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rwpark99 ritchey7 wanghaisheng ntatonetti rkboyce tdbennett seslava lucacian jingjingz shinseojeong sylviaxiaoyanwang chandryou yuxitian hojunpark solie rchen-cumc estone96 evidnet cephalization11 yoosoo0 yufenwang82 mintmountain89 hms1 mkim0710 abmi sigfried jswerdel seolpaik yoolande hl685 bdj5051 kmkostka dewittpe yorgosa shamim-active aostropolets gkovaig shrikantkuntestudyprotocols's Issues
CiCalibration: protocol link is broken
to find out details about what the CiCalibration study is trying to do, the link seems to be broken.
Alendronate study code fails with 0 counts in patients
Constructing treatment and comparator cohorts
^M |
^M |
| 0%^M |
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^M
|======================================================================|
100%
Executing SQL took 2.02 secs
Fetching cohorts from server
Error in data.frame(description = "Original cohorts", treatedPersons =
rawCount$exposedCount[rawCount$treatment == :
arguments imply differing number of rows: 1, 0
Calls: execute ... FUN -> do.call -> getDbCohortMethodData -> data.frame
Execution halted
Study 1 - Treatment Pathways - Version 2 minCellCount 2 - Postgres - sql code issues
Greetings,
It seems like the SQL code got a bit garbled up between lines 2500 and 2550 (roughly, it changes depending on Depression, HTN or T2DM SQL files. Some of the statements are throwing errors when I try to execute them AS-IS. I am attaching my fixed version of the files which I fixed using adapting the SQL code found on the MSSQL server version of the files. I successfully ran these files on my Postgres server and calculates the basic summary counts perfectly. Overall, the issue is with the first step of the attrition tables (0. count total persons for attrition table). This might also be found in the Version 2 minCellCount 1 files which I haven't looked at yet.
This seems to be an issue with the Oracle version of the files as well (I haven't checked the other ones) and only the MSSQL server ones seem to be complete. Was the code translated using some kind of automated software package?
Dropbox link to fixed files:
https://dl.dropboxusercontent.com/u/21004832/Study1-V2-MC2-fixedfiles.zip
CohortCount.csv generation - bug fix
The settings file that allows generation of several cohort using atlas ID is great.
I used that for a cancer study referenced here
http://forums.ohdsi.org/t/how-to-do-quick-feasibility-counts-from-r-given-public-server-cohort-definition-url-link/2831/3?u=vojtech_huser
It worked fine for 1 cohort.
With two cohorts, I was getting always only one cohort back.
I found a bug in the code:
On this line
https://github.com/OHDSI/StudyProtocols/blob/master/AlendronateVsRaloxifene/R/CreateCohorts.R#L79
part of code that has [i] must be removed.
bad code (current)
counts <- merge(counts, data.frame(cohortDefinitionId = cohortsToCreate$cohortId[i],
cohortName = cohortsToCreate$name[i]))
good code (fixed)
counts <- merge(counts, data.frame(cohortDefinitionId = cohortsToCreate$cohortId,
cohortName = cohortsToCreate$name))
Package version of FeatureExtraction and CohortMethod
Can anyone tell me which version of FeatureExtraction and CohortMethod was used in this study protocol?
As Feature Extraction becomes upgraded, I don't think current this study can run with the current Feature Extraction or CohortMethod package. (Mine too. I cannot remember the version of the package I used....)
Thanks!
KeppraAngioedema SQL potential issue
Looks like the SQL cohort code has the restriction of invalid_reason = NULL. Depending on the RDMBS flavor and how the vocabulary files are loaded this will be an issue. Loading the Athena files as-is on PostgreSQL will make invalid reason ='' rather than null.
While this is an easy fix, it might be worth making a note in the vocabulary load instructions that this should be the case. Otherwise, the study runs in a few seconds and gets no patients.
[OHDSI Large-Scale Population-Level Evidence Generation study] int size issue
Hello. I'm seojeong, a graduate student of Ajou university in Korea.
I have a issue while I tried to run the GitHub code proposed by this study.
