From 3c83e669aef8ec539bcff42d16d379e640c4b208 Mon Sep 17 00:00:00 2001 From: Chris Knoll Date: Mon, 8 Jul 2024 13:36:06 -0400 Subject: [PATCH] Added support for list of age breaks, supporting overlapping age break intervals. Using StandardAnalysisAPI 1.6.0-SNAPSHOT. Updated StrataSettings R6 class with new field: ageBreakList. Fixes #30. --- R/Builders.R | 4 +- R/Classes.R | 22 +- docs/articles/using-cohortincidence.html | 195 +++--------------- docs/news/index.html | 9 + docs/pkgdown.yml | 2 +- docs/reference/StrataSettings.html | 4 + docs/reference/createStrataSettings.html | 8 +- inst/java/CohortIncidence-4.0.0.jar | Bin 20325 -> 20925 bytes ...ardized-analysis-specs-1.6.0-SNAPSHOT.jar} | Bin 84531 -> 84660 bytes .../CohortIncidenceQueryBuilder.java | 60 +++--- .../cohortincidence/sql/ageGroupJoin.sql | 3 + .../cohortincidence/sql/incidenceAnalysis.sql | 14 +- .../sql/outcomeStrataQueryTemplate.sql | 1 + .../sql/tarStrataQueryTemplate.sql | 1 + .../cohortincidence/Incidence_5_0_Test.java | 29 +++ .../timeAtRisk/strataByAgeBreakListTest.json | 43 ++++ .../timeAtRisk/strataByAgeBreakList_PREP.json | 95 +++++++++ .../strataByAgeBreakList_VERIFY.json | 144 +++++++++++++ man/StrataSettings.Rd | 2 + man/createStrataSettings.Rd | 8 +- pom.xml | 2 +- vignettes/using-cohortincidence.Rmd | 26 ++- 22 files changed, 461 insertions(+), 211 deletions(-) rename inst/java/{standardized-analysis-specs-1.5.0.jar => standardized-analysis-specs-1.6.0-SNAPSHOT.jar} (76%) create mode 100644 java/main/resources/resources/cohortincidence/sql/ageGroupJoin.sql create mode 100644 java/test/resources/cohortincidence/timeAtRisk/strataByAgeBreakListTest.json create mode 100644 java/test/resources/cohortincidence/timeAtRisk/strataByAgeBreakList_PREP.json create mode 100644 java/test/resources/cohortincidence/timeAtRisk/strataByAgeBreakList_VERIFY.json diff --git a/R/Builders.R b/R/Builders.R index 97aa92c..12e7ad2 100644 --- a/R/Builders.R +++ b/R/Builders.R @@ -150,13 +150,13 @@ createCohortSubgroup <- function (id, name, description, cohortRef) { #' @param ageBreaks a vector of integers indicating the age group bounds. #' @return an R list containing name-value pairs that will serialize into a org.ohdsi.analysis.cohortincidence.design.StratifySettings JSON format. #' @export -createStrataSettings <- function (byAge = F, byGender = F, byYear = F, ageBreaks) { +createStrataSettings <- function (byAge = F, byGender = F, byYear = F, ageBreaks, ageBreakList) { strataSettings <- StrataSettings$new() strataSettings$byAge <- byAge; strataSettings$byGender <- byGender; strataSettings$byYear <- byYear; - if(byAge == T && missing(ageBreaks)) stop ("Error: ageBreaks must be a list of integers with at least 1 element") + if(byAge == T && (missing(ageBreaks) || missing(ageBreakList))) stop ("Error: when byAge = TRUE, ageBreaks or ageBreakList must be provided.") if (!missing(ageBreaks)) strataSettings$ageBreaks <- ageBreaks; return(strataSettings); diff --git a/R/Classes.R b/R/Classes.R index b5e3913..7e0633a 100644 --- a/R/Classes.R +++ b/R/Classes.R @@ -757,7 +757,8 @@ StrataSettings <- R6::R6Class("StrataSettings", .byAge = F, .byGender = F, .byYear = F, - .ageBreaks = NA + .ageBreaks = NA, + .ageBreakList = NA ), active = list ( #' @field byAge enables stratification by age @@ -803,6 +804,21 @@ StrataSettings <- R6::R6Class("StrataSettings", private$.ageBreaks <- ageBreaks self } + }, + #' @field ageBreakList a list of age breaks + ageBreakList = function(ageBreakList) { + if (missing(ageBreakList)) { + private$.ageBreakList + } else { + # check type + checkmate::assertList(as.list(ageBreakList), types="list") + checkmate::assertTRUE(all(sapply(ageBreakList, + function(x) { + checkmate::testList(x) && all(sapply(x, checkmate::testNumeric)) + }))) + private$.ageBreakList <- ageBreakList + self + } } ), public = list( @@ -816,6 +832,7 @@ StrataSettings <- R6::R6Class("StrataSettings", if ("byGender" %in% names (dataList)) self$byGender <- dataList$byGender if ("byYear" %in% names (dataList)) self$byYear <- dataList$byYear if ("ageBreaks" %in% names (dataList)) self$ageBreaks <- dataList$ageBreaks + if ("ageBreakList" %in% names (dataList)) self$ageBreakList <- dataList$ageBreakList }, #' @description @@ -825,7 +842,8 @@ StrataSettings <- R6::R6Class("StrataSettings", byAge = jsonlite::unbox(private$.byAge), byGender = jsonlite::unbox(private$.byGender), byYear = jsonlite::unbox(private$.byYear), - ageBreaks = .toJsonArray(private$.ageBreaks) + ageBreaks = .toJsonArray(private$.ageBreaks), + ageBreakList = lapply(private$.ageBreakList, .toJsonArray) )) }, #' @description diff --git a/docs/articles/using-cohortincidence.html b/docs/articles/using-cohortincidence.html index 5887fba..48eea8d 100644 --- a/docs/articles/using-cohortincidence.html +++ b/docs/articles/using-cohortincidence.html @@ -85,7 +85,7 @@

