diff --git a/README.Rmd b/README.Rmd index 44ecc52..b2428b0 100644 --- a/README.Rmd +++ b/README.Rmd @@ -12,13 +12,13 @@ knitr::opts_chunk$set( ) ``` -# metacore +# metacore Metacore Package Hex Sticker -[](https://RValidationHub.slack.com) +[Slack Status](https://RValidationHub.slack.com) [![R build status](https://github.com/atorus-research/metacore/workflows/R-CMD-check/badge.svg)](https://github.com/atorus-research/xportr/actions?workflow=R-CMD-check) -[](https://app.codecov.io/gh/atorus-research/metacore) -[](https://github.com/atorus-research/metacore/blob/master/LICENSE) +[Codecov Coverage](https://app.codecov.io/gh/atorus-research/metacore) +[MIT License](https://github.com/atorus-research/metacore/blob/master/LICENSE) [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental-1) [![CRAN status](https://www.r-pkg.org/badges/version/metacore)](https://CRAN.R-project.org/package=metacore) [![R-CMD-check](https://github.com/atorus-research/metacore/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/atorus-research/metacore/actions/workflows/R-CMD-check.yaml) @@ -56,9 +56,9 @@ A metacore object is made-up of 6 different tables, which are connected with a s Here is a schema of how all this fits together: -![](man/figures/schema-colors.png "man/figures/Metacore Schema") +![Schema diagram showing the relationships between all metacore tables (variable names not included)](man/figures/schema-colors.png "man/figures/Metacore Schema") -### ds_spec +### ds_spec Diagram of ds_spec table structure This table covers the basic information about each dataset. There is only a single row per dataset, with the following information: @@ -68,7 +68,7 @@ This table covers the basic information about each dataset. There is only a sing - *label*: Dataset label -### ds_vars +### ds_vars Diagram of ds_vars table structure This table contains the information that bridges between purely dataset level and purely variable level. There is one row per dataset per variable: @@ -86,7 +86,7 @@ This table contains the information that bridges between purely dataset level an - *supp_flag*: Logical to determine if the variable is in the supplemental datasets -### var_spec +### var_spec Diagram of var_spec table structure This table contains the purely variable level information. The goal is there is a single row per variable, which is common across all datasets. This helps ensure variables follow the CDISC standard. But, this isn't always possible, so if information for a given variable differs across datasets, the variable will be recorded as dataset.variable in the variable column. @@ -102,7 +102,7 @@ This table contains the purely variable level information. The goal is there is - *format*: Variable format -### value_spec +### value_spec Diagram of value_spec table structure This table contains the information the information at the value level. There will be at least one row per dataset/variable combination. There is more than one row per dataset/variable combination if the combination has values which have differing metadata. For instance LBORRES that are different data types depending on the value. The information contained are as follows: @@ -122,7 +122,7 @@ This table contains the information the information at the value level. There wi - *derivation_id*: ID for the derivation to match with the **derivation** table -### derivations +### derivations Diagram of derivation table structure This table has all the derivation information, with one row per derivation ID and the following information: @@ -130,7 +130,7 @@ This table has all the derivation information, with one row per derivation ID an - *derivation*: Text describing the derivation -### codelist +### codelist Diagram of codelist table structure This table contains the code lists, permitted value lists, and external libraries nested within a tibble. There is only a single row per list/library, with the following information: @@ -144,7 +144,7 @@ This table contains the code lists, permitted value lists, and external librarie -### supp +### supp Diagram of supp table structure This table contains the information needed to create supplemental tables. If you want to add a variable which will go into a supplemental qualifier then you can create as normal (i.e. label information going to the **var_spec** table and derivation and origin going into the **value_spec** table), but you need to flag it as supplemental in the **ds_vars** table and add a row to the **supp** table. There is only a single row per dataset/variable, with the following