When I executed codes like below,
---------------------------------------------------------------------------------------
execute(connectionDetails = connectionDetails,
cdmDatabaseSchema = "[Camel_DB].[dbo]",
#oracleTempSchema = NULL,
workDatabaseSchema = "[scratch_Shin_SJ].[dbo]",
studyCohortTable = "ohdsi_depression_cohorts",
exposureCohortSummaryTable = "ohdsi_depression_exposure_summary",
workFolder = "c:/temp/LargeScalePopEst",
maxCores = 4,
createCohorts = TRUE,
fetchAllDataFromServer = TRUE,
injectSignals = TRUE,
generateAllCohortMethodDataObjects = TRUE,
runCohortMethod = TRUE)
----------------------------------------------------------------------------------------
I got an error massage about the issue in readChar size. Please check the report I received.
-----------------------------------------------------------------------------------------
DBMS:
sql server
Error:
execute JDBC update query failed in dbSendUpdate
(Arithmetic overflow error converting expression to data type int.)
SQL:
SELECT pair_id,
t_cohort_definition_id,
c_cohort_definition_id,
t_cohort_definition_id * 1000 + pair_id AS tprime_cohort_definition_id,
c_cohort_definition_id * 1000 + pair_id AS cprime_cohort_definition_id,
min_cohort_date,
max_cohort_date
INTO #exposure_cohort_pairs
FROM (
SELECT ROW_NUMBER() OVER (
ORDER BY s1.cohort_definition_id,
s2.cohort_definition_id
) AS pair_id,
s1.cohort_definition_id AS t_cohort_definition_id,
s2.cohort_definition_id AS c_cohort_definition_id,
CASE
WHEN s1.min_cohort_date > s2.min_cohort_date
THEN s1.min_cohort_date
ELSE s2.min_cohort_date
END AS min_cohort_date,
CASE
WHEN s1.max_cohort_date < s2.max_cohort_date
THEN s1.max_cohort_date
ELSE s2.max_cohort_date
END AS max_cohort_date
FROM #exposure_cohort_summary s1,
#exposure_cohort_summary s2
WHERE s1.cohort_definition_id < s2.cohort_definition_id
) t1
-----------------------------------------------------------------------------------------
I think this query should be fixed as follows.
From. -------------------------------------------------------------------
s1.cohort_definition_id AS t_cohort_definition_id,
s2.cohort_definition_id AS c_cohort_definition_id,
-------------------------------------------------------------------------
To. ---------------------------------------------------------------------
CAST(s1.cohort_definition_id AS BIGINT) AS t_cohort_definition_id,
CAST(s2.cohort_definition_id AS BIGINT) AS c_cohort_definition_id,
-------------------------------------------------------------------------
When we tried to run the code with edited version, the result was good.
Could you review this issue and confirm the code that I fixed?
Thank you!
Amputation study: concept_sets folder missing
This document claims that value sets are in a folder
Where this folder can be found?
(excellent study btw. The drug-outcome pair was on short-list as well.
@pbr6cornell
Error in ff(initdata = initdata, length = length, levels = levels, ordered = ordered, : vmode 'character' not implemented
I'm still running keppra on Oracle, and ran into another bug.
Here's the error:
No outcome specified so not creating outcome and time variables
Error in ff(initdata = initdata, length = length, levels = levels, ordered = ordered, :
vmode 'character' not implemented
Calls: execute ... do.call -> as.ff -> as.ff.default -> clone.ff -> assign -> ff
In addition: Warning message:
replacing previous import ‘Rcpp::LdFlags’ by ‘RcppParallel::LdFlags’ when loading ‘Cyclops’
Execution halted
Full log:
R version 3.3.0 (2016-05-03) -- "Supposedly Educational"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(KeppraAngioedema)
Loading required package: DatabaseConnector
Loading required package: RJDBC
Loading required package: DBI
Loading required package: rJava
>
> # cohortTable = paste("ohdsi_keppra", Sys.getpid(), sep="_")
> cohortTable = "ohdsi_keppra_19239"
> print(paste("Cohort Table - ", cohortTable))
[1] "Cohort Table - ohdsi_keppra_19239"
>
> # outputDir = paste("/home/chilton/ohdsi_keppra/run", Sys.getpid(), sep="_")
> outputDir = "/home/chilton/ohdsi_keppra/run_19239"
