diff --git a/R/ds.glm.R b/R/ds.glm.R index b96decd4..332bb758 100644 --- a/R/ds.glm.R +++ b/R/ds.glm.R @@ -17,7 +17,7 @@ #' #' Many GLMs can be fitted very simply using a formula such as: #' -#' \deqn{y~a+b+c+d} +#' \eqn{y~a+b+c+d} #' #' which simply means fit a GLM with \code{y} as the outcome variable and #' \code{a}, \code{b}, \code{c} and \code{d} as covariates. @@ -26,7 +26,7 @@ #' Instead, if you need to fit a more complex #' model, for example: #' -#' \deqn{EVENT~1+TID+SEXF*AGE.60} +#' \eqn{EVENT~1+TID+SEXF*AGE.60} #' #' In the above model the outcome variable is \code{EVENT} #' and the covariates diff --git a/R/ds.glmSLMA.R b/R/ds.glmSLMA.R index d3aa9167..e21acfb3 100644 --- a/R/ds.glmSLMA.R +++ b/R/ds.glmSLMA.R @@ -61,7 +61,7 @@ #' #' Many glms can be fitted very simply using a formula such as: #' -#' \deqn{y~a+b+c+d} +#' \eqn{y~a+b+c+d} #' #' which simply means fit a glm with \code{y} as the outcome variable and #' \code{a}, \code{b}, \code{c} and \code{d} as covariates. @@ -70,7 +70,7 @@ #' Instead, if you need to fit a more complex #' model, for example: #' -#' \deqn{EVENT~1+TID+SEXF*AGE.60} +#' \eqn{EVENT~1+TID+SEXF*AGE.60} #' #' In the above model the outcome variable is \code{EVENT} #' and the covariates diff --git a/R/ds.glmerSLMA.R b/R/ds.glmerSLMA.R index efda6098..c2679444 100644 --- a/R/ds.glmerSLMA.R +++ b/R/ds.glmerSLMA.R @@ -18,17 +18,17 @@ #' In \code{formula} most shortcut notation allowed by \code{glmer()} function is #' also allowed by \code{ds.glmerSLMA}. #' Many GLMEs can be fitted very simply using a formula like: -#' \deqn{y~a+b+(1|c)} +#' \eqn{y~a+b+(1|c)} #' which simply means fit an GLME with \code{y} as the outcome variable (e.g. #' a binary case-control using a logistic regression model or a count or a survival #' time using a Poisson regression model), \code{a} and \code{b} #' as fixed effects, and \code{c} as a random effect or grouping factor. #' #' It is also possible to fit models with random slopes by specifying a model such as -#' \deqn{y~a+b+(1+b|c)} +#' \eqn{y~a+b+(1+b|c)} #' where the effect of \code{b} can vary randomly between groups defined by \code{c}. #' Implicit nesting can be specified with formulas such as: \eqn{y~a+b+(1|c/d)} -#' or \eqn{y~a+b+(1|c)+(1|c:d)}. +#' or \eqn{y~a+b+(1|c)+(1|c:d)}. #' #' #' The \code{dataName} argument avoids you having to specify the name of the diff --git a/R/ds.lmerSLMA.R b/R/ds.lmerSLMA.R index 5619d55b..1e8b247e 100644 --- a/R/ds.lmerSLMA.R +++ b/R/ds.lmerSLMA.R @@ -18,12 +18,12 @@ #' #' In \code{formula} most shortcut notation allowed by \code{lmer()} function is #' also allowed by \code{ds.lmerSLMA}. Many LMEs can be fitted very simply using a formula like: -#' \deqn{y ~ a + b + (1 | c)} +#' \eqn{y ~ a + b + (1 | c)} #' which simply means fit an LME with \code{y} as the outcome variable with \code{a} and \code{b} #' as fixed effects, and \code{c} as a random effect or grouping factor. #' #' It is also possible to fit models with random slopes by specifying a model such as -#' \deqn{y ~ a + b + (1 + b | c)} +#' \eqn{y ~ a + b + (1 + b | c)} #' where the effect of \code{b} can vary randomly between groups defined by \code{c}. #' Implicit nesting can be specified with formulae such as \eqn{y ~ a + b + (1 | c / d)} #' or \eqn{y ~ a + b + (1 | c) + (1 | c : d)}. diff --git a/docker-compose_armadillo.yml b/docker-compose_armadillo.yml index 2cbf5bdb..5e6ab2f5 100644 --- a/docker-compose_armadillo.yml +++ b/docker-compose_armadillo.yml @@ -3,7 +3,7 @@ services: hostname: armadillo ports: - 8080:8080 - image: datashield/armadillo_citest:4.11.1 + image: datashield/armadillo_citest:4.13.1 environment: LOGGING_CONFIG: 'classpath:logback-file.xml' AUDIT_LOG_PATH: '/app/logs/audit.log' @@ -16,6 +16,6 @@ services: default: hostname: default - image: datashield/rock-margin-donkey-permissive:draft + image: datashield/rock-margin-hammer-permissive:latest environment: DEBUG: "FALSE" diff --git a/docker-compose_opal.yml b/docker-compose_opal.yml index 41a3c8d7..fcdb93e4 100644 --- a/docker-compose_opal.yml +++ b/docker-compose_opal.yml @@ -1,6 +1,6 @@ services: opal: - image: obiba/opal:5.1.1 + image: obiba/opal:5.1.2 ports: - "8443:8443" links: @@ -20,4 +20,4 @@ services: - MONGO_INITDB_ROOT_USERNAME=root - MONGO_INITDB_ROOT_PASSWORD=foobar rock: - image: datashield/rock-margin-donkey-permissive:draft + image: datashield/rock-margin-hammer-permissive:latest diff --git a/docs/404.html b/docs/404.html index adefa480..c864294f 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 3f1def72..29e8c211 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/authors.html b/docs/authors.html index feb204c7..25c475fa 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 @@ -52,15 +52,15 @@

Citation

-

Developers D (2024). +

Developers D (2025). dsBaseClient: DataSHIELD Client Functions. -R package version 6.3.1. +R package version 6.3.2.9000. 

