-#> ---
-#> 196: US M 20170626 <NA> <NA> A US
-#> 197: CA F 20170627 <NA> <NA> <NA> CA
-#> 198: US <NA> 20170628 <NA> <NA> <NA> US
-#> 199: US F 20170628 <NA> <NA> <NA> US
-#> 200: CN M 20130620 <NA> <NA> <NA> CN
-#> occr_country
-#> <char>
-#> 1: <NA>
-#> 2: <NA>
-#> 3: <NA>
-#> 4: <NA>
-#> 5: <NA>
-#> ---
-#> 196: US
-#> 197: CA
-#> 198: US
-#> 199: US
-#> 200: CN
-Standardize and De-duplication
+faers_get(data2, "demo")
+#> year quarter primaryid caseid i_f_code foll_seq image event_dt
+#> <int> <char> <char> <char> <char> <int> <char> <int>
+#> 1: 2004 q1 4263742 4061110 I NA 4263742-7 20031115
+#> 2: 2004 q1 4264028 4064419 I NA 4264028-7 20031127
+#> 3: 2004 q1 4265584 4057482 I NA 4265584-5 20031029
+#> 4: 2004 q1 4268593 4066346 I NA 4268593-5 20031009
+#> 5: 2004 q1 4268863 4066975 I NA 4268863-0 20031228
+#> ---
+#> 196: 2017 q2 136878411 13687841 I NA <NA> 201704
+#> 197: 2017 q2 136932671 13693267 I NA <NA> 2016
+#> 198: 2017 q2 136959401 13695940 I NA <NA> NA
+#> 199: 2017 q2 136970751 13697075 I NA <NA> 20170623
+#> 200: 2017 q2 93588412 9358841 F NA <NA> 20120407
+#> mfr_dt fda_dt rept_cod mfr_num
+#> <int> <int> <char> <char>
+#> 1: 20031218 20040102 EXP DSA_23619_2003
+#> 2: 20031216 20040102 EXP GBT031201111
+#> 3: NA 20040107 DIR <NA>
+#> 4: 20031225 20040108 EXP K200301940
+#> 5: 20031230 20040108 EXP 2003UW17317
+#> ---
+#> 196: 20170616 20170626 EXP US-AMGEN-USASL2017093163
+#> 197: 20170621 20170627 EXP CA-ABBVIE-17K-028-2017994-00
+#> 198: 20170616 20170628 PER US-AMGEN-USASP2017095323
+#> 199: 20170626 20170628 EXP US-ABBVIE-17K-163-2020858-00
+#> 200: 20170518 20170522 EXP CN-PFIZER INC-2013181479
+#> mfr_sndr age age_cod sex e_sub wt wt_cod
+#> <char> <num> <char> <char> <char> <num> <char>
+#> 1: BIOVAIL PHARMACEUTICALS INC. 42 YR F N NA <NA>
+#> 2: ELI LILLY AND COMPANY 43 YR F N 71 KG
+#> 3: <NA> 44 YR F N 152 LBS
+#> 4: KING PHARMACEUTICALS, INC. 75 YR M N NA <NA>
+#> 5: ASTRAZENECA PHARMACEUTICALS 72 YR F N 109 LBS
+#> ---
+#> 196: AMGEN 64 YR M Y NA <NA>
+#> 197: ABBVIE NA <NA> F Y NA <NA>
+#> 198: AMGEN NA <NA> <NA> Y NA <NA>
+#> 199: ABBVIE 71 YR F Y NA <NA>
+#> 200: PFIZER 16 YR M Y 40 KG
+#> rept_dt occp_cod death_dt to_mfr confid v23 caseversion age_in_years
+#> <int> <char> <lgcl> <char> <char> <lgcl> <int> <num>
+#> 1: 20031231 OT NA <NA> <NA> NA 0 42
+#> 2: 20031223 MD NA <NA> <NA> NA 0 43
+#> 3: 20040106 MD NA N N NA 0 44
+#> 4: 20040107 OT NA <NA> <NA> NA 0 75
+#> 5: 20040107 <NA> NA <NA> <NA> NA 0 72
+#> ---
+#> 196: 20170625 OT NA <NA> <NA> NA 1 64
+#> 197: 20170627 CN NA <NA> <NA> NA 1 NA
+#> 198: 20170627 MD NA <NA> <NA> NA 1 NA
+#> 199: 20170628 CN NA <NA> <NA> NA 1 71
+#> 200: 20170522 OT NA <NA> <NA> NA 2 16
+#> country_code gender init_fda_dt auth_num lit_ref age_grp reporter_country
+#> <char> <char> <int> <char> <char> <char> <char>
+#> 1: <NA> F NA <NA> <NA> <NA> <NA>
+#> 2: <NA> F NA <NA> <NA> <NA> <NA>
+#> 3: <NA> F NA <NA> <NA> <NA> <NA>
+#> 4: <NA> M NA <NA> <NA> <NA> <NA>
+#> 5: <NA> F NA <NA> <NA> <NA> <NA>
+#> ---
+#> 196: US M 20170626 <NA> <NA> A US
+#> 197: CA F 20170627 <NA> <NA> <NA> CA
+#> 198: US <NA> 20170628 <NA> <NA> <NA> US
+#> 199: US F 20170628 <NA> <NA> <NA> US
+#> 200: CN M 20130620 <NA> <NA> <NA> CN
+#> occr_country
+#> <char>
+#> 1: <NA>
+#> 2: <NA>
+#> 3: <NA>
+#> 4: <NA>
+#> 5: <NA>
+#> ---
+#> 196: US
+#> 197: CA
+#> 198: US
+#> 199: US
+#> 200: CN
+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.
-# you must replace `meddra_path` with the path of uncompressed meddra data
-data <- faers_standardize(data2, meddra_path)
+# you must replace `meddra_path` with the path of uncompressed meddra data
+data <- faers_standardize(data2, meddra_path)
To proceed following steps, we just read a standardized data.
-data <- readRDS(system.file("extdata", "standardized_data.rds",
- package = "faers"
-))
-data
-#> Standardized FAERS data from 2 Quarterly ascii files
-#> Total reports: 200 (with duplicates)
+data <- readRDS(system.file("extdata", "standardized_data.rds",
+ package = "faers"
+))
+data
+#> Standardized FAERS data from 2 Quarterly ascii files
+#> Total reports: 200 (with duplicates)
The internal will save the complete MedDRA data in the @meddra slot, MedDRA consists of two components: hierarchy and SMQ data. We can specify these components using the use argument.
-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
+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. Additionally, the columns meddra_hierarchy_from, meddra_code, and meddra_pt will also be added which provide standardized names of the original PT (indi: indi_pt; reac: pt) (refer to ASC_NTS.pdf or ASC_NTS.docx in the FAERS quarterly file for the meanings of the original names, most original names will remain unchanged except for some names different between FAERS quarterly files, see ?faers_parse for details). We can retrieve this data using the faers_meddra() function. When we use faers_get() to retrieve indi or reac data from the standardized FAERSascii object, the meddra hierarchy columns are automatically added to the returned data.table.