> print(paste("Output Dir - ", outputDir))
[1] "Output Dir - /home/chilton/ohdsi_keppra/run_19239"
>
> connectionDetails <- createConnectionDetails(dbms = "oracle",
+ user = "OHDSI",
+ port = "1521",
+ password = "xxx",
+ server = "sasridg02.uits.iupui.edu/I2B21STG")
>
> execute(connectionDetails,
+ cdmDatabaseSchema = "OMOPV5_DE",
+ workDatabaseSchema = "OHDSI",
+ studyCohortTable = cohortTable,
+ oracleTempSchema = "OHDSI",
+ outputFolder = outputDir,
+ maxCores = 4,
+ createCohorts = FALSE)
Running analyses
*** Creating cohortMethodData objects ***
Loading required package: CohortMethod
Loading required package: Cyclops
Loading required package: FeatureExtraction
Connecting using Oracle driver
Constructing treatment and comparator cohorts
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Analysis took 23.5 secs
Fetching cohorts from server
Fetching cohorts took 0.729 secs
Constructing default covariates
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Analysis took 13.5 hours
Done
Fetching data from server
Loading took 24.8 secs
Removing redundant covariates
Removing redundant covariates took 22.3 secs
Normalizing covariates
Fetching outcomes from server
Fetching outcomes took 0.617 secs
*** Creating study populations ***
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*** Fitting shared propensity score models ***
Removing subject that are in both cohorts (if any)
No outcome specified so skipping removing people with prior outcomes
Removing subjects with less than 1 day(s) at risk (if any)
No outcome specified so not creating outcome and time variables
Error in ff(initdata = initdata, length = length, levels = levels, ordered = ordered, :
vmode 'character' not implemented
Calls: execute ... do.call -> as.ff -> as.ff.default -> clone.ff -> assign -> ff
In addition: Warning message:
replacing previous import ‘Rcpp::LdFlags’ by ‘RcppParallel::LdFlags’ when loading ‘Cyclops’
Execution halted
Also, if I rerun it (after it's fixed), can I start from createCohorts = FALSE, or do I need to start over?
Thanks.
Error when Generating outcomes (package AlendronateVsRaloxifene)
Hello,
I'm interested in this study but getting some errors running it.
Warning : the condition has length>1 and only the first element will be used
This warning doesn't look so probelmatic.
There were three chunks of error messages below.
I wonder if this is because I'm using Parallellogger of version 1.0.1 so I'm gonna update and run this package again but please tell me if you know what caused this issue.
Or I suspect that this error is caused becasue my institution hasn't converted some concepts.
Thread 1 returns error : "cannot oppen the connection" when using argument(s) : list(exposureID = NA, outcomeID = NA, modelFolder= NA, covarFileName = c("E:/DPJE001/Desktop/study_results/positiveControlSynthesis/CovarsForModel_gNA", .."
Thread 2 returns error : "argument is of length 0 when using argument(s) : list(exposureID = integer(0), outcomeID = integer(0), modelFolder= character(0), covarFileName = "E:/DPJE001/Desktop/study_results/positiveControlSynthesis/CovarsForModel_g"_, list(exposureID= c(99321,...,)"
Error in ParallelLogger:clusterapply(cluster,tasks,generateOutcomes, : Error(s) when calling function 'fun', see earlier messages for details
Oracle table names - not happy with the length of Depression12mo_drug_seq_summary
Hi,
While esting protocol 2 by running the MainAnalysis.R script configured for our dataset (Oracle >=11g, R 3.0) I ran into error "ORA-03291: Invalid truncate option - missing STORAGE keyword". This issue was triggered because I used a hyphen instead of an underscore in the "sourceName" variable - my bad. However, after correcting this, I found another issue that I think will require a slight change to the code. Specifically, the table prefix 'Depression12mo' leads to table names (e.g. 'Depression12mo_drug_seq_summary') that causes Oracle to trigger 'ORA-00972: identifier is too long'. The character limit on Oracle tables is 30. Going through the MainAnalysis.R and HelperFunctions.R and replacing 'Depression12mo' with 'Depr12mo' fixes this issue.