Using CohortIncidence

Christopher Knoll

-

2024-06-27

+

2024-07-08

Source: vignettes/using-cohortincidence.Rmd @@ -315,13 +315,27 @@

Using age, gender and start year strata settings with the CohortIncidence::createStrataSettings) function:

-irDesignWithStrata <- CohortIncidence::createIncidenceDesign(targetDefs = list(t1),
-                                                   outcomeDefs = list(o1),
-                                                   tars=list(tar1),
-                                                   analysisList = list(analysis1),
-                                                   subgroups = list(subgroup1),
-                                                   #add by age and by gender strata, but don't do by start year.
-                                                   strataSettings = CohortIncidence::createStrataSettings(byGender=T, byAge=T, ageBreaks = c(17,34,65)))
+irDesignWithStrata <- + CohortIncidence::createIncidenceDesign( + targetDefs = list(t1), + outcomeDefs = list(o1), + tars = list(tar1), + analysisList = list(analysis1), + subgroups = list(subgroup1), + #add by age and by gender strata, but don't do by start year. + strataSettings = CohortIncidence::createStrataSettings( + byGender = T, + byAge = T, + ageBreaks = list(17, 34, 65), + ageBreakList = list(list(25), list(65)) + ) + ) +

In the above example, thare are 2 ways of specifying the age breaks: +ageBreaks and ageBreakList. ageBreaks creates a single age break +specification, while ageBreakList allows you to specify a list of +breaks. All breaks defined in ageBreaks and ageBreakList will be used if +specified. If byAge is TRUE, you must specify at least one age break +specification either in ageBreaks or ageBreakList.

Using executeAnalysis() @@ -341,149 +355,11 @@

Using executeAnalysis()executeResults <- CohortIncidence::executeAnalysis(connectionDetails = connectionDetails, incidenceDesign = irDesign, buildOptions = buildOptions)

-

The results will contain the same table structure as the results -schema incidence_summary:

- ---- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
NameDescription
REF_IDThe reference id specified in buildOptions() to track results to the -analysis execution.
SOURCE_NAMEThe name of the source for these results
TARGET_COHORT_DEFIITION_IDThe cohort ID of the target population
TARGET_NAMEThe name of the target cohort
TAR_IDThe TAR identifier
TAR_START_WITHIndicates if the TAR starts with the ‘start’ or ‘end’ of the target -cohort episode
TAR_START_OFFSETThe days added to the date field specified in TAR_START_WITH
TAR_END_WITHIndicates if the TAR ends with the ‘start’ or ‘end’ of the target -cohort episode
TAR_END_OFFSETThe days added to the date field specified in TAR_END_WITH
SUBGROUP_IDThe subgroup identifier
SUBGROUP_NAMEThe name of the subgroup
OUTCOME_IDThe outcome identifier
OUTCOME_COHORT_DEFINITION_IDThe cohort ID of the outcome population
OUTCOME_NAMEThe outcome name
CLEAN_WINDOWThe clean window for this outcome definition
AGE_IDThe age ID for this strata representing the age band specified in -the strata settings
AGE_GROUP_NAMEThe name for this age group
GENDER_IDThe gender concept ID for this gender strata
GENDER_NAMEThe name of the gender
START_YEARThe year strata, defined by using the year the TAR started
PERSONS_AT_RISK_PEDistinct persons at risk before removing excluded time from TAR
PERSONS_AT_RISKDistinct persons at risk after removing excluded time from TAR. A -person must have at least 1 day TAR to be included.
PERSON_DAYS_PETotal TAR (in days) before excluded time was removed from TAR.
PERSON_DAYSTotal TAR (in days) after excluded time was removed from TAR.
PERSON_OUTCOMES_PEDistinct persons with outcome before removing excluded time from -TAR
PERSON_OUTCOMESDistinct persons with outcome after removing excluded time from TAR. -A person must have at least 1 day TAR to be included.
OUTCOMES_PENumber of cases before excluding TAR.
OUTCOMESNumber of cases after excluding TAR.
INCIDENCE_PROPORTION_P100PThe Incidence Proportion (per 100 people), calculated by -person_outcomes / persons_at_risk * 100
INCIDENCE_RATE_P100PYThe Incidence Rate (per 100 person years), calculated by outcomes / -person_days / 365.25 * 100
+

executeAnalysis() will return a list of dataframes with +the following fields: - incidenceSummary - targetDef - outcomeDef - +tarDef - ageGroupDef - subgroupDef

+

These dataframes follow the same structure as the corresponding +tables described in the Database Preparation section.

@@ -791,7 +667,7 @@

Build analysis SQL from design#> /* #> 5) aggregate tar and excluded+outcome #> */ -#> WITH tar_overall (target_cohort_definition_id, tar_id, subgroup_id, subject_id, start_date, end_date, age_group_id, gender_id, start_year) +#> WITH tar_overall (target_cohort_definition_id, tar_id, subgroup_id, subject_id, start_date, end_date, age, gender_id, start_year) #> AS ( #> SELECT te.cohort_definition_id as target_cohort_definition_id, #> te.tar_id, @@ -799,14 +675,11 @@

Build analysis SQL from design#> te.subject_id, #> te.start_date, #> te.end_date, -#> ag.age_group_id, +#> YEAR(te.start_date) - p.year_of_birth as age, #> p.gender_concept_id as gender_id, #> YEAR(te.start_date) as start_year #> FROM #TTAR_erafied te #> JOIN mycdm.person p on te.subject_id = p.person_id -#> LEFT JOIN myresults.age_group_def ag ON YEAR(te.start_date) - p.year_of_birth >= coalesce(ag.min_age, -999) -#> and YEAR(te.start_date) - p.year_of_birth < coalesce(ag.max_age, 999) -#> and ag.ref_id = 1 #> ) #> select target_cohort_definition_id, tar_id, subgroup_id, age_group_id, gender_id, start_year, person_days_pe, persons_at_risk_pe #> INTO #tar_agg @@ -820,11 +693,12 @@

