https://github.com/tansey/smoothfdr
Revision c5b693d0a66e83c9387433b33c0eab481bd4a763 authored by Wesley Tansey on 08 May 2020, 15:42:20 UTC, committed by Wesley Tansey on 08 May 2020, 15:42:20 UTC
1 parent 49cb69c
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Tip revision: c5b693d0a66e83c9387433b33c0eab481bd4a763 authored by Wesley Tansey on 08 May 2020, 15:42:20 UTC
Fixed bug in easy that created too large a support for the alternative distribution
Tip revision: c5b693d
errorReport.txt
DBMS:
postgresql

Error:
org.postgresql.util.PSQLException: ERROR: relation "achilles_results" does not exist
  Position: 580

SQL:
select   concept_hierarchy.concept_id,
  COALESCE(concept_hierarchy.soc_concept_name,'NA') || '||' || COALESCE(concept_hierarchy.hlgt_concept_name,'NA') || '||' || COALESCE(concept_hierarchy.hlt_concept_name,'NA') || '||' || COALESCE(concept_hierarchy.pt_concept_name,'NA') || '||' || COALESCE(concept_hierarchy.snomed_concept_name,'NA') concept_path,	ar1.count_value as num_persons, 
	ROUND(CAST(1.0*ar1.count_value / denom.count_value AS NUMERIC),5) as percent_persons,
	ROUND(CAST(1.0*ar2.count_value / ar1.count_value AS NUMERIC),5) as records_per_person
from (select * from ACHILLES_results where analysis_id = 400) ar1
	inner join
	(select * from ACHILLES_results where analysis_id = 401) ar2
	on ar1.stratum_1 = ar2.stratum_1
	inner join
	(
		select snomed.concept_id, 
			snomed.concept_name as snomed_concept_name,
			pt_to_hlt.pt_concept_name,
			hlt_to_hlgt.hlt_concept_name,
			hlgt_to_soc.hlgt_concept_name,
			soc.concept_name as soc_concept_name
		from	
		(
		select concept_id, concept_name
		from public.concept
		where vocabulary_id = 'SNOMED'
		) snomed
		left join
			(select c1.concept_id as snomed_concept_id, max(c2.concept_id) as pt_concept_id
			from
			public.concept c1
			inner join 
			public.concept_ancestor ca1
			on c1.concept_id = ca1.descendant_concept_id
			and c1.vocabulary_id = 'SNOMED'
			and ca1.min_levels_of_separation = 1
			inner join 
			public.concept c2
			on ca1.ancestor_concept_id = c2.concept_id
			and c2.vocabulary_id = 'MedDRA'
			group by c1.concept_id
			) snomed_to_pt
		on snomed.concept_id = snomed_to_pt.snomed_concept_id

		left join
			(select c1.concept_id as pt_concept_id, c1.concept_name as pt_concept_name, max(c2.concept_id) as hlt_concept_id
			from
			public.concept c1
			inner join 
			public.concept_ancestor ca1
			on c1.concept_id = ca1.descendant_concept_id
			and c1.vocabulary_id = 'MedDRA'
			and ca1.min_levels_of_separation = 1
			inner join 
		  public.concept c2
			on ca1.ancestor_concept_id = c2.concept_id
			and c2.vocabulary_id = 'MedDRA'
			group by c1.concept_id, c1.concept_name
			) pt_to_hlt
		on snomed_to_pt.pt_concept_id = pt_to_hlt.pt_concept_id

		left join
			(select c1.concept_id as hlt_concept_id, c1.concept_name as hlt_concept_name, max(c2.concept_id) as hlgt_concept_id
			from
			public.concept c1
			inner join 
			public.concept_ancestor ca1
			on c1.concept_id = ca1.descendant_concept_id
			and c1.vocabulary_id = 'MedDRA'
			and ca1.min_levels_of_separation = 1
			inner join 
			public.concept c2
			on ca1.ancestor_concept_id = c2.concept_id
			and c2.vocabulary_id = 'MedDRA'
			group by c1.concept_id, c1.concept_name
			) hlt_to_hlgt
		on pt_to_hlt.hlt_concept_id = hlt_to_hlgt.hlt_concept_id

		left join
			(select c1.concept_id as hlgt_concept_id, c1.concept_name as hlgt_concept_name, max(c2.concept_id) as soc_concept_id
			from
			public.concept c1
			inner join 
			public.concept_ancestor ca1
			on c1.concept_id = ca1.descendant_concept_id
			and c1.vocabulary_id = 'MedDRA'
			and ca1.min_levels_of_separation = 1
			inner join 
			public.concept c2
			on ca1.ancestor_concept_id = c2.concept_id
			and c2.vocabulary_id = 'MedDRA'
			group by c1.concept_id, c1.concept_name
			) hlgt_to_soc
		on hlt_to_hlgt.hlgt_concept_id = hlgt_to_soc.hlgt_concept_id

		left join public.concept soc
		 on hlgt_to_soc.soc_concept_id = soc.concept_id



	) concept_hierarchy
	on ar1.stratum_1 = CAST(concept_hierarchy.concept_id as VARCHAR)
	,
	(select count_value from ACHILLES_results where analysis_id = 1) denom

order by ar1.count_value desc


R version:
R version 3.1.1 (2014-07-10)

Platform:
x86_64-apple-darwin13.1.0

Attached base packages:
- splines
- stats
- graphics
- grDevices
- utils
- datasets
- methods
- base

Other attached packages:
- Achilles (1.0)
- rjson (0.2.15)
- DatabaseConnector (1.3.0)
- RJDBC (0.2-5)
- rJava (0.9-7)
- DBI (0.3.1)
- SqlRender (1.1.2)
- devtools (1.9.1)
- FDRreg (0.2)
- mvtnorm (1.0-0)
- BayesLogit (0.5.1)
- fda (2.4.3)
- foreach (1.4.2)
- glmgen (0.0.3)
- Matrix (1.1-4)
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