diff --git a/DESCRIPTION b/DESCRIPTION index 2baa5ed..5fff932 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: SelfControlledCaseSeries Type: Package Title: Self-Controlled Case Series Version: 5.2.3 -Date: 2024-06-20 +Date: 2024-08-12 Authors@R: c( person("Martijn", "Schuemie", , "schuemie@ohdsi.org", role = c("aut", "cre")), person("Patrick", "Ryan", role = c("aut")), @@ -19,7 +19,7 @@ Description: SelfControlledCaseSeries is an R package for performing self- included at once (MSCCS), with regularization on all coefficients except for the exposure of interest. VignetteBuilder: knitr -URL: https://github.com/OHDSI/SelfControlledCaseSeries +URL: https://ohdsi.github.io/SelfControlledCaseSeries/, https://github.com/OHDSI/SelfControlledCaseSeries BugReports: https://github.com/OHDSI/SelfControlledCaseSeries/issues Depends: R (>= 4.0.0), diff --git a/NEWS.md b/NEWS.md index a6b3c2a..fa6e2b5 100644 --- a/NEWS.md +++ b/NEWS.md @@ -5,7 +5,7 @@ Changes 1. More informative error messages when analysis specifications are inconsistent. -2. Throwing error when defining analysis that does not specify at least one era covariate that is the exposure of interest. +2. Throwing error when defining an analysis that does not specify at least one era covariate that is the exposure of interest. 3. The `includeEraIds` argument of `createEraCovariateSettings()` no longer has a default, forcing users to explicitly set this to avoid erroneously specifying all covariates. diff --git a/docs/404.html b/docs/404.html index 46a67ef..8574e29 100644 --- a/docs/404.html +++ b/docs/404.html @@ -6,7 +6,7 @@ Page not found (404) • SelfControlledCaseSeries - + @@ -18,7 +18,7 @@ - +
@@ -44,7 +44,7 @@
  • @@ -81,7 +81,7 @@
    • - +
    @@ -109,16 +109,16 @@

    Page not found (404)

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/MultipleAnalyses.html b/docs/articles/MultipleAnalyses.html index c98d679..5802a1c 100644 --- a/docs/articles/MultipleAnalyses.html +++ b/docs/articles/MultipleAnalyses.html @@ -6,13 +6,12 @@ Running multiple analyses at once using the SelfControlledCaseSeries package • SelfControlledCaseSeries - + - + - + - Articles • SelfControlledCaseSeriesArticles • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -85,15 +85,15 @@

    All vignettes

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/authors.html b/docs/authors.html index 511c8f0..f6a0991 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,9 +1,9 @@ -Authors and Citation • SelfControlledCaseSeriesAuthors and Citation • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    -

    Authors

    +

    Authors and Citation

    - +
    • -

      Martijn Schuemie. Author, maintainer. +

      Martijn Schuemie. Author, maintainer.

    • -

      Patrick Ryan. Author. +

      Patrick Ryan. Author.

    • -

      Trevor Shaddox. Author. +

      Trevor Shaddox. Author.

    • -

      Marc Suchard. Author. +

      Marc Suchard. Author.

    @@ -94,14 +94,14 @@

    Citation

    Schuemie M, Ryan P, Shaddox T, Suchard M (2024). SelfControlledCaseSeries: Self-Controlled Case Series. -R package version 5.2.2, https://github.com/OHDSI/SelfControlledCaseSeries. +R package version 5.2.3, https://github.com/OHDSI/SelfControlledCaseSeries, https://ohdsi.github.io/SelfControlledCaseSeries/. 

    @Manual{,
   title = {SelfControlledCaseSeries: Self-Controlled Case Series},
   author = {Martijn Schuemie and Patrick Ryan and Trevor Shaddox and Marc Suchard},
   year = {2024},
-  note = {R package version 5.2.2},
-  url = {https://github.com/OHDSI/SelfControlledCaseSeries},
+  note = {R package version 5.2.3, https://github.com/OHDSI/SelfControlledCaseSeries},
+  url = {https://ohdsi.github.io/SelfControlledCaseSeries/},
 }
    @@ -115,15 +115,15 @@

    Citation

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/index.html b/docs/index.html index d402564..3fddbc8 100644 --- a/docs/index.html +++ b/docs/index.html @@ -6,27 +6,20 @@ Self-Controlled Case Series • SelfControlledCaseSeries - + - + - +
    @@ -52,7 +45,7 @@
  • @@ -89,7 +82,7 @@
    • - +
    @@ -284,16 +277,16 @@

    Developers

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/news/index.html b/docs/news/index.html index 73ffa14..346fc4e 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -1,9 +1,9 @@ -Changelog • SelfControlledCaseSeriesChangelog • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -66,6 +66,17 @@

    Changelog

    Source: NEWS.md
    +
    +

    SelfControlledCaseSeries 5.2.3

    +

    Changes

    +

    1. More informative error messages when analysis specifications are inconsistent.

      2. +

    2. Throwing error when defining an analysis that does not specify at least one era covariate that is the exposure of interest.

      3. +

    3. The includeEraIds argument of createEraCovariateSettings() no longer has a default, forcing users to explicitly set this to avoid erroneously specifying all covariates.

      4. +

    Bugfixes

    +

    1. Fixed ‘ORDER BY is ignored in subqueries without LIMIT’ warning when calling createSccsIntervalData().

      2. +

    2. Fixed ‘std::bad_alloc’ error when any observation period start date is before 1970.

      3. +

    3. Fixed NA covariate values when age, season, or calendar time splines are removed because there are fewer cases than knots.

      4. +

    SelfControlledCaseSeries 5.2.2

    Bugfixes

    @@ -258,15 +269,15 @@

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index ab87bd4..02b3d41 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,9 +1,8 @@ -pandoc: 3.1.1 -pkgdown: 2.0.7 +pandoc: 3.1.11 +pkgdown: 2.1.0 pkgdown_sha: ~ articles: MultipleAnalyses: MultipleAnalyses.html ResultsSchema: ResultsSchema.html SingleStudies: SingleStudies.html -last_built: 2024-06-10T09:45Z - +last_built: 2024-08-12T06:42Z diff --git a/docs/reference/SccsData-class.html b/docs/reference/SccsData-class.html index 8bdf83a..3e8a94c 100644 --- a/docs/reference/SccsData-class.html +++ b/docs/reference/SccsData-class.html @@ -1,11 +1,11 @@ -SCCS Data — SccsData-class • SelfControlledCaseSeriesSCCS Data — SccsData-class • SelfControlledCaseSeries - +
    @@ -30,7 +30,7 @@
    • - +
    @@ -76,16 +76,18 @@

    SCCS Data

    - 
    # S4 method for SccsData
+    
    # S4 method for class 'SccsData'
 show(object)
 
-# S4 method for SccsData
+# S4 method for class 'SccsData'
 summary(object)

    Arguments

    -
    object
    + + +
    object

    An object of type SccsData.

    @@ -102,15 +104,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/SccsIntervalData-class.html b/docs/reference/SccsIntervalData-class.html index 3f18e00..2fa0c1a 100644 --- a/docs/reference/SccsIntervalData-class.html +++ b/docs/reference/SccsIntervalData-class.html @@ -1,12 +1,12 @@ -SCCS Interval Data — SccsIntervalData-class • SelfControlledCaseSeriesSCCS Interval Data — SccsIntervalData-class • SelfControlledCaseSeries - +
    @@ -31,7 +31,7 @@
    • - +
    @@ -78,16 +78,18 @@

    SCCS Interval Data

    - 
    # S4 method for SccsIntervalData
+    
    # S4 method for class 'SccsIntervalData'
 show(object)
 
-# S4 method for SccsIntervalData
+# S4 method for class 'SccsIntervalData'
 summary(object)

    Arguments

    -
    object
    + + +
    object

    An object of type SccsIntervalData.

    @@ -104,15 +106,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/SelfControlledCaseSeries-package.html b/docs/reference/SelfControlledCaseSeries-package.html index c63e43f..58aa050 100644 --- a/docs/reference/SelfControlledCaseSeries-package.html +++ b/docs/reference/SelfControlledCaseSeries-package.html @@ -1,9 +1,9 @@ -SelfControlledCaseSeries: Self-Controlled Case Series — SelfControlledCaseSeries-package • SelfControlledCaseSeriesSelfControlledCaseSeries: Self-Controlled Case Series — SelfControlledCaseSeries-package • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -98,15 +98,15 @@

    Author

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/computeMdrr.html b/docs/reference/computeMdrr.html index 770c628..a5fe8a9 100644 --- a/docs/reference/computeMdrr.html +++ b/docs/reference/computeMdrr.html @@ -1,9 +1,9 @@ -Compute the minimum detectable relative risk — computeMdrr • SelfControlledCaseSeriesCompute the minimum detectable relative risk — computeMdrr • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -84,29 +84,31 @@

    Compute the minimum detectable relative risk

    Arguments

    -
    object
    + + +
    object

    An object either of type SccsIntervalData as created using the createSccsIntervalData function, or an object of type SccsModel as created using the fitSccsModel() function.

    -
    exposureCovariateId
    +
    exposureCovariateId

    Covariate Id for the health exposure of interest.

    -
    alpha
    +
    alpha

    Type I error.

    -
    power
    +
    power

    1 - beta, where beta is the type II error.

    -
    twoSided
    +
    twoSided

    Consider a two-sided test?

    -
    method
    +
    method

    The type of sample size formula that will be used. Allowable values are "proportion", "binomial", "SRL1", "SRL2", or "ageEffects". Currently "ageEffects" is not supported.

    @@ -114,9 +116,7 @@

    Arguments

    Value

    - - -

    A data frame with the MDRR, number of events, time at risk, and total time.

    +

    A data frame with the MDRR, number of events, time at risk, and total time.

    Details

    @@ -143,15 +143,15 @@

    References

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/computePreExposureGainP.html b/docs/reference/computePreExposureGainP.html index ee06472..95c4b57 100644 --- a/docs/reference/computePreExposureGainP.html +++ b/docs/reference/computePreExposureGainP.html @@ -1,9 +1,9 @@ -Compute P for pre-exposure risk gain — computePreExposureGainP • SelfControlledCaseSeriesCompute P for pre-exposure risk gain — computePreExposureGainP • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,16 +77,18 @@

    Compute P for pre-exposure risk gain

    Arguments

    -
    sccsData
    + + +
    sccsData

    An object of type SccsData as created using the getDbSccsData function.

    -
    studyPopulation
    +
    studyPopulation

    An object created using the createStudyPopulation() function.

    -
    exposureEraId
    +
    exposureEraId

    The exposure to create the era data for. If not specified it is assumed to be the one exposure for which the data was loaded from the database.

    @@ -94,9 +96,7 @@

    Arguments

    Value

    - - -

    A one-sided p-value for whether the rate before exposure is higher than after, against +

    A one-sided p-value for whether the rate before exposure is higher than after, against the null of no change.

    @@ -120,15 +120,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/computeTimeStability.html b/docs/reference/computeTimeStability.html index 002d73f..fbf8ce0 100644 --- a/docs/reference/computeTimeStability.html +++ b/docs/reference/computeTimeStability.html @@ -1,9 +1,9 @@ -Compute stability of outcome rate over time — computeTimeStability • SelfControlledCaseSeriesCompute stability of outcome rate over time — computeTimeStability • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -82,33 +82,31 @@

    Compute stability of outcome rate over time

    Arguments

    -
    studyPopulation
    + + +
    studyPopulation

    An object created using the createStudyPopulation() function.

    -
    sccsModel
    +
    sccsModel

    Optional: A fitted SCCS model as created using fitSccsModel(). If the model contains splines for seasonality and or calendar time these will be adjusted for before computing stability.

    -
    maxRatio
    +
    maxRatio

    The maximum global ratio between the observed and expected count.

    -
    alpha
    +
    alpha

    The alpha (type 1 error) used to test for stability.

    Value

    - - -

    A tibble with one row and three columns: ratio indicates the estimated mean ratio between observed and expected. -p is the p-value against the null-hypothesis that the ratio is smaller than maxRatio, and stable is TRUE

    - - -

    if p is greater than alpha.

    +

    A tibble with one row and three columns: ratio indicates the estimated mean ratio between observed and expected. +p is the p-value against the null-hypothesis that the ratio is smaller than maxRatio, and stable is TRUE +if p is greater than alpha.

