From b5b8235ede0de562cdbd63f4c91af964062d0fb3 Mon Sep 17 00:00:00 2001
From: Meera <patelm9@mskcc.org>
Date: Fri, 27 Nov 2020 13:14:04 -0500
Subject: [PATCH] update Package and GitHub Page

---
 docs/pkgdown.yml                               | 2 +-
 docs/reference/chemidplus_tables_to_omop.html  | 2 +-
 docs/reference/export_schema_to_data_repo.html | 8 ++++----
 docs/reference/get_dictionary_and_links.html   | 2 +-
 docs/reference/get_drug_dictionary.html        | 2 +-
 docs/reference/get_ncit_synonym.html           | 2 +-
 docs/reference/isMultipleHits.html             | 2 +-
 docs/reference/lookup_ncit_synonym.html        | 2 +-
 docs/reference/process_drug_link_ncit.html     | 2 +-
 docs/reference/schema_status.html              | 2 +-
 docs/reference/update_schemas.html             | 4 ++--
 11 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index a04d9d0..68300d6 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 2.7.3
 pkgdown: 1.6.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2020-11-26T04:02Z
+last_built: 2020-11-27T18:13Z
 
diff --git a/docs/reference/chemidplus_tables_to_omop.html b/docs/reference/chemidplus_tables_to_omop.html
index 35d8239..fa37464 100644
--- a/docs/reference/chemidplus_tables_to_omop.html
+++ b/docs/reference/chemidplus_tables_to_omop.html
@@ -128,7 +128,7 @@ <h1>ETL the ChemiDPlus Tables to OMOP Vocabulary Architecture</h1>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='https://meerapatelmd.github.io/pg13/reference/lsTables.html'>lsTables</a></code>,<code><a href='https://meerapatelmd.github.io/pg13/reference/readTable.html'>readTable</a></code>,<code><a href='https://meerapatelmd.github.io/pg13/reference/query.html'>query</a></code>,<code><a href='https://meerapatelmd.github.io/pg13/reference/appendTable.html'>appendTable</a></code>
-<code><a href='https://rdrr.io/pkg/rubix/man/map_names_set.html'>map_names_set</a></code>, <code><a href='https://rdrr.io/pkg/rubix/man/normalize_all_to_na.html'>normalize_all_to_na</a></code>,<code><a href='https://rdrr.io/pkg/rubix/man/make_identifier.html'>make_identifier</a></code>
+<code><a href='https://meerapatelmd.github.io/rubix/reference/map_names_set.html'>map_names_set</a></code>, <code><a href='https://meerapatelmd.github.io/rubix/reference/normalize_all_to_na.html'>normalize_all_to_na</a></code>,<code><a href='https://meerapatelmd.github.io/rubix/reference/make_identifier.html'>make_identifier</a></code>
 <code><a href='https://purrr.tidyverse.org/reference/map.html'>map</a></code>,<code><a href='https://purrr.tidyverse.org/reference/map2.html'>map2</a></code>
 <code><a href='https://tibble.tidyverse.org/reference/as_tibble.html'>as_tibble</a></code>
 <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></code>,<code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></code>,<code><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></code>,<code><a href='https://dplyr.tidyverse.org/reference/distinct.html'>distinct</a></code>,<code><a href='https://dplyr.tidyverse.org/reference/mutate-joins.html'>mutate-joins</a></code>,<code><a href='https://dplyr.tidyverse.org/reference/filter_all.html'>filter_all</a></code>,<code><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></code>
diff --git a/docs/reference/export_schema_to_data_repo.html b/docs/reference/export_schema_to_data_repo.html
index a3bdcb5..43968d4 100644
--- a/docs/reference/export_schema_to_data_repo.html
+++ b/docs/reference/export_schema_to_data_repo.html
@@ -157,20 +157,20 @@ <h2 class="hasAnchor" id="exporting-schemas"><a class="anchor" href="#exporting-