--- output before fix ---
> source("MainAnalysis.R")
Loading required package: RJDBC
Loading required package: DBI
Loading required package: rJava
Created file 'TxPath autoTranslate oracle HTN12mo.sql'
Created file 'TxPath autoTranslate oracle T2DM12mo.sql'
Created file 'TxPath autoTranslate oracle Depression12mo.sql'
Connecting using Oracle driver
|============ | 17%Error executing SQL: Error in .local(conn, statement, ...): execute JDBC update query failed in dbSendUpdate (ORA-00972: identifier is too long
ORA-06512: at line 7
)
An error report has been created at /home/rdb20/OHDSI-code/StudyProtocols/Study 2 - Treatment Pathways 12mo/R Version/errorReport.txt
Error in value[[3L]](cond) : no loop for break/next, jumping to top level
after
> source("MainAnalysis.R")
Created file 'TxPath autoTranslate oracle HTN12mo.sql'
Created file 'TxPath autoTranslate oracle T2DM12mo.sql'
Created file 'TxPath autoTranslate oracle Depr12mo.sql'
Connecting using Oracle driver
|======================================================================| 100%
Analysis took 19.8 secs
|======================================================================| 100%
Analysis took 16.9 secs
|======================================================================| 100%
Analysis took 16.8 secs
Created file 'HTN12mo_GOHDSI_summary.csv'
Created file 'HTN12mo_GOHDSI_person_cnt.csv'
Created file 'HTN12mo_GOHDSI_seq_cnt.csv'
Created file 'T2DM12mo_GOHDSI_summary.csv'
Created file 'T2DM12mo_GOHDSI_person_cnt.csv'
Created file 'T2DM12mo_GOHDSI_seq_cnt.csv'
Created file 'Depr12mo_GOHDSI_summary.csv'
Created file 'Depr12mo_GOHDSI_person_cnt.csv'
Created file 'Depr12mo_GOHDSI_seq_cnt.csv'
Error running KeppraAngiodema
Hi,
We're trying to run Keppra Angiodema on Oracle, and I'm having issues when it is trying to create/select into cohort_person. It looks like it is creating the temp table in the CDM schema, and it should be coming from the workDatabaseSchema, right? Here's the error. It seems like it might be coming from a SELECT...INTO.
DBMS:
oracle
Error:
execute JDBC update query failed in dbSendUpdate (ORA-01031: insufficient privileges
)
SQL:
CREATE TABLE OMOPV5_DE.pwpkmcrscohort_person
AS
SELECT
ROW_NUMBER() OVER (ORDER BY person_id, cohort_start_date) AS row_id,
subject_id,
cohort_definition_id,
cohort_start_date,
( cohort_start_date - observation_period_start_date) AS days_from_obs_start,
( cohort_end_date - cohort_start_date)
AS days_to_cohort_end,
( observation_period_end_date - cohort_start_date)
AS days_to_obs_end
FROM
(SELECT subject_id,
cohort_definition_id,
cohort_start_date,
cohort_end_date
FROM OHDSI.ohdsi_keppra_19239 exposure_table
WHERE cohort_definition_id IN (1, 2)
) raw_cohorts
INNER JOIN OMOPV5_DE.observation_period
ON subject_id = person_id
WHERE cohort_start_date <= observation_period_end_date
AND cohort_start_date >= observation_period_start_date
R version:
R version 3.3.0 (2016-05-03)
Platform:
x86_64-pc-linux-gnu
Attached base packages:
- stats
- graphics
- grDevices
- utils
- datasets
- methods
- base
Other attached packages:
- CohortMethod (2.0.2)
- FeatureExtraction (1.0.0)
- Cyclops (1.2.0)
- KeppraAngioedema (0.1.0)
- DatabaseConnector (1.4.0)
- RJDBC (0.2-5)
- rJava (0.9-8)
- DBI (0.4-1)
Error in Data frame aggregation
Hello, I'm Seojeong, a graduate student of Ajou university in Korea.
I got a issue while I running the LargeScalePopEst Code.
I was trying to execute "injectionSignals" parameter especially for comfirming whether each step working rightly and then an error message was shown just like below. (Note that the parameters "createCohorts" and "fetchAllDataFromServer" worked well although one warning message poped up during executing the "createCohorts" step.)
↓ The warning message during "createCohort" step.
↓ The Error message during "injectSignals" step.
And I figured out that the length of [ unique(data$outcomeId) ] and [ negativeControlIds ] is different each other.
So I ask if it is possible that the code of LargeScalePopEst protocols can be altered.
↓ The Create outcomes file CODE
I think it would be better that the code should allow or skip the absent of some "outcomeId".
Could you modify this Code for us?
Please review this issue.
Thank you!