    Details

    @@ -130,15 +128,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createAgeCovariateSettings.html b/docs/reference/createAgeCovariateSettings.html index fd59d88..de8fd4a 100644 --- a/docs/reference/createAgeCovariateSettings.html +++ b/docs/reference/createAgeCovariateSettings.html @@ -1,9 +1,9 @@ -Create age covariate settings — createAgeCovariateSettings • SelfControlledCaseSeriesCreate age covariate settings — createAgeCovariateSettings • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -81,7 +81,9 @@

    Create age covariate settings

    Arguments

    -
    ageKnots
    + + +
    ageKnots

    If a single number is provided this is assumed to indicate the number of knots to use for the spline, and the knots are automatically spaced according to equal percentiles of the data. @@ -89,12 +91,12 @@

    Arguments

    exact location of the knots in age-days

    -
    allowRegularization
    +
    allowRegularization

    When fitting the model, should the covariates defined here be allowed to be regularized?

    -
    computeConfidenceIntervals
    +
    computeConfidenceIntervals

    Should confidence intervals be computed for the covariates defined here? Setting this to FALSE might save computing time when fitting the model. Will be turned to FALSE automatically @@ -103,9 +105,7 @@

    Arguments

    Value

    - - -

    An object of type AgeCovariateSettings.

    +

    An object of type AgeCovariateSettings.

    Details

    @@ -127,15 +127,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createCalendarTimeCovariateSettings.html b/docs/reference/createCalendarTimeCovariateSettings.html index 15d5a2a..bdba8f6 100644 --- a/docs/reference/createCalendarTimeCovariateSettings.html +++ b/docs/reference/createCalendarTimeCovariateSettings.html @@ -1,9 +1,9 @@ -Create calendar time settings — createCalendarTimeCovariateSettings • SelfControlledCaseSeriesCreate calendar time settings — createCalendarTimeCovariateSettings • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -81,19 +81,21 @@

    Create calendar time settings

    Arguments

    -
    calendarTimeKnots
    + + +
    calendarTimeKnots

    If a single number is provided this is assumed to indicate the number of knots to use for the spline. See details on how knots are placed. If a series of dates is provided these are assumed to be the exact location of the knots.

    -
    allowRegularization
    +
    allowRegularization

    When fitting the model, should the covariates defined here be allowed to be regularized?

    -
    computeConfidenceIntervals
    +
    computeConfidenceIntervals

    Should confidence intervals be computed for the covariates defined here? Setting this to FALSE might save computing time when fitting the model. Will be turned to FALSE automatically @@ -102,9 +104,7 @@

    Arguments

    Value

    - - -

    An object of type seasonalitySettings.

    +

    An object of type seasonalitySettings.

    Details

    @@ -132,15 +132,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createControlIntervalSettings.html b/docs/reference/createControlIntervalSettings.html index 9b25077..4f32ee1 100644 --- a/docs/reference/createControlIntervalSettings.html +++ b/docs/reference/createControlIntervalSettings.html @@ -1,9 +1,9 @@ -Create control interval settings — createControlIntervalSettings • SelfControlledCaseSeriesCreate control interval settings — createControlIntervalSettings • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -85,44 +85,44 @@

    Create control interval settings

    Arguments

    -
    includeEraIds
    + + +
    includeEraIds

    One or more IDs of variables in the SccsData object that should be used to construct this covariate. If no IDs are specified, all variables will be used.

    -
    excludeEraIds
    +
    excludeEraIds

    One or more IDs of variables in the [SccsData] object that should not be used to construct this covariate.

    -
    start
    +
    start

    The start of the control interval (in days) relative to the startAnchor.

    -
    startAnchor
    +
    startAnchor

    The anchor point for the start of the control interval. Can be "era start" or "era end".

    -
    end
    +
    end

    The end of the control interval (in days) relative to the endAnchor.

    -
    endAnchor
    +
    endAnchor

    The anchor point for the end of the control interval. Can be "era start" or "era end".

    -
    firstOccurrenceOnly
    +
    firstOccurrenceOnly

    Should only the first occurrence of the exposure be used?

    Value

    - - -

    An object of type ControlSettings.

    +

    An object of type ControlSettings.

    Details

    @@ -142,15 +142,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createCreateSccsIntervalDataArgs.html b/docs/reference/createCreateSccsIntervalDataArgs.html index 98deda3..69c4d62 100644 --- a/docs/reference/createCreateSccsIntervalDataArgs.html +++ b/docs/reference/createCreateSccsIntervalDataArgs.html @@ -1,9 +1,9 @@ -Create a parameter object for the function createSccsIntervalData — createCreateSccsIntervalDataArgs • SelfControlledCaseSeriesCreate a parameter object for the function createSccsIntervalData — createCreateSccsIntervalDataArgs • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -85,31 +85,33 @@

    Create a parameter object for the function createSccsIntervalData

    Arguments

    -
    eraCovariateSettings
    + + +
    eraCovariateSettings

    Either an object of type EraCovariateSettings as created using the createEraCovariateSettings() function, or a list of such objects.

    -
    ageCovariateSettings
    +
    ageCovariateSettings

    An object of type ageCovariateSettings as created using the createAgeCovariateSettings() function.

    -
    seasonalityCovariateSettings
    +
    seasonalityCovariateSettings

    An object of type seasonalityCovariateSettings as created using the createSeasonalityCovariateSettings() function.

    -
    calendarTimeCovariateSettings
    +
    calendarTimeCovariateSettings

    An object of type calendarTimeCovariateSettings as created using the createCalendarTimeCovariateSettings() function.

    -
    minCasesForAgeSeason
    +
    minCasesForAgeSeason

    DEPRECATED: Use minCasesForTimeCovariates instead.

    -
    minCasesForTimeCovariates
    +
    minCasesForTimeCovariates

    Minimum number of cases to use to fit age, season and calendar time splines. If needed (and available), cases that are not exposed will be included.

    -
    eventDependentObservation
    +
    eventDependentObservation

    Should the extension proposed by Farrington et al. be used to adjust for event-dependent observation time?

    @@ -130,15 +132,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createCreateScriIntervalDataArgs.html b/docs/reference/createCreateScriIntervalDataArgs.html index 40a8bcf..d374209 100644 --- a/docs/reference/createCreateScriIntervalDataArgs.html +++ b/docs/reference/createCreateScriIntervalDataArgs.html @@ -1,9 +1,9 @@ -Create a parameter object for the function createScriIntervalData — createCreateScriIntervalDataArgs • SelfControlledCaseSeriesCreate a parameter object for the function createScriIntervalData — createCreateScriIntervalDataArgs • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,11 +77,13 @@

    Create a parameter object for the function createScriIntervalData

    Arguments

    -
    eraCovariateSettings
    + + +
    eraCovariateSettings

    Either an object of type EraCovariateSettings as created using the createEraCovariateSettings() function, or a list of such objects.

    -
    controlIntervalSettings
    +
    controlIntervalSettings

    An object of type ControlIntervalSettings as created using the createControlIntervalSettings() function.

    @@ -102,15 +104,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createCreateStudyPopulationArgs.html b/docs/reference/createCreateStudyPopulationArgs.html index 18903a0..00c7493 100644 --- a/docs/reference/createCreateStudyPopulationArgs.html +++ b/docs/reference/createCreateStudyPopulationArgs.html @@ -1,9 +1,9 @@ -Create a parameter object for the function createStudyPopulation — createCreateStudyPopulationArgs • SelfControlledCaseSeriesCreate a parameter object for the function createStudyPopulation — createCreateStudyPopulationArgs • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -84,27 +84,29 @@

    Create a parameter object for the function createStudyPopulation

    Arguments

    -
    firstOutcomeOnly
    + + +
    firstOutcomeOnly

    Whether only the first occurrence of an outcome should be considered.

    -
    naivePeriod
    +
    naivePeriod

    The number of days at the start of a patient's observation period that should not be included in the risk calculations. Note that the naive period can be used to determine current covariate status right after the naive period, and whether an outcome is the first one.

    -
    minAge
    +
    minAge

    Minimum age at which patient time will be included in the analysis. Note that information prior to the min age is still used to determine exposure status after the minimum age (e.g. when a prescription was started just prior to reaching the minimum age). Also, outcomes occurring before the minimum age is reached will be considered as prior outcomes when using first outcomes only. Age should be specified in years, but non-integer values are allowed. If not specified, no age restriction will be applied.

    -
    maxAge
    +
    maxAge

    Maximum age at which patient time will be included in the analysis. Age should be specified in years, but non-integer values are allowed. If not specified, no age restriction will be applied.

    -
    genderConceptIds
    +
    genderConceptIds

    Set of gender concept IDs to restrict the population to. If not specified, no restriction on gender will be applied.

    -
    restrictTimeToEraId
    +
    restrictTimeToEraId

    If provided, study time (for all patients) will be restricted to the calender time when that era was observed in the data. For example, if the era ID refers to a drug, study time will be restricted to when the drug was on the market.

    @@ -125,15 +127,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createDefaultSccsMultiThreadingSettings.html b/docs/reference/createDefaultSccsMultiThreadingSettings.html index 3659b9f..557a855 100644 --- a/docs/reference/createDefaultSccsMultiThreadingSettings.html +++ b/docs/reference/createDefaultSccsMultiThreadingSettings.html @@ -1,10 +1,10 @@ -Create default SelfControlledCaseSeries multi-threading settings — createDefaultSccsMultiThreadingSettings • SelfControlledCaseSeriesCreate default SelfControlledCaseSeries multi-threading settings — createDefaultSccsMultiThreadingSettings • SelfControlledCaseSeries - +
    @@ -29,7 +29,7 @@
    • - +
    @@ -79,15 +79,15 @@

    Create default SelfControlledCaseSeries multi-threading settings

    Arguments

    -
    maxCores
    + + +
    maxCores

    Maximum number of CPU cores to use.

    Value

    - - -

    An object of type SccsMultiThreadingSettings.

    +

    An object of type SccsMultiThreadingSettings.

    See also

    @@ -112,15 +112,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createEraCovariateSettings.html b/docs/reference/createEraCovariateSettings.html index 42c3991..ec09905 100644 --- a/docs/reference/createEraCovariateSettings.html +++ b/docs/reference/createEraCovariateSettings.html @@ -1,9 +1,9 @@ -Create era covariate settings — createEraCovariateSettings • SelfControlledCaseSeriesCreate era covariate settings — createEraCovariateSettings • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -73,7 +73,7 @@

    Create era covariate settings

    createEraCovariateSettings(
-  includeEraIds = NULL,
+  includeEraIds,
   excludeEraIds = NULL,
   label = "Covariates",
   stratifyById = FALSE,
@@ -90,22 +90,24 @@ 
    Create era covariate settings
    
 
     
    
     
    Arguments
    
-    
    includeEraIds
    
+
+
+
    includeEraIds
    
 
    One or more IDs of variables in the SccsData object that should be
-used to construct this covariate. If no IDs are specified, all
+used to construct this covariate. If set to NULL, all
 variables will be used.
    
 
 
-
    excludeEraIds
    
+
    excludeEraIds
    
 
    One or more IDs of variables in the [SccsData] object that should not
 be used to construct this covariate.
    
 
 
-
    label
    
+
    label
    
 
    A label used to identify the covariates created using these settings.
    
 
 
-
    stratifyById
    
+
    stratifyById
    
 
    Should a single covariate be created for every ID in the SccsData
 object, or should a single covariate be constructed? For example, if
 the IDs identify exposures to different drugs, should a covariate be
@@ -113,34 +115,34 @@ 
    Arguments
    
 of these drugs. Note that overlap will be considered a single exposure.
    
 
 
-
    start
    
+
    start
    
 
    The start of the risk window (in days) relative to the startAnchor.
    
 
 
-
    startAnchor
    
+
    startAnchor
    
 
    The anchor point for the start of the risk window. Can be "era start"
 or "era end".
    
 
 
-
    end
    
+
    end
    
 
    The end of the risk window (in days) relative to the endAnchor.
    
 
 
-
    endAnchor
    
+
    endAnchor
    
 
    The anchor point for the end of the risk window. Can be "era start"
 or "era end".
    
 
 
-
    firstOccurrenceOnly
    
+
    firstOccurrenceOnly
    
 
    Should only the first occurrence of the exposure be used?
    
 
 
-
    allowRegularization
    
+
    allowRegularization
    
 
    When fitting the model, should the covariates defined here be allowed
 to be regularized?
    
 
 
-
    profileLikelihood
    
+
    profileLikelihood
    
 
    When fitting the model, should the likelihood profile be computed for
 the covariate defined here? The likelihood profile can be used to
 avoid making normal approximations on the likelihood and can be used in
@@ -148,7 +150,7 @@ 
    Arguments
    
 while to compute.
    
