Merge all FAERS field data into one
faers_merge(object, ...)
# S4 method for class 'FAERSascii'
faers_merge(object, fields = NULL, all = TRUE, all.x = all, all.y = all)
# S4 method for class 'FAERSxml'
faers_merge(object)
# S4 method for class 'ANY'
faers_merge(object)A FAERSascii or FAERSxml object.
Other arguments passed to specific methods.
A character vector specifying the fields to use. Only values "demo", "drug", "indi", "ther", "reac", "rpsr", and "outc" can be used.
logical; all = TRUE is shorthand to save setting both
all.x = TRUE and all.y = TRUE.
logical; if TRUE, rows from x which have no matching row
in y are included. These rows will have 'NA's in the columns that are usually
filled with values from y. The default is FALSE so that only rows with
data from both x and y are included in the output.
logical; analogous to all.x above.
A data.table object.
Each pair of field data are merged based on "year", "quarter" and
"primaryid". In cases where any pair of data contains information related to
"drug_seq" elements, such as "drug_seq", "indi_drug_seq", or "dsg_drug_seq",
"drug_seq" will be aligned as well. fields shall be organized in the
subsequent sequence: 'demo', 'drug', 'indi', 'reac', 'ther', 'rpsr', and
'outc' and the merging sequence will correspondingly adhere to this order.
Only the initial instance, of the "caseid" column will be preserved.
You'd better only merge necessary data, otherwise a lot of memory will be consumed to merge all fields data.
# you must change `dir`, as the file included in the package is sampled
data <- faers(2004, "q1",
dir = system.file("extdata", package = "faers"),
compress_dir = tempdir()
)
#> Finding 1 file already downloaded: aers_ascii_2004q1.zip
faers_merge(data, "indi") # only one field is just like faers_get()
#> year quarter primaryid indi_drug_seq
#> <int> <char> <char> <int>
#> 1: 2004 q1 4263927 1004493661
#> 2: 2004 q1 4264001 1004493811
#> 3: 2004 q1 4264001 1004520441
#> 4: 2004 q1 4264001 1004520538
#> 5: 2004 q1 4264319 1004494389
#> ---
#> 153: 2004 q1 4338901 1004786888
#> 154: 2004 q1 4346899 1004815291
#> 155: 2004 q1 4346899 1004815291
#> 156: 2004 q1 4347265 1004816501
#> 157: 2004 q1 4373559 1004923573
#> indi_pt
#> <char>
#> 1: DIABETES MELLITUS NON-INSULIN-DEPENDENT
#> 2: RHEUMATOID ARTHRITIS
#> 3: RHEUMATOID ARTHRITIS
#> 4: RHEUMATOID ARTHRITIS
#> 5: ANTIVIRAL PROPHYLAXIS
#> ---
#> 153: RHEUMATOID ARTHRITIS
#> 154: ATTENTION DEFICIT/HYPERACTIVITY DISORDER
#> 155: PERVASIVE DEVELOPMENTAL DISORDER
#> 156: FRACTURED SACRUM
#> 157: LIPIDS INCREASED
faers_merge(data, c("demo", "indi"))
#> year quarter primaryid caseid i_f_code foll_seq image event_dt
#> <int> <char> <char> <char> <char> <int> <char> <int>
#> 1: 2004 q1 4263764 4060920 I NA 4263764-6 20020101