Error on latest install of KeppraAngioedema
I am getting this for a few of the packages (on Windows):
Warning in install.packages :
cannot open URL 'http://OHDSI.github.io/drat/bin/windows/contrib/3.2/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'http://OHDSI.github.io/drat/bin/windows/contrib/3.2/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://OHDSI.github.io/drat/bin/windows/contrib/3.2:
cannot open URL 'http://OHDSI.github.io/drat/bin/windows/contrib/3.2/PACKAGES'
Warning in install.packages :
cannot open URL 'http://cloudyr.github.io/drat/bin/windows/contrib/3.2/PACKAGES.gz': HTTP status was '404 Not Found'
Warning in install.packages :
cannot open URL 'http://cloudyr.github.io/drat/bin/windows/contrib/3.2/PACKAGES': HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://cloudyr.github.io/drat/bin/windows/contrib/3.2:
cannot open URL 'http://cloudyr.github.io/drat/bin/windows/contrib/3.2/PACKAGES'
Heap Space Error on CSV Export
Running Oracle. First two exports work fine:
extractAndWriteToFile(conn, "person_count", resultsSchema, sourceName, "T2DM", dbms)
extractAndWriteToFile(conn, "person_count_year", resultsSchema, sourceName, "T2DM", dbms)
Last two exports throw an error:
extractAndWriteToFile(conn, "seq_count", resultsSchema, sourceName, "T2DM", dbms)
Error executing SQL: Error in .jcall(rp, "I", "fetch", stride): java.lang.OutOfMemoryError: Java heap space
Error in value[3L] : no loop for break/next, jumping to top levelextractAndWriteToFile(conn, "seq_count_year", resultsSchema, sourceName, "T2DM", dbms)
Error executing SQL: Error in .jcall(rp, "I", "fetch", stride): java.lang.OutOfMemoryError: Java heap space
Any ideas?
In CelecoxibVsNsNSAIDs, Error in ff::ff(1, length = nrow(covariates)) : unable to open and 17 warnings
Hi. I`m Minseok, a graduate student in Ajou univ.
I executed CelecoxibVsNsNSAIDs analysis R code and have some trouble.
My error message is
//Error in ff::ff(1, length = nrow(covariates)) : unable to open
In addition: There were 17 warnings (use warnings() to see them) //
and 17 warnings are almost
//In readChar(pathToSql, file.info(pathToSql)$size) :
can only read in bytes in a non-UTF-8 MBCS locale execute//
//In lowLevelQuerySql.ffdf(connection, sql) :
Data has zero rows, returning an empty data frame execute//
But I don`t know what the error is with just that text.
I attach running code log
Rcode
execute(connectionDetails,
cdmDatabaseSchema = "Camel_DB.dbo",
workDatabaseSchema = "Camel_nsnsaids_result.dbo",
studyCohortTable = "celecoxib_vs_nsnsaids",
oracleTempSchema = NULL,
outputFolder = "E:/R/OHDSI/study_results",
cdmVersion = "5")
console window
execute(connectionDetails,
-
cdmDatabaseSchema = "Camel_DB.dbo", -
workDatabaseSchema = "Camel_nsnsaids_result.dbo", -
studyCohortTable = "celecoxib_vs_nsnsaids", -
oracleTempSchema = NULL, -
outputFolder = "E:/R/OHDSI/study_results", -
cdmVersion = "5")
Creating exposure and outcome cohorts
Connecting using SQL Server driver
- Creating treatment cohort
|==================================================================================================================================================| 100%
Analysis took 3.03 secs - Creating comparator cohort
|==================================================================================================================================================| 100%
Analysis took 9.84 secs - Creating myocardial infarction cohort
|==================================================================================================================================================| 100%
Analysis took 4.06 secs - Creating myocardial infarction and ischemic death cohort
|==================================================================================================================================================| 100%
Analysis took 8.55 secs - Creating gastrointestinal hemorrhage cohort
|==================================================================================================================================================| 100%
Analysis took 5.47 secs - Creating angioedema cohort
|==================================================================================================================================================| 100%
Analysis took 1.27 secs - Creating acute renal failure cohort
|==================================================================================================================================================| 100%
Analysis took 3.45 secs - Creating drug induced liver injury cohort