@Manual{,
   title = {dsBaseClient: DataSHIELD Client Functions},
   author = {DataSHIELD Developers},
-  year = {2024},
-  note = {R package version 6.3.1},
+  year = {2025},
+  note = {R package version 6.3.2.9000},
 }
diff --git a/docs/index.html b/docs/index.html index 94baefd3..8be1b45e 100644 --- a/docs/index.html +++ b/docs/index.html @@ -33,7 +33,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 46a418da..e6db4552 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,4 +2,4 @@ pandoc: 3.1.3 pkgdown: 2.1.1 pkgdown_sha: ~ articles: {} -last_built: 2024-11-11T14:56Z +last_built: 2025-03-10T14:20Z diff --git a/docs/reference/checkClass.html b/docs/reference/checkClass.html index 8a4483b3..caa41c73 100644 --- a/docs/reference/checkClass.html +++ b/docs/reference/checkClass.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/colPercent.html b/docs/reference/colPercent.html index 4f2acdc8..17795547 100644 --- a/docs/reference/colPercent.html +++ b/docs/reference/colPercent.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.Boole.html b/docs/reference/ds.Boole.html index 2445ed80..fdc38402 100644 --- a/docs/reference/ds.Boole.html +++ b/docs/reference/ds.Boole.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.abs.html b/docs/reference/ds.abs.html index 65f8640c..191ad9d5 100644 --- a/docs/reference/ds.abs.html +++ b/docs/reference/ds.abs.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.asCharacter.html b/docs/reference/ds.asCharacter.html index df1c7cb9..24a4c421 100644 --- a/docs/reference/ds.asCharacter.html +++ b/docs/reference/ds.asCharacter.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.asDataMatrix.html b/docs/reference/ds.asDataMatrix.html index b8ceb870..0d88ac8f 100644 --- a/docs/reference/ds.asDataMatrix.html +++ b/docs/reference/ds.asDataMatrix.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.asFactor.html b/docs/reference/ds.asFactor.html index a75085f9..1eaca56d 100644 --- a/docs/reference/ds.asFactor.html +++ b/docs/reference/ds.asFactor.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.asFactorSimple.html b/docs/reference/ds.asFactorSimple.html index 2b19b9b3..81a92eb8 100644 --- a/docs/reference/ds.asFactorSimple.html +++ b/docs/reference/ds.asFactorSimple.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.asInteger.html b/docs/reference/ds.asInteger.html index 76cc6f13..f403a2d5 100644 --- a/docs/reference/ds.asInteger.html +++ b/docs/reference/ds.asInteger.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.asList.html b/docs/reference/ds.asList.html index d7fe3876..b7d6b7cd 100644 --- a/docs/reference/ds.asList.html +++ b/docs/reference/ds.asList.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.asLogical.html b/docs/reference/ds.asLogical.html index e07cc3c3..bc8682a6 100644 --- a/docs/reference/ds.asLogical.html +++ b/docs/reference/ds.asLogical.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.asMatrix.html b/docs/reference/ds.asMatrix.html index d3e7a9b3..f6972969 100644 --- a/docs/reference/ds.asMatrix.html +++ b/docs/reference/ds.asMatrix.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.asNumeric.html b/docs/reference/ds.asNumeric.html index 1bcda160..aaec72d3 100644 --- a/docs/reference/ds.asNumeric.html +++ b/docs/reference/ds.asNumeric.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.assign.html b/docs/reference/ds.assign.html index 8057c1a4..791c70af 100644 --- a/docs/reference/ds.assign.html +++ b/docs/reference/ds.assign.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.auc.html b/docs/reference/ds.auc.html index 28540596..2f487f0c 100644 --- a/docs/reference/ds.auc.html +++ b/docs/reference/ds.auc.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.boxPlot.html b/docs/reference/ds.boxPlot.html index 323aab95..208e468f 100644 --- a/docs/reference/ds.boxPlot.html +++ b/docs/reference/ds.boxPlot.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.boxPlotGG.html b/docs/reference/ds.boxPlotGG.html index 4736517a..7cb535ec 100644 --- a/docs/reference/ds.boxPlotGG.html +++ b/docs/reference/ds.boxPlotGG.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.boxPlotGG_data_Treatment.html b/docs/reference/ds.boxPlotGG_data_Treatment.html index 51205d21..e9299e3f 100644 --- a/docs/reference/ds.boxPlotGG_data_Treatment.html +++ b/docs/reference/ds.boxPlotGG_data_Treatment.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html b/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html index 476f6b4e..48ba2125 100644 --- a/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html +++ b/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.boxPlotGG_numeric.html b/docs/reference/ds.boxPlotGG_numeric.html index 4b9845e7..e6eae15f 100644 --- a/docs/reference/ds.boxPlotGG_numeric.html +++ b/docs/reference/ds.boxPlotGG_numeric.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.boxPlotGG_table.html b/docs/reference/ds.boxPlotGG_table.html index ad10740a..ba15598e 100644 --- a/docs/reference/ds.boxPlotGG_table.html +++ b/docs/reference/ds.boxPlotGG_table.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.bp_standards.html b/docs/reference/ds.bp_standards.html index 82247836..6b29404e 100644 --- a/docs/reference/ds.bp_standards.html +++ b/docs/reference/ds.bp_standards.