Running heel in newer versions of achilles

Implementers
1

Not sure if it’s an error, but in latest updated version of Achilles package I get this error message when launching the current analysis

achilles(connectionDetails,
          cdmDatabaseSchema = "omop",
          resultsDatabaseSchema="results",
          vocabDatabaseSchema = "omop",
          numThreads = 1,
          sourceName = "name",
          cdmVersion = "5.3.1",
          runHeel = TRUE,
          runCostAnalysis = FALSE)
Error in achilles(connectionDetails, cdmDatabaseSchema = "omop", resultsDatabaseSchema = "results",  : 
  unused arguments (runHeel = TRUE, runCostAnalysis = FALSE)

How is heel should be launched in this version?

2

Hi @Diego_Bosca_Tomas ,
I can not see connectionDetails in your error.
May I ask did you do like lines bellow for your connectionDetails?
connectionDetails ← createConnectionDetails(dbms = “postgresql”,
server = “localhost/synpuf”,
user = “cdm_user”,
password = “cdm_password”)

Best
Reza

3

Hi @Reza_Baharmand
createConnectionDetails creates without error, I can even launch DQD from that same connection

4

@Diego_Bosca_Tomas , I am sorry if I am mention more info.

vocabDatabaseSchema :

String name of database schema that contains OMOP Vocabulary. De- fault is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example ’results.dbo’.

Reza

5

It is a postgres db, and it’s the same as the cdm schema (in this case “omop”)

6

Ask @Ajit_Londhe ,
Reza

7

Looking at Achilles history https://github.com/OHDSI/Achilles/commits/master/R/Achilles.R, Achilles Heel has been removed. The Data Quality Dashboard is to replace Achilles Heel.

8

Is achilles heel run needed in the Atlas preparation? like creating some table (concept_hierarchy table?)

9

I think @DTorok is right, Heel is deprecated. @Frank correct me if I’m wrong, but although Atlas Data Sources has an Achilles Heel report, it should not be a problem if the Heel table is not present.

So @Diego_Bosca_Tomas – run Achilles using the instructions here: Running Achilles on Your CDM • Achilles, and then for Atlas, simply add the data source and invoke the caching of it in the Configuration module.

10

Ran achilles on the new database with an older version of achilles I had on an older server and now I see reports perfectly (was missing graphs in the reports before and achilles heel was throwing an error). So it seems something that was done during the heel analysis was needed to allow reports to be correctly shown.