-faers_get(data, "indi")
-#> year quarter primaryid indi_drug_seq
-#> <int> <char> <char> <int>
-#> 1: 2004 q1 4264028 1004493847
-#> 2: 2004 q1 4264028 1004530015
-#> 3: 2004 q1 4264028 1004530020
-#> 4: 2004 q1 4264028 1004530025
-#> 5: 2004 q1 4265584 1004498166
-#> ---
-#> 352: 2017 q2 136932671 1
-#> 353: 2017 q2 136959401 1
-#> 354: 2017 q2 136970751 1
-#> 355: 2017 q2 93588412 1
-#> 356: 2017 q2 93588412 2
-#> indi_pt caseid meddra_hierarchy_from
-#> <char> <char> <char>
-#> 1: BREAST CANCER <NA> llt
-#> 2: BREAST CANCER <NA> llt
-#> 3: BREAST CANCER <NA> llt
-#> 4: BREAST CANCER <NA> llt
-#> 5: ATTENTION DEFICIT/HYPERACTIVITY DISORDER <NA> llt
-#> ---
-#> 352: Psoriatic arthropathy 13693267 llt
-#> 353: Product used for unknown indication 13695940 llt
-#> 354: Crohn's disease 13697075 llt
-#> 355: Anti-infective therapy 9358841 llt
-#> 356: Anti-infective therapy 9358841 llt
-#> meddra_code meddra_pt llt_code
-#> <char> <char> <int>
-#> 1: 10006187 Breast cancer 10006187
-#> 2: 10006187 Breast cancer 10006187
-#> 3: 10006187 Breast cancer 10006187
-#> 4: 10006187 Breast cancer 10006187
-#> 5: 10003736 Attention deficit/hyperactivity disorder 10003736
-#> ---
-#> 352: 10037162 Psoriatic arthropathy 10037162
-#> 353: 10070592 Product used for unknown indication 10070592
-#> 354: 10011401 Crohn's disease 10011401
-#> 355: 10058316 Anti-infective therapy 10058316
-#> 356: 10058316 Anti-infective therapy 10058316
-#> llt_name pt_code
-#> <char> <int>
-#> 1: Breast cancer 10006187
-#> 2: Breast cancer 10006187
-#> 3: Breast cancer 10006187
-#> 4: Breast cancer 10006187
-#> 5: Attention deficit/hyperactivity disorder 10083622
-#> ---
-#> 352: Psoriatic arthropathy 10037162
-#> 353: Product used for unknown indication 10070592
-#> 354: Crohn's disease 10011401
-#> 355: Anti-infective therapy 10058316
-#> 356: Anti-infective therapy 10058316
-#> pt_name hlt_code
-#> <char> <int>
-#> 1: Breast cancer 10006290
-#> 2: Breast cancer 10006290
-#> 3: Breast cancer 10006290
-#> 4: Breast cancer 10006290
-#> 5: Attention deficit hyperactivity disorder 10003730
-#> ---
-#> 352: Psoriatic arthropathy 10037163
-#> 353: Product used for unknown indication 10027700
-#> 354: Crohn's disease 10009888
-#> 355: Anti-infective therapy 10002790
-#> 356: Anti-infective therapy 10002790
-#> hlt_name hlgt_code
-#> <char> <int>
-#> 1: Breast and nipple neoplasms malignant 10006291
-#> 2: Breast and nipple neoplasms malignant 10006291
-#> 3: Breast and nipple neoplasms malignant 10006291
-#> 4: Breast and nipple neoplasms malignant 10006291
-#> 5: Attention deficit and disruptive behaviour disorders 10009841
-#> ---
-#> 352: Psoriatic arthropathies 10023213
-#> 353: Therapeutic procedures NEC 10043413
-#> 354: Colitis (excl infective) 10017969
-#> 355: Antiinfective therapies 10043413
-#> 356: Antiinfective therapies 10043413
-#> hlgt_name soc_code
-#> <char> <int>
-#> 1: Breast neoplasms malignant and unspecified (incl nipple) 10029104
-#> 2: Breast neoplasms malignant and unspecified (incl nipple) 10029104
-#> 3: Breast neoplasms malignant and unspecified (incl nipple) 10029104
-#> 4: Breast neoplasms malignant and unspecified (incl nipple) 10029104
-#> 5: Cognitive and attention disorders and disturbances 10037175
-#> ---
-#> 352: Joint disorders 10028395
-#> 353: Therapeutic procedures and supportive care NEC 10042613
-#> 354: Gastrointestinal inflammatory conditions 10017947
-#> 355: Therapeutic procedures and supportive care NEC 10042613
-#> 356: Therapeutic procedures and supportive care NEC 10042613
-#> soc_name
-#> <char>
-#> 1: Neoplasms benign, malignant and unspecified (incl cysts and polyps)
-#> 2: Neoplasms benign, malignant and unspecified (incl cysts and polyps)
-#> 3: Neoplasms benign, malignant and unspecified (incl cysts and polyps)
-#> 4: Neoplasms benign, malignant and unspecified (incl cysts and polyps)
-#> 5: Psychiatric disorders
-#> ---
-#> 352: Musculoskeletal and connective tissue disorders
-#> 353: Surgical and medical procedures
-#> 354: Gastrointestinal disorders
-#> 355: Surgical and medical procedures
-#> 356: Surgical and medical procedures
-#> soc_abbrev primary_soc_fg
-#> <char> <char>
-#> 1: Neopl Y
-#> 2: Neopl Y
-#> 3: Neopl Y
-#> 4: Neopl Y
-#> 5: Psych Y
-#> ---
-#> 352: Musc Y
-#> 353: Surg Y
-#> 354: Gastr Y
-#> 355: Surg Y
-#> 356: Surg Y
-faers_get(data, "reac")
-#> year quarter primaryid pt v3 caseid
-#> <int> <char> <char> <char> <lgcl> <char>
-#> 1: 2004 q1 4263742 DIARRHOEA NA <NA>
-#> 2: 2004 q1 4263742 INTENTIONAL OVERDOSE NA <NA>
-#> 3: 2004 q1 4263742 MYDRIASIS NA <NA>
-#> 4: 2004 q1 4263742 NAUSEA NA <NA>
-#> 5: 2004 q1 4263742 PLATELET COUNT INCREASED NA <NA>
-#> ---
-#> 698: 2017 q2 136959401 Injection site reaction NA 13695940
-#> 699: 2017 q2 136970751 Intestinal obstruction NA 13697075
-#> 700: 2017 q2 93588412 Generalised tonic-clonic seizure NA 9358841
-#> 701: 2017 q2 93588412 Petit mal epilepsy NA 9358841
-#> 702: 2017 q2 93588412 Tic NA 9358841
-#> drug_rec_act meddra_hierarchy_from meddra_code
-#> <lgcl> <char> <char>
-#> 1: NA llt 10012735
-#> 2: NA llt 10022523
-#> 3: NA llt 10028521
-#> 4: NA llt 10028813
-#> 5: NA llt 10051608
-#> ---
-#> 698: NA llt 10022095
-#> 699: NA llt 10022687
-#> 700: NA llt 10018100
-#> 701: NA llt 10034759
-#> 702: NA llt 10043833
-#> meddra_pt llt_code llt_name
-#> <char> <int> <char>
-#> 1: Diarrhoea 10012735 Diarrhoea
-#> 2: Intentional overdose 10022523 Intentional overdose
-#> 3: Mydriasis 10028521 Mydriasis
-#> 4: Nausea 10028813 Nausea
-#> 5: Platelet count increased 10051608 Platelet count increased
-#> ---
-#> 698: Injection site reaction 10022095 Injection site reaction
-#> 699: Intestinal obstruction 10022687 Intestinal obstruction
-#> 700: Generalised tonic-clonic seizure 10018100 Generalised tonic-clonic seizure
-#> 701: Petit mal epilepsy 10034759 Petit mal epilepsy
-#> 702: Tic 10043833 Tic
-#> pt_code pt_name hlt_code
-#> <int> <char> <int>
-#> 1: 10012735 Diarrhoea 10012736
-#> 2: 10022523 Intentional overdose 10076292
-#> 3: 10028521 Mydriasis 10037514
-#> 4: 10028813 Nausea 10028817
-#> 5: 10051608 Platelet count increased 10035523
-#> ---
-#> 698: 10022095 Injection site reaction 10022097
-#> 699: 10022687 Intestinal obstruction 10018009
-#> 700: 10018100 Generalised tonic-clonic seizure 10018101
-#> 701: 10034759 Petit mal epilepsy 10000332
-#> 702: 10043833 Tic 10043835
-#> hlt_name hlgt_code
-#> <char> <int>
-#> 1: Diarrhoea (excl infective) 10017977
-#> 2: Overdoses NEC 10079159
-#> 3: Pupil disorders 10030061
-#> 4: Nausea and vomiting symptoms 10018012
-#> 5: Platelet analyses 10018851
-#> ---
-#> 698: Injection site reactions 10001316
-#> 699: Gastrointestinal stenosis and obstruction NEC 10018008
-#> 700: Generalised tonic-clonic seizures 10039911
-#> 701: Absence seizures 10039911