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.c.html b/docs/reference/ds.c.html index 7a04d7dd..0e26d688 100644 --- a/docs/reference/ds.c.html +++ b/docs/reference/ds.c.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.cbind.html b/docs/reference/ds.cbind.html index 7b771803..f49984b9 100644 --- a/docs/reference/ds.cbind.html +++ b/docs/reference/ds.cbind.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.changeRefGroup.html b/docs/reference/ds.changeRefGroup.html index 10fb7b25..3975f2d7 100644 --- a/docs/reference/ds.changeRefGroup.html +++ b/docs/reference/ds.changeRefGroup.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.class.html b/docs/reference/ds.class.html index 4bed09e2..89065a11 100644 --- a/docs/reference/ds.class.html +++ b/docs/reference/ds.class.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.colnames.html b/docs/reference/ds.colnames.html index 6dc70fbb..aded7484 100644 --- a/docs/reference/ds.colnames.html +++ b/docs/reference/ds.colnames.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.completeCases.html b/docs/reference/ds.completeCases.html index 2e200009..11d0ccac 100644 --- a/docs/reference/ds.completeCases.html +++ b/docs/reference/ds.completeCases.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.contourPlot.html b/docs/reference/ds.contourPlot.html index 2858a022..8e9c2a0b 100644 --- a/docs/reference/ds.contourPlot.html +++ b/docs/reference/ds.contourPlot.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.cor.html b/docs/reference/ds.cor.html index f86dd9b9..4e4ec7aa 100644 --- a/docs/reference/ds.cor.html +++ b/docs/reference/ds.cor.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.corTest.html b/docs/reference/ds.corTest.html index 8190dca4..228acd59 100644 --- a/docs/reference/ds.corTest.html +++ b/docs/reference/ds.corTest.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.cov.html b/docs/reference/ds.cov.html index b97c414b..4969a1c3 100644 --- a/docs/reference/ds.cov.html +++ b/docs/reference/ds.cov.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.dataFrame.html b/docs/reference/ds.dataFrame.html index f32cf6bc..0a428118 100644 --- a/docs/reference/ds.dataFrame.html +++ b/docs/reference/ds.dataFrame.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.dataFrameFill.html b/docs/reference/ds.dataFrameFill.html index e6c29795..cdcc80a3 100644 --- a/docs/reference/ds.dataFrameFill.html +++ b/docs/reference/ds.dataFrameFill.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.dataFrameSort.html b/docs/reference/ds.dataFrameSort.html index efa19b70..bc66c46a 100644 --- a/docs/reference/ds.dataFrameSort.html +++ b/docs/reference/ds.dataFrameSort.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.dataFrameSubset.html b/docs/reference/ds.dataFrameSubset.html index f1559f19..8c839ebe 100644 --- a/docs/reference/ds.dataFrameSubset.html +++ b/docs/reference/ds.dataFrameSubset.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.densityGrid.html b/docs/reference/ds.densityGrid.html index 03906004..5f1829ec 100644 --- a/docs/reference/ds.densityGrid.html +++ b/docs/reference/ds.densityGrid.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.dim.html b/docs/reference/ds.dim.html index 3469f8ad..df87e6e0 100644 --- a/docs/reference/ds.dim.html +++ b/docs/reference/ds.dim.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.dmtC2S.html b/docs/reference/ds.dmtC2S.html index 3b453ecb..2f4218ee 100644 --- a/docs/reference/ds.dmtC2S.html +++ b/docs/reference/ds.dmtC2S.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.elspline.html b/docs/reference/ds.elspline.html index 102add33..39bbfcbf 100644 --- a/docs/reference/ds.elspline.html +++ b/docs/reference/ds.elspline.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.exists.html b/docs/reference/ds.exists.html index 08944f12..fc2f1613 100644 --- a/docs/reference/ds.exists.html +++ b/docs/reference/ds.exists.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.exp.html b/docs/reference/ds.exp.html index 134f9743..1a033635 100644 --- a/docs/reference/ds.exp.html +++ b/docs/reference/ds.exp.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.extractQuantiles.html b/docs/reference/ds.extractQuantiles.html index 8056889b..e0bb5cd2 100644 --- a/docs/reference/ds.extractQuantiles.html +++ b/docs/reference/ds.extractQuantiles.html @@ -26,7 +26,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.forestplot.html b/docs/reference/ds.forestplot.html index a651872d..d0565013 100644 --- a/docs/reference/ds.forestplot.html +++ b/docs/reference/ds.forestplot.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.gamlss.html b/docs/reference/ds.gamlss.html index 4e92d7c7..ba5d4252 100644 --- a/docs/reference/ds.gamlss.html +++ b/docs/reference/ds.gamlss.html @@ -23,7 +23,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.getWGSR.html b/docs/reference/ds.getWGSR.html index 9f647c02..ac9e59a0 100644 --- a/docs/reference/ds.getWGSR.html +++ b/docs/reference/ds.getWGSR.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.glm.html b/docs/reference/ds.glm.html index 097d6a86..21a73a85 100644 --- a/docs/reference/ds.glm.html +++ b/docs/reference/ds.glm.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 @@ -196,13 +196,13 @@