 <p>Exporting schemas requires having a local clone of its Data Package Repository. The tables for the given schema are written to csvs in the "data-raw/", along with a refresh of DATASET.R where the usethis::use_raw_data() function is called. The R/data.R is also rewritten with updates on the dataframe dimensions. The updated local repo is then repackaged and pushed to the remote.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
-    <div class='dont-index'><p><code><a href='https://rdrr.io/pkg/cave/man/create_dir_if_not_exist.html'>create_dir_if_not_exist</a></code>
+    <div class='dont-index'><p><code><a href='https://meerapatelmd.github.io/cave/reference/create_dir_if_not_exist.html'>create_dir_if_not_exist</a></code>
 <code><a href='https://meerapatelmd.github.io/chariot/reference/connectAthena.html'>connectAthena</a></code>,<code><a href='https://meerapatelmd.github.io/chariot/reference/dcAthena.html'>dcAthena</a></code>
 <code><a href='https://meerapatelmd.github.io/pg13/reference/lsTables.html'>lsTables</a></code>,<code><a href='https://meerapatelmd.github.io/pg13/reference/readTable.html'>readTable</a></code>
-<code><a href='https://rdrr.io/pkg/rubix/man/map_names_set.html'>map_names_set</a></code>
+<code><a href='https://meerapatelmd.github.io/rubix/reference/map_names_set.html'>map_names_set</a></code>
 <code><a href='https://purrr.tidyverse.org/reference/map2.html'>map2</a></code>,<code><a href='https://purrr.tidyverse.org/reference/map.html'>map</a></code>
 <code><a href='https://meerapatelmd.github.io/broca/reference/simply_write_csv.html'>simply_write_csv</a></code>
 <code><a href='https://readr.tidyverse.org/reference/read_lines.html'>read_lines</a></code>
 <code><a href='https://rdrr.io/pkg/sinew/man/makeOxygen.html'>makeOxygen</a></code>
 <code><a href='https://stringr.tidyverse.org/reference/str_replace.html'>str_replace</a></code>
 <code><a href='https://rdrr.io/pkg/glitter/man/docPushInstall.html'>docPushInstall</a></code></p>
-<p><code><a href='https://rdrr.io/pkg/cave/man/create_dir_if_not_exist.html'>create_dir_if_not_exist</a></code>
+<p><code><a href='https://meerapatelmd.github.io/cave/reference/create_dir_if_not_exist.html'>create_dir_if_not_exist</a></code>
 <code><a href='https://meerapatelmd.github.io/chariot/reference/connectAthena.html'>connectAthena</a></code>,<code><a href='https://meerapatelmd.github.io/chariot/reference/dcAthena.html'>dcAthena</a></code>
 <code><a href='https://meerapatelmd.github.io/pg13/reference/lsTables.html'>lsTables</a></code>,<code><a href='https://meerapatelmd.github.io/pg13/reference/readTable.html'>readTable</a></code>
-<code><a href='https://rdrr.io/pkg/rubix/man/map_names_set.html'>map_names_set</a></code>
+<code><a href='https://meerapatelmd.github.io/rubix/reference/map_names_set.html'>map_names_set</a></code>
 <code><a href='https://purrr.tidyverse.org/reference/map2.html'>map2</a></code>,<code><a href='https://purrr.tidyverse.org/reference/map.html'>map</a></code>
 <code><a href='https://meerapatelmd.github.io/broca/reference/simply_write_csv.html'>simply_write_csv</a></code>
 <code><a href='https://readr.tidyverse.org/reference/read_lines.html'>read_lines</a></code>
diff --git a/docs/reference/get_dictionary_and_links.html b/docs/reference/get_dictionary_and_links.html
index 4d17b03..9f37b44 100644
--- a/docs/reference/get_dictionary_and_links.html
+++ b/docs/reference/get_dictionary_and_links.html
@@ -157,7 +157,7 @@ <h2 class="hasAnchor" id="drug-dictionary"><a class="anchor" href="#drug-diction
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='https://tibble.tidyverse.org/reference/tibble.html'>tibble</a></code>
-<code><a href='https://rdrr.io/pkg/secretary/man/typewrite.html'>typewrite</a></code>