Build analysis SQL from design#> SUM(CAST((DATEDIFF(day,t1.start_date,t1.end_date) + 1) as bigint)) as person_days_pe, #> COUNT(distinct t1.subject_id) as persons_at_risk_pe #> FROM tar_overall t1 +#> #> GROUP BY t1.target_cohort_definition_id, t1.tar_id, t1.subgroup_id #> ) T_OVERALL #> ; #> -#> WITH outcomes_overall (target_cohort_definition_id, tar_id, subgroup_id, outcome_id, subject_id, age_group_id, gender_id, start_year, excluded_days, tar_days, outcomes_pe, outcomes) +#> WITH outcomes_overall (target_cohort_definition_id, tar_id, subgroup_id, outcome_id, subject_id, age, gender_id, start_year, excluded_days, tar_days, outcomes_pe, outcomes) #> AS ( #> SELECT #> t1.cohort_definition_id as target_cohort_definition_id, @@ -832,7 +706,7 @@

Build analysis SQL from design#> t1.subgroup_id, #> op.outcome_id, #> t1.subject_id, -#> ag.age_group_id, +#> YEAR(t1.start_date) - p.year_of_birth as age, #> p.gender_concept_id as gender_id, #> YEAR(t1.start_date) as start_year, #> coalesce(e1.person_days, 0) as excluded_days, @@ -841,9 +715,6 @@

Build analysis SQL from design#> coalesce(o1.outcomes, 0) as outcomes #> FROM #TTAR_erafied t1 #> JOIN mycdm.person p ON t1.subject_id = p.person_id -#> LEFT JOIN myresults.age_group_def ag ON YEAR(t1.start_date) - p.year_of_birth >= coalesce(ag.min_age, -999) -#> AND YEAR(t1.start_date) - p.year_of_birth < coalesce(ag.max_age, 999) -#> AND ag.ref_id = 1 #> JOIN ( -- get the list of TTSO of anyone with excluded time or outcomes to limit result #> select target_cohort_definition_id, tar_id, subgroup_id, outcome_id, subject_id, start_date FROM #excluded_person_days #> UNION -- will remove dupes @@ -886,6 +757,7 @@

Build analysis SQL from design#> SUM(t1.outcomes_pe) as outcomes_pe, #> SUM(t1.outcomes) as outcomes #> FROM outcomes_overall t1 +#> #> GROUP BY target_cohort_definition_id, tar_id, subgroup_id, outcome_id #> ) O_OVERALL #> ; @@ -937,7 +809,6 @@

Build analysis SQL from design#> AND coalesce(ta.age_group_id,-1) = coalesce(oa.age_group_id,-1) #> AND coalesce(ta.gender_id,-1) = coalesce(oa.gender_id,-1) #> AND coalesce(ta.start_year, -1) = coalesce(oa.start_year,-1) -#> LEFT JOIN myresults.age_group_def ag on ag.age_group_id = ta.age_group_id #> LEFT JOIN mycdm.concept c on c.concept_id = ta.gender_id #> ; #> diff --git a/docs/news/index.html b/docs/news/index.html index 0d2d3ae..9ba26fc 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -60,6 +60,15 @@

Changelog

Source: NEWS.md

+
+

# CohortIncidence 4.0.0

+
+

Major Changes

+

The results DDL has been split into 5 tables: - incidence_summary - target_def - outcome_def - tar_def - age_group_def - subgroup_def

+

executeAnalysis() will return a list of dataframes with the following fields: - incidenceSummary - targetDef - outcomeDef - tarDef - ageGroupDef - subgroupDef

+

These dataframes follow the same structure as the corresponding table.

+
+

# CohortIncidence 3.3.1

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index fc41a56..0c78760 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,5 +3,5 @@ pkgdown: 2.0.9 pkgdown_sha: ~ articles: using-cohortincidence: using-cohortincidence.html -last_built: 2024-06-27T19:57Z +last_built: 2024-07-08T17:23Z diff --git a/docs/reference/StrataSettings.html b/docs/reference/StrataSettings.html index e4514e6..2ec25c0 100644 --- a/docs/reference/StrataSettings.html +++ b/docs/reference/StrataSettings.html @@ -93,6 +93,10 @@

Active bindings

a list of age breaks with at least 1 member

+
ageBreakList
+

a list of age breaks

+ +

diff --git a/docs/reference/createStrataSettings.html b/docs/reference/createStrataSettings.html index b3b9b3a..1ac774e 100644 --- a/docs/reference/createStrataSettings.html +++ b/docs/reference/createStrataSettings.html @@ -66,7 +66,13 @@

