documentation:software:atlas:achilles_v_1_5
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documentation:software:atlas:achilles_v_1_5 [2017/10/11 16:12] anthonysena |
documentation:software:atlas:achilles_v_1_5 [2018/03/12 14:36] anthonysena [Concept Hierarchy] |
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| ===== TL;DR ===== | ===== TL;DR ===== | ||
| - | If you complete a full run of Achilles v.1.5.0 on your OMOP CDM v5 with the default settings, you will not need to complete any of the steps in this article. If you have an OMOP CDM v5 and you ran Achilles in the past (prior to v.1.5.0) then you will need to read and complete the steps below to work with WebAPI/Atlas V2.2.0. | + | If you complete a full run of Achilles v.1.5.0 on your OMOP CDM v5 with the default settings, you will not need to complete any of the steps in this article. If you have an OMOP CDM v5 and you ran Achilles in the past (prior to v.1.5.0) then you will need to read and complete the steps below to work with WebAPI/Atlas V2.2.0. If you'd like to run a command to apply all of the new changes, scroll to the bottom of the article. |
| Resources: | Resources: | ||
| Line 17: | Line 17: | ||
| ====== Achilles v1.5.0 Changes Impacting WebAPI/Atlas ====== | ====== Achilles v1.5.0 Changes Impacting WebAPI/Atlas ====== | ||
| - | The following sections will describe the additions in Achilles V1.5.0, how to verify if you have the additional dependencies required by WebAPI/Atlas and how to run Achilles R commands to make your Achilles installation compatible with WebAPI/Atlas V2.2.0. | + | The following sections will describe the additions in Achilles V1.5.0, how to verify if you have the additional dependencies required by WebAPI/Atlas and how to run Achilles R commands to make your Achilles installation compatible with WebAPI/Atlas V2.2.0. Each section will describe the changes and how to make each change individually. If you would like to apply all of the changes in a single step, skip to the bottom as this can be done in a single command. |
| ===== Concept Hierarchy ===== | ===== Concept Hierarchy ===== | ||
| Line 23: | Line 23: | ||
| Achilles will now construct a new table in the results schema labeled ''concept_hierarchy'' using the OMOP vocabulary found in the CDM. This one-time operation is used to optimize query performance when by WebAPI against the ''ACHILLES_results'' table. | Achilles will now construct a new table in the results schema labeled ''concept_hierarchy'' using the OMOP vocabulary found in the CDM. This one-time operation is used to optimize query performance when by WebAPI against the ''ACHILLES_results'' table. | ||
| + | **Please Note**: If you update the vocabulary in your CDM, you should re-create (and re-index) the concept_hierarchy table. | ||
| ==== Creating the Concept Hierarchy ==== | ==== Creating the Concept Hierarchy ==== | ||
| Line 56: | Line 57: | ||
| resultsDatabaseSchema = resultsSchema) | resultsDatabaseSchema = resultsSchema) | ||
| | | ||
| - | Once these steps are complete, you are ready to start using WebAPI/Atlas 2.2! | + | ===== New Frequency Distribution Analyses ===== |
| + | |||
| + | While these analyses are not mandatory to run WebAPI/Atlas 2.2, these new analyses will be surfaced in Atlas. These new analyses will compute the distribution of a concept, how often the concept is used and the percentage of people with the count of that concept. | ||
| + | |||
| + | ==== Creating the analyses ==== | ||
| + | |||
| + | The following command will be used to create these new analyses: | ||
| + | |||
| + | connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "postgresql", | ||
| + | server = "localhost/ohdsi", | ||
| + | user = "joe", | ||
| + | password = "supersecret") | ||
| + | cdmDatabaseSchema <- "my_cdm_schema_goes_here" | ||
| + | resultsDatabaseSchema <- "my_results_schema_goes_here" | ||
| + | vocabDatabaseSchema <- "my_vocabulary_schema_goes_here" | ||
| + | db <- "my_cdm_database_name" | ||
| + | achillesResults <- Achilles::achilles(connectionDetails, | ||
| + | cdmDatabaseSchema = cdmDatabaseSchema, | ||
| + | oracleTempSchema = NULL, | ||
| + | resultsDatabaseSchema = resultsDatabaseSchema, | ||
| + | sourceName = db, | ||
| + | analysisIds = c(691,791,891,1891), | ||
| + | createTable = FALSE, | ||
| + | smallcellcount = 5, | ||
| + | cdmVersion = "5", | ||
| + | runHeel = FALSE, | ||
| + | validateSchema = FALSE, | ||
| + | vocabDatabaseSchema = vocabDatabaseSchema, | ||
| + | runCostAnalysis = FALSE, | ||
| + | sqlOnly = FALSE, | ||
| + | conceptHierarchy = FALSE, | ||
| + | createIndices = FALSE) | ||
| + | |||
| + | Please note the command above sets both the conceptHierarchy and createIndices parameters to **FALSE**. | ||
| + | |||
| + | ====== Apply All Changes In One Step ====== | ||
| + | |||
| + | The following command can be used to apply all of the changes above in a single step: | ||
| + | |||
| + | connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "postgresql", | ||
| + | server = "localhost/ohdsi", | ||
| + | user = "joe", | ||
| + | password = "supersecret") | ||
| + | cdmDatabaseSchema <- "my_cdm_schema_goes_here" | ||
| + | resultsDatabaseSchema <- "my_results_schema_goes_here" | ||
| + | vocabDatabaseSchema <- "my_vocabulary_schema_goes_here" | ||
| + | db <- "my_cdm_database_name" | ||
| + | achillesResults <- Achilles::achilles(connectionDetails, | ||
| + | cdmDatabaseSchema = cdmDatabaseSchema, | ||
| + | oracleTempSchema = NULL, | ||
| + | resultsDatabaseSchema = resultsDatabaseSchema, | ||
| + | sourceName = db, | ||
| + | analysisIds = c(691,791,891,1891), | ||
| + | createTable = FALSE, | ||
| + | smallcellcount = 5, | ||
| + | cdmVersion = "5", | ||
| + | runHeel = FALSE, | ||
| + | validateSchema = FALSE, | ||
| + | vocabDatabaseSchema = vocabDatabaseSchema, | ||
| + | runCostAnalysis = FALSE, | ||
| + | sqlOnly = FALSE, | ||
| + | conceptHierarchy = TRUE, | ||
| + | createIndices = TRUE) | ||
documentation/software/atlas/achilles_v_1_5.txt · Last modified: 2018/03/12 14:36 by anthonysena
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