counts the occurrences of reactions/indications/substance for a given set of primary IDs. Calculates % as the proportion of individuals recording the event.
Usage
reporting_rates(
pids_cases,
entity = "reaction",
level = "pt",
drug_role = c("PS", "SS", "I", "C"),
drug_indi = NA,
temp_reac = Reac,
temp_drug = Drug,
temp_indi = Indi
)Arguments
- pids_cases
Vector of primary IDs to consider for counting reactions.
- entity
Entity investigated. It can be one of the following:
reaction;
indication;
substance.
- level
The desired MedDRA or ATC level for counting (default is "pt").
- drug_role
is only used for substances. By default both suspect and concomitant drugs are included.
- drug_indi
is only used for indications. By default the indications of all the drugs of the selected primaryids are considered, but you can specify a vector of drugs.
- temp_reac
Reac dataset. Can be set to sample_Reac for testing
- temp_drug
Drug dataset. Can be set to sample_Drug for testing
- temp_indi
Indi dataset. Can be set to sample_Indi for testing
Value
A data.table containing counts and percentages of the investigated entity at the specified level and in descending order.
Examples
# select only reports recording paracetamol from the sample dataset,
# and provide the most reported events (at the pt level),
# drugs, and indications (at the PT level).
pids_cases <-
reporting_rates(unique(sample_Drug[substance == "paracetamol"]$primaryid),
"reaction", "pt",
temp_reac = sample_Reac,
temp_drug = sample_Drug, temp_indi = sample_Indi
)
reporting_rates(unique(sample_Drug[substance == "paracetamol"]$primaryid),
"indication", "pt",
temp_reac = sample_Reac,
temp_drug = sample_Drug, temp_indi = sample_Indi
)
#> pt
#> <ord>
#> 1: rheumatoid arthritis
#> 2: plasma cell myeloma
#> 3: multiple sclerosis
#> 4: psoriasis
#> 5: hypertension
#> ---
#> 378: endometriosis
#> 379: fabry's disease
#> 380: ovarian cancer recurrent
#> 381: pancreatic carcinoma metastatic
#> 382: antibiotic prophylaxis
#> label_pt N_pt
#> <char> <int>
#> 1: rheumatoid arthritis (7.58%) [55] 55
#> 2: plasma cell myeloma (3.99%) [29] 29
#> 3: multiple sclerosis (3.44%) [25] 25
#> 4: psoriasis (3.44%) [25] 25
#> 5: hypertension (3.03%) [22] 22
#> ---
#> 378: endometriosis (0.14%) [1] 1
#> 379: fabry's disease (0.14%) [1] 1
#> 380: ovarian cancer recurrent (0.14%) [1] 1
#> 381: pancreatic carcinoma metastatic (0.14%) [1] 1
#> 382: antibiotic prophylaxis (0.14%) [1] 1
reporting_rates(unique(sample_Drug[substance == "paracetamol"]$primaryid),
entity = "substance",
temp_reac = sample_Reac, temp_drug = sample_Drug,
temp_indi = sample_Indi
)
#> substance label_substance N_substance
#> <fctr> <char> <int>
#> 1: paracetamol paracetamol (5.1%) [51] 51
#> 2: acetylsalicylic acid acetylsalicylic acid (4.9%) [49] 49
#> 3: adalimumab adalimumab (4.5%) [45] 45
#> 4: <NA> NA (3.8%) [38] 38
#> 5: etanercept etanercept (3.8%) [38] 38
#> ---
#> 717: water water (0.1%) [1] 1
#> 718: entecavir entecavir (0.1%) [1] 1
#> 719: canagliflozin canagliflozin (0.1%) [1] 1
#> 720: ofatumumab ofatumumab (0.1%) [1] 1
#> 721: cefepime cefepime (0.1%) [1] 1