Creates R6 object for StrataSettings

- 
createStrataSettings(byAge = F, byGender = F, byYear = F, ageBreaks)
+ 
createStrataSettings(
+  byAge = F,
+  byGender = F,
+  byYear = F,
+  ageBreaks,
+  ageBreakList
+)
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zF^yQvGoNTC6*Q`7`R#FQqTTbL+h_o(=(MTN3VJ%q1Z^0ThiW=xj!!#lE<21^baQoB z?6>1gF=@U)m3a&r7Eku2Ayx&_HfAw(;R#>hphur@?qt-T=b;H4i`G9od8ZhFOT>Wz zv%DBCUuk%&91>JRg6xB;r4)cQQotMv{6v#@j~`GM&y;5DhOosC9YdI(OVD*iReXHh z2}=0`Z9UrbRcRcx&tG_)@$nzH0P0Rcx1tz-B+G=S_#@ea*gnl%bWfD#uzqZr$l=WR kEJPoq2e|O9KM2tMe|KIM>zXXha)EgPKz%|9JyOp90lf9_h5!Hn diff --git a/java/main/java/org/ohdsi/cohortincidence/CohortIncidenceQueryBuilder.java b/java/main/java/org/ohdsi/cohortincidence/CohortIncidenceQueryBuilder.java index 80939c3..620dcfa 100644 --- a/java/main/java/org/ohdsi/cohortincidence/CohortIncidenceQueryBuilder.java +++ b/java/main/java/org/ohdsi/cohortincidence/CohortIncidenceQueryBuilder.java @@ -26,6 +26,7 @@ public class CohortIncidenceQueryBuilder { private static final String COHORT_SUBGROUP_TEMPTABLE_TEMPLATE = ResourceHelper.GetResourceAsString("/resources/cohortincidence/sql/cohortSubgroupTempTable.sql"); private static final String TAR_STRATA_QUERY_TEMPTABLE_TEMPLATE = ResourceHelper.GetResourceAsString("/resources/cohortincidence/sql/tarStrataQueryTemplate.sql"); private static final String OUTCOME_STRATA_QUERY_TEMPTABLE_TEMPLATE = ResourceHelper.GetResourceAsString("/resources/cohortincidence/sql/outcomeStrataQueryTemplate.sql"); + private static final String AGE_GROUP_JOIN = ResourceHelper.GetResourceAsString("/resources/cohortincidence/sql/ageGroupJoin.sql"); private static final String AGE_GROUP_SELECT_TEMPLATE = "select CAST(%d as int) as age_group_id, '%s' as age_group_name, cast(%s as int) as min_age, cast(%s as int) as max_age"; private static final String NULL_STRATA = "cast(null as int)"; @@ -273,9 +274,11 @@ private String buildStrataQuery(String strataTemplate, String[] selectCols, Stri private String getStrataQueries(String strataTemplate) { ArrayList queries = new ArrayList<>(); + // Note: because age strata can contain overlapping (ie: non-stratified) age breaks, we need to + // apply the ageGroupJoin only on the subqueries that involve age group stratification. // overall strata queries.add(buildStrataQuery( - strataTemplate, + StringUtils.replace(strataTemplate, "@ageGroupJoin", ""), new String[] {NULL_STRATA + " as age_group_id", NULL_STRATA + " as gender_id", NULL_STRATA + " as start_year"}, new String[] {} )); @@ -283,35 +286,35 @@ private String getStrataQueries(String strataTemplate) { // by age if (this.design.strataSettings != null && this.design.strataSettings.byAge) { queries.add(buildStrataQuery( - strataTemplate, - new String[] {"t1.age_group_id", NULL_STRATA + " as gender_id", NULL_STRATA + " as start_year"}, - new String[] {"t1.age_group_id"} + StringUtils.replace(strataTemplate, "@ageGroupJoin", AGE_GROUP_JOIN), + new String[]{"ag.age_group_id", NULL_STRATA + " as gender_id", NULL_STRATA + " as start_year"}, + new String[]{"ag.age_group_id"} )); // by age, by gender if (this.design.strataSettings.byGender) { queries.add(buildStrataQuery( - strataTemplate, - new String[] {"t1.age_group_id", "t1.gender_id", NULL_STRATA + " as start_year"}, - new String[] {"t1.age_group_id", "t1.gender_id"} + StringUtils.replace(strataTemplate, "@ageGroupJoin", AGE_GROUP_JOIN), + new String[]{"ag.age_group_id", "t1.gender_id", NULL_STRATA + " as start_year"}, + new String[]{"ag.age_group_id", "t1.gender_id"} )); } // by age, by year if (this.design.strataSettings.byYear) { queries.add(buildStrataQuery( - strataTemplate, - new String[] {"t1.age_group_id", NULL_STRATA + " as gender_id", "t1.start_year"}, - new String[] {"t1.age_group_id", "t1.start_year"} + StringUtils.replace(strataTemplate, "@ageGroupJoin", AGE_GROUP_JOIN), + new String[] {"ag.age_group_id", NULL_STRATA + " as gender_id", "t1.start_year"}, + new String[] {"ag.age_group_id", "t1.start_year"} )); } // by age, by gender, by year if (this.design.strataSettings.byGender && this.design.strataSettings.byYear) { queries.add(buildStrataQuery( - strataTemplate, - new String[] {"t1.age_group_id", "t1.gender_id", "t1.start_year"}, - new String[] {"t1.age_group_id", "t1.gender_id", "t1.start_year"} + StringUtils.replace(strataTemplate, "@ageGroupJoin", AGE_GROUP_JOIN), + new String[] {"ag.age_group_id", "t1.gender_id", "t1.start_year"}, + new String[] {"ag.age_group_id", "t1.gender_id", "t1.start_year"} )); } } @@ -319,7 +322,7 @@ private String getStrataQueries(String strataTemplate) { // by gender if (this.design.strataSettings != null && this.design.strataSettings.byGender) { queries.add(buildStrataQuery( - strataTemplate, + StringUtils.replace(strataTemplate, "@ageGroupJoin", ""), new String[]{NULL_STRATA + " as age_group_id", "t1.gender_id", NULL_STRATA + " as start_year"}, new