-#> 702: Tic disorders 10008401
-#> hlgt_name soc_code
-#> <char> <int>
-#> 1: Gastrointestinal motility and defaecation conditions 10017947
-#> 2: Overdoses and underdoses NEC 10022117
-#> 3: Ocular neuromuscular disorders 10015919
-#> 4: Gastrointestinal signs and symptoms 10017947
-#> 5: Haematology investigations (incl blood groups) 10022891
-#> ---
-#> 698: Administration site reactions 10018065
-#> 699: Gastrointestinal stenosis and obstruction 10017947
-#> 700: Seizures (incl subtypes) 10029205
-#> 701: Seizures (incl subtypes) 10029205
-#> 702: Changes in physical activity 10037175
-#> soc_name soc_abbrev
-#> <char> <char>
-#> 1: Gastrointestinal disorders Gastr
-#> 2: Injury, poisoning and procedural complications Inj&P
-#> 3: Eye disorders Eye
-#> 4: Gastrointestinal disorders Gastr
-#> 5: Investigations Inv
-#> ---
-#> 698: General disorders and administration site conditions Genrl
-#> 699: Gastrointestinal disorders Gastr
-#> 700: Nervous system disorders Nerv
-#> 701: Nervous system disorders Nerv
-#> 702: Psychiatric disorders Psych
-#> primary_soc_fg
-#> <char>
-#> 1: Y
-#> 2: Y
-#> 3: Y
-#> 4: Y
-#> 5: Y
-#> ---
-#> 698: Y
-#> 699: Y
-#> 700: Y
-#> 701: Y
-#> 702: Y
+faers_get(data, "indi")
+#> year quarter primaryid indi_drug_seq
+#> <int> <char> <char> <int>
+#> 1: 2004 q1 4264028 1004493847
+#> 2: 2004 q1 4264028 1004530015
+#> 3: 2004 q1 4264028 1004530020
+#> 4: 2004 q1 4264028 1004530025
+#> 5: 2004 q1 4265584 1004498166
+#> ---
+#> 352: 2017 q2 136932671 1
+#> 353: 2017 q2 136959401 1
+#> 354: 2017 q2 136970751 1
+#> 355: 2017 q2 93588412 1
+#> 356: 2017 q2 93588412 2
+#> indi_pt caseid meddra_hierarchy_from
+#> <char> <char> <char>
+#> 1: BREAST CANCER <NA> llt
+#> 2: BREAST CANCER <NA> llt
+#> 3: BREAST CANCER <NA> llt
+#> 4: BREAST CANCER <NA> llt
+#> 5: ATTENTION DEFICIT/HYPERACTIVITY DISORDER <NA> llt
+#> ---
+#> 352: Psoriatic arthropathy 13693267 llt
+#> 353: Product used for unknown indication 13695940 llt
+#> 354: Crohn's disease 13697075 llt
+#> 355: Anti-infective therapy 9358841 llt
+#> 356: Anti-infective therapy 9358841 llt
+#> meddra_code meddra_pt llt_code
+#> <char> <char> <int>
+#> 1: 10006187 Breast cancer 10006187
+#> 2: 10006187 Breast cancer 10006187
+#> 3: 10006187 Breast cancer 10006187
+#> 4: 10006187 Breast cancer 10006187
+#> 5: 10003736 Attention deficit/hyperactivity disorder 10003736
+#> ---
+#> 352: 10037162 Psoriatic arthropathy 10037162
+#> 353: 10070592 Product used for unknown indication 10070592
+#> 354: 10011401 Crohn's disease 10011401
+#> 355: 10058316 Anti-infective therapy 10058316
+#> 356: 10058316 Anti-infective therapy 10058316
+#> llt_name pt_code
+#> <char> <int>
+#> 1: Breast cancer 10006187
+#> 2: Breast cancer 10006187
+#> 3: Breast cancer 10006187
+#> 4: Breast cancer 10006187
+#> 5: Attention deficit/hyperactivity disorder 10083622
+#> ---
+#> 352: Psoriatic arthropathy 10037162
+#> 353: Product used for unknown indication 10070592
+#> 354: Crohn's disease 10011401
+#> 355: Anti-infective therapy 10058316
+#> 356: Anti-infective therapy 10058316
+#> pt_name hlt_code
+#> <char> <int>
+#> 1: Breast cancer 10006290
+#> 2: Breast cancer 10006290
+#> 3: Breast cancer 10006290
+#> 4: Breast cancer 10006290
+#> 5: Attention deficit hyperactivity disorder 10003730
+#> ---
+#> 352: Psoriatic arthropathy 10037163
+#> 353: Product used for unknown indication 10027700
+#> 354: Crohn's disease 10009888
+#> 355: Anti-infective therapy 10002790
+#> 356: Anti-infective therapy 10002790
+#> hlt_name hlgt_code
+#> <char> <int>
+#> 1: Breast and nipple neoplasms malignant 10006291
+#> 2: Breast and nipple neoplasms malignant 10006291
+#> 3: Breast and nipple neoplasms malignant 10006291
+#> 4: Breast and nipple neoplasms malignant 10006291
+#> 5: Attention deficit and disruptive behaviour disorders 10009841
+#> ---
+#> 352: Psoriatic arthropathies 10023213
+#> 353: Therapeutic procedures NEC 10043413
+#> 354: Colitis (excl infective) 10017969
+#> 355: Antiinfective therapies 10043413
+#> 356: Antiinfective therapies 10043413
+#> hlgt_name soc_code
+#> <char> <int>
+#> 1: Breast neoplasms malignant and unspecified (incl nipple) 10029104
+#> 2: Breast neoplasms malignant and unspecified (incl nipple) 10029104
+#> 3: Breast neoplasms malignant and unspecified (incl nipple) 10029104
+#> 4: Breast neoplasms malignant and unspecified (incl nipple) 10029104
+#> 5: Cognitive and attention disorders and disturbances 10037175
+#> ---
+#> 352: Joint disorders 10028395
+#> 353: Therapeutic procedures and supportive care NEC 10042613
+#> 354: Gastrointestinal inflammatory conditions 10017947
+#> 355: Therapeutic procedures and supportive care NEC 10042613
+#> 356: Therapeutic procedures and supportive care NEC 10042613
+#> soc_name
+#> <char>
+#> 1: Neoplasms benign, malignant and unspecified (incl cysts and polyps)
+#> 2: Neoplasms benign, malignant and unspecified (incl cysts and polyps)
+#> 3: Neoplasms benign, malignant and unspecified (incl cysts and polyps)
+#> 4: Neoplasms benign, malignant and unspecified (incl cysts and polyps)
+#> 5: Psychiatric disorders
+#> ---
+#> 352: Musculoskeletal and connective tissue disorders
+#> 353: Surgical and medical procedures
+#> 354: Gastrointestinal disorders
+#> 355: Surgical and medical procedures
+#> 356: Surgical and medical procedures
+#> soc_abbrev primary_soc_fg
+#> <char> <char>
+#> 1: Neopl Y
+#> 2: Neopl Y
+#> 3: Neopl Y
+#> 4: Neopl Y
+#> 5: Psych Y
+#> ---
+#> 352: Musc Y
+#> 353: Surg Y
+#> 354: Gastr Y
+#> 355: Surg Y
+#> 356: Surg Y
+faers_get(data, "reac")
+#> year quarter primaryid pt v3 caseid
+#> <int> <char> <char> <char> <lgcl> <char>
+#> 1: 2004 q1 4263742 DIARRHOEA NA <NA>
+#> 2: 2004 q1 4263742 INTENTIONAL OVERDOSE NA <NA>
+#> 3: 2004 q1 4263742 MYDRIASIS NA <NA>
+#> 4: 2004 q1 4263742 NAUSEA NA <NA>
+#> 5: 2004 q1 4263742 PLATELET COUNT INCREASED NA <NA>
+#> ---
+#> 698: 2017 q2 136959401 Injection site reaction NA 13695940
+#> 699: 2017 q2 136970751 Intestinal obstruction NA 13697075
+#> 700: 2017 q2 93588412 Generalised tonic-clonic seizure NA 9358841
+#> 701: 2017 q2 93588412 Petit mal epilepsy NA 9358841
+#> 702: 2017 q2 93588412 Tic NA 9358841
+#> drug_rec_act meddra_hierarchy_from meddra_code
+#> <lgcl> <char> <char>
+#> 1: NA llt 10012735
+#> 2: NA llt 10022523
+#> 3: NA llt 10028521
+#> 4: NA llt 10028813
+#> 5: NA llt 10051608
+#> ---
+#> 698: NA llt 10022095
+#> 699: NA llt 10022687
+#> 700: NA llt 10018100
+#> 701: NA llt 10034759
+#> 702: NA llt 10043833
+#> meddra_pt llt_code llt_name
+#> <char> <int> <char>
+#> 1: Diarrhoea 10012735 Diarrhoea
+#> 2: Intentional overdose 10022523 Intentional overdose
+#> 3: Mydriasis 10028521 Mydriasis
+#> 4: Nausea 10028813 Nausea
+#> 5: Platelet count increased 10051608 Platelet count increased