Details

In formula most shortcut notation for formulas allowed under R's standard glm() function is also allowed by ds.glm.

Many GLMs can be fitted very simply using a formula such as:

-

$$y~a+b+c+d$$

+

\(y~a+b+c+d\)

which simply means fit a GLM with y as the outcome variable and a, b, c and d as covariates. By default all such models also include an intercept (regression constant) term.

Instead, if you need to fit a more complex model, for example:

-

$$EVENT~1+TID+SEXF*AGE.60$$

+

\(EVENT~1+TID+SEXF*AGE.60\)

In the above model the outcome variable is EVENT and the covariates TID (factor variable with level values between 1 and 6 denoting the period time), @@ -237,7 +237,7 @@

Details

The data argument avoids you having to specify the name of the data frame in front of each covariate in the formula. For example, if the data frame is called DataFrame you -avoid having to write: \(DataFrame$y ~ DataFrame$a + DataFrame$b + DataFrame$c + DataFrame$d\)

+avoid having to write: \(DataFrame\$y ~ DataFrame\$a + DataFrame\$b + DataFrame\$c + DataFrame\$d\)

The checks argument verifies that the variables in the model are all defined (exist) on the server-side at every study and that they have the correct characteristics required to fit the model. diff --git a/docs/reference/ds.glmPredict.html b/docs/reference/ds.glmPredict.html index 228bed88..d72f2306 100644 --- a/docs/reference/ds.glmPredict.html +++ b/docs/reference/ds.glmPredict.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.glmSLMA.html b/docs/reference/ds.glmSLMA.html index b429327a..89ffce26 100644 --- a/docs/reference/ds.glmSLMA.html +++ b/docs/reference/ds.glmSLMA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 @@ -281,13 +281,13 @@

Details

In formula Most shortcut notation for formulas allowed under R's standard glm() function is also allowed by ds.glmSLMA.

Many glms can be fitted very simply using a formula such as:

-

$$y~a+b+c+d$$

+

\(y~a+b+c+d\)

which simply means fit a glm with y as the outcome variable and a, b, c and d as covariates. By default all such models also include an intercept (regression constant) term.

Instead, if you need to fit a more complex model, for example:

-

$$EVENT~1+TID+SEXF*AGE.60$$

+

\(EVENT~1+TID+SEXF*AGE.60\)

In the above model the outcome variable is EVENT and the covariates TID (factor variable with level values between 1 and 6 denoting the period time), @@ -355,7 +355,7 @@

Details

The dataName argument avoids you having to specify the name of the data frame in front of each covariate in the formula. For example, if the data frame is called DataFrame you -avoid having to write: \(DataFrame$y ~ DataFrame$a + DataFrame$b + DataFrame$c + DataFrame$d\)

+avoid having to write: \(DataFrame\$y ~ DataFrame\$a + DataFrame\$b + DataFrame\$c + DataFrame\$d\)

The checks argument verifies that the variables in the model are all defined (exist) on the server-site at every study and that they have the correct characteristics required to fit the model. diff --git a/docs/reference/ds.glmSummary.html b/docs/reference/ds.glmSummary.html index 327060d8..9f063a2b 100644 --- a/docs/reference/ds.glmSummary.html +++ b/docs/reference/ds.glmSummary.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.glmerSLMA.html b/docs/reference/ds.glmerSLMA.html index 8d8a3b6c..8c4c2d1f 100644 --- a/docs/reference/ds.glmerSLMA.html +++ b/docs/reference/ds.glmerSLMA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 @@ -235,13 +235,13 @@

Details

In formula most shortcut notation allowed by glmer() function is also allowed by ds.glmerSLMA. Many GLMEs can be fitted very simply using a formula like: -$$y~a+b+(1|c)$$ +\(y~a+b+(1|c)\) which simply means fit an GLME with y as the outcome variable (e.g. a binary case-control using a logistic regression model or a count or a survival time using a Poisson regression model), a and b as fixed effects, and c as a random effect or grouping factor.

It is also possible to fit models with random slopes by specifying a model such as -$$y~a+b+(1+b|c)$$ +\(y~a+b+(1+b|c)\) where the effect of b can vary randomly between groups defined by c. Implicit nesting can be specified with formulas such as: \(y~a+b+(1|c/d)\) or \(y~a+b+(1|c)+(1|c:d)\).

@@ -249,7 +249,7 @@

Details

The dataName argument avoids you having to specify the name of the data frame in front of each covariate in the formula. For example, if the data frame is called DataFrame you avoid having to write: -\(DataFrame$y ~ DataFrame$a + DataFrame$b + (1 | DataFrame$c)\).

+\(DataFrame\$y ~ DataFrame\$a + DataFrame\$b + (1 | DataFrame\$c)\).

