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Read cohort incidence options from lookup tables #309

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Read cohort incidence options from lookup tables #309

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5c62a73
Update characterization-incidence.R to use lookup tables.
chrisknoll Jul 23, 2024
16612ce
Switch coldef json to CSV.
chrisknoll Jul 30, 2024
5967f82
Removed dead code.
chrisknoll Jul 30, 2024
9888845
fixing tests
jreps Jul 31, 2024
ab7f958
fixing example sqlite database_ids
jreps Jul 31, 2024
a285c60
Merge branch 'prerelease' into estimation-updated-cohortIncidence
jreps Aug 1, 2024
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18 changes: 9 additions & 9 deletions R/characterization-caseSeries.R
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Original file line number Diff line number Diff line change
Expand Up @@ -190,7 +190,7 @@ characterizationGetCaseSeriesOptions <- function(
and s.database_id = cd.database_id
and cd.target_cohort_id = @target_id
and cd.outcome_cohort_id = @outcome_id
and cd.cohort_type = 'TnO'
and cd.cohort_type = 'Cases'

inner join
@schema.@cg_table_prefixcohort_definition ct1
Expand Down Expand Up @@ -256,9 +256,9 @@ characterizationGetCaseSeriesData <- function(

sql <- "SELECT
case
when cov.cohort_type = 'TnO' then 'Before'
when cov.cohort_type = 'TnObetween' then 'During'
when cov.cohort_type = 'OnT' then 'After'
when cov.cohort_type = 'CasesBefore' then 'Before'
when cov.cohort_type = 'CasesBetween' then 'During'
when cov.cohort_type = 'CaseAfter' then 'After'
end as type,
cr.covariate_name,
s.min_prior_observation, s.outcome_washout_days,
Expand All @@ -277,7 +277,7 @@ characterizationGetCaseSeriesData <- function(

where cov.target_cohort_id = @target_id
and cov.outcome_cohort_id = @outcome_id
and cov.cohort_type in ('TnObetween','OnT','TnO')
and cov.cohort_type in ('CasesBetween','CasesAfter','CasesBefore')
--and cov.setting_id = @setting_id
and s.risk_window_start = @risk_window_start
and s.risk_window_end = @risk_window_end
Expand Down Expand Up @@ -309,9 +309,9 @@ characterizationGetCaseSeriesData <- function(

sql <- "SELECT
case
when cov.cohort_type = 'TnO' then 'Before'
when cov.cohort_type = 'TnObetween' then 'During'
when cov.cohort_type = 'OnT' then 'After'
when cov.cohort_type = 'CasesBefore' then 'Before'
when cov.cohort_type = 'CasesBetween' then 'During'
when cov.cohort_type = 'CasesAfter' then 'After'
end as type,
cr.covariate_name,
s.min_prior_observation, s.outcome_washout_days,
Expand All @@ -333,7 +333,7 @@ characterizationGetCaseSeriesData <- function(

where cov.target_cohort_id = @target_id
and cov.outcome_cohort_id = @outcome_id
and cov.cohort_type in ('TnObetween','OnT','TnO')
and cov.cohort_type in ('CasesBetween','CasesAfter','CasesBefore')
and s.risk_window_start = @risk_window_start
and s.risk_window_end = @risk_window_end
and s.start_anchor = '@start_anchor'
Expand Down
2 changes: 1 addition & 1 deletion R/characterization-cohorts.R
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Expand Up @@ -968,7 +968,7 @@ characterizatonGetCohortComparisonDataContinuous <- function(
res <- res %>% dplyr::select(-"cohortDefinitionId", -"databaseId", -"type",
-"settingId", -"targetCohortId", -"outcomeCohortId",
-"cohortType") %>%
dplyr::relocate(.data$databaseName, .after = .data$covariateName)
dplyr::relocate("databaseName", .after = "covariateName")
}

shiny::incProgress(4/4, detail = paste("Done"))
Expand Down
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