#711: External Validation for Acute Kidney Injury(AKI) Predictive Models using
PCORnet CDM data
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Reporter: meiliu | Owner: xsong
Type: task | Status: new
Priority: major | Milestone:
Component: data-sharing | Resolution:
Keywords: aki cdm | Blocked By:
Blocking: |
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Comment (by xsong):
received feedback from UIOWA about code testing and made the following
fixes
{{{
change dbSendQuery to dbSendUpdate if the query is not getting any result
set.
--it seems both DBI and RJDBC have function dbSendQuery, with former
performs similarly as RJDBC::dbSendUpdate. So I modified the codes as
DBI::dbSendQuery to keep it simply (works on Oracle)
util.R
1. use RJDBC instead of odbc
--merged the change
2. change tSQL parameter
--merged the change
extract_cohort.R
1. change parameter from cdm_db_server=" " to cdm_db_server
--modified the “cdm_db_server” to “cdm_db_name” to keep it consistent with
the configuration file.
2. removed wrong query if(DBMS_type=="tSQL") statements.
--merged the change
3. change aki_enc<-dbGetQuery(conn, "select * from AKI_onsets") to
aki_enc<-dbGetQuery(conn, "select * from #AKI_onsets") (temporary file
name in oracle is AKI_onsets but #AKI_onsets in tSQL
--merged the change
4. change drop_temp<-paste("drop table",parse_out$tbl_out,"purge") to
drop_temp<-paste("drop table",parse_out$tbl_out)
--merged the change
AKI_CDM_EXT_VALID_p1_QA.Rmd
1. change config_file_path<-"../config.csv" to
config_file_path<-"./config.csv"
current directory is AKI_CDM-master
--merged the change
2. add extra parameter cdm_db_server=config_file$cdm_db_server in function
extract_cohort
pass database and schema name.
--changed the parameter name to “cdm_db_server” to “cdm_db_name” to be
consistent with configuration file
3. run names(consort_tbl) = toupper(names(consort_tbl)) change column name
of table consort_tbl to upper case
--merged the change
Error: “Per Gi-Yung, the consort_tbl has 16 columns but in the VIZ.r file
when it attempts to apply labels to the consort_tbl it thinks there are
only 15 columns”
--fixed by removing one exclusion chunk from
‘inst/tSQL/cohort_exclude.sql’
}}}
--
Ticket URL:
<http://informatics.gpcnetwork.org/trac/Project/ticket/711#comment:7>
gpc-informatics <http://informatics.gpcnetwork.org/>
Greater Plains Network - Informatics
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