+#> ---
+#> 698: Injection site reaction 10022095 Injection site reaction
+#> 699: Intestinal obstruction 10022687 Intestinal obstruction
+#> 700: Generalised tonic-clonic seizure 10018100 Generalised tonic-clonic seizure
+#> 701: Petit mal epilepsy 10034759 Petit mal epilepsy
+#> 702: Tic 10043833 Tic
+#> pt_code pt_name hlt_code
+#> <int> <char> <int>
+#> 1: 10012735 Diarrhoea 10012736
+#> 2: 10022523 Intentional overdose 10076292
+#> 3: 10028521 Mydriasis 10037514
+#> 4: 10028813 Nausea 10028817
+#> 5: 10051608 Platelet count increased 10035523
+#> ---
+#> 698: 10022095 Injection site reaction 10022097
+#> 699: 10022687 Intestinal obstruction 10018009
+#> 700: 10018100 Generalised tonic-clonic seizure 10018101
+#> 701: 10034759 Petit mal epilepsy 10000332
+#> 702: 10043833 Tic 10043835
+#> hlt_name hlgt_code
+#> <char> <int>
+#> 1: Diarrhoea (excl infective) 10017977
+#> 2: Overdoses NEC 10079159
+#> 3: Pupil disorders 10030061
+#> 4: Nausea and vomiting symptoms 10018012
+#> 5: Platelet analyses 10018851
+#> ---
+#> 698: Injection site reactions 10001316
+#> 699: Gastrointestinal stenosis and obstruction NEC 10018008
+#> 700: Generalised tonic-clonic seizures 10039911
+#> 701: Absence seizures 10039911
+#> 702: Tic disorders 10008401
+#> hlgt_name soc_code
+#> <char> <int>
+#> 1: Gastrointestinal motility and defaecation conditions 10017947
+#> 2: Overdoses and underdoses NEC 10022117
+#> 3: Ocular neuromuscular disorders 10015919
+#> 4: Gastrointestinal signs and symptoms 10017947
+#> 5: Haematology investigations (incl blood groups) 10022891
+#> ---
+#> 698: Administration site reactions 10018065
+#> 699: Gastrointestinal stenosis and obstruction 10017947
+#> 700: Seizures (incl subtypes) 10029205
+#> 701: Seizures (incl subtypes) 10029205
+#> 702: Changes in physical activity 10037175
+#> soc_name soc_abbrev
+#> <char> <char>
+#> 1: Gastrointestinal disorders Gastr
+#> 2: Injury, poisoning and procedural complications Inj&P
+#> 3: Eye disorders Eye
+#> 4: Gastrointestinal disorders Gastr
+#> 5: Investigations Inv
+#> ---
+#> 698: General disorders and administration site conditions Genrl
+#> 699: Gastrointestinal disorders Gastr
+#> 700: Nervous system disorders Nerv
+#> 701: Nervous system disorders Nerv
+#> 702: Psychiatric disorders Psych
+#> primary_soc_fg
+#> <char>
+#> 1: Y
+#> 2: Y
+#> 3: Y
+#> 4: Y
+#> 5: Y
+#> ---
+#> 698: Y
+#> 699: Y
+#> 700: Y
+#> 701: Y
+#> 702: Y
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.
-data <- faers_dedup(data)
-#> → deduplication from the same source by retain the most recent report
-#> → merging `drug`, `indi`, `ther`, and `reac` data
-#> → deduplication from multiple sources by matching gender, age, reporting country, event date, start date, drug indications, drugs administered, and adverse reactions
-data
-#> Standardized and De-duplicated FAERS data from 2 Quarterly ascii files
-#> Total unique reports: 200
-Pharmacovigilance analysis
+data <- faers_dedup(data)
+#> → deduplication from the same source by retain the most recent report
+#> → merging `drug`, `indi`, `ther`, and `reac` data
+#> → deduplication from multiple sources by matching gender, age, reporting country, event date, start date, drug indications, drugs administered, and adverse reactions
+data
+#> Standardized and De-duplicated FAERS data from 2 Quarterly ascii files
+#> Total unique reports: 200
+Pharmacovigilance analysis
Pharmacovigilance is the science and activities relating to the detection, assessment, understanding and prevention of adverse effects or any other medicine/vaccine related problem.
To mine the signals of “insulin”, we start by using the faers_filter() function. In this function, the .fn argument should be a function that accepts data specified in .field. It is important to note that .fn should always return the primaryid that you want to keep.
To enhance our analysis, it would be advantageous to include all drug synonym names for insulin. These synonyms can be obtained by querying sources such as https://go.drugbank.com/ or alternative databases. Furthermore, we extract the brand names of insulin from the Drugs@FDA dataset, which can be easily obtained using the fda_drugs() function.
-insulin_pattern <- "insulin"
-insulin_pattern <- paste(insulin_pattern, collapse = "|")
-fda_insulin <- fda_drugs()[
- grepl(insulin_pattern, ActiveIngredient, ignore.case = TRUE)
-]
-#> → Using Drugs@FDA data from cached
-#> '/home/yun/.cache/R/faers/fdadrugs/fda_drugs_data_2023-12-16.zip'
-#> Snapshot date: 2023-12-16
-#> Warning: One or more parsing issues, call `problems()` on your data frame for details,
-#> e.g.:
-#> dat <- vroom(...)
-#> problems(dat)
-insulin_pattern <- paste0(
- unique(tolower(c(insulin_pattern, fda_insulin$DrugName))),
- collapse = "|"
-)
-insulin_data <- faers_filter(data, .fn = function(x) {
- idx <- grepl(insulin_pattern, x$drugname, ignore.case = TRUE) |
- grepl(insulin_pattern, x$prod_ai, ignore.case = TRUE)
- x[idx, primaryid]
-}, .field = "drug")
-insulin_data
-#> Standardized and De-duplicated FAERS data from 2 Quarterly ascii files
-#> Total unique reports: 3
+insulin_pattern <- "insulin"
+insulin_pattern <- paste(insulin_pattern, collapse = "|")
+fda_insulin <- fda_drugs()[
+ grepl(insulin_pattern, ActiveIngredient, ignore.case = TRUE)
+]
+#> → Using Drugs@FDA data from cached
+#> '/home/yun/.cache/R/faers/fdadrugs/fda_drugs_data_2024-01-13.zip'
+#> Snapshot date: 2024-01-13
+#> Warning: One or more parsing issues, call `problems()` on your data frame for details,
+#> e.g.:
+#> dat <- vroom(...)
+#> problems(dat)
+insulin_pattern <- paste0(
+ unique(tolower(c(insulin_pattern, fda_insulin$DrugName))),
+ collapse = "|"
+)
+insulin_data <- faers_filter(data, .fn = function(x) {
+ idx <- grepl(insulin_pattern, x$drugname, ignore.case = TRUE) |
+ grepl(insulin_pattern, x$prod_ai, ignore.case = TRUE)
+ x[idx, primaryid]
+}, .field = "drug")
+insulin_data
+#> Standardized and De-duplicated FAERS data from 2 Quarterly ascii files
+#> Total unique reports: 3
Then, signal can be easily obtained with faers_phv_signal() which internally use faers_phv_table() to create a contingency table and use phv_signal() to do signal analysis specified in .methods argument. By default, all supported signal analysis methods will be run, including “ror”, “prr”, “chisq”, “bcpnn_norm”, “bcpnn_mcmc”, “obsexp_shrink”, “fisher”, and “ebgm”.
The most important argument for this function is .object, which should be a de-duplicated FAERSascii object containing the data for the drugs or traits of interest. Additionally, you must specify either .full, which represents the background distributions data (usually the entire FAERS data), or you can specify .object2, which should be the control data or another drug of interest for comparison.