information: @@ -159,7 +159,7 @@ This table contains the information needed to create supplemental tables. If you To get more information about the metacore objects and how to build a specification reader, please see our vignettes. -![](man/figures/labeled_schema.png "man/figures/Metacore Schema") +![Schema diagram showing the relationships between all metacore tables](man/figures/labeled_schema.png "man/figures/Metacore Schema") ## Future Development diff --git a/README.md b/README.md index 6413cf5..511b4f2 100644 --- a/README.md +++ b/README.md @@ -1,15 +1,15 @@ -# metacore +# metacore Metacore Package Hex Sticker -[](https://RValidationHub.slack.com) +[Slack Status](https://RValidationHub.slack.com) [![R build status](https://github.com/atorus-research/metacore/workflows/R-CMD-check/badge.svg)](https://github.com/atorus-research/xportr/actions?workflow=R-CMD-check) -[](https://app.codecov.io/gh/atorus-research/metacore) -[](https://github.com/atorus-research/metacore/blob/master/LICENSE) +[Codecov Coverage](https://app.codecov.io/gh/atorus-research/metacore) +[MIT License](https://github.com/atorus-research/metacore/blob/master/LICENSE) [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental-1) [![CRAN @@ -74,9 +74,15 @@ remember. They are as follows: Here is a schema of how all this fits together: -![](man/figures/schema-colors.png "man/figures/Metacore Schema") +
+ + +
-### ds_spec +### ds_spec Diagram of ds_spec table structure This table covers the basic information about each dataset. There is only a single row per dataset, with the following information: @@ -87,7 +93,7 @@ only a single row per dataset, with the following information: - *label*: Dataset label -### ds_vars +### ds_vars Diagram of ds_vars table structure This table contains the information that bridges between purely dataset level and purely variable level. There is one row per dataset per @@ -116,7 +122,7 @@ variable: - *supp_flag*: Logical to determine if the variable is in the supplemental datasets -### var_spec +### var_spec Diagram of var_spec table structure This table contains the purely variable level information. The goal is there is a single row per variable, which is common across all datasets. @@ -141,7 +147,7 @@ variable column. - *format*: Variable format -### value_spec +### value_spec Diagram of value_spec table structure This table contains the information the information at the value level. There will be at least one row per dataset/variable combination. There @@ -169,7 +175,7 @@ are as follows: - *derivation_id*: ID for the derivation to match with the **derivation** table -### derivations +### derivations Diagram of derivation table structure This table has all the derivation information, with one row per derivation ID and the following information: @@ -178,7 +184,7 @@ derivation ID and the following information: - *derivation*: Text describing the derivation -### codelist +### codelist Diagram of codelist table structure This table contains the code lists, permitted value lists, and external libraries nested within a tibble. There is only a single row per @@ -195,7 +201,7 @@ list/library, with the following information: - *type*: An indicator of if the information in the code column is a code/decode table, permitted value, or external library -### supp +### supp Diagram of supp table structure This table contains the information needed to create supplemental tables. If you want to add a variable which will go into a supplemental @@ -218,7 +224,13 @@ single row per dataset/variable, with the following information: To get more information about the metacore objects and how to build a specification reader, please see our vignettes. -![](man/figures/labeled_schema.png "man/figures/Metacore Schema") +
+ + +
## Future Development diff --git a/vignettes/Building_Specification_Readers.Rmd b/vignettes/Building_Specification_Readers.Rmd index 5bb7574..9ba7582 100644 --- a/vignettes/Building_Specification_Readers.Rmd +++ b/vignettes/Building_Specification_Readers.Rmd @@ -47,7 +47,7 @@ As we can see, the mock spec we are using here doesn't match the format. Therefo Here is a schema of how all this fits together -![](../man/figures/labeled_schema.png "Metacore Schema") +![Schema diagram showing the relationships between all metacore tables](../man/figures/labeled_schema.png "Metacore Schema") ds_spec is connected to ds_vars by the 'dataset' variable and ds_vars is connected to var_spec by the 'variable' variable, etc. For more information on the make-up of metacore objects please see the README.