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# Installation
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## R package
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Achilles is a R package available [here](https://github.com/OHDSI/Achilles).
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To install Achilles package, you need to use `devtools::install_github()` function.
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```r
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devtools::install_github("OHDSI/Achilles")
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```
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## SQL results tables
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The output table of the Achilles statistic computation need to be created before run Achilles analysis:
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- ACHILLES_RESULTS
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- ACHILLES_HEEL
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- ACHILLES_RESULTS_CONCEPT_COUNT
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- ACHILLES_RESULTS_DIST
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The scripts are available bellow. They must be run in the OMOP result scheme.
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```sql
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CREATE TABLE ACHILLES_RESULTS
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(
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ANALYSIS_ID NUMBER(38)
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, STRATUM_1 VARCHAR2(255)
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, STRATUM_2 VARCHAR2(255)
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, STRATUM_3 VARCHAR2(255)
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, STRATUM_4 VARCHAR2(255)
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, STRATUM_5 VARCHAR2(255)
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, COUNT_VALUE NUMBER(38)
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);
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```
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```sql
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CREATE TABLE ACHILLES_HEEL
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(
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ANALYSIS_ID NUMBER(38)
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, ACHILLES_HEEL_WARNING VARCHAR2(255)
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, RULE_ID NUMBER(38)
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, RECORD_COUNT NUMBER(38)
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);
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```
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```sql
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CREATE TABLE ACHILLES_RESULTS_CONCEPT_COUNT
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(
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CONCEPT_ID NUMBER(38)
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, RECORD_COUNT NUMBER(38)
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, DESCENDANT_RECORD_COUNT NUMBER(38)
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);
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```
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```sql
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CREATE TABLE ACHILLES_RESULTS_DIST
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(
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ANALYSIS_ID NUMBER(38)
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, STRATUM_1 VARCHAR2(255)
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, STRATUM_2 VARCHAR2(255)
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, STRATUM_3 VARCHAR2(255)
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, STRATUM_4 VARCHAR2(255)
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, STRATUM_5 VARCHAR2(255)
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, COUNT_VALUE NUMBER(38)
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, MIN_VALUE FLOAT
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, MAX_VALUE FLOAT
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, AVG_VALUE FLOAT
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, STDEV_VALUE FLOAT
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, MEDIAN_VALUE FLOAT
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, P10_VALUE FLOAT
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, P25_VALUE FLOAT
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, P75_VALUE FLOAT
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, P90_VALUE FLOAT
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);
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```
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# Statistic computation
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## Connexion
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A connexion to the OMOP database is created by the `Achilles::createConnectionDetails()` function.
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An example of connexion is avalable bellow.
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```r
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connectionDetails <- Achilles::createConnectionDetails(
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dbms = 'oracle',
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user = '[USER]',
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password = '[PASSWORD]',
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connectionString = 'jdbc:oracle:thin:@[SID]:[PORT]:[DBNAME]'
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)
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```
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## Analysis
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Statistic computation are generated by the `Achilles::achilles()` function.
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```r
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Achilles::achilles(
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connectionDetails = connectionDetails,
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cdmDatabaseSchema = 'omop',
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resultsDatabaseSchema = 'omop_temp',
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vocabDatabaseSchema = 'omop',
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numThreads = 1,
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sourceName = 'Achilles',
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cdmVersion = '5.3.0',
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runHeel = FALSE,
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optimizeAtlasCache = TRUE,
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createTable = FALSE
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)
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``` |