 
 
-
    exposureOfInterest
    
+
    exposureOfInterest
    
 
    If TRUE, the fitted coefficient for this variable will be reported when
 using runSccsAnalyses(). Requires includeEraIds to be a exposure
 reference ID as defined in createExposure().
    
@@ -156,9 +158,7 @@ 
    Arguments
    
 
    
     
    
     
    Value
    
-    
-
-
    An object of type EraCovariateSettings.
    
+    
    An object of type EraCovariateSettings.
    
     
    
     
    
     
    Details
    
@@ -177,15 +177,15 @@ 
    Details
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    - - + + diff --git a/docs/reference/createExposure.html b/docs/reference/createExposure.html index 44b5b8b..91cfd65 100644 --- a/docs/reference/createExposure.html +++ b/docs/reference/createExposure.html @@ -1,9 +1,9 @@ -Create exposure definition — createExposure • SelfControlledCaseSeriesCreate exposure definition — createExposure • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,16 +77,18 @@

    Create exposure definition

    Arguments

    -
    exposureId
    + + +
    exposureId

    An integer used to identify the exposure in the exposure cohort table.

    -
    exposureIdRef
    +
    exposureIdRef

    A string used to refer to the exposure when defining covariates using the createEraCovariateSettings() function.

    -
    trueEffectSize
    +
    trueEffectSize

    For negative and positive controls: the known true effect size. To be used for empirical calibration. Negative controls have trueEffectSize = 1. If the true effect size is unknown, use @@ -95,9 +97,7 @@

    Arguments

    Value

    - - -

    An object of type Exposure.

    +

    An object of type Exposure.

    Details

    @@ -116,15 +116,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createExposuresOutcome.html b/docs/reference/createExposuresOutcome.html index c24104d..849af6a 100644 --- a/docs/reference/createExposuresOutcome.html +++ b/docs/reference/createExposuresOutcome.html @@ -1,9 +1,9 @@ -Create a exposures-outcome combination. — createExposuresOutcome • SelfControlledCaseSeriesCreate a exposures-outcome combination. — createExposuresOutcome • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,23 +77,23 @@

    Create a exposures-outcome combination.

    Arguments

    -
    outcomeId
    + + +
    outcomeId

    An integer used to identify the outcome in the outcome cohort table.

    -
    exposures
    +
    exposures

    A list of object of type Exposure as created by createExposure().

    -
    nestingCohortId
    +
    nestingCohortId

    (Optional) the nesting cohort ID.

    Value

    - - -

    An object of type ExposuresOutcome.

    +

    An object of type ExposuresOutcome.

    Details

    @@ -112,15 +112,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createFitSccsModelArgs.html b/docs/reference/createFitSccsModelArgs.html index 80671bc..7178fab 100644 --- a/docs/reference/createFitSccsModelArgs.html +++ b/docs/reference/createFitSccsModelArgs.html @@ -1,9 +1,9 @@ -Create a parameter object for the function fitSccsModel — createFitSccsModelArgs • SelfControlledCaseSeriesCreate a parameter object for the function fitSccsModel — createFitSccsModelArgs • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,19 +83,21 @@

    Create a parameter object for the function fitSccsModel

    Arguments

    -
    prior
    + + +
    prior

    The prior used to fit the model. See Cyclops::createPrior for details.

    -
    control
    +
    control

    The control object used to control the cross-validation used to determine the hyperparameters of the prior (if applicable). See Cyclops::createControl for details.

    -
    profileGrid
    +
    profileGrid

    A one-dimensional grid of points on the log(relative risk) scale where the likelihood for coefficient of variables is sampled. See details.

    -
    profileBounds
    +
    profileBounds

    The bounds (on the log relative risk scale) for the adaptive sampling of the likelihood function.

    @@ -116,15 +118,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createGetDbSccsDataArgs.html b/docs/reference/createGetDbSccsDataArgs.html index 55e134d..d653799 100644 --- a/docs/reference/createGetDbSccsDataArgs.html +++ b/docs/reference/createGetDbSccsDataArgs.html @@ -1,9 +1,9 @@ -Create a parameter object for the function getDbSccsData — createGetDbSccsDataArgs • SelfControlledCaseSeriesCreate a parameter object for the function getDbSccsData — createGetDbSccsDataArgs • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -89,47 +89,49 @@

    Create a parameter object for the function getDbSccsData

    Arguments

    -
    useCustomCovariates
    + + +
    useCustomCovariates

    DEPRECATED. Set customCovariateIds to non-null value to use custom cohorts.

    -
    useNestingCohort
    +
    useNestingCohort

    DEPRECATED. Set nestingCohortId to non-null value to use a nesting cohort.

    -
    nestingCohortId
    +
    nestingCohortId

    A cohort definition ID identifying the records in the nestingCohortTable to use as nesting cohort.

    -
    deleteCovariatesSmallCount
    +
    deleteCovariatesSmallCount

    The minimum count for a covariate to appear in the data to be kept.

    -
    studyStartDate
    +
    studyStartDate

    DEPRECATED. Use studyStartDates instead.

    -
    studyEndDate
    +
    studyEndDate

    DEPRECATED. Use studyEndDates instead.

    -
    studyStartDates
    +
    studyStartDates

    A character object specifying the minimum dates where data is used. Date format is 'yyyymmdd'. Use "" to indicate all time prior. See section for more information.

    -
    studyEndDates
    +
    studyEndDates

    A character object specifying the maximum dates where data is used. Date format is 'yyyymmdd'. Use "" to indicate to the end of observation. See section for more information.

    -
    maxCasesPerOutcome
    +
    maxCasesPerOutcome

    If there are more than this number of cases for a single outcome cases will be sampled to this size. maxCasesPerOutcome = 0 indicates no maximum size.

    -
    exposureIds
    +
    exposureIds

    A list of identifiers to extract from the exposure table. If exposureTable = DRUG_ERA, exposureIds should be CONCEPT_ID. If exposureTable = "drug_era", exposureIds is used to select the drug_concept_id. If no exposure IDs are provided, all drugs or cohorts in the exposureTable are included as exposures.

    -
    customCovariateIds
    +
    customCovariateIds

    A list of cohort definition IDs identifying the records in the customCovariateTable to use for building custom covariates.

    @@ -150,15 +152,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createResultsDataModel.html b/docs/reference/createResultsDataModel.html index ec200a4..14ecbcc 100644 --- a/docs/reference/createResultsDataModel.html +++ b/docs/reference/createResultsDataModel.html @@ -1,9 +1,9 @@ -Create the results data model tables on a database server. — createResultsDataModel • SelfControlledCaseSeriesCreate the results data model tables on a database server. — createResultsDataModel • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -81,15 +81,17 @@

    Create the results data model tables on a database server.

    Arguments

    -
    connectionDetails
    + + +
    connectionDetails

    DatabaseConnector connectionDetails instance @seealsoDatabaseConnector::createConnectionDetails

    -
    databaseSchema
    +
    databaseSchema

    The schema on the server where the tables will be created.

    -
    tablePrefix
    +
    tablePrefix

    (Optional) string to insert before table names for database table names

    @@ -110,15 +112,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createSccsAnalysis.html b/docs/reference/createSccsAnalysis.html index 70c512f..c75f885 100644 --- a/docs/reference/createSccsAnalysis.html +++ b/docs/reference/createSccsAnalysis.html @@ -1,9 +1,9 @@ -Create a SelfControlledCaseSeries analysis specification — createSccsAnalysis • SelfControlledCaseSeriesCreate a SelfControlledCaseSeries analysis specification — createSccsAnalysis • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,47 +77,47 @@

    Create a SelfControlledCaseSeries analysis specification

    description = "", getDbSccsDataArgs, createStudyPopulationArgs, - createIntervalDataArgs = NULL, + createIntervalDataArgs, fitSccsModelArgs )

    Arguments

    -
    analysisId
    + + +
    analysisId

    An integer that will be used later to refer to this specific set of analysis choices.

    -
    description
    +
    description

    A short description of the analysis.

    -
    getDbSccsDataArgs
    +
    getDbSccsDataArgs

    An object representing the arguments to be used when calling the getDbSccsData function.

    -
    createStudyPopulationArgs
    +
    createStudyPopulationArgs

    An object representing the arguments to be used when calling the getDbSccsData function.

    -
    createIntervalDataArgs
    +
    createIntervalDataArgs

    An object representing the arguments to be used when calling the createSccsIntervalData or createScriIntervalData function.

    -
    fitSccsModelArgs
    +
    fitSccsModelArgs

    An object representing the arguments to be used when calling the fitSccsModel function.

    Value

    - - -

    An object of type SccsAnalysis, to be used with the runSccsAnalyses function.

    +

    An object of type SccsAnalysis, to be used with the runSccsAnalyses function.

    @@ -132,15 +132,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createSccsDiagnosticThresholds.html b/docs/reference/createSccsDiagnosticThresholds.html index 00a61ae..b840dcb 100644 --- a/docs/reference/createSccsDiagnosticThresholds.html +++ b/docs/reference/createSccsDiagnosticThresholds.html @@ -1,9 +1,9 @@ -Create SCCS diagnostics thresholds — createSccsDiagnosticThresholds • SelfControlledCaseSeriesCreate SCCS diagnostics thresholds — createSccsDiagnosticThresholds • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -82,31 +82,31 @@

    Create SCCS diagnostics thresholds

    Arguments

    -
    mdrrThreshold
    + + +
    mdrrThreshold

    What is the maximum allowed minimum detectable relative risk (MDRR)?

    -
    easeThreshold
    +
    easeThreshold

    What is the maximum allowed expected absolute systematic error (EASE).

    -
    timeTrendPThreshold
    +
    timeTrendPThreshold

    What p-value threshold (alpha) will be used to determine temporal instability?

    -
    preExposurePThreshold
    +
    preExposurePThreshold

    What p-value threshold (alpha) will be used to determine whether the rate of the outcome was higher just before exposure initiation?

    Value

    - - -

    An object of type SccsDiagnosticThresholds.

    +

    An object of type SccsDiagnosticThresholds.

    @@ -121,15 +121,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createSccsIntervalData.html b/docs/reference/createSccsIntervalData.html index ced44ba..55a0fd5 100644 --- a/docs/reference/createSccsIntervalData.html +++ b/docs/reference/createSccsIntervalData.html @@ -1,9 +1,9 @@ -Create SCCS era data — createSccsIntervalData • SelfControlledCaseSeriesCreate SCCS era data — createSccsIntervalData • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -87,55 +87,55 @@

    Create SCCS era data

    Arguments

    -
    studyPopulation
    + + +
    studyPopulation

    An object created using the createStudyPopulation() function.

    -
    sccsData
    +
    sccsData

    An object of type SccsData as created using the getDbSccsData function.

    -
    eraCovariateSettings
    +
    eraCovariateSettings

    Either an object of type EraCovariateSettings as created using the createEraCovariateSettings() function, or a list of such objects.

    -
    ageCovariateSettings
    +
    ageCovariateSettings

    An object of type ageCovariateSettings as created using the createAgeCovariateSettings() function.

    -
    seasonalityCovariateSettings
    +
    seasonalityCovariateSettings

    An object of type seasonalityCovariateSettings as created using the createSeasonalityCovariateSettings() function.

    -
    calendarTimeCovariateSettings
    +
    calendarTimeCovariateSettings

    An object of type calendarTimeCovariateSettings as created using the createCalendarTimeCovariateSettings() function.

    -
    minCasesForAgeSeason
    +
    minCasesForAgeSeason

    DEPRECATED: Use minCasesForTimeCovariates instead.

    -
    minCasesForTimeCovariates
    +
    minCasesForTimeCovariates

    Minimum number of cases to use to fit age, season and calendar time splines. If needed (and available), cases that are not exposed will be included.

    -
    eventDependentObservation
    +
    eventDependentObservation

    Should the extension proposed by Farrington et al. be used to adjust for event-dependent observation time?

    Value

    - - -

    An object of type SccsIntervalData.

    +

    An object of type SccsIntervalData.

    Details

    @@ -163,15 +163,15 @@

    References

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createSccsMultiThreadingSettings.html b/docs/reference/createSccsMultiThreadingSettings.html index f156437..af986fb 100644 --- a/docs/reference/createSccsMultiThreadingSettings.html +++ b/docs/reference/createSccsMultiThreadingSettings.html @@ -1,9 +1,9 @@ -Create SelfControlledCaseSeries multi-threading settings — createSccsMultiThreadingSettings • SelfControlledCaseSeriesCreate SelfControlledCaseSeries multi-threading settings — createSccsMultiThreadingSettings • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -84,42 +84,42 @@

    Create SelfControlledCaseSeries multi-threading settings

    Arguments

    -
    getDbSccsDataThreads
    + + +
    getDbSccsDataThreads

    The number of parallel threads to use for building the SccsData objects.