String[]{"t1.gender_id"} )); @@ -327,7 +330,7 @@ private String getStrataQueries(String strataTemplate) { // by gender, by year if (this.design.strataSettings.byYear) { queries.add(buildStrataQuery( - strataTemplate, + StringUtils.replace(strataTemplate, "@ageGroupJoin", ""), new String[] {NULL_STRATA + " as age_group_id", "t1.gender_id", "t1.start_year"}, new String[] {"t1.gender_id", "t1.start_year"} )); @@ -337,7 +340,7 @@ private String getStrataQueries(String strataTemplate) { // by year if (this.design.strataSettings != null && this.design.strataSettings.byYear) { queries.add(buildStrataQuery( - strataTemplate, + StringUtils.replace(strataTemplate, "@ageGroupJoin", ""), new String[]{NULL_STRATA + " as age_group_id", NULL_STRATA + "as gender_id", "t1.start_year"}, new String[]{"t1.start_year"} )); @@ -356,18 +359,27 @@ private String getAgeGroupInsert() { if (this.design.strataSettings == null || this.design.strataSettings.byAge == false) return ""; - if (this.design.strataSettings.ageBreaks.isEmpty()) - throw new IllegalArgumentException("Invalid strataSettings: ageBreaks can not be empty."); + if (this.design.strataSettings.ageBreaks.isEmpty() && + (this.design.strataSettings.ageBreakList.isEmpty() || this.design.strataSettings.ageBreakList.stream().anyMatch(List::isEmpty))) + throw new IllegalArgumentException("Invalid strataSettings: ageBreaks and ageBreaksList can not both be empty."); ArrayList selects = new ArrayList<>(); - List ageBreaks = this.design.strataSettings.ageBreaks; - selects.add(String.format(AGE_GROUP_SELECT_TEMPLATE, 1, "<" + ageBreaks.get(0),"null", ageBreaks.get(0))); + List> ageBreakList = new ArrayList<>(this.design.strataSettings.ageBreakList); + if (!this.design.strataSettings.ageBreaks.isEmpty()) { + // put the breaks from ageBreaks in the front of the list (for backwards compatability) + ageBreakList.add(0,this.design.strataSettings.ageBreaks); + } - for (int i = 0; i < ageBreaks.size() - 1; i++) - { - selects.add(String.format(AGE_GROUP_SELECT_TEMPLATE, i+2, "" + ageBreaks.get(i) + " - " + (ageBreaks.get(i+1)-1),ageBreaks.get(i), ageBreaks.get(i+1))); + int ageGroupId = 1; + for (List ageBreaks : ageBreakList) { + selects.add(String.format(AGE_GROUP_SELECT_TEMPLATE, ageGroupId++, "<" + ageBreaks.get(0),"null", ageBreaks.get(0))); + + for (int i = 0; i < ageBreaks.size() - 1; i++) + { + selects.add(String.format(AGE_GROUP_SELECT_TEMPLATE, ageGroupId++, "" + ageBreaks.get(i) + " - " + (ageBreaks.get(i+1)-1),ageBreaks.get(i), ageBreaks.get(i+1))); + } + selects.add(String.format(AGE_GROUP_SELECT_TEMPLATE, ageGroupId++, ">=" + ageBreaks.get(ageBreaks.size()-1),ageBreaks.get(ageBreaks.size()-1), "null")); } - selects.add(String.format(AGE_GROUP_SELECT_TEMPLATE, ageBreaks.size()+1, ">=" + ageBreaks.get(ageBreaks.size()-1),ageBreaks.get(ageBreaks.size()-1), "null")); return String.format("insert into @results_database_schema.age_group_def (ref_id, age_group_id, age_group_name, min_age, max_age)\nselect CAST(@ref_id as int) as ref_id, age_group_id, age_group_name, min_age, max_age from (\n%s\n) ag;", StringUtils.join(selects, "\nUNION ALL\n")); diff --git a/java/main/resources/resources/cohortincidence/sql/ageGroupJoin.sql b/java/main/resources/resources/cohortincidence/sql/ageGroupJoin.sql new file mode 100644 index 0000000..31b6401 --- /dev/null +++ b/java/main/resources/resources/cohortincidence/sql/ageGroupJoin.sql @@ -0,0 +1,3 @@ + LEFT JOIN @results_database_schema.age_group_def ag ON ag.ref_id = @ref_id + and t1.age >= coalesce(ag.min_age, -999) + and t1.age < coalesce(ag.max_age, 999) \ No newline at end of file diff --git a/java/main/resources/resources/cohortincidence/sql/incidenceAnalysis.sql b/java/main/resources/resources/cohortincidence/sql/incidenceAnalysis.sql index ebe4217..0b6c445 100644 --- a/java/main/resources/resources/cohortincidence/sql/incidenceAnalysis.sql +++ b/java/main/resources/resources/cohortincidence/sql/incidenceAnalysis.sql @@ -231,7 +231,7 @@ FROM ( /* 5) aggregate tar and excluded+outcome */ -WITH tar_overall (target_cohort_definition_id, tar_id, subgroup_id, subject_id, start_date, end_date, age_group_id, gender_id, start_year) +WITH tar_overall (target_cohort_definition_id, tar_id, subgroup_id, subject_id, start_date, end_date, age, gender_id, start_year) AS ( SELECT te.cohort_definition_id as target_cohort_definition_id, te.tar_id, @@ -239,14 +239,11 @@ AS ( te.subject_id, te.start_date, te.end_date, - ag.age_group_id, + YEAR(te.start_date) - p.year_of_birth as age, p.gender_concept_id as gender_id, YEAR(te.start_date) as start_year FROM #TTAR_erafied te JOIN @cdm_database_schema.person p on te.subject_id = p.person_id - LEFT JOIN @results_database_schema.age_group_def ag ON YEAR(te.start_date) - p.year_of_birth >= coalesce(ag.min_age, -999) - and YEAR(te.start_date) - p.year_of_birth < coalesce(ag.max_age, 999) - and ag.ref_id = @ref_id ) select target_cohort_definition_id, tar_id, subgroup_id, age_group_id, gender_id, start_year, person_days_pe, persons_at_risk_pe INTO #tar_agg @@ -255,7 +252,7 @@ FROM ( ) T_OVERALL ; -WITH outcomes_overall (target_cohort_definition_id, tar_id, subgroup_id, outcome_id, subject_id, age_group_id, gender_id, start_year, excluded_days, tar_days, outcomes_pe, outcomes) +WITH outcomes_overall (target_cohort_definition_id, tar_id, subgroup_id, outcome_id, subject_id, age, gender_id, start_year, excluded_days, tar_days, outcomes_pe, outcomes) AS ( SELECT t1.cohort_definition_id as target_cohort_definition_id, @@ -263,7 +260,7 @@ WITH outcomes_overall (target_cohort_definition_id, tar_id, subgroup_id, outcome t1.subgroup_id, op.outcome_id, t1.subject_id, - ag.age_group_id, + YEAR(t1.start_date) - p.year_of_birth as age, p.gender_concept_id as gender_id, YEAR(t1.start_date) as start_year, coalesce(e1.person_days, 0) as excluded_days, @@ -272,9 +269,6 @@ WITH outcomes_overall (target_cohort_definition_id, tar_id, subgroup_id, outcome coalesce(o1.outcomes, 0) as outcomes FROM #TTAR_erafied t1 JOIN @cdm_database_schema.person p ON t1.subject_id = p.person_id - LEFT JOIN @results_database_schema.age_group_def ag ON YEAR(t1.start_date) - p.year_of_birth >= coalesce(ag.min_age, -999) - AND YEAR(t1.start_date) - p.year_of_birth < coalesce(ag.max_age, 999) - AND ag.ref_id = @ref_id JOIN ( -- get the list of TTSO of anyone with excluded time or outcomes to limit result select target_cohort_definition_id, tar_id, subgroup_id, outcome_id, subject_id, start_date FROM #excluded_person_days UNION -- will remove dupes diff --git a/java/main/resources/resources/cohortincidence/sql/outcomeStrataQueryTemplate.sql b/java/main/resources/resources/cohortincidence/sql/outcomeStrataQueryTemplate.sql index 60a149b..e746d7f 100644 --- a/java/main/resources/resources/cohortincidence/sql/outcomeStrataQueryTemplate.sql +++ b/java/main/resources/resources/cohortincidence/sql/outcomeStrataQueryTemplate.sql @@ -12,4 +12,5 @@ SUM(t1.outcomes_pe) as outcomes_pe, SUM(t1.outcomes) as outcomes FROM outcomes_overall t1 +@ageGroupJoin GROUP BY target_cohort_definition_id, tar_id, subgroup_id, outcome_id@groupCols \ No newline at end of file diff --git a/java/main/resources/resources/cohortincidence/sql/tarStrataQueryTemplate.sql b/java/main/resources/resources/cohortincidence/sql/tarStrataQueryTemplate.sql index 850a2fd..7a25dca 100644 --- a/java/main/resources/resources/cohortincidence/sql/tarStrataQueryTemplate.sql +++ b/java/main/resources/resources/cohortincidence/sql/tarStrataQueryTemplate.sql @@ -5,4 +5,5 @@ SUM(CAST((DATEDIFF(day,t1.start_date,t1.end_date) + 1) as bigint)) as person_days_pe, COUNT(distinct t1.subject_id) as persons_at_risk_pe FROM tar_overall t1 +@ageGroupJoin GROUP BY t1.target_cohort_definition_id, t1.tar_id, t1.subgroup_id@groupCols \ No newline at end of file diff --git a/java/test/java/org/ohdsi/cohortincidence/Incidence_5_0_Test.java b/java/test/java/org/ohdsi/cohortincidence/Incidence_5_0_Test.java index cb0fd33..214bd9e 100644 --- a/java/test/java/org/ohdsi/cohortincidence/Incidence_5_0_Test.java +++ b/java/test/java/org/ohdsi/cohortincidence/Incidence_5_0_Test.java @@ -398,6 +398,35 @@ public void strataByAgeTest() throws Exception { this.executeTest(params); } + /** + * Tests multiple people with different age/gender/year strata, but only requests by-age strata + * Person 1: Male, 2 outcomes, 1 excluded, 2 TARs (age 32 and 37). + * Person 2: Female, 2 outcomes, 0 excluded, 2 TARs (age 35 and 37) + * Special notes: Person 1 will start in 1 year but have the TAR exclusion make followup start in next year + * to test that start_year is correct (it should use the erafied-start date) + * + * @throws Exception + */ + @Test + public void strataByAgeBreakListTest() throws Exception { + TestParams params = new TestParams(); + + params.resultSchema = "strata_age_list"; // this must be all lower case for DBUnit to work + params.prepDataSets = new String[]{ + "/datasets/vocabulary.json", + "/cohortincidence/timeAtRisk/strataByAgeBreakList_PREP.json" + }; + params.designJson = ResourceHelper.GetResourceAsString("/cohortincidence/timeAtRisk/strataByAgeBreakListTest.json"); + params.verifyDataSets = new String[]{"/cohortincidence/timeAtRisk/strataByAgeBreakList_VERIFY.json"}; + params.verifyCols = Arrays.asList(new String[]{COL_REF_ID, COL_TARGET_COHORT_ID, COL_TAR_ID, COL_SUBGROUP_ID, COL_OUTCOME_ID, + COL_AGE_GROUP_ID, COL_GENDER_ID, COL_YEAR_ID, + COL_PERSONS_PRE_EXCLUDE, COL_PERSONS_AT_RISK, COL_PERSONS_DAYS_PRE_EXCLUDE, COL_PERSON_DAYS, + COL_PERSON_OUTCOMES_PRE_EXCLUDE, COL_PERSON_OUTCOMES, COL_OUTCOMES_PRE_EXCLUDE, COL_OUTCOMES, + COL_INCIDENCE_PROPORTION_P100P, COL_INCIDENCE_RATE_P100PY}); + + this.executeTest(params); + } + /** * Tests multiple people with different age/gender/year strata, but only requests