+<code><a href='https://meerapatelmd.github.io/secretary/reference/typewrite.html'>typewrite</a></code>
 <code><a href='http://xml2.r-lib.org/reference/read_xml.html'>read_xml</a></code>
 <code><a href='https://rvest.tidyverse.org/reference/html_nodes.html'>html_nodes</a></code>,<code><a href='https://rvest.tidyverse.org/reference/html_text.html'>html_text</a></code>
 <code><a href='https://purrr.tidyverse.org/reference/map.html'>map</a></code>,<code><a href='https://purrr.tidyverse.org/reference/keep.html'>keep</a></code>,<code><a href='https://purrr.tidyverse.org/reference/transpose.html'>transpose</a></code>
diff --git a/docs/reference/get_drug_dictionary.html b/docs/reference/get_drug_dictionary.html
index b6d3e05..249f99b 100644
--- a/docs/reference/get_drug_dictionary.html
+++ b/docs/reference/get_drug_dictionary.html
@@ -149,7 +149,7 @@ <h2 class="hasAnchor" id="drug-dictionary"><a class="anchor" href="#drug-diction
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='https://tibble.tidyverse.org/reference/tibble.html'>tibble</a></code>
-<code><a href='https://rdrr.io/pkg/secretary/man/typewrite.html'>typewrite</a></code>
+<code><a href='https://meerapatelmd.github.io/secretary/reference/typewrite.html'>typewrite</a></code>
 <code><a href='http://xml2.r-lib.org/reference/read_xml.html'>read_xml</a></code>
 <code><a href='https://rvest.tidyverse.org/reference/html_nodes.html'>html_nodes</a></code>,<code><a href='https://rvest.tidyverse.org/reference/html_text.html'>html_text</a></code>
 <code><a href='https://purrr.tidyverse.org/reference/map.html'>map</a></code>,<code><a href='https://purrr.tidyverse.org/reference/keep.html'>keep</a></code>,<code><a href='https://purrr.tidyverse.org/reference/transpose.html'>transpose</a></code>
diff --git a/docs/reference/get_ncit_synonym.html b/docs/reference/get_ncit_synonym.html
index 21fb3eb..4f83157 100644
--- a/docs/reference/get_ncit_synonym.html
+++ b/docs/reference/get_ncit_synonym.html
@@ -145,7 +145,7 @@ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See a
 <code><a href='https://rvest.tidyverse.org/reference/html_nodes.html'>html_nodes</a></code>,<code><a href='https://rvest.tidyverse.org/reference/html_table.html'>html_table</a></code>
 <code><a href='https://purrr.tidyverse.org/reference/keep.html'>keep</a></code>
 <code><a href='https://dplyr.tidyverse.org/reference/bind.html'>bind</a></code>,<code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></code>,<code><a href='https://dplyr.tidyverse.org/reference/select_all.html'>select_all</a></code>
-<code><a href='https://rdrr.io/pkg/rubix/man/format_colnames.html'>format_colnames</a></code></p></div>
+<code><a href='https://meerapatelmd.github.io/rubix/reference/format_colnames.html'>format_colnames</a></code></p></div>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='cn'>FALSE</span><span class='op'>)</span> <span class='op'>{</span>
diff --git a/docs/reference/isMultipleHits.html b/docs/reference/isMultipleHits.html
index 67230e1..a69b07a 100644
--- a/docs/reference/isMultipleHits.html
+++ b/docs/reference/isMultipleHits.html
@@ -137,7 +137,7 @@ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See a
 
     <div class='dont-index'><p><code><a href='https://rvest.tidyverse.org/reference/html_nodes.html'>html_nodes</a></code>,<code><a href='https://rvest.tidyverse.org/reference/html_text.html'>html_text</a></code>
 <code><a href='https://tibble.tidyverse.org/reference/as_tibble.html'>as_tibble</a></code>
-<code><a href='https://rdrr.io/pkg/rubix/man/filter_at_grepl.html'>filter_at_grepl</a></code>
+<code><a href='https://meerapatelmd.github.io/rubix/reference/filter_at_grepl.html'>filter_at_grepl</a></code>
