Files in hugheylab/pmparser
Create and Maintain a Relational Database of Data from PubMed/MEDLINE
.Rbuildignore
.github/workflows/check-deploy.yaml
.github/workflows/pkgdown.yaml
.github/workflows/rhub.yaml
.github/workflows/test-coverage.yaml
.gitignore
CRAN-SUBMISSION
DESCRIPTION
NAMESPACE
NEWS.md
R/bigquery.R
R/clickhouse.R
R/drop_pmid_version.R
R/get_citation.R
R/get_parsing_tables.R
R/get_pubmed_files.R
R/get_test_standard.R
R/modify_pubmed_db.R
R/parse_element.R
R/parse_person.R
R/parse_pubmed_xml.R
R/utilities.R
README.md
_pkgdown.yml
codecov.yml
cran-comments.md
data-raw/clickhouse/compare_postgres_clickhouse.R
data-raw/clickhouse/create_clickhouse_from_postgres.R
data-raw/copy_postgres_to_bigquery.R
data-raw/create_and_dump.sh
data-raw/dump_pubmed_db.R
data-raw/modify_zenodo.py
data-raw/pubmed20n0000.xml
data-raw/setup_ubuntu.sh
data-raw/update_and_dump.sh
data-raw/wrap_get_test_standard.R
data-raw/wrap_modify_pubmed_db.R
data-raw/wrap_modify_pubmed_db.yml
inst/extdata/data_dictionary.csv
inst/extdata/pgpass
inst/extdata/pubmed20n1016.xml.gz
lint_ignore.csv
man/getCitation.Rd
man/getPgParams.Rd
man/modifyPubmedDb.Rd
man/parseElement.Rd
pmparser.Rproj
tests/testthat.R
tests/testthat/parsing_tables/create_parsing_tables_no_suffix.db
tests/testthat/parsing_tables/create_parsing_tables_with_suffix.db
tests/testthat/parsing_tables/get_parsing_tables_no_suffix.rds
tests/testthat/parsing_tables/get_parsing_tables_with_suffix.rds
tests/testthat/pgpass
tests/testthat/pubmed_no_rows.xml
tests/testthat/pubmed_sample/baseline/pubmed25n1274.xml.gz
tests/testthat/pubmed_sample/baseline/pubmed25n1274.xml.gz.md5
tests/testthat/pubmed_sample/file_info_postdown.csv
tests/testthat/pubmed_sample/file_info_predown_all.csv
tests/testthat/pubmed_sample/file_info_predown_baseline.csv
tests/testthat/pubmed_sample/open_citation_collection.zip
tests/testthat/pubmed_sample/pmdb_sample_create.db
tests/testthat/pubmed_sample/pmdb_sample_update.db
tests/testthat/pubmed_sample/pubmed25n1274.rds
tests/testthat/pubmed_sample/pubmed25n1275.rds
tests/testthat/pubmed_sample/updatefiles/pubmed25n1275.xml.gz
tests/testthat/pubmed_sample/updatefiles/pubmed25n1275.xml.gz.md5
tests/testthat/setup.R
tests/testthat/test_get_citation.R
tests/testthat/test_get_parse_funcs.R
tests/testthat/test_get_parsing_tables.R
tests/testthat/test_get_pubmed_files.R
tests/testthat/test_get_xml_info.R
tests/testthat/test_modify_pubmed_db_dup.R
tests/testthat/test_modify_pubmed_db_std.R
tests/testthat/test_parse_element.R
tests/testthat/test_parse_element_no_rows.R
tests/testthat/test_utilities.R
vignettes/.gitignore
vignettes/data_dictionary.Rmd