    -
    createStudyPopulationThreads
    +
    createStudyPopulationThreads

    The number of parallel threads to use for building the studyPopulation objects.

    -
    createIntervalDataThreads
    +
    createIntervalDataThreads

    The number of parallel threads to use for building the SccsIntervalData objects.

    -
    fitSccsModelThreads
    +
    fitSccsModelThreads

    The number of parallel threads to use for fitting the models.

    -
    cvThreads
    +
    cvThreads

    The number of parallel threads to use for the cross- validation when estimating the hyperparameter for the outcome model. Note that the total number of CV threads at one time could be fitSccsModelThreads * cvThreads.

    -
    calibrationThreads
    +
    calibrationThreads

    The number of parallel threads to use for empirical calibration.

    Value

    - - -

    An object of type SccsMultiThreadingSettings.

    +

    An object of type SccsMultiThreadingSettings.

    See also

    @@ -138,15 +138,15 @@

    See also

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createSccsSimulationSettings.html b/docs/reference/createSccsSimulationSettings.html index 1d758c4..420d9ce 100644 --- a/docs/reference/createSccsSimulationSettings.html +++ b/docs/reference/createSccsSimulationSettings.html @@ -1,9 +1,9 @@ -Create SCCS simulation settings — createSccsSimulationSettings • SelfControlledCaseSeriesCreate SCCS simulation settings — createSccsSimulationSettings • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -100,98 +100,98 @@

    Create SCCS simulation settings

    Arguments

    -
    meanPatientTime
    + + +
    meanPatientTime

    Mean number of observation days per patient.

    -
    sdPatientTime
    +
    sdPatientTime

    Standard deviation of the observation days per patient.

    -
    minAge
    +
    minAge

    The minimum age in days.

    -
    maxAge
    +
    maxAge

    The maximum age in days.

    -
    minBaselineRate
    +
    minBaselineRate

    The minimum baseline rate (per day).

    -
    maxBaselineRate
    +
    maxBaselineRate

    The maximum baseline rate (per day).

    -
    minCalendarTime
    +
    minCalendarTime

    The minimum date patients are to be observed.

    -
    maxCalendarTime
    +
    maxCalendarTime

    The maximum date patients are to be observed.

    -
    eraIds
    +
    eraIds

    The IDs for the covariates to be generated.

    -
    patientUsages
    +
    patientUsages

    The fraction of patients that use the drugs.

    -
    usageRate
    +
    usageRate

    The rate of prescriptions per person that uses the drug.

    -
    meanPrescriptionDurations
    +
    meanPrescriptionDurations

    The mean duration of a prescription, per drug.

    -
    sdPrescriptionDurations
    +
    sdPrescriptionDurations

    The standard deviation of the duration of a prescription, per drug.

    -
    simulationRiskWindows
    +
    simulationRiskWindows

    One or a list of objects of type SimulationRiskWindow as created using the createSimulationRiskWindow() function. function.

    -
    includeAgeEffect
    +
    includeAgeEffect

    Include an age effect for the outcome?

    -
    ageKnots
    +
    ageKnots

    Number of knots in the age spline.

    -
    includeSeasonality
    +
    includeSeasonality

    Include seasonality for the outcome?

    -
    seasonKnots
    +
    seasonKnots

    Number of knots in the seasonality spline.

    -
    includeCalendarTimeEffect
    +
    includeCalendarTimeEffect

    Include a calendar time effect for the outcome?

    -
    calendarTimeKnots
    +
    calendarTimeKnots

    Number of knots in the calendar time spline.

    -
    outcomeId
    +
    outcomeId

    The ID to be used for the outcome.

    Value

    - - -

    An object of type SccsSimulationSettings.

    +

    An object of type SccsSimulationSettings.

    Details

    @@ -210,15 +210,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createScriIntervalData.html b/docs/reference/createScriIntervalData.html index 7772b58..fbca0c1 100644 --- a/docs/reference/createScriIntervalData.html +++ b/docs/reference/createScriIntervalData.html @@ -1,9 +1,9 @@ -Create Self-Controlled Risk Interval (SCRI) era data — createScriIntervalData • SelfControlledCaseSeriesCreate Self-Controlled Risk Interval (SCRI) era data — createScriIntervalData • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -82,31 +82,31 @@

    Create Self-Controlled Risk Interval (SCRI) era data

    Arguments

    -
    studyPopulation
    + + +
    studyPopulation

    An object created using the createStudyPopulation() function.

    -
    sccsData
    +
    sccsData

    An object of type SccsData as created using the getDbSccsData function.

    -
    eraCovariateSettings
    +
    eraCovariateSettings

    Either an object of type EraCovariateSettings as created using the createEraCovariateSettings() function, or a list of such objects.

    -
    controlIntervalSettings
    +
    controlIntervalSettings

    An object of type ControlIntervalSettings as created using the createControlIntervalSettings() function.

    Value

    - - -

    An object of type SccsIntervalData.

    +

    An object of type SccsIntervalData.

    Details

    @@ -136,15 +136,15 @@

    References

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createSeasonalityCovariateSettings.html b/docs/reference/createSeasonalityCovariateSettings.html index 3e7643e..05147b9 100644 --- a/docs/reference/createSeasonalityCovariateSettings.html +++ b/docs/reference/createSeasonalityCovariateSettings.html @@ -1,9 +1,9 @@ -Create seasonality settings — createSeasonalityCovariateSettings • SelfControlledCaseSeriesCreate seasonality settings — createSeasonalityCovariateSettings • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -81,7 +81,9 @@

    Create seasonality settings

    Arguments

    -
    seasonKnots
    + + +
    seasonKnots

    If a single number is provided this is assumed to indicate the number of knots to use for the spline, and the knots are automatically equally spaced across the year. If more than one @@ -89,12 +91,12 @@

    Arguments

    the knots in days relative to the start of the year.

    -
    allowRegularization
    +
    allowRegularization

    When fitting the model, should the covariates defined here be allowed to be regularized?

    -
    computeConfidenceIntervals
    +
    computeConfidenceIntervals

    Should confidence intervals be computed for the covariates defined here? Setting this to FALSE might save computing time when fitting the model. Will be turned to FALSE automatically @@ -103,9 +105,7 @@

    Arguments

    Value

    - - -

    An object of type seasonalitySettings.

    +

    An object of type seasonalitySettings.

    Details

    @@ -127,15 +127,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createSimulationRiskWindow.html b/docs/reference/createSimulationRiskWindow.html index 5d944bc..7d3d56d 100644 --- a/docs/reference/createSimulationRiskWindow.html +++ b/docs/reference/createSimulationRiskWindow.html @@ -1,9 +1,9 @@ -Create a risk window definition for simulation — createSimulationRiskWindow • SelfControlledCaseSeriesCreate a risk window definition for simulation — createSimulationRiskWindow • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -83,24 +83,26 @@

    Create a risk window definition for simulation

    Arguments

    -
    start
    + + +
    start

    Start of the risk window relative to exposure start.

    -
    end
    +
    end

    The end of the risk window (in days) relative to the endAnchor.

    -
    endAnchor
    +
    endAnchor

    The anchor point for the end of the risk window. Can be "era start" or "era end".

    -
    splitPoints
    +
    splitPoints

    Subdivision of the risk window in to smaller sub-windows.

    -
    relativeRisks
    +
    relativeRisks

    Either a single number representing the relative risk in the risk window, or when splitPoints have been defined a vector of relative risks, one for each sub-window.

    @@ -108,9 +110,7 @@

    Arguments

    Value

    - - -

    An object of type SimulationRiskWindow.

    +

    An object of type SimulationRiskWindow.

    @@ -125,15 +125,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/createStudyPopulation.html b/docs/reference/createStudyPopulation.html index 880aed8..05d76e7 100644 --- a/docs/reference/createStudyPopulation.html +++ b/docs/reference/createStudyPopulation.html @@ -1,9 +1,9 @@ -Create a study population — createStudyPopulation • SelfControlledCaseSeriesCreate a study population — createStudyPopulation • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -86,23 +86,25 @@

    Create a study population

    Arguments

    -
    sccsData
    + + +
    sccsData

    An object of type SccsData as created using the getDbSccsData function.

    -
    outcomeId
    +
    outcomeId

    The outcome to create the era data for. If not specified it is assumed to be the one outcome for which the data was loaded from the database.

    -
    firstOutcomeOnly
    +
    firstOutcomeOnly

    Whether only the first occurrence of an outcome should be considered.

    -
    naivePeriod
    +
    naivePeriod

    The number of days at the start of a patient's observation period that should not be included in the risk calculations. Note that the naive period can be used to determine current covariate @@ -110,7 +112,7 @@

    Arguments

    the first one.

    -
    minAge
    +
    minAge

    Minimum age at which patient time will be included in the analysis. Note that information prior to the min age is still used to determine exposure status after the minimum age (e.g. when a prescription was started just prior @@ -120,18 +122,18 @@

    Arguments

    specified, no age restriction will be applied.

    -
    maxAge
    +
    maxAge

    Maximum age at which patient time will be included in the analysis. Age should be specified in years, but non-integer values are allowed. If not specified, no age restriction will be applied.

    -
    genderConceptIds
    +
    genderConceptIds

    Set of gender concept IDs to restrict the population to. If not specified, no restriction on gender will be applied.

    -
    restrictTimeToEraId
    +
    restrictTimeToEraId

    If provided, study time (for all patients) will be restricted to the calender time when that era was observed in the data. For example, if the era ID refers to a drug, study time will be restricted to when the drug was on the market.

    @@ -139,9 +141,7 @@

    Arguments

    Value

    - - -

    A list specifying the study population, with the following items:

    • cases: A tibble with one row per observation period of a person with the outcome.

      • +

      A list specifying the study population, with the following items:

      • cases: A tibble with one row per observation period of a person with the outcome.

      • outcomes: A tibble listing the days when a case has the outcome.

      • metaData: A list with meta data about the study population, including the attrition.

    @@ -162,15 +162,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/cyclicSplineDesign.html b/docs/reference/cyclicSplineDesign.html index 9b4d426..daaa616 100644 --- a/docs/reference/cyclicSplineDesign.html +++ b/docs/reference/cyclicSplineDesign.html @@ -1,9 +1,9 @@ -Create a design matrix for a cyclic spline — cyclicSplineDesign • SelfControlledCaseSeriesCreate a design matrix for a cyclic spline — cyclicSplineDesign • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,15 +77,17 @@

    Create a design matrix for a cyclic spline

    Arguments

    -
    x
    + + +
    x

    Vector of coordinates of the points to be interpolated.

    -
    knots
    +
    knots

    Location of the knots.

    -
    ord
    +
    ord

    Order of the spline function. ord = 3 implies quadratic.

    @@ -106,15 +108,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/exportToCsv.html b/docs/reference/exportToCsv.html index 4c0945a..ee7d757 100644 --- a/docs/reference/exportToCsv.html +++ b/docs/reference/exportToCsv.html @@ -1,9 +1,9 @@ -Export SCCSresults to CSV files — exportToCsv • SelfControlledCaseSeriesExport SCCSresults to CSV files — exportToCsv • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -84,42 +84,40 @@

    Export SCCSresults to CSV files

    Arguments

    -
    outputFolder
    + + +
    outputFolder

    The folder where runCmAnalyses() generated all results.

    -
    exportFolder
    +
    exportFolder

    The folder where the CSV files will written.

    -
    databaseId
    +
    databaseId

    A unique ID for the database. This will be appended to most tables.

    -
    minCellCount
    +
    minCellCount

    To preserve privacy: the minimum number of subjects contributing to a count before it can be included in the results. If the count is below this threshold, it will be set to -minCellCount.

    -
    maxCores
    +
    maxCores

    Maximum number of CPU cores to use.

    -
    sccsDiagnosticThresholds
    +
    sccsDiagnosticThresholds

    An object of type SccsDiagnosticThresholds as created using createSccsDiagnosticThresholds().

    Value

    - - -

    Does not return anything. Is called for the side-effect of populating the exportFolder

    - - -

    with CSV files.

    +

    Does not return anything. Is called for the side-effect of populating the exportFolder +with CSV files.