The checks argument verifies that the variables in the model are all defined (exist) on the server-site at every study and that they have the correct characteristics required to fit the model. diff --git a/docs/reference/ds.heatmapPlot.html b/docs/reference/ds.heatmapPlot.html index dd26dbd3..09c22fe8 100644 --- a/docs/reference/ds.heatmapPlot.html +++ b/docs/reference/ds.heatmapPlot.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.hetcor.html b/docs/reference/ds.hetcor.html index 5373fbae..fc514632 100644 --- a/docs/reference/ds.hetcor.html +++ b/docs/reference/ds.hetcor.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.histogram.html b/docs/reference/ds.histogram.html index 777c4278..7b86ea95 100644 --- a/docs/reference/ds.histogram.html +++ b/docs/reference/ds.histogram.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.igb_standards.html b/docs/reference/ds.igb_standards.html index e59a5413..b8c641ec 100644 --- a/docs/reference/ds.igb_standards.html +++ b/docs/reference/ds.igb_standards.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.isNA.html b/docs/reference/ds.isNA.html index 9f81d806..ad75f9b1 100644 --- a/docs/reference/ds.isNA.html +++ b/docs/reference/ds.isNA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.isValid.html b/docs/reference/ds.isValid.html index d34ddbd6..375d794b 100644 --- a/docs/reference/ds.isValid.html +++ b/docs/reference/ds.isValid.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.kurtosis.html b/docs/reference/ds.kurtosis.html index 896113ff..313c4392 100644 --- a/docs/reference/ds.kurtosis.html +++ b/docs/reference/ds.kurtosis.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.length.html b/docs/reference/ds.length.html index fa6be208..0758e262 100644 --- a/docs/reference/ds.length.html +++ b/docs/reference/ds.length.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.levels.html b/docs/reference/ds.levels.html index d4eda89f..41cac992 100644 --- a/docs/reference/ds.levels.html +++ b/docs/reference/ds.levels.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.lexis.html b/docs/reference/ds.lexis.html index 72b4fc78..b237b5e0 100644 --- a/docs/reference/ds.lexis.html +++ b/docs/reference/ds.lexis.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.list.html b/docs/reference/ds.list.html index 209dcb5b..208ec5ba 100644 --- a/docs/reference/ds.list.html +++ b/docs/reference/ds.list.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.listClientsideFunctions.html b/docs/reference/ds.listClientsideFunctions.html index 6f6570e6..4b8c9695 100644 --- a/docs/reference/ds.listClientsideFunctions.html +++ b/docs/reference/ds.listClientsideFunctions.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.listDisclosureSettings.html b/docs/reference/ds.listDisclosureSettings.html index 45969706..f4e04bce 100644 --- a/docs/reference/ds.listDisclosureSettings.html +++ b/docs/reference/ds.listDisclosureSettings.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.listOpals.html b/docs/reference/ds.listOpals.html index 5ab10679..461de157 100644 --- a/docs/reference/ds.listOpals.html +++ b/docs/reference/ds.listOpals.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.listServersideFunctions.html b/docs/reference/ds.listServersideFunctions.html index 757fbc03..cd3c5966 100644 --- a/docs/reference/ds.listServersideFunctions.html +++ b/docs/reference/ds.listServersideFunctions.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.lmerSLMA.html b/docs/reference/ds.lmerSLMA.html index efd0e6f9..0f147aa2 100644 --- a/docs/reference/ds.lmerSLMA.html +++ b/docs/reference/ds.lmerSLMA.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 @@ -229,18 +229,18 @@

Details

obtained using R help for lmer and the lme4 package.

In formula most shortcut notation allowed by lmer() function is also allowed by ds.lmerSLMA. Many LMEs can be fitted very simply using a formula like: -$$y ~ a + b + (1 | c)$$ +\(y ~ a + b + (1 | c)\) which simply means fit an LME with y as the outcome variable with a and b as fixed effects, and c as a random effect or grouping factor.

It is also possible to fit models with random slopes by specifying a model such as -$$y ~ a + b + (1 + b | c)$$ +\(y ~ a + b + (1 + b | c)\) where the effect of b can vary randomly between groups defined by c. Implicit nesting can be specified with formulae such as \(y ~ a + b + (1 | c / d)\) or \(y ~ a + b + (1 | c) + (1 | c : d)\).

The dataName argument avoids you having to specify the name of the data frame in front of each covariate in the formula. For example, if the data frame is called DataFrame you avoid having to write: -\(DataFrame$y ~ DataFrame$a + DataFrame$b + (1 | DataFrame$c)\).

+\(DataFrame\$y ~ DataFrame\$a + DataFrame\$b + (1 | DataFrame\$c)\).

