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KidSIDES

pkgdown R-CMD-check Codecov test coverage CRAN status

This R data package contains observation, summary, and model-level data from pediatric drug safety research developed by Nicholas Giangreco for his PhD dissertation in the Tatonetti lab at Columbia University.

Installation

The database is downloaded after consent is given when using the package. Installing the package will not download the database, but it will make it easier to download and connect to the database from your R session.

install.packages('kidsides')
remotes::install_github("ngiangre/kidsides")

Summary

The database is comprised of 17 tables including a table with descriptions of the fields in each table. The main table, ade_nichd, contains quantitative data from nearly 500,000 pediatric drug safety signals across 7 child development stages spanning from birth through late adolescence (21 years of age).

The database was created using the methods and analyses in the references.

This data resource can be used under the CC BY 4.0 license agreement.

See the Overview vignette for more details on the data and the online portal

Usage

library(kidsides)
kidsides::download_sqlite_db(force=TRUE)
## kidsides would like to download a 0.9GB 'sqlite' database to your cache. Is that okay?
## The file will be located at at: /Users/nickgiangreco/Library/Caches/org.R-project.R/R/kidsides
##  (Yes/no/cancel)
con <- kidsides::connect_sqlite_db()

DBI::dbListTables(con)
##  [1] "ade"                                           
##  [2] "ade_nichd"                                     
##  [3] "ade_nichd_enrichment"                          
##  [4] "ade_null"                                      
##  [5] "ade_null_distribution"                         
##  [6] "ade_raw"                                       
##  [7] "atc_raw_map"                                   
##  [8] "cyp_gene_expression_substrate_risk_information"
##  [9] "dictionary"                                    
## [10] "drug"                                          
## [11] "drug_gene"                                     
## [12] "event"                                         
## [13] "gene"                                          
## [14] "gene_expression"                               
## [15] "grip"                                          
## [16] "ryan"                                          
## [17] "sider"
library(dplyr)
## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
dplyr::tbl(con,"dictionary") %>% 
    dplyr::collect()
## # A tibble: 152 × 4
##    table field             description                                     type 
##    <chr> <chr>             <chr>                                           <chr>
##  1 drug  atc_concept_id    The ATC 5th level OMOP concept identifier.      int  
##  2 drug  atc_concept_name  The ATC 5th level OMOP concept name. In the ad… char…
##  3 drug  atc_concept_code  The ATC 5th level OMOP concept code.            char…
##  4 drug  ndrugreports      The number of reports of the drug in Pediatric… int  
##  5 drug  atc4_concept_name The ATC 4th level OMOP concept name.            char…
##  6 drug  atc4_concept_code The ATC 4th level OMOP concept code.            char…
##  7 drug  atc3_concept_name The ATC 3rd level OMOP concept name.            char…
##  8 drug  atc3_concept_code The ATC 3rd level OMOP concept code.            char…
##  9 drug  atc2_concept_name The ATC 2nd level OMOP concept name.            char…
## 10 drug  atc2_concept_code The ATC 2nd level OMOP concept code.            char…
## # … with 142 more rows
dplyr::tbl(con,"ade_nichd") %>% 
    dplyr::collect()
