minor clean-ups in R and SQL code (#135)

* extras folder creation

* update to rule overview file

* some changes hinted in #133

* #133 documentation improvement and cleanup of sql code

.Rbuildignore

@@ -1,2 +1,3 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^.travis.yml$

DESCRIPTION

@@ -3,7 +3,7 @@ Type: Package
 Title: Creates descriptive statistics summary for an entire OMOP CDM instance.
 Version: 1.3
 Date: 2016-06-10
-Author: Patrick Ryan, Martijn Schuemie
+Author: Patrick Ryan, Martijn Schuemie, Vojtech Huser, Chris Knoll
 Maintainer: Patrick Ryan <[email protected]>
 LazyData: true
 Description: creates descriptive statistics summary for an entire OMOP CDM

R/Achilles.R

@@ -172,6 +172,27 @@ achilles <- function (connectionDetails,
   result
 }
 
+#' execution of data quality rules 
+#'
+#' @description
+#' \code{achillesHeel} executes data quality rules (or checks) on pre-computed analyses (or measures).
+#'
+#' @details
+#' \code{achillesHeel} contains number of rules (authored in SQL) that are executed againts achilles results tables.
+#' 
+#' @param connectionDetails  An R object of type ConnectionDetail (details for the function that contains server info, database type, optionally username/password, port)
+#' @param cdmDatabaseSchema    	string name of database schema that contains OMOP CDM. On SQL Server, this should specifiy both the database and the schema, so for example 'cdm_instance.dbo'.
+#' @param oracleTempSchema    For Oracle only: the name of the database schema where you want all temporary tables to be managed. Requires create/insert permissions to this database. 
+#' @param resultsDatabaseSchema		string name of database schema that we can write results to. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.
+#' @param sourceName		string name of the database, as recorded in results
+#' @param cdmVersion     Define the OMOP CDM version used:  currently support "4" and "5".  Default = "4"
+#' @param vocabDatabaseSchema		string name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.
+#' 
+#' @return nothing is returned
+#' @examples \dontrun{
+#'   connectionDetails <- createConnectionDetails(dbms="sql server", server="RNDUSRDHIT07.jnj.com")
+#'   achillesHeel <- achilles(connectionDetails, cdmDatabaseSchema="mycdm", resultsDatabaseSchema="scratch", vocabDatabaseSchema="vocabulary")
+#' }
 #' @export
 achillesHeel <- function (connectionDetails, 
                       cdmDatabaseSchema, 

inst/csv/achilles_rule.csv

@@ -28,5 +28,8 @@ rule_id,rule_name,severity,rule_description
 26,implausible quantity for drug,warning,quantity > 600
 27,more than 1 percent of unmapped rows (concept_0 rows),warning,for multiple analyses (4xx;6xx;7xx;8xx;18xx)
 28,percentage of deceased patients,warning,fires if (deceased/all person count * 100)  is less than 1 (anusual if dataset represents a general healthcare data warehouse)
-29,infant diagnosis at senior age,error,mecconium condition
-31,ratio of providers to total patients,notification,ratio
+29,infant diagnosis at senior age of over 50yo,error,mecconium condition 195075; This rule is example of a terminology depended data quality tool
+31,ratio of providers to total patients,notification,ratio
+32,NOTIFICATION: Percentage of patients with no visits exceeds threshold,notification, checks if there are too many patients with no visits
+33,NOTIFICATION: [GeneralPopulationOnly] Not all deciles represented at first observation,notification, the rule only applies to general population datasets
+34,NOTIFICATION: Count of unmapped source values in a domain exceeds threshold,notification,looks at values that are mapped to concept0 and their source values by table