-insulin_signals <- faers_phv_signal(insulin_data, .full = data)
-insulin_signals
-#> Key: <soc_name>
-#> soc_name a
-#> <char> <int>
-#> 1: Blood and lymphatic system disorders 0
-#> 2: Cardiac disorders 1
-#> 3: Congenital, familial and genetic disorders 0
-#> 4: Ear and labyrinth disorders 0
-#> 5: Endocrine disorders 0
-#> 6: Eye disorders 1
-#> 7: Gastrointestinal disorders 1
-#> 8: General disorders and administration site conditions 1
-#> 9: Hepatobiliary disorders 0
-#> 10: Immune system disorders 0
-#> 11: Infections and infestations 2
-#> 12: Injury, poisoning and procedural complications 1
-#> 13: Investigations 2
-#> 14: Metabolism and nutrition disorders 2
-#> 15: Musculoskeletal and connective tissue disorders 0
-#> b c d expected ror ror_ci_low ror_ci_high prr
-#> <int> <int> <int> <num> <num> <num> <num> <num>
-#> 1: 3 14 183 0.210 0.0000000 0.00000000 NaN 0.0000000
-#> 2: 2 7 190 0.120 13.5714286 1.09612571 168.031524 9.3809524
-#> 3: 3 1 196 0.015 0.0000000 0.00000000 NaN 0.0000000
-#> 4: 3 4 193 0.060 0.0000000 0.00000000 NaN 0.0000000
-#> 5: 3 1 196 0.015 0.0000000 0.00000000 NaN 0.0000000
-#> 6: 2 9 188 0.150 10.4444444 0.86432480 126.209985 7.2962963
-#> 7: 2 33 164 0.510 2.4848485 0.21888790 28.208376 1.9898990
-#> 8: 2 79 118 1.200 0.7468354 0.06658895 8.376212 0.8312236
-#> 9: 3 9 188 0.135 0.0000000 0.00000000 NaN 0.0000000
-#> 10: 3 4 193 0.060 0.0000000 0.00000000 NaN 0.0000000
-#> 11: 1 30 167 0.480 11.1333333 0.97846354 126.679335 4.3777778
-#> 12: 2 30 167 0.465 2.7833333 0.24461589 31.669834 2.1888889
-#> 13: 1 30 167 0.480 11.1333333 0.97846354 126.679335 4.3777778
-#> 14: 1 10 187 0.180 37.4000000 3.12161662 448.088336 13.1333333
-#> 15: 3 19 178 0.285 0.0000000 0.00000000 NaN 0.0000000
-#> prr_ci_low prr_ci_high chisq chisq_pvalue bcpnn_norm_ic
-#> <num> <num> <num> <num> <num>
-#> 1: 0.0000000 NaN 4.096414e-31 1.000000000 -0.97458175
-#> 2: 1.6173190 54.412435 1.272561e+00 0.259286856 0.63833534
-#> 3: 0.0000000 NaN 1.265951e-26 1.000000000 -0.31739140
-#> 4: 0.0000000 NaN 2.866117e-32 1.000000000 -0.63762418
-#> 5: 0.0000000 NaN 1.265951e-26 1.000000000 -0.31739140
-#> 6: 1.3027676 40.863727 8.727402e-01 0.350197814 0.57607008
-#> 7: 0.3897628 10.159250 6.459270e-31 1.000000000 0.05900067
-#> 8: 0.1662546 4.155871 1.762340e-31 1.000000000 -0.57013768
-#> 9: 0.0000000 NaN 6.503567e-28 1.000000000 -0.83645056
-#> 10: 0.0000000 NaN 2.866117e-32 1.000000000 -0.63762418
-#> 11: 1.8426662 10.400656 2.619652e+00 0.105547591 0.81550390
-#> 12: 0.4272128 11.215100 3.165120e-03 0.955135161 0.11209704
-#> 13: 1.8426662 10.400656 2.619652e+00 0.105547591 0.81550390
-#> 14: 4.8197010 35.787374 1.045469e+01 0.001223383 1.24133970
-#> 15: 0.0000000 NaN 4.555566e-29 1.000000000 -1.09198678
-#> bcpnn_norm_ic_ci_low bcpnn_norm_ic_ci_high bcpnn_mcmc_ic
-#> <num> <num> <num>
-#> 1: -4.960069 3.010906 -0.50449401
-#> 2: -2.239177 3.515848 1.27660894
-#> 3: -4.844759 4.209977 -0.03947607
-#> 4: -4.773808 3.498560 -0.16092798
-#> 5: -4.844759 4.209977 -0.03947607
-#> 6: -2.270036 3.422176 1.20821022
-#> 7: -2.690902 2.808903 0.57112278
-#> 8: -3.294337 2.154062 -0.18051848
-#> 9: -4.858428 3.185527 -0.34296004
-#> 10: -4.773808 3.498560 -0.16092798
-#> 11: -1.546257 3.177265 1.35163975
-#> 12: -2.641970 2.866165 0.63695385
-#> 13: -1.546257 3.177265 1.35163975
-#> 14: -1.203821 3.686501 1.87988617
-#> 15: -5.059438 2.875465 -0.64969772
-#> bcpnn_mcmc_ic_ci_low bcpnn_mcmc_ic_ci_high oe_ratio oe_ratio_ci_low
-#> <num> <num> <num> <num>
-#> 1: -10.3317489 1.7283623 -0.50589093 -10.3237654
-#> 2: -2.3407886 2.7726499 1.27462238 -2.5084784
-#> 3: -10.0061093 2.2571416 -0.04264434 -9.9756850
-#> 4: -9.9713561 2.1185831 -0.16349873 -10.1277161
-#> 5: -9.9641434 2.2527566 -0.04264434 -9.9882612
-#> 6: -2.3672567 2.6862853 1.20645088 -2.5766499
-#> 7: -2.8497824 1.9008600 0.57060721 -3.2124936
-#> 8: -3.4967615 0.9876046 -0.18057225 -3.9636731
-#> 9: -10.0901076 1.9077602 -0.34482850 -10.1872240
-#> 10: -10.0098865 2.1076118 -0.16349873 -10.0083530
-#> 11: -0.7573926 2.3128579 1.35107444 -1.2419932
-#> 12: -2.8328941 1.9837945 0.63636165 -3.1467392
-#> 13: -0.7555282 2.3084890 1.35107444 -1.2419932
-#> 14: -0.4210446 3.0214754 1.87832144 -0.7147462
-#> 15: -10.4857578 1.5524149 -0.65076456 -10.5334635
-#> oe_ratio_ci_high odds_ratio odds_ratio_ci_low odds_ratio_ci_high
-#> <num> <num> <num> <num>
-#> 1: 1.734787 0.0000000 0.00000000 33.68585
-#> 2: 2.962049 13.0303800 0.20150028 279.21542
-#> 3: 2.259942 0.0000000 0.00000000 2462.50000
-#> 4: 2.108052 0.0000000 0.00000000 145.21133
-#> 5: 2.257014 0.0000000 0.00000000 2462.50000
-#> 6: 2.893877 10.1233187 0.15947006 211.87117
-#> 7: 2.258033 2.4701675 0.04089140 48.73410
-#> 8: 1.506854 0.7478897 0.01250834 14.59249
-#> 9: 1.901575 0.0000000 0.00000000 55.53664
-#> 10: 2.130614 0.0000000 0.00000000 145.21133
-#> 11: 2.742477 10.9151800 0.55237709 657.45882
-#> 12: 2.323788 2.7642969 0.04567010 54.61951
-#> 13: 2.742477 10.9151800 0.55237709 657.45882
-#> 14: 3.269724 35.2158110 1.70522393 2176.34560
-#> 15: 1.577846 0.0000000 0.00000000 23.77817
-#> fisher_pvalue ebgm ebgm_ci_low ebgm_ci_high
-#> <num> <num> <num> <num>
-#> 1: 1.00000000 2.421502 2.38 2.46
-#> 2: 0.11582153 2.421743 2.38 2.46
-#> 3: 1.00000000 2.421595 2.38 2.46
-#> 4: 1.00000000 2.421574 2.38 2.46
-#> 5: 1.00000000 2.421595 2.38 2.46
-#> 6: 0.14330745 2.421729 2.38 2.46
-#> 7: 0.42998325 2.421556 2.38 2.46
-#> 8: 1.00000000 2.421225 2.38 2.46
-#> 9: 1.00000000 2.421538 2.38 2.46
-#> 10: 1.00000000 2.421574 2.38 2.46
-#> 11: 0.06722095 2.421769 2.38 2.46
-#> 12: 0.39832191 2.421578 2.38 2.46
-#> 13: 0.06722095 2.421769 2.38 2.46
-#> 14: 0.00961474 2.421913 2.38 2.46
-#> 15: 1.00000000 2.421466 2.38 2.46
-#> [ reached getOption("max.print") -- omitted 12 rows ]
+set.seed(1L)
+insulin_signals <- faers_phv_signal(insulin_data, .full = data)
+insulin_signals
+#> Key: <soc_name>
+#> soc_name a
+#> <char> <int>