    Details

    @@ -140,15 +138,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/fitSccsModel.html b/docs/reference/fitSccsModel.html index 23995b7..ddc3230 100644 --- a/docs/reference/fitSccsModel.html +++ b/docs/reference/fitSccsModel.html @@ -1,9 +1,9 @@ -Fit the SCCS model — fitSccsModel • SelfControlledCaseSeriesFit the SCCS model — fitSccsModel • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -84,37 +84,37 @@

    Fit the SCCS model

    Arguments

    -
    sccsIntervalData
    + + +
    sccsIntervalData

    An object of type SccsIntervalData as created using the createSccsIntervalData function.

    -
    prior
    +
    prior

    The prior used to fit the model. See Cyclops::createPrior for details.

    -
    control
    +
    control

    The control object used to control the cross-validation used to determine the hyperparameters of the prior (if applicable). See Cyclops::createControl for details.

    -
    profileGrid
    +
    profileGrid

    A one-dimensional grid of points on the log(relative risk) scale where the likelihood for coefficient of variables is sampled. See details.

    -
    profileBounds
    +
    profileBounds

    The bounds (on the log relative risk scale) for the adaptive sampling of the likelihood function.

    Value

    - - -

    An object of type SccsModel. Generic functions print, coef, and +

    An object of type SccsModel. Generic functions print, coef, and confint are available.

    @@ -145,15 +145,15 @@

    References

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/getAttritionTable.html b/docs/reference/getAttritionTable.html index 8dfed57..4c021ca 100644 --- a/docs/reference/getAttritionTable.html +++ b/docs/reference/getAttritionTable.html @@ -1,9 +1,9 @@ -Get the attrition table for a population — getAttritionTable • SelfControlledCaseSeriesGet the attrition table for a population — getAttritionTable • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,7 +77,9 @@

    Get the attrition table for a population

    Arguments

    -
    object
    + + +
    object

    Either an object of type SccsData, a population object generated by functions like createStudyPopulation(), or an object of type outcomeModel.

    @@ -85,9 +87,7 @@

    Arguments

    Value

    - - -

    A tibble specifying the number of people and exposures in the population after specific steps +

    A tibble specifying the number of people and exposures in the population after specific steps of filtering.

    @@ -103,15 +103,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/getDataMigrator.html b/docs/reference/getDataMigrator.html index 9125c3c..ccd68ed 100644 --- a/docs/reference/getDataMigrator.html +++ b/docs/reference/getDataMigrator.html @@ -1,9 +1,9 @@ -Get database migrations instance — getDataMigrator • SelfControlledCaseSeriesGet database migrations instance — getDataMigrator • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,23 +77,23 @@

    Get database migrations instance

    Arguments

    -
    connectionDetails
    + + +
    connectionDetails

    DatabaseConnector connection details object

    -
    databaseSchema
    +
    databaseSchema

    String schema where database schema lives

    -
    tablePrefix
    +
    tablePrefix

    (Optional) Use if a table prefix is used before table names (e.g. "cd_")

    Value

    - - -

    Instance of ResultModelManager::DataMigrationManager that has interface for converting existing data models

    +

    Instance of ResultModelManager::DataMigrationManager that has interface for converting existing data models

    @@ -108,15 +108,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/getDbSccsData.html b/docs/reference/getDbSccsData.html index a197d93..5037f2c 100644 --- a/docs/reference/getDbSccsData.html +++ b/docs/reference/getDbSccsData.html @@ -1,9 +1,9 @@ -Load data for SCCS from the database — getDbSccsData • SelfControlledCaseSeriesLoad data for SCCS from the database — getDbSccsData • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -102,45 +102,47 @@

    Load data for SCCS from the database

    Arguments

    -
    connectionDetails
    + + +
    connectionDetails

    An R object of type ConnectionDetails created using the function DatabaseConnector::createConnectionDetails() function.

    -
    cdmDatabaseSchema
    +
    cdmDatabaseSchema

    The name of the database schema that contains the OMOP CDM instance. Requires read permissions to this database. On SQL Server, this should specify both the database and the schema, so for example 'cdm_instance.dbo'.

    -
    tempEmulationSchema
    +
    tempEmulationSchema

    Some database platforms like Oracle and Impala do not truly support temp tables. To emulate temp tables, provide a schema with write privileges where temp tables can be created.

    -
    outcomeDatabaseSchema
    +
    outcomeDatabaseSchema

    The name of the database schema that is the location where the data used to define the outcome cohorts is available. If outcomeTable = "condition_era", outcomeDatabaseSchema is not used. Requires read permissions to this database.

    -
    outcomeTable
    +
    outcomeTable

    The table name that contains the outcome cohorts. If outcomeTable is not "condition_era", then expectation is outcomeTable has format of cohort table (see details).

    -
    outcomeIds
    +
    outcomeIds

    A list of IDs used to define outcomes. If outcomeTable is not "condition_era" the list contains records found in the cohort_definition_id field.

    -
    exposureDatabaseSchema
    +
    exposureDatabaseSchema

    The name of the database schema that is the location where the exposure data used to define the exposure eras is available. If exposureTable = "drug_era", @@ -148,13 +150,13 @@

    Arguments

    cdmDatabaseSchema. Requires read permissions to this database.

    -
    exposureTable
    +
    exposureTable

    The tablename that contains the exposure cohorts. If exposureTable is not "drug_era", then expectation is exposureTable has format of a cohort table (see details).

    -
    exposureIds
    +
    exposureIds

    A list of identifiers to extract from the exposure table. If exposureTable = DRUG_ERA, exposureIds should be CONCEPT_ID. If exposureTable = "drug_era", exposureIds is used to select @@ -162,75 +164,75 @@

    Arguments

    or cohorts in the exposureTable are included as exposures.

    -
    useCustomCovariates
    +
    useCustomCovariates

    DEPRECATED. Set customCovariateIds to non-null value to use custom cohorts.

    -
    customCovariateDatabaseSchema
    +
    customCovariateDatabaseSchema

    The name of the database schema that is the location where the custom covariate data is available.

    -
    customCovariateTable
    +
    customCovariateTable

    Name of the table holding the custom covariates. This table should have the same structure as the cohort table (see details).

    -
    customCovariateIds
    +
    customCovariateIds

    A list of cohort definition IDs identifying the records in the customCovariateTable to use for building custom covariates.

    -
    useNestingCohort
    +
    useNestingCohort

    DEPRECATED. Set nestingCohortId to non-null value to use a nesting cohort.

    -
    nestingCohortDatabaseSchema
    +
    nestingCohortDatabaseSchema

    The name of the database schema that is the location where the nesting cohort is defined.

    -
    nestingCohortTable
    +
    nestingCohortTable

    Name of the table holding the nesting cohort. This table should have the same structure as the cohort table (see details).

    -
    nestingCohortId
    +
    nestingCohortId

    A cohort definition ID identifying the records in the nestingCohortTable to use as nesting cohort.

    -
    deleteCovariatesSmallCount
    +
    deleteCovariatesSmallCount

    The minimum count for a covariate to appear in the data to be kept.

    -
    studyStartDate
    +
    studyStartDate

    DEPRECATED. Use studyStartDates instead.

    -
    studyEndDate
    +
    studyEndDate

    DEPRECATED. Use studyEndDates instead.

    -
    studyStartDates
    +
    studyStartDates

    A character object specifying the minimum dates where data is used. Date format is 'yyyymmdd'. Use "" to indicate all time prior. See section for more information.

    -
    studyEndDates
    +
    studyEndDates

    A character object specifying the maximum dates where data is used. Date format is 'yyyymmdd'. Use "" to indicate to the end of observation. See section for more information.

    -
    cdmVersion
    +
    cdmVersion

    Define the OMOP CDM version used: currently supports "5".

    -
    maxCasesPerOutcome
    +
    maxCasesPerOutcome

    If there are more than this number of cases for a single outcome cases will be sampled to this size. maxCasesPerOutcome = 0 indicates no maximum size.

    @@ -238,9 +240,7 @@

    Arguments

    Value

    - - -

    An SccsData object.

    +

    An SccsData object.

    Details

    @@ -262,7 +262,7 @@

    Details

    Study period start and end dates

    - +

    A study start and end date define a period when patient data will be included in the analysis. Multiple non-overlapping periods can be defined, which for example will allow @@ -281,15 +281,15 @@

    Study period start and end dates

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/getFileReference.html b/docs/reference/getFileReference.html index 8a75d0a..3ab701c 100644 --- a/docs/reference/getFileReference.html +++ b/docs/reference/getFileReference.html @@ -1,9 +1,9 @@ -Get file reference — getFileReference • SelfControlledCaseSeriesGet file reference — getFileReference • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,15 +77,15 @@

    Get file reference

    Arguments

    -
    outputFolder
    + + +
    outputFolder

    Name of the folder where all the outputs have been written to.

    Value

    - - -

    A tibble containing the names of the files for various artifacts created for each outcome-exposures set.

    +

    A tibble containing the names of the files for various artifacts created for each outcome-exposures set.

    @@ -100,15 +100,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/getModel.html b/docs/reference/getModel.html index e829cbd..3f64137 100644 --- a/docs/reference/getModel.html +++ b/docs/reference/getModel.html @@ -1,9 +1,9 @@ -Output the full model — getModel • SelfControlledCaseSeriesOutput the full model — getModel • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,16 +77,16 @@

    Output the full model

    Arguments

    -
    sccsModel
    + + +
    sccsModel

    An object of type SccsModel as created using the fitSccsModel() function.

    Value

    - - -

    A tibble with the coefficients and confidence intervals (when not-regularized) for all +

    A tibble with the coefficients and confidence intervals (when not-regularized) for all covariates in the model.

    @@ -102,15 +102,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/getResultsDataModelSpecifications.html b/docs/reference/getResultsDataModelSpecifications.html index fae2f58..0bbf436 100644 --- a/docs/reference/getResultsDataModelSpecifications.html +++ b/docs/reference/getResultsDataModelSpecifications.html @@ -1,9 +1,9 @@ -Get specifications for SelfControlledCaseSeries results data model — getResultsDataModelSpecifications • SelfControlledCaseSeriesGet specifications for SelfControlledCaseSeries results data model — getResultsDataModelSpecifications • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,9 +77,7 @@

    Get specifications for SelfControlledCaseSeries results data model

    Value

    - - -

    A tibble data frame object with specifications

    +

    A tibble data frame object with specifications

    @@ -94,15 +92,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/getResultsSummary.html b/docs/reference/getResultsSummary.html index d846bd8..b1ddee3 100644 --- a/docs/reference/getResultsSummary.html +++ b/docs/reference/getResultsSummary.html @@ -1,9 +1,9 @@ -Get a summary report of the analyses results — getResultsSummary • SelfControlledCaseSeriesGet a summary report of the analyses results — getResultsSummary • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,15 +77,15 @@

    Get a summary report of the analyses results

    Arguments

    -
    outputFolder
    + + +
    outputFolder

    Name of the folder where all the outputs have been written to.

    Value

    - - -

    A tibble containing summary statistics for each outcome-covariate-analysis combination.

    +

    A tibble containing summary statistics for each outcome-covariate-analysis combination.

    @@ -100,15 +100,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/hasAgeEffect.html b/docs/reference/hasAgeEffect.html index 9f1235f..c9c72b7 100644 --- a/docs/reference/hasAgeEffect.html +++ b/docs/reference/hasAgeEffect.html @@ -1,9 +1,9 @@ -Does the model contain an age effect? — hasAgeEffect • SelfControlledCaseSeriesDoes the model contain an age effect? — hasAgeEffect • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,16 +77,16 @@

    Does the model contain an age effect?

    Arguments

    -
    sccsModel
    + + +
    sccsModel

    An object of type SccsModel as created using the fitSccsModel() function.

    Value

    - - -

    TRUE if the model contains an age effect, otherwise FALSE.

    +

    TRUE if the model contains an age effect, otherwise FALSE.

    @@ -101,15 +101,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/hasCalendarTimeEffect.html b/docs/reference/hasCalendarTimeEffect.html index ea0f5d9..9691ce5 100644 --- a/docs/reference/hasCalendarTimeEffect.html +++ b/docs/reference/hasCalendarTimeEffect.html @@ -1,9 +1,9 @@ -Does the model contain an age effect? — hasCalendarTimeEffect • SelfControlledCaseSeriesDoes the model contain an age effect? — hasCalendarTimeEffect • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,16 +77,16 @@

    Does the model contain an age effect?

    Arguments

    -
    sccsModel
    + + +
    sccsModel

    An object of type SccsModel as created using the fitSccsModel() function.

    Value

    - - -

    TRUE if the model contains an age effect, otherwise FALSE.

    +

    TRUE if the model contains an age effect, otherwise FALSE.

