From 9e3740e38c681c46106ba27d1a0fc82c4ed184d1 Mon Sep 17 00:00:00 2001 From: Adam Black Date: Sun, 7 Jul 2024 20:20:42 +0200 Subject: [PATCH] remove visR. update docs --- .github/workflows/R-CMD-check.yaml | 1 - CRAN-SUBMISSION | 3 + DESCRIPTION | 1 - docs/404.html | 2 +- docs/CONTRIBUTING.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/a01_getting-started.html | 150 ++++++----- docs/articles/a02_cohorts.html | 249 +++++++++--------- docs/articles/a03_dbplyr.html | 2 +- .../articles/a04_DBI_connection_examples.html | 2 +- docs/articles/a05_cdm_reference_backends.html | 2 +- docs/articles/a06_using_cdm_attributes.html | 51 ++-- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 24 +- docs/news/index.html | 11 +- docs/pkgdown.yml | 2 +- docs/reference/CDMConnector-package.html | 2 +- docs/reference/appendPermanent.html | 2 +- docs/reference/asDate.html | 2 +- docs/reference/assert_tables.html | 2 +- docs/reference/assert_write_schema.html | 2 +- docs/reference/benchmarkCDMConnector.html | 2 +- docs/reference/cdmCon.html | 2 +- docs/reference/cdmDisconnect.html | 15 +- docs/reference/cdmFlatten.html | 2 +- docs/reference/cdmName.html | 2 +- docs/reference/cdmSample.html | 2 +- docs/reference/cdmSubset.html | 2 +- docs/reference/cdmSubsetCohort.html | 2 +- docs/reference/cdmWriteSchema.html | 2 +- docs/reference/cdm_from_con.html | 78 +++++- docs/reference/cdm_from_environment.html | 2 +- docs/reference/cdm_from_files.html | 2 +- docs/reference/cdm_from_tables.html | 145 ++++++++++ docs/reference/cdm_select_tbl.html | 2 +- docs/reference/cohortAttrition.html | 2 +- docs/reference/cohortSet.html | 2 +- docs/reference/cohort_count.html | 2 +- docs/reference/cohort_erafy.html | 2 +- docs/reference/cohort_union.html | 2 +- docs/reference/computeQuery.html | 2 +- docs/reference/copy_cdm_to.html | 2 +- docs/reference/dateadd.html | 2 +- docs/reference/datediff.html | 2 +- docs/reference/datepart.html | 2 +- docs/reference/dbSource.html | 2 +- docs/reference/dbms.html | 2 +- docs/reference/downloadEunomiaData.html | 2 +- docs/reference/eunomiaDir.html | 2 +- docs/reference/eunomia_is_available.html | 2 +- docs/reference/exampleDatasets.html | 2 +- docs/reference/generateCohortSet.html | 2 +- docs/reference/generateConceptCohortSet.html | 2 +- docs/reference/inSchema.html | 2 +- docs/reference/index.html | 7 +- docs/reference/intersect_cohorts.html | 2 +- docs/reference/list_tables.html | 2 +- docs/reference/new_generated_cohort_set.html | 2 +- docs/reference/pipe.html | 2 +- docs/reference/read_cohort_set.html | 2 +- docs/reference/recordCohortAttrition.html | 2 +- docs/reference/reexports.html | 24 +- docs/reference/snapshot.html | 2 +- docs/reference/stow.html | 2 +- docs/reference/summarise_quantile.html | 2 +- docs/reference/tbl_group.html | 2 +- docs/reference/union_cohorts.html | 2 +- docs/reference/uniqueTableName.html | 2 +- docs/reference/validate_cdm.html | 2 +- docs/reference/version.html | 2 +- docs/search.json | 2 +- docs/sitemap.xml | 3 + vignettes/a02_cohorts.Rmd | 9 - 74 files changed, 586 insertions(+), 303 deletions(-) create mode 100644 CRAN-SUBMISSION create mode 100644 docs/reference/cdm_from_tables.html diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 191fc481..c9f55f02 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -57,7 +57,6 @@ jobs: install.packages("bigrquery") install.packages("arrow") install.packages("tibble") - install.packages("visR") install.packages("tictoc") install.packages("palmerpenguins") shell: Rscript {0} diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION new file mode 100644 index 00000000..5c644a8e --- /dev/null +++ b/CRAN-SUBMISSION @@ -0,0 +1,3 @@ +Version: 1.4.1 +Date: 2024-07-05 11:03:50 UTC +SHA: 5c74d7f8ffed89fce7208f9f38102e99259ef821 diff --git a/DESCRIPTION b/DESCRIPTION index b6319e66..90b55c92 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -61,7 +61,6 @@ Suggests: testthat (>= 3.0.0), pool, snakecase, - visR, palmerpenguins, tictoc Enhances: diff --git a/docs/404.html b/docs/404.html index df839c96..d860495d 100644 --- a/docs/404.html +++ b/docs/404.html @@ -24,7 +24,7 @@ CDMConnector - 1.4.0 + 1.4.1 + + + + + +
+
+
+

Create a cdm object from local tables

+ Source: R/reexports-omopgenerics.R +
cdm_from_tables.Rd
+
+ +
+

Create a cdm object from local tables

+
+ +
+

Usage

+ 
cdm_from_tables(tables, cdm_name, cohort_tables = list(), cdm_version = NULL)
+
+ +
+

Arguments

+
tables
+

List of tables to be part of the cdm object.

+ + +
cdm_name
+

Name of the cdm object.

+ + +
cohort_tables
+

List of tables that contains cohort, cohort_set and +cohort_attrition can be provided as attributes.

+ + +
cdm_version
+

Version of the cdm_reference

+ +
+
+

Value

+ + +

A cdm_reference object.

+
+ +
+

Examples

+ 
# \donttest{
+library(omopgenerics)
+#> Warning: package ‘omopgenerics’ was built under R version 4.3.3
+#> 
+#> Attaching package: ‘omopgenerics’
+#> The following objects are masked from ‘package:CDMConnector’:
+#> 
+#>     cdmName, recordCohortAttrition, uniqueTableName
+#> The following object is masked from ‘package:stats’:
+#> 
+#>     filter
+library(dplyr, warn.conflicts = FALSE)
+
+person <- tibble(
+  person_id = 1, gender_concept_id = 0, year_of_birth = 1990,
+  race_concept_id = 0, ethnicity_concept_id = 0
+)
+observation_period <- tibble(
+  observation_period_id = 1, person_id = 1,
+  observation_period_start_date = as.Date("2000-01-01"),
+  observation_period_end_date = as.Date("2025-12-31"),
+  period_type_concept_id = 0
+)
+cdm <- cdm_from_tables(
+  tables = list("person" = person, "observation_period" = observation_period),
+  cdm_name = "test"
+)
+# }
+
+
+
+ + +
+

Developed by Adam Black, Artem Gorbachev, Edward Burn, Marti Catala Sabate.

+
+ +
+

Site built with pkgdown 2.0.9.

+
+ +
+ + + + + + + diff --git a/docs/reference/cdm_select_tbl.html b/docs/reference/cdm_select_tbl.html index c21cd1ed..7a137177 100644 --- a/docs/reference/cdm_select_tbl.html +++ b/docs/reference/cdm_select_tbl.html @@ -12,7 +12,7 @@ CDMConnector - 1.4.0 + 1.4.1