 <code><a href='https://tidyr.tidyverse.org/reference/extract.html'>extract</a></code>
 <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></code>,<code><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_all</a></code>
 <code><a href='https://stringr.tidyverse.org/reference/str_remove.html'>str_remove</a></code></p>
diff --git a/docs/reference/lookup_ncit_synonym.html b/docs/reference/lookup_ncit_synonym.html
index b2485cd..a9889fe 100644
--- a/docs/reference/lookup_ncit_synonym.html
+++ b/docs/reference/lookup_ncit_synonym.html
@@ -145,7 +145,7 @@ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See a
 <code><a href='https://rvest.tidyverse.org/reference/html_nodes.html'>html_nodes</a></code>,<code><a href='https://rvest.tidyverse.org/reference/html_table.html'>html_table</a></code>
 <code><a href='https://purrr.tidyverse.org/reference/keep.html'>keep</a></code>
 <code><a href='https://dplyr.tidyverse.org/reference/bind.html'>bind</a></code>,<code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></code>,<code><a href='https://dplyr.tidyverse.org/reference/select_all.html'>select_all</a></code>
-<code><a href='https://rdrr.io/pkg/rubix/man/format_colnames.html'>format_colnames</a></code></p></div>
+<code><a href='https://meerapatelmd.github.io/rubix/reference/format_colnames.html'>format_colnames</a></code></p></div>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/reference/process_drug_link_ncit.html b/docs/reference/process_drug_link_ncit.html
index 643601e..d6e4cbe 100644
--- a/docs/reference/process_drug_link_ncit.html
+++ b/docs/reference/process_drug_link_ncit.html
@@ -145,7 +145,7 @@ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See a
 
     <div class='dont-index'><p><code><a href='https://meerapatelmd.github.io/pg13/reference/lsTables.html'>lsTables</a></code>,<code><a href='https://meerapatelmd.github.io/pg13/reference/query.html'>query</a></code>,<code><a href='https://meerapatelmd.github.io/pg13/reference/buildQuery.html'>buildQuery</a></code>,<code><a href='https://meerapatelmd.github.io/pg13/reference/readTable.html'>readTable</a></code>,<code><a href='https://meerapatelmd.github.io/pg13/reference/dropTable.html'>dropTable</a></code>,<code><a href='https://meerapatelmd.github.io/pg13/reference/writeTable.html'>writeTable</a></code>,<code><a href='https://meerapatelmd.github.io/pg13/reference/appendTable.html'>appendTable</a></code>
 <code><a href='https://dplyr.tidyverse.org/reference/mutate-joins.html'>mutate-joins</a></code>,<code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></code>,<code><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></code>,<code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></code>
-<code><a href='https://rdrr.io/pkg/rubix/man/filter_at_grepl.html'>filter_at_grepl</a></code>
+<code><a href='https://meerapatelmd.github.io/rubix/reference/filter_at_grepl.html'>filter_at_grepl</a></code>
 <code><a href='https://tidyr.tidyverse.org/reference/extract.html'>extract</a></code></p>
 <p>Other cancergov: 
 <code><a href='get_dictionary_and_links.html'>get_dictionary_and_links</a>()</code>,
diff --git a/docs/reference/schema_status.html b/docs/reference/schema_status.html
index ec72b9e..fc33464 100644
--- a/docs/reference/schema_status.html
+++ b/docs/reference/schema_status.html
@@ -127,7 +127,7 @@ <h2 class="hasAnchor" id="check-schema-status"><a class="anchor" href="#check-sc