    @@ -101,15 +101,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/hasSeasonality.html b/docs/reference/hasSeasonality.html index 970149e..1e222e9 100644 --- a/docs/reference/hasSeasonality.html +++ b/docs/reference/hasSeasonality.html @@ -1,9 +1,9 @@ -Does the model contain an age effect? — hasSeasonality • SelfControlledCaseSeriesDoes the model contain an age effect? — hasSeasonality • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,16 +77,16 @@

    Does the model contain an age effect?

    Arguments

    -
    sccsModel
    + + +
    sccsModel

    An object of type SccsModel as created using the fitSccsModel() function.

    Value

    - - -

    TRUE if the model contains an age effect, otherwise FALSE.

    +

    TRUE if the model contains an age effect, otherwise FALSE.

    @@ -101,15 +101,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/index.html b/docs/reference/index.html index 94130d7..e9a3256 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,9 +1,9 @@ -Function reference • SelfControlledCaseSeriesPackage index • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -358,15 +358,15 @@

    Helper functions -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/isSccsData.html b/docs/reference/isSccsData.html index eb8953a..951ea40 100644 --- a/docs/reference/isSccsData.html +++ b/docs/reference/isSccsData.html @@ -1,9 +1,9 @@ -Check whether an object is a SccsData object — isSccsData • SelfControlledCaseSeriesCheck whether an object is a SccsData object — isSccsData • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,15 +77,15 @@

    Check whether an object is a SccsData object

    Arguments

    -
    x
    + + +
    x

    The object to check.

    Value

    - - -

    A logical value.

    +

    A logical value.

    @@ -100,15 +100,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/isSccsIntervalData.html b/docs/reference/isSccsIntervalData.html index e808e8d..6a3471e 100644 --- a/docs/reference/isSccsIntervalData.html +++ b/docs/reference/isSccsIntervalData.html @@ -1,9 +1,9 @@ -Check whether an object is a SccsIntervalData object — isSccsIntervalData • SelfControlledCaseSeriesCheck whether an object is a SccsIntervalData object — isSccsIntervalData • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,15 +77,15 @@

    Check whether an object is a SccsIntervalData object

    Arguments

    -
    x
    + + +
    x

    The object to check.

    Value

    - - -

    A logical value.

    +

    A logical value.

    @@ -100,15 +100,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/loadExposuresOutcomeList.html b/docs/reference/loadExposuresOutcomeList.html index ac6a0fa..5d0b2a9 100644 --- a/docs/reference/loadExposuresOutcomeList.html +++ b/docs/reference/loadExposuresOutcomeList.html @@ -1,9 +1,9 @@ -Load a list of ExposuresOutcome from file — loadExposuresOutcomeList • SelfControlledCaseSeriesLoad a list of ExposuresOutcome from file — loadExposuresOutcomeList • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,15 +77,15 @@

    Load a list of ExposuresOutcome from file

    Arguments

    -
    file
    + + +
    file

    The name of the file

    Value

    - - -

    A list of objects of type ExposuresOutcome.

    +

    A list of objects of type ExposuresOutcome.

    @@ -100,15 +100,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/loadSccsAnalysisList.html b/docs/reference/loadSccsAnalysisList.html index 0ea5d6b..9954d23 100644 --- a/docs/reference/loadSccsAnalysisList.html +++ b/docs/reference/loadSccsAnalysisList.html @@ -1,9 +1,9 @@ -Load a list of sccsAnalysis from file — loadSccsAnalysisList • SelfControlledCaseSeriesLoad a list of sccsAnalysis from file — loadSccsAnalysisList • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,15 +77,15 @@

    Load a list of sccsAnalysis from file

    Arguments

    -
    file
    + + +
    file

    The name of the file

    Value

    - - -

    A list of objects of type SccsAnalysis.

    +

    A list of objects of type SccsAnalysis.

    @@ -100,15 +100,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/loadSccsData.html b/docs/reference/loadSccsData.html index 61eed0c..5ef3f17 100644 --- a/docs/reference/loadSccsData.html +++ b/docs/reference/loadSccsData.html @@ -1,9 +1,9 @@ -Load the cohort method data from a file — loadSccsData • SelfControlledCaseSeriesLoad the cohort method data from a file — loadSccsData • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,15 +77,15 @@

    Load the cohort method data from a file

    Arguments

    -
    file
    + + +
    file

    The name of the file containing the data.

    Value

    - - -

    An object of class SccsData.

    +

    An object of class SccsData.

    @@ -100,15 +100,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/loadSccsIntervalData.html b/docs/reference/loadSccsIntervalData.html index fcce32c..f0f2ec4 100644 --- a/docs/reference/loadSccsIntervalData.html +++ b/docs/reference/loadSccsIntervalData.html @@ -1,9 +1,9 @@ -Load the cohort method data from a file — loadSccsIntervalData • SelfControlledCaseSeriesLoad the cohort method data from a file — loadSccsIntervalData • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,15 +77,15 @@

    Load the cohort method data from a file

    Arguments

    -
    file
    + + +
    file

    The name of the file containing the data.

    Value

    - - -

    An object of class SccsIntervalData.

    +

    An object of class SccsIntervalData.

    @@ -100,15 +100,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/migrateDataModel.html b/docs/reference/migrateDataModel.html index 32fa942..6b9de5b 100644 --- a/docs/reference/migrateDataModel.html +++ b/docs/reference/migrateDataModel.html @@ -1,11 +1,11 @@ -Migrate Data model — migrateDataModel • SelfControlledCaseSeriesMigrate Data model — migrateDataModel • SelfControlledCaseSeries - +
    @@ -30,7 +30,7 @@
    • - +
    @@ -81,15 +81,17 @@

    Migrate Data model

    Arguments

    -
    connectionDetails
    + + +
    connectionDetails

    DatabaseConnector connection details object

    -
    databaseSchema
    +
    databaseSchema

    String schema where database schema lives

    -
    tablePrefix
    +
    tablePrefix

    (Optional) Use if a table prefix is used before table names (e.g. "cd_")

    @@ -106,15 +108,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/plotAgeEffect.html b/docs/reference/plotAgeEffect.html index f2407b7..8544086 100644 --- a/docs/reference/plotAgeEffect.html +++ b/docs/reference/plotAgeEffect.html @@ -1,9 +1,9 @@ -Plot the age effect — plotAgeEffect • SelfControlledCaseSeriesPlot the age effect — plotAgeEffect • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,29 +77,29 @@

    Plot the age effect

    Arguments

    -
    sccsModel
    + + +
    sccsModel

    An object of type sccsModel as created using the fitSccsModel function.

    -
    rrLim
    +
    rrLim

    The limits on the incidence rate ratio scale in the plot.

    -
    title
    +
    title

    Optional: the main title for the plot

    -
    fileName
    +
    fileName

    Name of the file where the plot should be saved, for example 'plot.png'. See the function ggsave in the ggplot2 package for supported file formats.

    Value

    - - -

    A Ggplot object. Use the ggsave function to save to file.

    +

    A Ggplot object. Use the ggsave function to save to file.

    Details

    @@ -118,15 +118,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/plotAgeSpans.html b/docs/reference/plotAgeSpans.html index e4309f3..974a4d4 100644 --- a/docs/reference/plotAgeSpans.html +++ b/docs/reference/plotAgeSpans.html @@ -1,9 +1,9 @@ -Plot the age ranges spanned by each observation period. — plotAgeSpans • SelfControlledCaseSeriesPlot the age ranges spanned by each observation period. — plotAgeSpans • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -82,29 +82,29 @@

    Plot the age ranges spanned by each observation period.

    Arguments

    -
    studyPopulation
    + + +
    studyPopulation

    An object created using the createStudyPopulation() function.

    -
    maxPersons
    +
    maxPersons

    The maximum number of persons to plot. If there are more than this number of persons a random sample will be taken to avoid visual clutter.

    -
    title
    +
    title

    Optional: the main title for the plot

    -
    fileName
    +
    fileName

    Name of the file where the plot should be saved, for example 'plot.png'. See the function ggplot2::ggsave() for supported file formats.

    Value

    - - -

    A ggplot object. Use the ggplot2::ggsave() function to save to file in a different +

    A ggplot object. Use the ggplot2::ggsave() function to save to file in a different format.

    @@ -124,15 +124,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/plotCalendarTimeEffect.html b/docs/reference/plotCalendarTimeEffect.html index 587b13d..788516c 100644 --- a/docs/reference/plotCalendarTimeEffect.html +++ b/docs/reference/plotCalendarTimeEffect.html @@ -1,9 +1,9 @@ -Plot the calendar time effect — plotCalendarTimeEffect • SelfControlledCaseSeriesPlot the calendar time effect — plotCalendarTimeEffect • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -82,29 +82,29 @@

    Plot the calendar time effect

    Arguments

    -
    sccsModel
    + + +
    sccsModel

    An object of type sccsModel as created using the fitSccsModel function.

    -
    rrLim
    +
    rrLim

    The limits on the incidence rate ratio scale in the plot.

    -
    title
    +
    title

    Optional: the main title for the plot

    -
    fileName
    +
    fileName

    Name of the file where the plot should be saved, for example 'plot.png'. See the function ggsave in the ggplot2 package for supported file formats.

    Value

    - - -

    A Ggplot object. Use the ggsave function to save to file.

    +

    A Ggplot object. Use the ggsave function to save to file.

    Details

    @@ -123,15 +123,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/plotCalendarTimeSpans.html b/docs/reference/plotCalendarTimeSpans.html index 622d67d..2a34b5c 100644 --- a/docs/reference/plotCalendarTimeSpans.html +++ b/docs/reference/plotCalendarTimeSpans.html @@ -1,9 +1,9 @@ -Plot the calendar time ranges spanned by each observation period. — plotCalendarTimeSpans • SelfControlledCaseSeriesPlot the calendar time ranges spanned by each observation period. — plotCalendarTimeSpans • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -82,29 +82,29 @@

    Plot the calendar time ranges spanned by each observation period.

    Arguments

    -
    studyPopulation
    + + +
    studyPopulation

    An object created using the createStudyPopulation() function.

    -
    maxPersons
    +
    maxPersons

    The maximum number of persons to plot. If there are more than this number of persons a random sample will be taken to avoid visual clutter.

    -
    title
    +
    title

    Optional: the main title for the plot

    -
    fileName
    +
    fileName

    Name of the file where the plot should be saved, for example 'plot.png'. See the function ggplot2::ggsave() for supported file formats.

    Value

    - - -

    A ggplot object. Use the ggplot2::ggsave() function to save to file in a different +

    A ggplot object. Use the ggplot2::ggsave() function to save to file in a different format.

    @@ -124,15 +124,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/plotEventObservationDependence.html b/docs/reference/plotEventObservationDependence.html index 0a1ed72..1fa7f4e 100644 --- a/docs/reference/plotEventObservationDependence.html +++ b/docs/reference/plotEventObservationDependence.html @@ -1,9 +1,9 @@ -Plot time from event to observation end for censored and uncensored time. — plotEventObservationDependence • SelfControlledCaseSeriesPlot time from event to observation end for censored and uncensored time. — plotEventObservationDependence • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,24 +77,24 @@

    Plot time from event to observation end for censored and uncensored time.

    Arguments

    -
    studyPopulation
    + + +
    studyPopulation

    An object created using the createStudyPopulation() function.

    -
    title
    +
    title

    Optional: the main title for the plot

    -
    fileName
    +
    fileName

    Name of the file where the plot should be saved, for example 'plot.png'. See the function ggplot2::ggsave() for supported file formats.

    Value

    - - -

    A ggplot object. Use the ggplot2::ggsave() function to save to file in a different +

    A ggplot object. Use the ggplot2::ggsave() function to save to file in a different format.

    @@ -124,15 +124,15 @@

    References

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/plotEventToCalendarTime.html b/docs/reference/plotEventToCalendarTime.html index 69ca997..e45b69f 100644 --- a/docs/reference/plotEventToCalendarTime.html +++ b/docs/reference/plotEventToCalendarTime.html @@ -1,9 +1,9 @@ -Plot the ratio of observed to expected events over calendar time. — plotEventToCalendarTime • SelfControlledCaseSeriesPlot the ratio of observed to expected events over calendar time. — plotEventToCalendarTime • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -82,30 +82,30 @@

    Plot the ratio of observed to expected events over calendar time.

    Arguments

    -
    studyPopulation
    + + +
    studyPopulation

    An object created using the createStudyPopulation() function.

    -
    sccsModel
    +
    sccsModel

    Optional: A fitted SCCS model as created using fitSccsModel(). If the model contains splines for seasonality and or calendar time a panel will be added with outcome counts adjusted for these splines.