|==================================================================================================================================================| 100%
Analysis took 11.9 secs - Creating heart failure cohort
|==================================================================================================================================================| 100%
Analysis took 3.56 secs - Creating negative control outcome cohort
|==================================================================================================================================================| 100%
Analysis took 23.7 secs
cohortDefinitionId count cohortName
1 1 634 Treatment
2 2 3069 Comparator
3 10 4757 Myocardial infarction
4 11 5633 Myocardial infarction and ischemic death
5 12 6126 Gastrointestinal hemorrhage
6 13 4437 Angioedema
7 14 4896 Acute renal failure
8 15 10888 Drug induced liver injury
9 16 2389 Heart failure
10 72418 224
11 72712 133
12 73302 296
13 74855 59
14 76737 2985
15 77650 128
16 78804 578
17 79072 421
18 80509 294
19 81250 746
20 81336 163
21 133141 617
22 133228 968
23 133551 96
24 134118 13
25 134222 8122
26 134765 9
27 136937 3257
28 137054 2
29 139099 155
30 140362 151
31 140641 442
32 141216 29
33 141825 2967
34 192606 1004
35 194702 4621
36 194997 1405
37 195212 943
38 195501 276
39 197036 702
40 198075 325
41 199876 1159
42 201388 305
43 253796 13828
44 261326 1395
45 261880 1268
46 315288 1262
47 317305 266
48 317376 2151
49 317585 1875
50 317895 83
51 319845 536
52 373478 10
53 373766 382
54 374384 129
55 376132 27
56 376712 196
57 378160 57
58 378256 15
59 378424 75
60 379769 1739
61 380395 29
62 380731 857
63 381581 82
64 432851 67152
65 433163 196
66 433440 315
67 434309 360
68 434319 9
69 434630 4
70 435140 685
71 436740 1661
72 437222 687
73 437409 17427
74 438134 99
75 438407 25
76 439237 789
77 439840 35
78 440389 612
79 440676 577
80 440695 3
81 440814 970
82 441267 9
83 441788 458
84 442274 51
85 443361 201
86 443605 447
87 443767 9271
88 444130 6071
89 444191 30951
90 4018050 513
91 4028970 5370
92 4029582 276
93 4029966 2786
94 4044391 2097
95 4047269 3
96 4052648 121
97 4083964 19578
98 4085156 24
99 4087647 16743
100 4092565 599
101 4095288 37
102 4112853 16496
103 4114197 1359
104 4114222 33241
105 4129880 7847
106 4130061 1359
107 4131595 3437
108 4131616 16378
109 4132130 1875
110 4132546 5125
111 4140510 200
112 4146239 5
113 4147672 458
114 4153380 536
115 4153877 346
116 4163232 102
117 4164337 2170
118 4171549 1042
119 4171915 116
120 4172458 14
121 4174977 4784
122 4186392 580
123 4195698 56
124 4207688 4874
125 4209011 424
126 4215978 448
127 4218106 895
128 4223947 1827
129 4224118 2799
130 4242416 1
131 4256228 563
132 4262178 163
133 4270490 5407
134 4285569 25
135 4286201 192
136 4288544 7600
137 4295888 170
138 4297984 346
139 4305304 514
140 4307254 329
141 4322737 968
142 4339088 296
Running analyses
*** Creating cohortMethodData objects ***
Connecting using SQL Server driver
Constructing treatment and comparator cohorts
Executing multiple queries. This could take a while
|==================================================================================================================================================| 100%
Analysis took 56.5 secs
Fetching data from server
Loading took 0.521 secs
Constructing baseline covariates
Constructing covariates
|==================================================================================================================================================| 100%
Analysis took 21.4 secs
Done
Fetching data from server
Loading took 0.11 secs
Removing redundant covariates
Error in ff::ff(1, length = nrow(covariates)) : unable to open
In addition: There were 17 warnings (use warnings() to see them)
Database related error when calling CiCalibration::execute
I am attempting to run CiCalibration::execute function by following the instructions at
https://github.com/OHDSI/StudyProtocols/tree/master/CiCalibration
I have installed the dependencies R packages, installed PostgreSQL server and created the database, as well as the cdm_data and results schemas. When I ran the code shown at the web page, I get this error
Creating exposure and outcome cohorts Connecting using PostgreSQL driver Creating cohort: DabigatranSouthworth |== | 3%Error: Error executing SQL: org.postgresql.util.PSQLException: ERROR: relation "cdm_data.concept" does not exist Position: 155
Am I supposed to setup other tables before I can run CiCalibration::execute?
Thanks!
Median time-to-event
Return median time-to-event and its 95%CI for T and C cohorts in StudyResults artifacts.
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