 <p>All the Data Packages in the Schema Map returned by <code><a href='load_schema_map.html'>load_schema_map</a></code> are installed if there are changes to the SHA hash. An "updated" field is added to the Schema Map that contain the values of TRUE if a new installation occurred and FALSE otherwise. If an update to the schema is desired after running this function, <code><a href='import_schemas.html'>update_schemas</a></code>, should be run with <code>force_update</code> set to <code>TRUE</code>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
-    <div class='dont-index'><p><code><a href='https://rdrr.io/pkg/rubix/man/filter_for.html'>filter_for</a></code>
+    <div class='dont-index'><p><code><a href='https://meerapatelmd.github.io/rubix/reference/filter_for.html'>filter_for</a></code>
 <code><a href='https://purrr.tidyverse.org/reference/map.html'>map</a></code>
 <code><a href='https://rdrr.io/r/utils/capture.output.html'>capture.output</a></code>
 <code><a href='https://devtools.r-lib.org//reference/remote-reexports.html'>remote-reexports</a></code></p>
diff --git a/docs/reference/update_schemas.html b/docs/reference/update_schemas.html
index 4763340..b19f313 100644
--- a/docs/reference/update_schemas.html
+++ b/docs/reference/update_schemas.html
@@ -163,14 +163,14 @@ <h2 class="hasAnchor" id="update-schemas"><a class="anchor" href="#update-schema
 <p>Checking Schema Status is not a required prerequisite to update skyscraper schemas. However, if the status is checked before running an update, the update needs to be run with force_update set to <code>TRUE</code> since the execution of the update occurs on the condition of requiring a new installation, which the <code><a href='schema_status.html'>schema_status</a></code> would have already executed.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
-    <div class='dont-index'><p><code><a href='https://rdrr.io/pkg/rubix/man/filter_for.html'>filter_for</a></code>,<code><a href='https://rdrr.io/pkg/rubix/man/map_names_set.html'>map_names_set</a></code>
+    <div class='dont-index'><p><code><a href='https://meerapatelmd.github.io/rubix/reference/filter_for.html'>filter_for</a></code>,<code><a href='https://meerapatelmd.github.io/rubix/reference/map_names_set.html'>map_names_set</a></code>
 <code><a href='https://purrr.tidyverse.org/reference/map.html'>map</a></code>,<code><a href='https://purrr.tidyverse.org/reference/map2.html'>map2</a></code>
 <code><a href='https://rdrr.io/r/utils/capture.output.html'>capture.output</a></code>
 <code><a href='https://devtools.r-lib.org//reference/remote-reexports.html'>remote-reexports</a></code>
 <code><a href='https://meerapatelmd.github.io/pg13/reference/dropSchema.html'>dropSchema</a></code>,<code><a href='https://meerapatelmd.github.io/pg13/reference/createSchema.html'>createSchema</a></code>,<code><a href='https://meerapatelmd.github.io/pg13/reference/writeTable.html'>writeTable</a></code>
 <code><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_all</a></code>
 <code><a href='http://lubridate.tidyverse.org/reference/ymd_hms.html'>ymd_hms</a></code></p>
-<p><code><a href='https://rdrr.io/pkg/rubix/man/filter_for.html'>filter_for</a></code>,<code><a href='https://rdrr.io/pkg/rubix/man/map_names_set.html'>map_names_set</a></code>
+<p><code><a href='https://meerapatelmd.github.io/rubix/reference/filter_for.html'>filter_for</a></code>,<code><a href='https://meerapatelmd.github.io/rubix/reference/map_names_set.html'>map_names_set</a></code>
 <code><a href='https://purrr.tidyverse.org/reference/map.html'>map</a></code>,<code><a href='https://purrr.tidyverse.org/reference/map2.html'>map2</a></code>
 <code><a href='https://rdrr.io/r/utils/capture.output.html'>capture.output</a></code>
 <code><a href='https://devtools.r-lib.org//reference/remote-reexports.html'>remote-reexports</a></code>