## # A tibble: 3,225,859 × 13
##    atc_c…¹ meddr…² ade   nichd gam_s…³  norm gam_s…⁴ gam_s…⁵ gam_s…⁶     D     E
##      <int>   <int> <chr> <chr>   <dbl> <dbl>   <dbl>   <dbl>   <dbl> <int> <int>
##  1 1588648  3.58e7 1588… term…  -0.131 0        2.48 -4.21      3.95     0    20
##  2 1588648  3.58e7 1588… infa…   0.947 0.166    1.98 -2.31      4.21     0    80
##  3 1588648  3.58e7 1588… todd…   2.03  0.332    1.79 -0.923     4.98     0   107
##  4 1588648  3.58e7 1588… earl…   3.11  0.499    1.86  0.0553    6.17     0   294
##  5 1588648  3.58e7 1588… midd…   4.21  0.667    2.10  0.745     7.67     0  1046
##  6 1588648  3.58e7 1588… earl…   5.30  0.834    2.52  1.15      9.44     1  2697
##  7 1588648  3.58e7 1588… late…   6.38  1        3.14  1.21     11.5      0  1729
##  8 1588648  3.63e7 1588… term…  -0.310 0        5.61 -9.53      8.91     0     0
##  9 1588648  3.63e7 1588… infa…   2.25  0.166    4.43 -5.05      9.54     0     2
## 10 1588648  3.63e7 1588… todd…   4.81  0.332    3.79 -1.43     11.1      0     6
## # … with 3,225,849 more rows, 2 more variables: DE <int>, ade_name <chr>, and
## #   abbreviated variable names ¹​atc_concept_id, ²​meddra_concept_id, ³​gam_score,
## #   ⁴​gam_score_se, ⁵​gam_score_90mse, ⁶​gam_score_90pse
dplyr::tbl(con,"ade") %>% 
    dplyr::collect()
## # A tibble: 460,823 × 9
##    ade           atc_c…¹ meddr…² clust…³ gt_nu…⁴ gt_nu…⁵ max_s…⁶ clust…⁷ ade_n…⁸
##    <chr>           <int>   <int> <chr>     <dbl>   <dbl> <chr>   <chr>   <chr>  
##  1 1588648_3580… 1588648  3.58e7 2             1       0 late_a… Increa… 1      
##  2 1588648_3631… 1588648  3.63e7 2             1       1 late_a… Increa… 1      
##  3 1588648_3641… 1588648  3.64e7 2             1       0 late_a… Increa… 1      
##  4 1588648_3701… 1588648  3.70e7 2             1       0 late_a… Increa… 1      
##  5 1588648_3701… 1588648  3.70e7 2             1       1 late_a… Increa… 1      
##  6 1588648_3752… 1588648  3.75e7 2             1       0 late_a… Increa… 1      
##  7 1588697_3510… 1588697  3.51e7 4             0       0 term_n… Decrea… 1      
##  8 1588697_3510… 1588697  3.51e7 2             0       0 late_a… Increa… 1      
##  9 1588697_3510… 1588697  3.51e7 2             0       0 late_a… Increa… 3      
## 10 1588697_3510… 1588697  3.51e7 4             0       0 term_n… Decrea… 1      
## # … with 460,813 more rows, and abbreviated variable names ¹​atc_concept_id,
## #   ²​meddra_concept_id, ³​cluster_id, ⁴​gt_null_statistic, ⁵​gt_null_99,
## #   ⁶​max_score_nichd, ⁷​cluster_name, ⁸​ade_nreports
dplyr::tbl(con,"ade_raw") %>% 
    dplyr::collect()
## # A tibble: 2,326,383 × 23
##    safetyr…¹ ade   atc_c…² meddr…³ nichd sex   repor…⁴ recei…⁵    XA    XB    XC
##    <chr>     <chr>   <int>   <int> <chr> <chr> <chr>   <chr>   <dbl> <dbl> <dbl>
##  1 10003357  2160…  2.16e7  3.67e7 midd… Male  Other … 2014-0…     0     0     0
##  2 10003357  2160…  2.16e7  4.29e7 midd… Male  Other … 2014-0…     0     0     0
##  3 10003357  2160…  2.16e7  3.67e7 midd… Male  Other … 2014-0…     0     0     0
##  4 10003357  2160…  2.16e7  3.67e7 midd… Male  Other … 2014-0…     0     0     0
##  5 10003357  2160…  2.16e7  4.29e7 midd… Male  Other … 2014-0…     0     0     0
##  6 10003357  2160…  2.16e7  3.67e7 midd… Male  Other … 2014-0…     0     0     0
##  7 10003388  2160…  2.16e7  3.52e7 late… Fema… Consum… 2014-0…     0     0     1
##  8 10003388  2160…  2.16e7  3.52e7 late… Fema… Consum… 2014-0…     0     0     1
##  9 10003388  2160…  2.16e7  3.58e7 late… Fema… Consum… 2014-0…     0     0     1
## 10 10003401  2160…  2.16e7  3.61e7 earl… Fema… Consum… 2014-0…     0     0     1
## # … with 2,326,373 more rows, 12 more variables: XD <dbl>, XG <dbl>, XH <dbl>,
## #   XJ <dbl>, XL <dbl>, XM <dbl>, XN <dbl>, XP <dbl>, XR <dbl>, XS <dbl>,
## #   XV <dbl>, polypharmacy <int>, and abbreviated variable names
## #   ¹​safetyreportid, ²​atc_concept_id, ³​meddra_concept_id,
## #   ⁴​reporter_qualification, ⁵​receive_date
kidsides::disconnect_sqlite_db(con)

References

Giangreco, Nicholas. Mind the developmental gap: Identifying adverse drug effects across childhood to evaluate biological mechanisms from growth and development. 2022. Columbia University, PhD dissertation.

Giangreco NP, Tatonetti NP. A database of pediatric drug effects to evaluate ontogenic mechanisms from child growth and development. Med (N Y). 2022 Aug 12;3(8):579-595.e7. doi: 10.1016/j.medj.2022.06.001. Epub 2022 Jun 24. PMID: 35752163; PMCID: PMC9378670.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.