Nothing
## ----setup, include = FALSE----------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ---- eval=FALSE---------------------------------------------------------
# install.packages("pubtatordb")
## ---- eval=FALSE---------------------------------------------------------
# install.packages("devtools")
# devtools::install_github("mamc-dci/pubtatordb")
## ----message=FALSE, warning=FALSE----------------------------------------
# Load the package.
library(pubtatordb)
## ---- eval=FALSE---------------------------------------------------------
# # Download the data.
# # Use the full path. Writing to the temp directory is not recommended.
# download_dir <- tempdir()
# download_pt(download_dir)
## ---- eval=FALSE---------------------------------------------------------
# # Define the data directory, a subdirectory of the above directory.
# pubtator_path <- file.path(download_dir, "PubTator")
#
# # Create the database.
# pt_to_sql(
# pubtator_path,
# skip_behavior = FALSE,
# remove_behavior = TRUE
# )
## ---- eval=FALSE---------------------------------------------------------
# # Create a connection to the database.
# db_con <- pt_connector(pubtator_path)
## ---- eval=FALSE---------------------------------------------------------
# # Query the data.
# pt_select(
# db_con,
# "gene",
# columns = NULL,
# keys = NULL,
# keytype = NULL,
# limit = 5
# )
## ---- eval=FALSE---------------------------------------------------------
# # Query the data.
# pt_select(
# db_con,
# "gene",
# columns = c("PMID", "ENTREZID"),
# keys = c("7356", "4199"),
# keytype = "ENTREZID",
# limit = 5
# )
## ---- eval=FALSE---------------------------------------------------------
# pt_tables(db_con)
## ---- eval=FALSE---------------------------------------------------------
# pt_columns(db_con, "species")
## ------------------------------------------------------------------------
pubtator_citations()
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