In meerapatelmd/oldamphora: Create Reingold-Tilford tree diagrams of the OMOP Vocabularies

library(tidyverse)
library(pg13)
conn <- pg13::local_connect()

input <-
tibble::tribble(~rxnorm_ingredient_name,
        "filgrastim",
        "benralizumab",
        "cyclosporine",
        "dihematoporphyrin ether",
        "eculizumab",
        "ethoglucid",
        "fosfestrol",
        "fostamatinib",
        "herpesvirus 1, human",
        "mesna",
        "pravastatin",
        "ravulizumab",
        "ruxolitinib",
        "tranexamic acid",
        "valproate",
        "levamisole",
        "methyl 5-aminolevulinate",
        "phenytoin",
        "zidovudine",
        "mepolizumab",
        "mycophenolate mofetil",
        "ketoconazole",
        "pirfenidone",
        "sargramostim",
        "octreotide",
        "quinine",
        "tacrolimus",
        "megestrol",
        "miltefosine",
        "medroxyprogesterone",
        "methylprednisolone",
        "omeprazole",
        "tocilizumab",
        "leucovorin",
        "levoleucovorin",
        "hydrocortisone",
        "cortisone",
        "danazol",
        "doxycycline",
        "estradiol",
        "dexamethasone",
        "denosumab",
        "amoxicillin",
        "aspirin",
        "azathioprine",
        "sirolimus",
        "isotretinoin",
        "diethylstilbestrol",
        "dutasteride",
        "prednisolone",
        "prednisone",
)

staging_table_name <- 
        pg13::write_staging_table(conn = conn, 
                                  schema = "public",
                                  drop_existing = TRUE,
                                  data = input)

sql_statement <-
pg13::build_join_query(distinct = TRUE,
                 schema = "public",
                 table = staging_table_name,
                 column = "rxnorm_ingredient_name",
                 join_on_schema = "omop_vocabulary",
                 join_on_table = "concept",
                 join_on_column = "concept_name",
                 case_insensitive = TRUE,
                 where_in_join_on_field = "vocabulary_id",
                 where_in_join_on_vector = "RxNorm")

false_positive_concepts <-
        pg13::query(conn = conn, 
                    sql_statement = sql_statement) 

false_positive_concepts <-
        input %>%
        left_join(false_positive_concepts) %>%
        select(-rxnorm_ingredient_name) %>%
        distinct()

false_positive_concepts

pg13::dc(conn = conn)

meerapatelmd/oldamphora documentation built on Jan. 4, 2021, 12:33 a.m.