    -
    title
    +
    title

    Optional: the main title for the plot

    -
    fileName
    +
    fileName

    Name of the file where the plot should be saved, for example 'plot.png'. See the function ggplot2::ggsave() for supported file formats.

    Value

    - - -

    A ggplot object. Use the ggplot2::ggsave() function to save to file in a different +

    A ggplot object. Use the ggplot2::ggsave() function to save to file in a different format.

    @@ -127,15 +127,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/plotExposureCentered.html b/docs/reference/plotExposureCentered.html index b086309..866126e 100644 --- a/docs/reference/plotExposureCentered.html +++ b/docs/reference/plotExposureCentered.html @@ -1,9 +1,9 @@ -Plot information centered around the start of exposure — plotExposureCentered • SelfControlledCaseSeriesPlot information centered around the start of exposure — plotExposureCentered • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -84,39 +84,39 @@

    Plot information centered around the start of exposure

    Arguments

    -
    studyPopulation
    + + +
    studyPopulation

    An object created using the createStudyPopulation() function.

    -
    sccsData
    +
    sccsData

    An object of type SccsData as created using the getDbSccsData function.

    -
    exposureEraId
    +
    exposureEraId

    The exposure to create the era data for. If not specified it is assumed to be the one exposure for which the data was loaded from the database.

    -
    highlightExposedEvents
    +
    highlightExposedEvents

    Highlight events that occurred during the exposure era using a different color?

    -
    title
    +
    title

    Optional: the main title for the plot

    -
    fileName
    +
    fileName

    Name of the file where the plot should be saved, for example 'plot.png'. See the function ggplot2::ggsave() for supported file formats.

    Value

    - - -

    A ggplot object. Use the ggplot2::ggsave() function to save to file in a different +

    A ggplot object. Use the ggplot2::ggsave() function to save to file in a different format.

    @@ -137,15 +137,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/plotSeasonality.html b/docs/reference/plotSeasonality.html index ae120ee..3dc4cd9 100644 --- a/docs/reference/plotSeasonality.html +++ b/docs/reference/plotSeasonality.html @@ -1,9 +1,9 @@ -Plot the seasonality effect — plotSeasonality • SelfControlledCaseSeriesPlot the seasonality effect — plotSeasonality • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,29 +77,29 @@

    Plot the seasonality effect

    Arguments

    -
    sccsModel
    + + +
    sccsModel

    An object of type sccsModel as created using the fitSccsModel function.

    -
    rrLim
    +
    rrLim

    The limits on the incidence rate ratio scale in the plot.

    -
    title
    +
    title

    Optional: the main title for the plot

    -
    fileName
    +
    fileName

    Name of the file where the plot should be saved, for example 'plot.png'. See the function ggsave in the ggplot2 package for supported file formats.

    Value

    - - -

    A Ggplot object. Use the ggsave function to save to file.

    +

    A Ggplot object. Use the ggsave function to save to file.

    Details

    @@ -118,15 +118,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/runSccsAnalyses.html b/docs/reference/runSccsAnalyses.html index 340e8c3..1ad4119 100644 --- a/docs/reference/runSccsAnalyses.html +++ b/docs/reference/runSccsAnalyses.html @@ -1,9 +1,9 @@ -Run a list of analyses — runSccsAnalyses • SelfControlledCaseSeriesRun a list of analyses — runSccsAnalyses • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -96,25 +96,27 @@

    Run a list of analyses

    Arguments

    -
    connectionDetails
    + + +
    connectionDetails

    An R object of type ConnectionDetails created using the function DatabaseConnector::createConnectionDetails().

    -
    cdmDatabaseSchema
    +
    cdmDatabaseSchema

    The name of the database schema that contains the OMOP CDM instance. Requires read permissions to this database. On SQL Server, this should specify both the database and the schema, so for example 'cdm_instance.dbo'.

    -
    tempEmulationSchema
    +
    tempEmulationSchema

    Some database platforms like Oracle and Impala do not truly support temp tables. To emulate temp tables, provide a schema with write privileges where temp tables can be created.

    -
    exposureDatabaseSchema
    +
    exposureDatabaseSchema

    The name of the database schema that is the location where the exposure data used to define the exposure cohorts is available. If exposureTable = "DRUG_ERA", @@ -122,74 +124,74 @@

    Arguments

    cdmDatabaseSchema. Requires read permissions to this database.

    -
    exposureTable
    +
    exposureTable

    The table name that contains the exposure cohorts. If exposureTable <> "DRUG_ERA", then expectation is exposureTable has format of COHORT table: cohort_concept_id, SUBJECT_ID, COHORT_START_DATE, COHORT_END_DATE.

    -
    outcomeDatabaseSchema
    +
    outcomeDatabaseSchema

    The name of the database schema that is the location where the data used to define the outcome cohorts is available. Requires read permissions to this database.

    -
    outcomeTable
    +
    outcomeTable

    The table name that contains the outcome cohorts.

    -
    customCovariateDatabaseSchema
    +
    customCovariateDatabaseSchema

    The name of the database schema that is the location where the custom covariate data is available.

    -
    customCovariateTable
    +
    customCovariateTable

    Name of the table holding the custom covariates. This table should have the same structure as the cohort table.

    -
    nestingCohortDatabaseSchema
    +
    nestingCohortDatabaseSchema

    The name of the database schema that is the location where the nesting cohort is defined.

    -
    nestingCohortTable
    +
    nestingCohortTable

    Name of the table holding the nesting cohort. This table should have the same structure as the cohort table.

    -
    cdmVersion
    +
    cdmVersion

    Define the OMOP CDM version used: currently supports "5".

    -
    outputFolder
    +
    outputFolder

    Name of the folder where all the outputs will written to.

    -
    sccsAnalysisList
    +
    sccsAnalysisList

    A list of objects of SccsAnalysis as created using the createSccsAnalysis() function.

    -
    exposuresOutcomeList
    +
    exposuresOutcomeList

    A list of objects of type ExposuresOutcome as created using the createExposuresOutcome() function.

    -
    analysesToExclude
    +
    analysesToExclude

    Analyses to exclude. See the Analyses to Exclude section for details.

    -
    combineDataFetchAcrossOutcomes
    +
    combineDataFetchAcrossOutcomes

    Should fetching data from the database be done one outcome at a time, or for all outcomes in one fetch? Combining fetches will be more efficient if there is large overlap in the subjects that have the different outcomes.

    -
    sccsMultiThreadingSettings
    +
    sccsMultiThreadingSettings

    An object of type SccsMultiThreadingSettings as created using the createSccsMultiThreadingSettings() or createDefaultSccsMultiThreadingSettings() functions.

    @@ -197,9 +199,7 @@

    Arguments

    Value

    - - -

    A tibble describing for each exposure-outcome-analysisId combination where the intermediary and +

    A tibble describing for each exposure-outcome-analysisId combination where the intermediary and outcome model files can be found, relative to the outputFolder.

    @@ -238,15 +238,15 @@

    Analyses to Exclude -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/saveExposuresOutcomeList.html b/docs/reference/saveExposuresOutcomeList.html index 405b3bf..68fd55e 100644 --- a/docs/reference/saveExposuresOutcomeList.html +++ b/docs/reference/saveExposuresOutcomeList.html @@ -1,9 +1,9 @@ -Save a list of ExposuresOutcome to file — saveExposuresOutcomeList • SelfControlledCaseSeriesSave a list of ExposuresOutcome to file — saveExposuresOutcomeList • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,11 +77,13 @@

    Save a list of ExposuresOutcome to file

    Arguments

    -
    exposuresOutcomeList
    + + +
    exposuresOutcomeList

    The ExposuresOutcome list to be written to file

    -
    file
    +
    file

    The name of the file where the results will be written

    @@ -98,15 +100,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/saveSccsAnalysisList.html b/docs/reference/saveSccsAnalysisList.html index 364c449..3007757 100644 --- a/docs/reference/saveSccsAnalysisList.html +++ b/docs/reference/saveSccsAnalysisList.html @@ -1,9 +1,9 @@ -Save a list of SccsAnalysis to file — saveSccsAnalysisList • SelfControlledCaseSeriesSave a list of SccsAnalysis to file — saveSccsAnalysisList • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,11 +77,13 @@

    Save a list of SccsAnalysis to file

    Arguments

    -
    sccsAnalysisList
    + + +
    sccsAnalysisList

    The SccsAnalysis list to be written to file

    -
    file
    +
    file

    The name of the file where the results will be written

    @@ -98,15 +100,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/saveSccsData.html b/docs/reference/saveSccsData.html index e940131..29c2d8e 100644 --- a/docs/reference/saveSccsData.html +++ b/docs/reference/saveSccsData.html @@ -1,9 +1,9 @@ -Save the cohort method data to file — saveSccsData • SelfControlledCaseSeriesSave the cohort method data to file — saveSccsData • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,21 +77,21 @@

    Save the cohort method data to file

    Arguments

    -
    sccsData
    + + +
    sccsData

    An object of type SccsData as created using the getDbSccsData function.

    -
    file
    +
    file

    The name of the file where the data will be written. If the file already exists it will be overwritten.

    Value

    - - -

    Returns no output.

    +

    Returns no output.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/saveSccsIntervalData.html b/docs/reference/saveSccsIntervalData.html index 7801187..15ce3e1 100644 --- a/docs/reference/saveSccsIntervalData.html +++ b/docs/reference/saveSccsIntervalData.html @@ -1,9 +1,9 @@ -Save the cohort method data to file — saveSccsIntervalData • SelfControlledCaseSeriesSave the cohort method data to file — saveSccsIntervalData • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,21 +77,21 @@

    Save the cohort method data to file

    Arguments

    -
    sccsIntervalData
    + + +
    sccsIntervalData

    An object of type SccsIntervalData as created using the createSccsIntervalData function.

    -
    file
    +
    file

    The name of the file where the data will be written. If the file already exists it will be overwritten.

    Value

    - - -

    Returns no output.

    +

    Returns no output.

    @@ -106,15 +106,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/simulateSccsData.html b/docs/reference/simulateSccsData.html index 784652c..4316026 100644 --- a/docs/reference/simulateSccsData.html +++ b/docs/reference/simulateSccsData.html @@ -1,9 +1,9 @@ -Simulate SCCS data — simulateSccsData • SelfControlledCaseSeriesSimulate SCCS data — simulateSccsData • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -77,20 +77,20 @@

    Simulate SCCS data

    Arguments

    -
    nCases
    + + +
    nCases

    The number of cases to simulate.

    -
    settings
    +
    settings

    An object of type SccsSimulationSettings as created using the createSccsSimulationSettings() function.

    Value

    - - -

    An object of type SccsData.

    +

    An object of type SccsData.

    @@ -105,15 +105,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/uploadResults.html b/docs/reference/uploadResults.html index 385d748..5fbf850 100644 --- a/docs/reference/uploadResults.html +++ b/docs/reference/uploadResults.html @@ -1,9 +1,9 @@ -Upload results to the database server. — uploadResults • SelfControlledCaseSeriesUpload results to the database server. — uploadResults • SelfControlledCaseSeries - +
    @@ -28,7 +28,7 @@
    • - +
    @@ -86,43 +86,45 @@

    Upload results to the database server.

    Arguments

    -
    connectionDetails
    + + +
    connectionDetails

    An object of type connectionDetails as created using the createConnectionDetails function in the DatabaseConnector package.

    -
    schema
    +
    schema

    The schema on the server where the tables have been created.

    -
    zipFileName
    +
    zipFileName

    The name of the zip file.

    -
    forceOverWriteOfSpecifications
    +
    forceOverWriteOfSpecifications

    If TRUE, specifications of the phenotypes, cohort definitions, and analysis will be overwritten if they already exist on the database. Only use this if these specifications have changed since the last upload.

    -
    purgeSiteDataBeforeUploading
    +
    purgeSiteDataBeforeUploading

    If TRUE, before inserting data for a specific databaseId all the data for that site will be dropped. This assumes the input zip file contains the full data for that data site.

    -
    tempFolder
    +
    tempFolder

    A folder on the local file system where the zip files are extracted to. Will be cleaned up when the function is finished. Can be used to specify a temp folder on a drive that has sufficient space if the default system temp space is too limited.

    -
    tablePrefix
    +
    tablePrefix

    (Optional) string to insert before table names for database table names

    -
    ...
    +
    ...