by-age strata * Person 1: Male, 2 outcomes, 1 excluded, 2 TARs (age 32 and 37). diff --git a/java/test/resources/cohortincidence/timeAtRisk/strataByAgeBreakListTest.json b/java/test/resources/cohortincidence/timeAtRisk/strataByAgeBreakListTest.json new file mode 100644 index 0000000..dd5527a --- /dev/null +++ b/java/test/resources/cohortincidence/timeAtRisk/strataByAgeBreakListTest.json @@ -0,0 +1,43 @@ +{ + "targetDefs": [ + { + "id": 100, + "name": "Target Cohort 1" + } + ], + "outcomeDefs": [ + { + "id": 1, + "name": "Outcome Cohort 1", + "cohortId": 200, + "cleanWindow": 30 + } + ], + "timeAtRiskDefs": [ + { + "id": 1, + "start": { + "dateField": "start", + "offset": 0 + }, + "end": { + "dateField": "start", + "offset": 90 + } + } + ], + "strataSettings": { + "byAge": true, + "byGender": false, + "byYear": false, + "ageBreaks": [17, 35, 65], + "ageBreakList": [[17], [35], [65]] + }, + "analysisList": [ + { + "targets": [100], + "outcomes": [1], + "tars": [1] + } + ] +} diff --git a/java/test/resources/cohortincidence/timeAtRisk/strataByAgeBreakList_PREP.json b/java/test/resources/cohortincidence/timeAtRisk/strataByAgeBreakList_PREP.json new file mode 100644 index 0000000..2401c02 --- /dev/null +++ b/java/test/resources/cohortincidence/timeAtRisk/strataByAgeBreakList_PREP.json @@ -0,0 +1,95 @@ +{ + "cdm.person": [ + { + "person_id": 1, + "gender_concept_id": 8507, + "year_of_birth": 1970, + "race_concept_id": 0, + "ethnicity_concept_id": 0 + }, + { + "person_id": 2, + "gender_concept_id": 8532, + "year_of_birth": 1968, + "race_concept_id": 0, + "ethnicity_concept_id": 0 + } + ], + "cdm.observation_period": [ + { + "observation_period_id": 1, + "person_id": 1, + "observation_period_start_date": "2000-01-01", + "observation_period_end_date": "2010-01-01", + "period_type_concept_id": 0 + },{ + "observation_period_id": 2, + "person_id": 2, + "observation_period_start_date": "2000-01-01", + "observation_period_end_date": "2010-01-01", + "period_type_concept_id": 0 + } + ], + "strata_age_list.cohort": [ + { + "cohort_definition_id": 100, + "subject_id": 1, + "cohort_start_date": "2002-12-25", + "cohort_end_date": "2002-12-25" + }, + { + "cohort_definition_id": 100, + "subject_id": 1, + "cohort_start_date": "2007-03-01", + "cohort_end_date": "2007-03-01" + }, + { + "cohort_definition_id": 200, + "subject_id": 1, + "cohort_start_date": "2002-12-15", + "cohort_end_date": "2002-12-15" + }, + { + "cohort_definition_id": 200, + "subject_id": 1, + "cohort_start_date": "2003-02-15", + "cohort_end_date": "2003-02-15" + }, + { + "cohort_definition_id": 200, + "subject_id": 1, + "cohort_start_date": "2007-04-01", + "cohort_end_date": "2007-04-01" + }, + { + "cohort_definition_id": 200, + "subject_id": 1, + "cohort_start_date": "2007-04-05", + "cohort_end_date": "2007-04-05" + }, + { + "cohort_definition_id": 100, + "subject_id": 2, + "cohort_start_date": "2003-03-01", + "cohort_end_date": "2003-03-01" + }, + { + "cohort_definition_id": 100, + "subject_id": 2, + "cohort_start_date": "2005-03-01", + "cohort_end_date": "2005-03-01" + }, + { + "cohort_definition_id": 200, + "subject_id": 2, + "cohort_start_date": "2003-02-01", + "cohort_end_date": "2003-02-01" + }, + { + "cohort_definition_id": 200, + "subject_id": 2, + "cohort_start_date": "2003-05-01", + "cohort_end_date": "2003-05-01" + } + ] +} \ No newline at end of file diff --git a/java/test/resources/cohortincidence/timeAtRisk/strataByAgeBreakList_VERIFY.json b/java/test/resources/cohortincidence/timeAtRisk/strataByAgeBreakList_VERIFY.json new file mode 100644 index 0000000..20921a0 --- /dev/null +++ b/java/test/resources/cohortincidence/timeAtRisk/strataByAgeBreakList_VERIFY.json @@ -0,0 +1,144 @@ +{ + "strata_age_list.incidence_summary": [ + { + "ref_id": 1, + "target_cohort_definition_id": 100, + "tar_id": 1, + "subgroup_id": 0, + "outcome_id": 1, + "age_group_id": 2, + "gender_id": null, + "start_year": null, + "persons_at_risk_pe": 1, + "persons_at_risk": 1, + "person_days_pe": 91, + "person_days": 40, + "person_outcomes_pe": 1, + "person_outcomes": 1, + "outcomes_pe": 1, + "outcomes": 1, + "incidence_proportion_p100p": 100, + "incidence_rate_p100py": 913.125 + }, + { + "ref_id": 1, + "target_cohort_definition_id": 100, + "tar_id": 1, + "subgroup_id": 0, + "outcome_id": 1, + "age_group_id": 3, + "gender_id": null, + "start_year": null, + "persons_at_risk_pe": 2, + "persons_at_risk": 2, + "person_days_pe": 273, + "person_days": 207, + "person_outcomes_pe": 2, + "person_outcomes": 2, + "outcomes_pe": 3, + "outcomes": 2, + "incidence_proportion_p100p": 100, + "incidence_rate_p100py": 352.8986 + }, + { + "ref_id": 1, + "target_cohort_definition_id": 100, + "tar_id": 1, + "subgroup_id": 0, + "outcome_id": 1, + "age_group_id": 6, + "gender_id": null, + "start_year": null, + "persons_at_risk_pe": 2, + "persons_at_risk": 2, + "person_days_pe": 