The checks argument verifies that the variables in the model are all defined (exist) on the server-site at every study and that they have the correct characteristics required to fit the model. diff --git a/docs/reference/ds.log.html b/docs/reference/ds.log.html index 30f10ae2..9a2c2cfb 100644 --- a/docs/reference/ds.log.html +++ b/docs/reference/ds.log.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.look.html b/docs/reference/ds.look.html index ae0d0cc7..9fbdc316 100644 --- a/docs/reference/ds.look.html +++ b/docs/reference/ds.look.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.ls.html b/docs/reference/ds.ls.html index e0086831..4655046f 100644 --- a/docs/reference/ds.ls.html +++ b/docs/reference/ds.ls.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.lspline.html b/docs/reference/ds.lspline.html index 188e4632..74a950d5 100644 --- a/docs/reference/ds.lspline.html +++ b/docs/reference/ds.lspline.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.make.html b/docs/reference/ds.make.html index 7d4ae3e2..401858f4 100644 --- a/docs/reference/ds.make.html +++ b/docs/reference/ds.make.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.matrix.html b/docs/reference/ds.matrix.html index 0b7c0d61..fe4bd91d 100644 --- a/docs/reference/ds.matrix.html +++ b/docs/reference/ds.matrix.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.matrixDet.html b/docs/reference/ds.matrixDet.html index 8d94a581..d91adb54 100644 --- a/docs/reference/ds.matrixDet.html +++ b/docs/reference/ds.matrixDet.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.matrixDet.report.html b/docs/reference/ds.matrixDet.report.html index f216c851..61e94a82 100644 --- a/docs/reference/ds.matrixDet.report.html +++ b/docs/reference/ds.matrixDet.report.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.matrixDiag.html b/docs/reference/ds.matrixDiag.html index 66e8c6c4..76602f24 100644 --- a/docs/reference/ds.matrixDiag.html +++ b/docs/reference/ds.matrixDiag.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.matrixDimnames.html b/docs/reference/ds.matrixDimnames.html index 24230307..5c315156 100644 --- a/docs/reference/ds.matrixDimnames.html +++ b/docs/reference/ds.matrixDimnames.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.matrixInvert.html b/docs/reference/ds.matrixInvert.html index 07f7e00c..da639cd2 100644 --- a/docs/reference/ds.matrixInvert.html +++ b/docs/reference/ds.matrixInvert.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.matrixMult.html b/docs/reference/ds.matrixMult.html index 55623b50..f0897f58 100644 --- a/docs/reference/ds.matrixMult.html +++ b/docs/reference/ds.matrixMult.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.matrixTranspose.html b/docs/reference/ds.matrixTranspose.html index 524e7531..d4ab339a 100644 --- a/docs/reference/ds.matrixTranspose.html +++ b/docs/reference/ds.matrixTranspose.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.mean.html b/docs/reference/ds.mean.html index 301e391e..ae22f7a2 100644 --- a/docs/reference/ds.mean.html +++ b/docs/reference/ds.mean.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.meanByClass.html b/docs/reference/ds.meanByClass.html index 8b081930..b0456d96 100644 --- a/docs/reference/ds.meanByClass.html +++ b/docs/reference/ds.meanByClass.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.meanSdGp.html b/docs/reference/ds.meanSdGp.html index 51702b22..f33c3d84 100644 --- a/docs/reference/ds.meanSdGp.html +++ b/docs/reference/ds.meanSdGp.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.merge.html b/docs/reference/ds.merge.html index 87767638..3535577c 100644 --- a/docs/reference/ds.merge.html +++ b/docs/reference/ds.merge.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.message.html b/docs/reference/ds.message.html index 7c94b88e..3460bb6a 100644 --- a/docs/reference/ds.message.html +++ b/docs/reference/ds.message.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.metadata.html b/docs/reference/ds.metadata.html index 0d807090..d06c827f 100644 --- a/docs/reference/ds.metadata.html +++ b/docs/reference/ds.metadata.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.mice.html b/docs/reference/ds.mice.html index 871cd3c2..27428cc8 100644 --- a/docs/reference/ds.mice.html +++ b/docs/reference/ds.mice.html @@ -25,7 +25,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.names.html b/docs/reference/ds.names.html index 69c83c36..a70c16e5 100644 --- a/docs/reference/ds.names.html +++ b/docs/reference/ds.names.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.ns.html b/docs/reference/ds.ns.html index 4cb30d13..6cf4ef13 100644 --- a/docs/reference/ds.ns.html +++ b/docs/reference/ds.ns.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.numNA.html b/docs/reference/ds.numNA.html index 2bb4270f..c1727486 100644 --- a/docs/reference/ds.numNA.html +++ b/docs/reference/ds.numNA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.qlspline.html b/docs/reference/ds.qlspline.html index d1a702dd..b66e8e1e 100644 --- a/docs/reference/ds.qlspline.html +++ b/docs/reference/ds.qlspline.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.quantileMean.html b/docs/reference/ds.quantileMean.html index bcc80bc5..cb52a2d8 100644 --- a/docs/reference/ds.quantileMean.html +++ b/docs/reference/ds.quantileMean.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.rBinom.html b/docs/reference/ds.rBinom.html index 63e174a8..3694921c 100644 --- a/docs/reference/ds.rBinom.html +++ b/docs/reference/ds.rBinom.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.rNorm.html b/docs/reference/ds.rNorm.html index 164ac708..e7973dca 100644 --- a/docs/reference/ds.rNorm.html +++ b/docs/reference/ds.rNorm.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.rPois.html b/docs/reference/ds.rPois.html index aaacd484..1efd53d6 100644 --- a/docs/reference/ds.rPois.html +++ b/docs/reference/ds.rPois.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.rUnif.html b/docs/reference/ds.rUnif.html index a9c582ce..a7d6d832 100644 --- a/docs/reference/ds.rUnif.html +++ b/docs/reference/ds.rUnif.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.ranksSecure.html b/docs/reference/ds.ranksSecure.html index f29d764c..1c069c40 100644 --- a/docs/reference/ds.ranksSecure.html +++ b/docs/reference/ds.ranksSecure.