+#> 1: Blood and lymphatic system disorders 0
+#> 2: Cardiac disorders 1
+#> 3: Congenital, familial and genetic disorders 0
+#> 4: Ear and labyrinth disorders 0
+#> 5: Endocrine disorders 0
+#> 6: Eye disorders 1
+#> 7: Gastrointestinal disorders 1
+#> 8: General disorders and administration site conditions 1
+#> 9: Hepatobiliary disorders 0
+#> 10: Immune system disorders 0
+#> 11: Infections and infestations 2
+#> 12: Injury, poisoning and procedural complications 1
+#> 13: Investigations 2
+#> 14: Metabolism and nutrition disorders 2
+#> 15: Musculoskeletal and connective tissue disorders 0
+#> b c d expected ror ror_ci_low ror_ci_high prr
+#> <int> <int> <int> <num> <num> <num> <num> <num>
+#> 1: 3 14 183 0.210 0.0000000 0.00000000 NaN 0.0000000
+#> 2: 2 7 190 0.120 13.5714286 1.09612571 168.031524 9.3809524
+#> 3: 3 1 196 0.015 0.0000000 0.00000000 NaN 0.0000000
+#> 4: 3 4 193 0.060 0.0000000 0.00000000 NaN 0.0000000
+#> 5: 3 1 196 0.015 0.0000000 0.00000000 NaN 0.0000000
+#> 6: 2 9 188 0.150 10.4444444 0.86432480 126.209985 7.2962963
+#> 7: 2 33 164 0.510 2.4848485 0.21888790 28.208376 1.9898990
+#> 8: 2 79 118 1.200 0.7468354 0.06658895 8.376212 0.8312236
+#> 9: 3 9 188 0.135 0.0000000 0.00000000 NaN 0.0000000
+#> 10: 3 4 193 0.060 0.0000000 0.00000000 NaN 0.0000000
+#> 11: 1 30 167 0.480 11.1333333 0.97846354 126.679335 4.3777778
+#> 12: 2 30 167 0.465 2.7833333 0.24461589 31.669834 2.1888889
+#> 13: 1 30 167 0.480 11.1333333 0.97846354 126.679335 4.3777778
+#> 14: 1 10 187 0.180 37.4000000 3.12161662 448.088336 13.1333333
+#> 15: 3 19 178 0.285 0.0000000 0.00000000 NaN 0.0000000
+#> prr_ci_low prr_ci_high chisq chisq_pvalue bcpnn_norm_ic
+#> <num> <num> <num> <num> <num>
+#> 1: 0.0000000 NaN 4.096414e-31 1.000000000 -0.97458175
+#> 2: 1.6173190 54.412435 1.272561e+00 0.259286856 0.63833534
+#> 3: 0.0000000 NaN 1.265951e-26 1.000000000 -0.31739140
+#> 4: 0.0000000 NaN 2.866117e-32 1.000000000 -0.63762418
+#> 5: 0.0000000 NaN 1.265951e-26 1.000000000 -0.31739140
+#> 6: 1.3027676 40.863727 8.727402e-01 0.350197814 0.57607008
+#> 7: 0.3897628 10.159250 6.459270e-31 1.000000000 0.05900067
+#> 8: 0.1662546 4.155871 1.762340e-31 1.000000000 -0.57013768
+#> 9: 0.0000000 NaN 6.503567e-28 1.000000000 -0.83645056
+#> 10: 0.0000000 NaN 2.866117e-32 1.000000000 -0.63762418
+#> 11: 1.8426662 10.400656 2.619652e+00 0.105547591 0.81550390
+#> 12: 0.4272128 11.215100 3.165120e-03 0.955135161 0.11209704
+#> 13: 1.8426662 10.400656 2.619652e+00 0.105547591 0.81550390
+#> 14: 4.8197010 35.787374 1.045469e+01 0.001223383 1.24133970
+#> 15: 0.0000000 NaN 4.555566e-29 1.000000000 -1.09198678
+#> bcpnn_norm_ic_ci_low bcpnn_norm_ic_ci_high bcpnn_mcmc_ic
+#> <num> <num> <num>
+#> 1: -4.960069 3.010906 -0.50449401
+#> 2: -2.239177 3.515848 1.27660894
+#> 3: -4.844759 4.209977 -0.03947607
+#> 4: -4.773808 3.498560 -0.16092798
+#> 5: -4.844759 4.209977 -0.03947607
+#> 6: -2.270036 3.422176 1.20821022
+#> 7: -2.690902 2.808903 0.57112278
+#> 8: -3.294337 2.154062 -0.18051848
+#> 9: -4.858428 3.185527 -0.34296004
+#> 10: -4.773808 3.498560 -0.16092798
+#> 11: -1.546257 3.177265 1.35163975
+#> 12: -2.641970 2.866165 0.63695385
+#> 13: -1.546257 3.177265 1.35163975
+#> 14: -1.203821 3.686501 1.87988617
+#> 15: -5.059438 2.875465 -0.64969772
+#> bcpnn_mcmc_ic_ci_low bcpnn_mcmc_ic_ci_high oe_ratio oe_ratio_ci_low
+#> <num> <num> <num> <num>
+#> 1: -10.2469847 1.7329970 -0.50589093 -10.3355050
+#> 2: -2.3687685 2.7746570 1.27462238 -2.5084784
+#> 3: -10.0299469 2.2485350 -0.04264434 -9.8952571
+#> 4: -10.0496990 2.1208626 -0.16349873 -9.9729602
+#> 5: -9.9443639 2.2546058 -0.04264434 -10.0159789
+#> 6: -2.3721307 2.6989335 1.20645088 -2.5766499
+#> 7: -2.8497104 1.8982781 0.57060721 -3.2124936
+#> 8: -3.4827207 0.9902367 -0.18057225 -3.9636731
+#> 9: -10.2104872 1.9009499 -0.34482850 -10.1693395
+#> 10: -10.0393748 2.1095254 -0.16349873 -9.9466376
+#> 11: -0.7632789 2.3062119 1.35107444 -1.2419932
+#> 12: -2.8130859 1.9851334 0.63636165 -3.1467392
+#> 13: -0.7832653 2.3098357 1.35107444 -1.2419932
+#> 14: -0.4409460 3.0182365 1.87832144 -0.7147462
+#> 15: -10.4784638 1.5675396 -0.65076456 -10.5718176
+#> oe_ratio_ci_high odds_ratio odds_ratio_ci_low odds_ratio_ci_high
+#> <num> <num> <num> <num>
+#> 1: 1.726128 0.0000000 0.00000000 33.68585
+#> 2: 2.962049 13.0303800 0.20150028 279.21542
+#> 3: 2.236123 0.0000000 0.00000000 2462.50000
+#> 4: 2.129039 0.0000000 0.00000000 145.21133
+#> 5: 2.268819 0.0000000 0.00000000 2462.50000
+#> 6: 2.893877 10.1233187 0.15947006 211.87117
+#> 7: 2.258033 2.4701675 0.04089140 48.73410
+#> 8: 1.506854 0.7478897 0.01250834 14.59249
+#> 9: 1.914874 0.0000000 0.00000000 55.53664
+#> 10: 2.114262 0.0000000 0.00000000 145.21133
+#> 11: 2.742477 10.9151800 0.55237709 657.45882
+#> 12: 2.323788 2.7642969 0.04567010 54.61951
+#> 13: 2.742477 10.9151800 0.55237709 657.45882
+#> 14: 3.269724 35.2158110 1.70522393 2176.34560
+#> 15: 1.557832 0.0000000 0.00000000 23.77817
+#> fisher_pvalue ebgm ebgm_ci_low ebgm_ci_high
+#> <num> <num> <num> <num>
+#> 1: 1.00000000 2.421502 2.38 2.46
+#> 2: 0.11582153 2.421743 2.38 2.46
+#> 3: 1.00000000 2.421595 2.38 2.46
+#> 4: 1.00000000 2.421574 2.38 2.46
+#> 5: 1.00000000 2.421595 2.38 2.46
+#> 6: 0.14330745 2.421729 2.38 2.46
+#> 7: 0.42998325 2.421556 2.38 2.46
+#> 8: 1.00000000 2.421225 2.38 2.46
+#> 9: 1.00000000 2.421538 2.38 2.46
+#> 10: 1.00000000 2.421574 2.38 2.46
+#> 11: 0.06722095 2.421769 2.38 2.46
+#> 12: 0.39832191 2.421578 2.38 2.46
+#> 13: 0.06722095 2.421769 2.38 2.46
+#> 14: 0.00961474 2.421913 2.38 2.46
+#> 15: 1.00000000 2.421466 2.38 2.46
+#> [ reached getOption("max.print") -- omitted 12 rows ]
The column containing the events of interest can be specified using an atomic character in the .events (default: “soc_name”) argument. The combination of all specified columns will define the unique event. Additionally, we can control which field data to find the columns in the .field (default: “reac”) argument.