#> 2: 2004 q1 4263927 4064250 I NA 4263927-X NA
#> 3: 2004 q1 4264001 4062524 I NA 4264001-9 20031218
#> 4: 2004 q1 4264001 4062524 I NA 4264001-9 20031218
#> 5: 2004 q1 4264001 4062524 I NA 4264001-9 20031218
#> ---
#> 167: 2004 q1 4346899 4135105 I NA 4346899-9 20030101
#> 168: 2004 q1 4347265 4133168 I NA 4347265-2 20040128
#> 169: 2004 q1 4373559 4151463 F 1 4373559-0 20030923
#> 170: 2004 q1 4373586 4111031 I NA 4373586-3 20040123
#> 171: 2004 q1 4373706 4151560 I NA 4373706-0 NA
#> mfr_dt fda_dt rept_cod mfr_num
#> <int> <int> <char> <char>
#> 1: 20031219 20040102 EXP USA031255171
#> 2: 20031209 20040102 EXP B0317710A
#> 3: 20031219 20040102 EXP JP-JNJFOC-20031204393
#> 4: 20031219 20040102 EXP JP-JNJFOC-20031204393
#> 5: 20031219 20040102 EXP JP-JNJFOC-20031204393
#> ---
#> 167: 20031222 20040329 PER USA031255274
#> 168: 20040217 20040325 PER USA040158011
#> 169: 20031209 20040305 PER 2003UW14133
#> 170: 20040123 20040305 PER 2004UW01678
#> 171: 20040106 20040305 PER 2004UW00207
#> mfr_sndr age age_cod gender e_sub wt
#> <char> <num> <char> <char> <char> <num>
#> 1: ELI LILLY AND COMPANY 68 YR F N 82.0
#> 2: GLAXOSMITHKLINE GLOBAL CLINICAL SAFETY 58 YR F N NA
#> 3: CENTOCOR, INC. 53 YR F N 36.8
#> 4: CENTOCOR, INC. 53 YR F N 36.8
#> 5: CENTOCOR, INC. 53 YR F N 36.8
#> ---
#> 167: ELI LILLY AND COMPANY 6 YR M N 27.0
#> 168: ELI LILLY AND COMPANY 76 YR F N NA
#> 169: ASTRAZENECA PHARMACEUTICALS 78 YR M N 243.0
#> 170: ASTRAZENECA PHARMACEUTICALS 56 YR M N NA
#> 171: ASTRAZENECA PHARMACEUTICALS NA <NA> <NA> N NA
#> wt_cod rept_dt occp_cod death_dt to_mfr confid v23 caseversion
#> <char> <int> <char> <lgcl> <char> <char> <lgcl> <int>
#> 1: KG 20031223 <NA> NA <NA> <NA> NA 0
#> 2: <NA> 20031219 <NA> NA <NA> <NA> NA 0
#> 3: KG 20031231 MD NA <NA> <NA> NA 0
#> 4: KG 20031231 MD NA <NA> <NA> NA 0
#> 5: KG 20031231 MD NA <NA> <NA> NA 0
#> ---
#> 167: KG 20040301 <NA> NA <NA> <NA> NA 0
#> 168: <NA> 20040309 <NA> NA <NA> <NA> NA 0
#> 169: LBS 20040223 MD NA <NA> <NA> NA 0
#> 170: <NA> 20040223 MD NA <NA> <NA> NA 0
#> 171: <NA> 20040223 <NA> NA <NA> <NA> NA 0
#> age_in_years country_code sex indi_drug_seq
#> <num> <char> <char> <int>
#> 1: 68 <NA> Female NA
#> 2: 58 <NA> Female 1004493661
#> 3: 53 <NA> Female 1004493811
#> 4: 53 <NA> Female 1004520441
#> 5: 53 <NA> Female 1004520538
#> ---
#> 167: 6 <NA> Male 1004815291
#> 168: 76 <NA> Female 1004816501
#> 169: 78 <NA> Male 1004923573
#> 170: 56 <NA> Male NA
#> 171: NA <NA> <NA> NA
#> indi_pt
#> <char>
#> 1: <NA>
#> 2: DIABETES MELLITUS NON-INSULIN-DEPENDENT
#> 3: RHEUMATOID ARTHRITIS
#> 4: RHEUMATOID ARTHRITIS
#> 5: RHEUMATOID ARTHRITIS
#> ---
#> 167: PERVASIVE DEVELOPMENTAL DISORDER
#> 168: FRACTURED SACRUM
#> 169: LIPIDS INCREASED
#> 170: <NA>
#> 171: <NA>