364, + "person_days": 247, + "person_outcomes_pe": 2, + "person_outcomes": 2, + "outcomes_pe": 4, + "outcomes": 3, + "incidence_proportion_p100p": 100, + "incidence_rate_p100py": 443.6235 + }, + { + "ref_id": 1, + "target_cohort_definition_id": 100, + "tar_id": 1, + "subgroup_id": 0, + "outcome_id": 1, + "age_group_id": 7, + "gender_id": null, + "start_year": null, + "persons_at_risk_pe": 1, + "persons_at_risk": 1, + "person_days_pe": 91, + "person_days": 40, + "person_outcomes_pe": 1, + "person_outcomes": 1, + "outcomes_pe": 1, + "outcomes": 1, + "incidence_proportion_p100p": 100, + "incidence_rate_p100py": 913.1250 + }, + { + "ref_id": 1, + "target_cohort_definition_id": 100, + "tar_id": 1, + "subgroup_id": 0, + "outcome_id": 1, + "age_group_id": 8, + "gender_id": null, + "start_year": null, + "persons_at_risk_pe": 2, + "persons_at_risk": 2, + "person_days_pe": 273, + "person_days": 207, + "person_outcomes_pe": 2, + "person_outcomes": 2, + "outcomes_pe": 3, + "outcomes": 2, + "incidence_proportion_p100p": 100, + "incidence_rate_p100py": 352.8986 + }, + { + "ref_id": 1, + "target_cohort_definition_id": 100, + "tar_id": 1, + "subgroup_id": 0, + "outcome_id": 1, + "age_group_id": 9, + "gender_id": null, + "start_year": null, + "persons_at_risk_pe": 2, + "persons_at_risk": 2, + "person_days_pe": 364, + "person_days": 247, + "person_outcomes_pe": 2, + "person_outcomes": 2, + "outcomes_pe": 4, + "outcomes": 3, + "incidence_proportion_p100p": 100, + "incidence_rate_p100py": 443.6235 + }, + { + "ref_id": 1, + "target_cohort_definition_id": 100, + "tar_id": 1, + "subgroup_id": 0, + "outcome_id": 1, + "age_group_id": null, + "gender_id": null, + "start_year": null, + "persons_at_risk_pe": 2, + "persons_at_risk": 2, + "person_days_pe": 364, + "person_days": 247, + "person_outcomes_pe": 2, + "person_outcomes": 2, + "outcomes_pe": 4, + "outcomes": 3, + "incidence_proportion_p100p": 100, + "incidence_rate_p100py": 443.6235 + } + ] +} \ No newline at end of file diff --git a/man/StrataSettings.Rd b/man/StrataSettings.Rd index e56790f..6021e94 100644 --- a/man/StrataSettings.Rd +++ b/man/StrataSettings.Rd @@ -26,6 +26,8 @@ before calling jsonlite::toJSON(). \item{\code{byYear}}{enables stratification by start year of TAR} \item{\code{ageBreaks}}{a list of age breaks with at least 1 member} + +\item{\code{ageBreakList}}{a list of age breaks} } \if{html}{\out{
}} } diff --git a/man/createStrataSettings.Rd b/man/createStrataSettings.Rd index 31de637..3e868e4 100644 --- a/man/createStrataSettings.Rd +++ b/man/createStrataSettings.Rd @@ -4,7 +4,13 @@ \alias{createStrataSettings} \title{Creates R6 object for StrataSettings} \usage{ -createStrataSettings(byAge = F, byGender = F, byYear = F, ageBreaks) +createStrataSettings( + byAge = F, + byGender = F, + byYear = F, + ageBreaks, + ageBreakList +) } \arguments{ \item{byAge}{a boolean indicating to stratify by age, defaults to F} diff --git a/pom.xml b/pom.xml index da490c6..387fa70 100644 --- a/pom.xml +++ b/pom.xml @@ -149,7 +149,7 @@ org.ohdsi standardized-analysis-specs - 1.5.0 + 1.6.0-SNAPSHOT org.springframework.boot diff --git a/vignettes/using-cohortincidence.Rmd b/vignettes/using-cohortincidence.Rmd index e4d65fc..cf781f8 100644 --- a/vignettes/using-cohortincidence.Rmd +++ b/vignettes/using-cohortincidence.Rmd @@ -119,15 +119,27 @@ The IR design can also include settings to specify if an analysis should be done To use this function, you create the strata settings with the `CohortIncidence::createStrataSettings)` function: ```{r} -irDesignWithStrata <- CohortIncidence::createIncidenceDesign(targetDefs = list(t1), - outcomeDefs = list(o1), - tars=list(tar1), - analysisList = list(analysis1), - subgroups = list(subgroup1), - #add by age and by gender strata, but don't do by start year. - strataSettings = CohortIncidence::createStrataSettings(byGender=T, byAge=T, ageBreaks = c(17,34,65))) +irDesignWithStrata <- + CohortIncidence::createIncidenceDesign( + targetDefs = list(t1), + outcomeDefs = list(o1), + tars = list(tar1), + analysisList = list(analysis1), + subgroups = list(subgroup1), + #add by age and by gender strata, but don't do by start year. + strataSettings = CohortIncidence::createStrataSettings( + byGender = T, + byAge = T, + ageBreaks = list(17, 34, 65), + ageBreakList = list(list(25), list(65)) + ) + ) ``` +In the above example, thare are 2 ways of specifying the age breaks: ageBreaks and ageBreakList. ageBreaks creates a single age +break specification, while ageBreakList allows you to specify a list of breaks. All breaks defined in ageBreaks and ageBreakList will be +used if specified. If byAge is TRUE, you must specify at least one age break specification either in ageBreaks or ageBreakList. + ## Using executeAnalysis() If there is no need to see the analysis sql or control the output of the analysis to a permenant table, the `executeAnalysis()` function