    See ResultModelManager::uploadResults

    @@ -139,15 +141,15 @@

    Arguments

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index e4d939f..3445f23 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -1,264 +1,89 @@ - - - - /404.html - - - /articles/index.html - - - /articles/MultipleAnalyses.html - - - /articles/ResultsSchema.html - - - /articles/SingleStudies.html - - - /authors.html - - - /index.html - - - /news/index.html - - - /pull_request_template.html - - - /reference/computeMdrr.html - - - /reference/computePreExposureGainP.html - - - /reference/computeTimeStability.html - - - /reference/createAgeCovariateSettings.html - - - /reference/createAgeSettings.html - - - /reference/createCalendarTimeCovariateSettings.html - - - /reference/createControlIntervalSettings.html - - - /reference/createCovariateSettings.html - - - /reference/createCreateSccsEraDataArgs.html - - - /reference/createCreateSccsIntervalDataArgs.html - - - /reference/createCreateScriIntervalDataArgs.html - - - /reference/createCreateStudyPopulationArgs.html - - - /reference/createDefaultSccsMultiThreadingSettings.html - - - /reference/createEraCovariateSettings.html - - - /reference/createExposure.html - - - /reference/createExposureOutcome.html - - - /reference/createExposuresOutcome.html - - - /reference/createFitSccsModelArgs.html - - - /reference/createGetDbSccsDataArgs.html - - - /reference/createResultsDataModel.html - - - /reference/createSccsAnalysis.html - - - /reference/createSccsDiagnosticThresholds.html - - - /reference/createSccsEraData.html - - - /reference/createSccsIntervalData.html - - - /reference/createSccsMultiThreadingSettings.html - - - /reference/createSccsSimulationSettings.html - - - /reference/createScriIntervalData.html - - - /reference/createSeasonalityCovariateSettings.html - - - /reference/createSeasonalitySettings.html - - - /reference/createSimulationRiskWindow.html - - - /reference/createStudyPopulation.html - - - /reference/cyclicSplineDesign.html - - - /reference/exportToCsv.html - - - /reference/fitSccsModel.html - - - /reference/forceSccsEraDataIntoRam.html - - - /reference/getAttritionTable.html - - - /reference/getDataMigrator.html - - - /reference/getDbSccsData.html - - - /reference/getFileReference.html - - - /reference/getModel.html - - - /reference/getResultsDataModelSpecifications.html - - - /reference/getResultsSummary.html - - - /reference/hasAgeEffect.html - - - /reference/hasCalendarTimeEffect.html - - - /reference/hasSeasonality.html - - - /reference/index.html - - - /reference/isSccsData.html - - - /reference/isSccsIntervalData.html - - - /reference/loadExposureOutcomeList.html - - - /reference/loadExposuresOutcomeList.html - - - /reference/loadSccsAnalysisList.html - - - /reference/loadSccsData.html - - - /reference/loadSccsEraData.html - - - /reference/loadSccsIntervalData.html - - - /reference/migrateDataModel.html - - - /reference/plotAgeEffect.html - - - /reference/plotAgeSpans.html - - - /reference/plotCalendarTimeEffect.html - - - /reference/plotCalendarTimeSpans.html - - - /reference/plotEventObservationDependence.html - - - /reference/plotEventToCalendarTime.html - - - /reference/plotExposureCentered.html - - - /reference/plotPerPersonData.html - - - /reference/plotSeasonality.html - - - /reference/runSccsAnalyses.html - - - /reference/saveExposureOutcomeList.html - - - /reference/saveExposuresOutcomeList.html - - - /reference/saveSccsAnalysisList.html - - - /reference/saveSccsData.html - - - /reference/saveSccsEraData.html - - - /reference/saveSccsIntervalData.html - - - /reference/SccsData-class.html - - - /reference/SccsIntervalData-class.html - - - /reference/SelfControlledCaseSeries-package.html - - - /reference/SelfControlledCaseSeries.html - - - /reference/simulateSccsData.html - - - /reference/summarizeSccsAnalyses.html - - - /reference/uploadResults.html - + +/404.html +/articles/index.html +/articles/MultipleAnalyses.html +/articles/ResultsSchema.html +/articles/SingleStudies.html +/authors.html +/index.html +/news/index.html +/pull_request_template.html +/reference/computeMdrr.html +/reference/computePreExposureGainP.html +/reference/computeTimeStability.html +/reference/createAgeCovariateSettings.html +/reference/createAgeSettings.html +/reference/createCalendarTimeCovariateSettings.html +/reference/createControlIntervalSettings.html +/reference/createCovariateSettings.html +/reference/createCreateSccsEraDataArgs.html +/reference/createCreateSccsIntervalDataArgs.html +/reference/createCreateScriIntervalDataArgs.html +/reference/createCreateStudyPopulationArgs.html +/reference/createDefaultSccsMultiThreadingSettings.html +/reference/createEraCovariateSettings.html +/reference/createExposure.html +/reference/createExposureOutcome.html +/reference/createExposuresOutcome.html +/reference/createFitSccsModelArgs.html +/reference/createGetDbSccsDataArgs.html +/reference/createResultsDataModel.html +/reference/createSccsAnalysis.html +/reference/createSccsDiagnosticThresholds.html +/reference/createSccsEraData.html +/reference/createSccsIntervalData.html +/reference/createSccsMultiThreadingSettings.html +/reference/createSccsSimulationSettings.html +/reference/createScriIntervalData.html +/reference/createSeasonalityCovariateSettings.html +/reference/createSeasonalitySettings.html +/reference/createSimulationRiskWindow.html +/reference/createStudyPopulation.html +/reference/cyclicSplineDesign.html +/reference/exportToCsv.html +/reference/fitSccsModel.html +/reference/forceSccsEraDataIntoRam.html +/reference/getAttritionTable.html +/reference/getDataMigrator.html +/reference/getDbSccsData.html +/reference/getFileReference.html +/reference/getModel.html +/reference/getResultsDataModelSpecifications.html +/reference/getResultsSummary.html +/reference/hasAgeEffect.html +/reference/hasCalendarTimeEffect.html +/reference/hasSeasonality.html +/reference/index.html +/reference/isSccsData.html +/reference/isSccsIntervalData.html +/reference/loadExposureOutcomeList.html +/reference/loadExposuresOutcomeList.html +/reference/loadSccsAnalysisList.html +/reference/loadSccsData.html +/reference/loadSccsEraData.html +/reference/loadSccsIntervalData.html +/reference/migrateDataModel.html +/reference/plotAgeEffect.html +/reference/plotAgeSpans.html +/reference/plotCalendarTimeEffect.html +/reference/plotCalendarTimeSpans.html +/reference/plotEventObservationDependence.html +/reference/plotEventToCalendarTime.html +/reference/plotExposureCentered.html +/reference/plotPerPersonData.html +/reference/plotSeasonality.html +/reference/runSccsAnalyses.html +/reference/saveExposureOutcomeList.html +/reference/saveExposuresOutcomeList.html +/reference/saveSccsAnalysisList.html +/reference/saveSccsData.html +/reference/saveSccsEraData.html +/reference/saveSccsIntervalData.html +/reference/SccsData-class.html +/reference/SccsIntervalData-class.html +/reference/SelfControlledCaseSeries-package.html +/reference/simulateSccsData.html +/reference/summarizeSccsAnalyses.html +/reference/uploadResults.html + diff --git a/extras/MultiAnalysesVignetteDataFetch.R b/extras/MultiAnalysesVignetteDataFetch.R index 9810992..6dd4018 100644 --- a/extras/MultiAnalysesVignetteDataFetch.R +++ b/extras/MultiAnalysesVignetteDataFetch.R @@ -278,6 +278,7 @@ exportToCsv( ) # Upload results to SQLite ----------------------------------------------------- +library(SelfControlledCaseSeries) databaseFile <- file.path(outputFolder, "export", "SccsResults.sqlite") connectionDetails <- DatabaseConnector::createConnectionDetails( dbms = "sqlite", @@ -298,7 +299,11 @@ uploadResults( connection <- DatabaseConnector::connect(connectionDetails) cohorts <- tibble( cohortDefinitionId = c(diclofenac, giBleed, ppis, negativeControls), - cohortName = c("Diclofenac", "GI Bleed", paste0("PPI_", seq_along(ppis)), paste0("NegativeControl_", seq_along(negativeControls))) + cohortName = c("Diclofenac", "GI Bleed", paste0("PPI_", seq_along(ppis)), paste0("NegativeControl_", seq_along(negativeControls))), + isCohort = 0, + description = "", + json = "{}", + sqlCommand = "" ) DatabaseConnector::insertTable( connection = connection, @@ -324,12 +329,15 @@ DatabaseConnector::insertTable( ) DatabaseConnector::disconnect(connection) -# Launch Shiny app: +# Launch Shiny app ------------------------------------------------------------- +library(dplyr) +outputFolder <- "d:/temp/sccsVignette2" databaseFile <- file.path(outputFolder, "export", "SccsResults.sqlite") connectionDetails <- DatabaseConnector::createConnectionDetails( dbms = "sqlite", server = databaseFile ) +# conn <- DatabaseConnector::connect(connectionDetails) resultDatabaseDetails <- list( dbms = connectionDetails$dbms, tablePrefix = 'sccs_', @@ -338,11 +346,11 @@ resultDatabaseDetails <- list( schema = "main", databaseTable = 'database_meta_data' ) -sccsModule <- ShinyAppBuilder::createDefaultSccsConfig() +estimationModule <- ShinyAppBuilder::createDefaultEstimationConfig() aboutModule <- ShinyAppBuilder::createDefaultAboutConfig() shinyAppConfig <- ShinyAppBuilder::initializeModuleConfig() %>% ShinyAppBuilder::addModuleConfig(aboutModule) %>% - ShinyAppBuilder::addModuleConfig(sccsModule) + ShinyAppBuilder::addModuleConfig(estimationModule) connectionHandler <- ResultModelManager::ConnectionHandler$new(connectionDetails) ShinyAppBuilder::viewShiny(shinyAppConfig, connectionHandler) connectionHandler$closeConnection() diff --git a/extras/PackageMaintenance.R b/extras/PackageMaintenance.R index a0f402f..9e8094a 100644 --- a/extras/PackageMaintenance.R +++ b/extras/PackageMaintenance.R @@ -1,4 +1,4 @@ -# Copyright 2023 Observational Health Data Sciences and Informatics +# Copyright 2024 Observational Health Data Sciences and Informatics # # This file is part of SelfControlledCaseSeries # diff --git a/extras/SelfControlledCaseSeries.pdf b/extras/SelfControlledCaseSeries.pdf index d17c0b9..776e1e2 100644 Binary files a/extras/SelfControlledCaseSeries.pdf and b/extras/SelfControlledCaseSeries.pdf differ diff --git a/extras/SingleStudyVignetteDataFetch.R b/extras/SingleStudyVignetteDataFetch.R index b49ac47..361a03e 100644 --- a/extras/SingleStudyVignetteDataFetch.R +++ b/extras/SingleStudyVignetteDataFetch.R @@ -220,6 +220,7 @@ model <- fitSccsModel(sccsIntervalData, cvRepetitions = 1, threads = 10)) saveRDS(model, file.path(folder, "seasonCalendarTimeCovidBlipModel.rds")) +model <- readRDS(file.path(folder, "seasonCalendarTimeCovidBlipModel.rds")) model plot <- plotEventToCalendarTime(studyPopulation = studyPop, diff --git a/inst/doc/MultipleAnalyses.pdf b/inst/doc/MultipleAnalyses.pdf index 196e042..83785f2 100644 Binary files a/inst/doc/MultipleAnalyses.pdf and b/inst/doc/MultipleAnalyses.pdf differ diff --git a/inst/doc/ResultsSchema.pdf b/inst/doc/ResultsSchema.pdf index fb5ec3c..4269019 100644 Binary files a/inst/doc/ResultsSchema.pdf and b/inst/doc/ResultsSchema.pdf differ diff --git a/inst/doc/SingleStudies.pdf b/inst/doc/SingleStudies.pdf index e03be86..9844f8e 100644 Binary files a/inst/doc/SingleStudies.pdf and b/inst/doc/SingleStudies.pdf differ diff --git a/vignettes/SingleStudies.Rmd b/vignettes/SingleStudies.Rmd index c2d54b2..2f54389 100644 --- a/vignettes/SingleStudies.Rmd +++ b/vignettes/SingleStudies.Rmd @@ -619,7 +619,7 @@ To gain a better understanding of when the event occurs relative to the start of ```{r eval=FALSE} plotExposureCentered(studyPop, sccsData, exposureEraId = aspirin) ``` -```{r echo=FALSE,message=FALSE,fig.width=6.5, fig.height=5} +```{r echo=FALSE,message=FALSE,warning=FALSE,fig.width=6.5, fig.height=5} if (folderExists) { plotExposureCentered(studyPop, sccsData, exposureEraId = aspirin) }