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.rbind.html b/docs/reference/ds.rbind.html index 30de9105..87e7221f 100644 --- a/docs/reference/ds.rbind.html +++ b/docs/reference/ds.rbind.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.reShape.html b/docs/reference/ds.reShape.html index cbd97a29..9e2210bd 100644 --- a/docs/reference/ds.reShape.html +++ b/docs/reference/ds.reShape.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.recodeLevels.html b/docs/reference/ds.recodeLevels.html index 008e5014..6c91d43b 100644 --- a/docs/reference/ds.recodeLevels.html +++ b/docs/reference/ds.recodeLevels.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.recodeValues.html b/docs/reference/ds.recodeValues.html index 80bff411..7584d358 100644 --- a/docs/reference/ds.recodeValues.html +++ b/docs/reference/ds.recodeValues.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.rep.html b/docs/reference/ds.rep.html index 56413642..9be83c19 100644 --- a/docs/reference/ds.rep.html +++ b/docs/reference/ds.rep.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.replaceNA.html b/docs/reference/ds.replaceNA.html index 144448a8..3b46cf45 100644 --- a/docs/reference/ds.replaceNA.html +++ b/docs/reference/ds.replaceNA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.rm.html b/docs/reference/ds.rm.html index 47cbcb7a..b40547ef 100644 --- a/docs/reference/ds.rm.html +++ b/docs/reference/ds.rm.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.rowColCalc.html b/docs/reference/ds.rowColCalc.html index 59560072..cf8ebf12 100644 --- a/docs/reference/ds.rowColCalc.html +++ b/docs/reference/ds.rowColCalc.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.sample.html b/docs/reference/ds.sample.html index 8ebc307c..23be1fa5 100644 --- a/docs/reference/ds.sample.html +++ b/docs/reference/ds.sample.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.scatterPlot.html b/docs/reference/ds.scatterPlot.html index 5c792f45..c1107e91 100644 --- a/docs/reference/ds.scatterPlot.html +++ b/docs/reference/ds.scatterPlot.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.seq.html b/docs/reference/ds.seq.html index 2235f610..1a9a70cf 100644 --- a/docs/reference/ds.seq.html +++ b/docs/reference/ds.seq.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.setDefaultOpals.html b/docs/reference/ds.setDefaultOpals.html index 2753f52a..73beb9fa 100644 --- a/docs/reference/ds.setDefaultOpals.html +++ b/docs/reference/ds.setDefaultOpals.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.setSeed.html b/docs/reference/ds.setSeed.html index f20baffa..d9303021 100644 --- a/docs/reference/ds.setSeed.html +++ b/docs/reference/ds.setSeed.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.skewness.html b/docs/reference/ds.skewness.html index 86ff4c8c..560b9eb9 100644 --- a/docs/reference/ds.skewness.html +++ b/docs/reference/ds.skewness.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.sqrt.html b/docs/reference/ds.sqrt.html index 46c711cb..e79da88b 100644 --- a/docs/reference/ds.sqrt.html +++ b/docs/reference/ds.sqrt.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.subset.html b/docs/reference/ds.subset.html index 69240cf0..a2077f3c 100644 --- a/docs/reference/ds.subset.html +++ b/docs/reference/ds.subset.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.subsetByClass.html b/docs/reference/ds.subsetByClass.html index 8a8fad3b..fa4482f1 100644 --- a/docs/reference/ds.subsetByClass.html +++ b/docs/reference/ds.subsetByClass.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.summary.html b/docs/reference/ds.summary.html index 309c6a0d..e790322b 100644 --- a/docs/reference/ds.summary.html +++ b/docs/reference/ds.summary.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.table.html b/docs/reference/ds.table.html index 4c524ddd..b1e9d826 100644 --- a/docs/reference/ds.table.html +++ b/docs/reference/ds.table.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.table1D.html b/docs/reference/ds.table1D.html index cd8e6c28..dac3b0c5 100644 --- a/docs/reference/ds.table1D.html +++ b/docs/reference/ds.table1D.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.table2D.html b/docs/reference/ds.table2D.html index 96270839..ea824f2f 100644 --- a/docs/reference/ds.table2D.html +++ b/docs/reference/ds.table2D.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.tapply.assign.html b/docs/reference/ds.tapply.assign.html index c65eeacf..08aa0775 100644 --- a/docs/reference/ds.tapply.assign.html +++ b/docs/reference/ds.tapply.assign.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.tapply.html b/docs/reference/ds.tapply.html index d1d6d8d8..575ac8d2 100644 --- a/docs/reference/ds.tapply.html +++ b/docs/reference/ds.tapply.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.testObjExists.html b/docs/reference/ds.testObjExists.html index 2dc6b97d..00b66492 100644 --- a/docs/reference/ds.testObjExists.html +++ b/docs/reference/ds.testObjExists.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.unList.html b/docs/reference/ds.unList.html index 1a0b9c55..71600af2 100644 --- a/docs/reference/ds.unList.html +++ b/docs/reference/ds.unList.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.unique.html b/docs/reference/ds.unique.html index 5d1cd79b..e34a6454 100644 --- a/docs/reference/ds.unique.html +++ b/docs/reference/ds.unique.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.var.html b/docs/reference/ds.var.html index 030dc4cd..11fd7b8c 100644 --- a/docs/reference/ds.var.html +++ b/docs/reference/ds.var.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/ds.vectorCalc.html b/docs/reference/ds.vectorCalc.html index 43e81df9..61895f85 100644 --- a/docs/reference/ds.vectorCalc.html +++ b/docs/reference/ds.vectorCalc.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/extract.html b/docs/reference/extract.html index eacb3fcf..4db46a1b 100644 --- a/docs/reference/extract.html +++ b/docs/reference/extract.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/getPooledMean.html b/docs/reference/getPooledMean.html index 4986842d..be701654 100644 --- a/docs/reference/getPooledMean.html +++ b/docs/reference/getPooledMean.