-insulin_signals_hlgt <- faers_phv_signal(
- insulin_data,
- .events = "hlgt_name",
- .full = data
-)
-insulin_signals_hlgt
-#> Key: <hlgt_name>
-#> hlgt_name a b
-#> <char> <int> <int>
-#> 1: Acid-base disorders 0 3
-#> 2: Administration site reactions 0 3
-#> 3: Allergic conditions 0 3
-#> 4: Anaemias nonhaemolytic and marrow depression 0 3
-#> 5: Angioedema and urticaria 0 3
-#> ---
-#> 138: Viral infectious disorders 0 3
-#> 139: Vision disorders 1 2
-#> 140: Vulvovaginal disorders (excl infections and inflammations) 0 3
-#> 141: Water, electrolyte and mineral investigations 1 2
-#> 142: White blood cell disorders 0 3
-#> c d expected ror ror_ci_low ror_ci_high prr prr_ci_low
-#> <int> <int> <num> <num> <num> <num> <num> <num>
-#> 1: 1 196 0.015 0.00 0.000000 NaN 0.00000 0.000000
-#> 2: 9 188 0.135 0.00 0.000000 NaN 0.00000 0.000000
-#> 3: 3 194 0.045 0.00 0.000000 NaN 0.00000 0.000000
-#> 4: 2 195 0.030 0.00 0.000000 NaN 0.00000 0.000000
-#> 5: 1 196 0.015 0.00 0.000000 NaN 0.00000 0.000000
-#> ---
-#> 138: 6 191 0.090 0.00 0.000000 NaN 0.00000 0.000000
-#> 139: 2 195 0.045 48.75 3.038446 782.1638 32.83333 3.971134
-#> 140: 1 196 0.015 0.00 0.000000 NaN 0.00000 0.000000
-#> 141: 1 196 0.030 98.00 4.405403 2180.0503 65.66667 5.249564
-#> 142: 6 191 0.090 0.00 0.000000 NaN 0.00000 0.000000
-#> prr_ci_high chisq chisq_pvalue bcpnn_norm_ic bcpnn_norm_ic_ci_low
-#> <num> <num> <num> <num> <num>
-#> 1: NaN 1.265951e-26 1.000000000 -0.3173914 -4.844759
-#> 2: NaN 6.503567e-28 1.000000000 -0.8364506 -4.858428
-#> 3: NaN 3.579029e-27 1.000000000 -0.5729454 -4.769182
-#> 4: NaN 1.292402e-30 1.000000000 -0.4806767 -4.781546
-#> 5: NaN 1.265951e-26 1.000000000 -0.3173914 -4.844759
-#> ---
-#> 138: NaN 2.800437e-31 1.000000000 -0.7316939 -4.801687
-#> 139: 271.4660 4.741741e+00 0.029439266 0.8697497 -2.230719
-#> 140: NaN 1.265951e-26 1.000000000 -0.3173914 -4.844759
-#> 141: 821.4227 7.550975e+00 0.005997761 0.9620184 -2.278658
-#> 142: NaN 2.800437e-31 1.000000000 -0.7316939 -4.801687
-#> bcpnn_norm_ic_ci_high bcpnn_mcmc_ic bcpnn_mcmc_ic_ci_low
-#> <num> <num> <num>
-#> 1: 4.209977 -0.03947607 -10.031838
-#> 2: 3.185527 -0.34296004 -10.196627
-#> 3: 3.623291 -0.12157646 -9.983107
-#> 4: 3.820193 -0.08111417 -10.000743
-#> 5: 4.209977 -0.03947607 -9.979654
-#> ---
-#> 138: 3.338300 -0.23653305 -10.165525
-#> 139: 3.970219 1.46338605 -2.203669
-#> 140: 4.209977 -0.03947607 -9.960982
-#> 141: 4.202695 1.50384833 -2.184148
-#> 142: 3.338300 -0.23653305 -10.066983
-#> bcpnn_mcmc_ic_ci_high oe_ratio oe_ratio_ci_low oe_ratio_ci_high
-#> <num> <num> <num> <num>
-#> 1: 2.256211 -0.04264434 -9.903524 2.254197
-#> 2: 1.904126 -0.34482850 -10.340359 1.913541
-#> 3: 2.145214 -0.12432814 -10.088559 2.169377
-#> 4: 2.213887 -0.08406426 -10.005938 2.221035
-#> 5: 2.253682 -0.04264434 -10.005551 2.241251
-#> ---
-#> 138: 2.010294 -0.23878686 -10.131488 2.023390
-#> 139: 3.002075 1.46063437 -2.322466 3.148061
-#> 140: 2.240702 -0.04264434 -9.925329 2.259773
-#> 141: 3.050325 1.50089824 -2.282203 3.188325
-#> 142: 2.042342 -0.23878686 -10.130615 2.022234
-#> odds_ratio odds_ratio_ci_low odds_ratio_ci_high fisher_pvalue ebgm
-#> <num> <num> <num> <num> <num>
-#> 1: 0.00000 0.0000000 2462.50000 1.00000000 3.670936
-#> 2: 0.00000 0.0000000 55.53664 1.00000000 3.459110
-#> 3: 0.00000 0.0000000 213.09160 1.00000000 3.615584
-#> 4: 0.00000 0.0000000 408.94448 1.00000000 3.643050
-#> 5: 0.00000 0.0000000 2462.50000 1.00000000 3.670936
-#> ---
-#> 138: 0.00000 0.0000000 88.65547 1.00000000 3.535617
-#> 139: 43.06704 0.5524356 1247.00745 0.04454850 4.117845
-#> 140: 0.00000 0.0000000 2462.50000 1.00000000 3.670936
-#> 141: 80.16649 0.8340751 7069.12541 0.02984925 4.149126
-#> 142: 0.00000 0.0000000 88.65547 1.00000000 3.535617
-#> ebgm_ci_low ebgm_ci_high
-#> <num> <num>
-#> 1: 1.66 7.14
-#> 2: 1.56 6.73
-#> 3: 1.63 7.03
-#> 4: 1.65 7.09
-#> 5: 1.66 7.14
-#> ---
-#> 138: 1.60 6.88
-#> 139: 1.96 7.71
-#> 140: 1.66 7.14
-#> 141: 1.98 7.77
-#> 142: 1.60 6.88
-sessionInfo
-sessionInfo()
-#> R version 4.3.1 (2023-06-16)
-#> Platform: x86_64-pc-linux-gnu (64-bit)
-#> Running under: Ubuntu 22.04.3 LTS
-#>
-#> Matrix products: default
-#> BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libmkl_rt.so; LAPACK version 3.8.0
-#>
-#> locale:
-#> [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
-#> [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
-#> [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
-#> [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
-#>
-#> time zone: Asia/Shanghai
-#> tzcode source: system (glibc)
-#>
-#> attached base packages:
-#> [1] stats graphics grDevices utils datasets methods base
-#>
-#> other attached packages:
-#> [1] faers_0.99.3
-#>
-#> loaded via a namespace (and not attached):
-#> [1] generics_0.1.3 rappdirs_0.3.3 utf8_1.2.4 xml2_1.3.6
-#> [5] stringi_1.8.3 openEBGM_0.9.1 lattice_0.22-5 digest_0.6.33
-#> [9] magrittr_2.0.3 evaluate_0.23 grid_4.3.1 MCMCpack_1.6-3
-#> [13] fastmap_1.1.1 Matrix_1.6-4 survival_3.5-7 mcmc_0.9-7
-#> [17] httr_1.4.7 rvest_1.0.3 fansi_1.0.6 selectr_0.4-2
-#> [21] scales_1.3.0 cli_3.6.2 rlang_1.1.2 crayon_1.5.2
-#> [25] munsell_0.5.0 bit64_4.0.5 splines_4.3.1 yaml_2.3.8
-#> [29] tools_4.3.1 parallel_4.3.1 SparseM_1.81 tzdb_0.4.0
-#> [33] MatrixModels_0.5-2 coda_0.19-4 dplyr_1.1.4 colorspace_2.1-0
-#> [37] ggplot2_3.4.4 curl_5.2.0 vctrs_0.6.5 R6_2.5.1
-#> [41] lifecycle_1.0.4 stringr_1.5.1 bit_4.0.5 vroom_1.6.5
-#> [45] MASS_7.3-60 pkgconfig_2.0.3 archive_1.1.6 pillar_1.9.0
-#> [49] gtable_0.3.4 data.table_1.14.9 glue_1.6.2 xfun_0.41
-#> [53] tibble_3.2.1 tidyselect_1.2.0 knitr_1.45 htmltools_0.5.7
-#> [57] rmarkdown_2.25 compiler_4.3.1 quantreg_5.96
