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: pain
#> 2: rheumatoid arthritis
#> 3: back pain
#> 4: anxiety
#> 5: gastrooesophageal reflux disease
#> 6: depression
#> 7: hypertension
#> 8: plasma cell myeloma
#> 9: psoriasis
#> 10: asthma
#> 11: type 2 diabetes mellitus
#> 12: premedication
#> 13: covid-19
#> 14: psoriatic arthropathy
#> 15: affective disorder
#> 16: psychotic disorder
#> 17: intentional self-injury
#> 18: candida infection
#> 19: ill-defined disorder
#> 20: low density lipoprotein increased
#> 21: abdominal pain upper
#> 22: muscle spasms
#> 23: neuralgia
#> 24: breakthrough pain
#> 25: migraine
#> 26: insomnia
#> 27: systemic lupus erythematosus
#> 28: chemotherapy
#> 29: hypersensitivity
#> 30: contraception
#> 31: mucopolysaccharidosis vi
#> 32: chronic myeloid leukaemia
#> 33: multiple sclerosis
#> 34: oral fungal infection
#> 35: atrial fibrillation
#> 36: postoperative care
#> 37: cardiac failure congestive
#> 38: cachexia
#> 39: tonsillitis
#> 40: dyspepsia
#> 41: gout
#> 42: calcium deficiency
#> 43: vitamin d deficiency
#> 44: blood phosphorus
#> 45: renal failure
#> 46: anaemia
#> 47: leukopenia
#> 48: crohn's disease
#> 49: infection prophylaxis
#> 50: essential thrombocythaemia
#> 51: immunodeficiency common variable
#> 52: acute myeloid leukaemia
#> 53: pancreatic carcinoma
#> 54: influenza like illness
#> 55: pyrexia
#> 56: chills
#> 57: infection
#> 58: blood pressure abnormal
#> 59: renal injury
#> 60: blood cholesterol abnormal
#> 61: cardiac disorder
#> 62: cough
#> 63: rhinorrhoea
#> 64: upper-airway cough syndrome
#> 65: fabry's disease
#> 66: colitis ulcerative
#> 67: covid-19 immunisation
#> pt
#> label_pt N_pt
#> <char> <int>
#> 1: pain (17.95%) [7] 7
#> 2: rheumatoid arthritis (7.69%) [3] 3
#> 3: back pain (7.69%) [3] 3
#> 4: anxiety (7.69%) [3] 3
#> 5: gastrooesophageal reflux disease (7.69%) [3] 3
#> 6: depression (7.69%) [3] 3
#> 7: hypertension (5.13%) [2] 2
#> 8: plasma cell myeloma (5.13%) [2] 2
#> 9: psoriasis (5.13%) [2] 2
#> 10: asthma (5.13%) [2] 2
#> 11: type 2 diabetes mellitus (5.13%) [2] 2
#> 12: premedication (5.13%) [2] 2
#> 13: covid-19 (5.13%) [2] 2
#> 14: psoriatic arthropathy (5.13%) [2] 2
#> 15: affective disorder (2.56%) [1] 1
#> 16: psychotic disorder (2.56%) [1] 1
#> 17: intentional self-injury (2.56%) [1] 1
#> 18: candida infection (2.56%) [1] 1
#> 19: ill-defined disorder (2.56%) [1] 1
#> 20: low density lipoprotein increased (2.56%) [1] 1
#> 21: abdominal pain upper (2.56%) [1] 1
#> 22: muscle spasms (2.56%) [1] 1
#> 23: neuralgia (2.56%) [1] 1
#> 24: breakthrough pain (2.56%) [1] 1
#> 25: migraine (2.56%) [1] 1
#> 26: insomnia (2.56%) [1] 1
#> 27: systemic lupus erythematosus (2.56%) [1] 1
#> 28: chemotherapy (2.56%) [1] 1
#> 29: hypersensitivity (2.56%) [1] 1
#> 30: contraception (2.56%) [1] 1
#> 31: mucopolysaccharidosis vi (2.56%) [1] 1
#> 32: chronic myeloid leukaemia (2.56%) [1] 1
#> 33: multiple sclerosis (2.56%) [1] 1
#> 34: oral fungal infection (2.56%) [1] 1
#> 35: atrial fibrillation (2.56%) [1] 1
#> 36: postoperative care (2.56%) [1] 1
#> 37: cardiac failure congestive (2.56%) [1] 1
#> 38: cachexia (2.56%) [1] 1
#> 39: tonsillitis (2.56%) [1] 1
#> 40: dyspepsia (2.56%) [1] 1
#> 41: gout (2.56%) [1] 1
#> 42: calcium deficiency (2.56%) [1] 1
#> 43: vitamin d deficiency (2.56%) [1] 1
#> 44: blood phosphorus (2.56%) [1] 1
#> 45: renal failure (2.56%) [1] 1
#> 46: anaemia (2.56%) [1] 1
#> 47: leukopenia (2.56%) [1] 1
#> 48: crohn's disease (2.56%) [1] 1
#> 49: infection prophylaxis (2.56%) [1] 1
#> 50: essential thrombocythaemia (2.56%) [1] 1
#> 51: immunodeficiency common variable (2.56%) [1] 1
#> 52: acute myeloid leukaemia (2.56%) [1] 1
#> 53: pancreatic carcinoma (2.56%) [1] 1
#> 54: influenza like illness (2.56%) [1] 1
#> 55: pyrexia (2.56%) [1] 1
#> 56: chills (2.56%) [1] 1
#> 57: infection (2.56%) [1] 1
#> 58: blood pressure abnormal (2.56%) [1] 1
#> 59: renal injury (2.56%) [1] 1
#> 60: blood cholesterol abnormal (2.56%) [1] 1
#> 61: cardiac disorder (2.56%) [1] 1
#> 62: cough (2.56%) [1] 1
#> 63: rhinorrhoea (2.56%) [1] 1
#> 64: upper-airway cough syndrome (2.56%) [1] 1
#> 65: fabry's disease (2.56%) [1] 1
#> 66: colitis ulcerative (2.56%) [1] 1
#> 67: covid-19 immunisation (2.56%) [1] 1
#> label_pt N_pt
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 (100%) [51] 51
#> 2: oxycodone oxycodone (31.37%) [16] 16
#> 3: hydrocodone hydrocodone (25.49%) [13] 13
#> 4: acetylsalicylic acid acetylsalicylic acid (19.61%) [10] 10
#> 5: salbutamol salbutamol (17.65%) [9] 9
#> ---
#> 264: enalapril enalapril (1.96%) [1] 1
#> 265: aciclovir aciclovir (1.96%) [1] 1
#> 266: nifedipine nifedipine (1.96%) [1] 1
#> 267: upadacitinib upadacitinib (1.96%) [1] 1
#> 268: covid-19 vaccine covid-19 vaccine (1.96%) [1] 1