+set.seed(1L)
+insulin_signals_hlgt <- faers_phv_signal(
+ insulin_data,
+ .events = "hlgt_name",
+ .full = data
+)
+insulin_signals_hlgt
+#> Key: <hlgt_name>
+#> hlgt_name a b
+#> <char> <int> <int>
+#> 1: Acid-base disorders 0 3
+#> 2: Administration site reactions 0 3
+#> 3: Allergic conditions 0 3
+#> 4: Anaemias nonhaemolytic and marrow depression 0 3
+#> 5: Angioedema and urticaria 0 3
+#> ---
+#> 138: Viral infectious disorders 0 3
+#> 139: Vision disorders 1 2
+#> 140: Vulvovaginal disorders (excl infections and inflammations) 0 3
+#> 141: Water, electrolyte and mineral investigations 1 2
+#> 142: White blood cell disorders 0 3
+#> c d expected ror ror_ci_low ror_ci_high prr prr_ci_low
+#> <int> <int> <num> <num> <num> <num> <num> <num>
+#> 1: 1 196 0.015 0.00 0.000000 NaN 0.00000 0.000000
+#> 2: 9 188 0.135 0.00 0.000000 NaN 0.00000 0.000000
+#> 3: 3 194 0.045 0.00 0.000000 NaN 0.00000 0.000000
+#> 4: 2 195 0.030 0.00 0.000000 NaN 0.00000 0.000000
+#> 5: 1 196 0.015 0.00 0.000000 NaN 0.00000 0.000000
+#> ---
+#> 138: 6 191 0.090 0.00 0.000000 NaN 0.00000 0.000000
+#> 139: 2 195 0.045 48.75 3.038446 782.1638 32.83333 3.971134
+#> 140: 1 196 0.015 0.00 0.000000 NaN 0.00000 0.000000
+#> 141: 1 196 0.030 98.00 4.405403 2180.0503 65.66667 5.249564
+#> 142: 6 191 0.090 0.00 0.000000 NaN 0.00000 0.000000
+#> prr_ci_high chisq chisq_pvalue bcpnn_norm_ic bcpnn_norm_ic_ci_low
+#> <num> <num> <num> <num> <num>
+#> 1: NaN 1.265951e-26 1.000000000 -0.3173914 -4.844759
+#> 2: NaN 6.503567e-28 1.000000000 -0.8364506 -4.858428
+#> 3: NaN 3.579029e-27 1.000000000 -0.5729454 -4.769182
+#> 4: NaN 1.292402e-30 1.000000000 -0.4806767 -4.781546
+#> 5: NaN 1.265951e-26 1.000000000 -0.3173914 -4.844759
+#> ---
+#> 138: NaN 2.800437e-31 1.000000000 -0.7316939 -4.801687
+#> 139: 271.4660 4.741741e+00 0.029439266 0.8697497 -2.230719
+#> 140: NaN 1.265951e-26 1.000000000 -0.3173914 -4.844759
+#> 141: 821.4227 7.550975e+00 0.005997761 0.9620184 -2.278658
+#> 142: NaN 2.800437e-31 1.000000000 -0.7316939 -4.801687
+#> bcpnn_norm_ic_ci_high bcpnn_mcmc_ic bcpnn_mcmc_ic_ci_low
+#> <num> <num> <num>
+#> 1: 4.209977 -0.03947607 -9.870668
+#> 2: 3.185527 -0.34296004 -10.137252
+#> 3: 3.623291 -0.12157646 -10.072216
+#> 4: 3.820193 -0.08111417 -10.027072
+#> 5: 4.209977 -0.03947607 -9.920536
+#> ---
+#> 138: 3.338300 -0.23653305 -10.119996
+#> 139: 3.970219 1.46338605 -2.221526
+#> 140: 4.209977 -0.03947607 -9.976006
+#> 141: 4.202695 1.50384833 -2.215082
+#> 142: 3.338300 -0.23653305 -10.139379
+#> bcpnn_mcmc_ic_ci_high oe_ratio oe_ratio_ci_low oe_ratio_ci_high
+#> <num> <num> <num> <num>
+#> 1: 2.262782 -0.04264434 -9.901054 2.248909
+#> 2: 1.905408 -0.34482850 -10.194800 1.912105
+#> 3: 2.155367 -0.12432814 -9.995913 2.168232
+#> 4: 2.209895 -0.08406426 -10.144027 2.209777
+#> 5: 2.256206 -0.04264434 -10.092572 2.265663
+#> ---
+#> 138: 2.032943 -0.23878686 -10.201472 2.039077
+#> 139: 3.013392 1.46063437 -2.322466 3.148061
+#> 140: 2.253660 -0.04264434 -9.954685 2.252572
+#> 141: 3.064956 1.50089824 -2.282203 3.188325
+#> 142: 2.052593 -0.23878686 -10.221601 2.044580
+#> odds_ratio odds_ratio_ci_low odds_ratio_ci_high fisher_pvalue ebgm
+#> <num> <num> <num> <num> <num>
+#> 1: 0.00000 0.0000000 2462.50000 1.00000000 3.670936
+#> 2: 0.00000 0.0000000 55.53664 1.00000000 3.459110
+#> 3: 0.00000 0.0000000 213.09160 1.00000000 3.615584
+#> 4: 0.00000 0.0000000 408.94448 1.00000000 3.643050
+#> 5: 0.00000 0.0000000 2462.50000 1.00000000 3.670936
+#> ---
+#> 138: 0.00000 0.0000000 88.65547 1.00000000 3.535617
+#> 139: 43.06704 0.5524356 1247.00745 0.04454850 4.117845
+#> 140: 0.00000 0.0000000 2462.50000 1.00000000 3.670936
+#> 141: 80.16649 0.8340751 7069.12541 0.02984925 4.149126
+#> 142: 0.00000 0.0000000 88.65547 1.00000000 3.535617
+#> ebgm_ci_low ebgm_ci_high
+#> <num> <num>
+#> 1: 1.66 7.14
+#> 2: 1.56 6.73
+#> 3: 1.63 7.03
+#> 4: 1.65 7.09
+#> 5: 1.66 7.14
+#> ---
+#> 138: 1.60 6.88
+#> 139: 1.96 7.71
+#> 140: 1.66 7.14
+#> 141: 1.98 7.77
+#> 142: 1.60 6.88
+sessionInfo
+sessionInfo()
+#> R version 4.3.1 (2023-06-16)
+#> Platform: x86_64-pc-linux-gnu (64-bit)
+#> Running under: Ubuntu 22.04.3 LTS
+#>
+#> Matrix products: default
+#> BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libmkl_rt.so; LAPACK version 3.8.0
+#>
+#> locale:
+#> [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
+#> [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
+#> [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
+#> [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
+#>
+#> time zone: Asia/Shanghai
+#> tzcode source: system (glibc)
+#>
+#> attached base packages:
+#> [1] stats graphics grDevices utils datasets methods base
+#>
+#> other attached packages:
+#> [1] faers_0.99.3
+#>
+#> loaded via a namespace (and not attached):
+#> [1] generics_0.1.3 rappdirs_0.3.3 utf8_1.2.4 xml2_1.3.6
+#> [5] stringi_1.8.3 openEBGM_0.9.1 lattice_0.22-5 digest_0.6.33
+#> [9] magrittr_2.0.3 evaluate_0.23 grid_4.3.1 MCMCpack_1.6-3
+#> [13] fastmap_1.1.1 Matrix_1.6-4 survival_3.5-7 mcmc_0.9-7
+#> [17] httr_1.4.7 rvest_1.0.3 fansi_1.0.6 selectr_0.4-2
+#> [21] scales_1.3.0 cli_3.6.2 rlang_1.1.2 crayon_1.5.2
+#> [25] munsell_0.5.0 bit64_4.0.5 splines_4.3.1 yaml_2.3.8
+#> [29] tools_4.3.1 parallel_4.3.1 SparseM_1.81 tzdb_0.4.0
+#> [33] MatrixModels_0.5-2 coda_0.19-4 dplyr_1.1.4 colorspace_2.1-0
+#> [37] ggplot2_3.4.4 curl_5.2.0 vctrs_0.6.5 R6_2.5.1
+#> [41] lifecycle_1.0.4 stringr_1.5.1 bit_4.0.5 vroom_1.6.5
+#> [45] MASS_7.3-60 pkgconfig_2.0.3 archive_1.1.6 pillar_1.9.0
+#> [49] gtable_0.3.4 data.table_1.14.99 glue_1.6.2 xfun_0.41
+#> [53] tibble_3.2.1 tidyselect_1.2.0 knitr_1.45 htmltools_0.5.7
+#> [57] rmarkdown_2.25 compiler_4.3.1 quantreg_5.96