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/getPooledVar.html b/docs/reference/getPooledVar.html index 0286fd8e..dbdf9e8f 100644 --- a/docs/reference/getPooledVar.html +++ b/docs/reference/getPooledVar.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/glmChecks.html b/docs/reference/glmChecks.html index 5a944f9e..9e9d2ebb 100644 --- a/docs/reference/glmChecks.html +++ b/docs/reference/glmChecks.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/index.html b/docs/reference/index.html index 0ceeb7bf..c1c14d93 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/isAssigned.html b/docs/reference/isAssigned.html index b3d66e75..a48eb911 100644 --- a/docs/reference/isAssigned.html +++ b/docs/reference/isAssigned.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/isDefined.html b/docs/reference/isDefined.html index 54184020..1119a36c 100644 --- a/docs/reference/isDefined.html +++ b/docs/reference/isDefined.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/logical2int.html b/docs/reference/logical2int.html index ac52dac1..bef4be20 100644 --- a/docs/reference/logical2int.html +++ b/docs/reference/logical2int.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/meanByClassHelper0a.html b/docs/reference/meanByClassHelper0a.html index 8d6cfebe..733c3acf 100644 --- a/docs/reference/meanByClassHelper0a.html +++ b/docs/reference/meanByClassHelper0a.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/meanByClassHelper0b.html b/docs/reference/meanByClassHelper0b.html index f35054ef..8409233b 100644 --- a/docs/reference/meanByClassHelper0b.html +++ b/docs/reference/meanByClassHelper0b.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/meanByClassHelper1.html b/docs/reference/meanByClassHelper1.html index 810f46d7..f29979f3 100644 --- a/docs/reference/meanByClassHelper1.html +++ b/docs/reference/meanByClassHelper1.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/meanByClassHelper2.html b/docs/reference/meanByClassHelper2.html index 7540f66f..ed8110e9 100644 --- a/docs/reference/meanByClassHelper2.html +++ b/docs/reference/meanByClassHelper2.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/meanByClassHelper3.html b/docs/reference/meanByClassHelper3.html index c5eb79f5..bc5a7e58 100644 --- a/docs/reference/meanByClassHelper3.html +++ b/docs/reference/meanByClassHelper3.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/meanByClassHelper4.html b/docs/reference/meanByClassHelper4.html index ef479e86..c137c7e4 100644 --- a/docs/reference/meanByClassHelper4.html +++ b/docs/reference/meanByClassHelper4.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/rowPercent.html b/docs/reference/rowPercent.html index da5df3fd..3d10c804 100644 --- a/docs/reference/rowPercent.html +++ b/docs/reference/rowPercent.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/docs/reference/subsetHelper.html b/docs/reference/subsetHelper.html index 33f96c87..16ffe6f4 100644 --- a/docs/reference/subsetHelper.html +++ b/docs/reference/subsetHelper.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2.9000 diff --git a/man/ds.glm.Rd b/man/ds.glm.Rd index 6bd50a4c..f2d05ffc 100644 --- a/man/ds.glm.Rd +++ b/man/ds.glm.Rd @@ -138,7 +138,7 @@ function is also allowed by \code{ds.glm}. Many GLMs can be fitted very simply using a formula such as: -\deqn{y~a+b+c+d} +\eqn{y~a+b+c+d} which simply means fit a GLM with \code{y} as the outcome variable and \code{a}, \code{b}, \code{c} and \code{d} as covariates. @@ -147,7 +147,7 @@ By default all such models also include an intercept (regression constant) term. Instead, if you need to fit a more complex model, for example: - \deqn{EVENT~1+TID+SEXF*AGE.60} + \eqn{EVENT~1+TID+SEXF*AGE.60} In the above model the outcome variable is \code{EVENT} and the covariates diff --git a/man/ds.glmSLMA.Rd b/man/ds.glmSLMA.Rd index f64e6a5c..10c66a56 100644 --- a/man/ds.glmSLMA.Rd +++ b/man/ds.glmSLMA.Rd @@ -241,7 +241,7 @@ function is also allowed by \code{ds.glmSLMA}. Many glms can be fitted very simply using a formula such as: -\deqn{y~a+b+c+d} +\eqn{y~a+b+c+d} which simply means fit a glm with \code{y} as the outcome variable and \code{a}, \code{b}, \code{c} and \code{d} as covariates. @@ -250,7 +250,7 @@ By default all such models also include an intercept (regression constant) term. Instead, if you need to fit a more complex model, for example: - \deqn{EVENT~1+TID+SEXF*AGE.60} +\eqn{EVENT~1+TID+SEXF*AGE.60} In the above model the outcome variable is \code{EVENT} and the covariates diff --git a/man/ds.glmerSLMA.Rd b/man/ds.glmerSLMA.Rd index 8ee7cdfd..6b04a75a 100644 --- a/man/ds.glmerSLMA.Rd +++ b/man/ds.glmerSLMA.Rd @@ -169,17 +169,17 @@ If it did not some information about the reason for this is reported. In \code{formula} most shortcut notation allowed by \code{glmer()} function is also allowed by \code{ds.glmerSLMA}. Many GLMEs can be fitted very simply using a formula like: -\deqn{y~a+b+(1|c)} +\eqn{y~a+b+(1|c)} which simply means fit an GLME with \code{y} as the outcome variable (e.g. a binary case-control using a logistic regression model or a count or a survival time using a Poisson regression model), \code{a} and \code{b} as fixed effects, and \code{c} as a random effect or grouping factor. It is also possible to fit models with random slopes by specifying a model such as -\deqn{y~a+b+(1+b|c)} +\eqn{y~a+b+(1+b|c)} where the effect of \code{b} can vary randomly between groups defined by \code{c}. Implicit nesting can be specified with formulas such as: \eqn{y~a+b+(1|c/d)} -or \eqn{y~a+b+(1|c)+(1|c:d)}. +or \eqn{y~a+b+(1|c)+(1|c:d)}. The \code{dataName} argument avoids you having to specify the name of the diff --git a/man/ds.lmerSLMA.Rd b/man/ds.lmerSLMA.Rd index 68489737..4ec9b612 100644 --- a/man/ds.lmerSLMA.Rd +++ b/man/ds.lmerSLMA.Rd @@ -168,12 +168,12 @@ obtained using R help for \code{lmer} and the \code{lme4} package. In \code{formula} most shortcut notation allowed by \code{lmer()} function is also allowed by \code{ds.lmerSLMA}. Many LMEs can be fitted very simply using a formula like: -\deqn{y ~ a + b + (1 | c)} +\eqn{y ~ a + b + (1 | c)} which simply means fit an LME with \code{y} as the outcome variable with \code{a} and \code{b} as fixed effects, and \code{c} as a random effect or grouping factor. It is also possible to fit models with random slopes by specifying a model such as -\deqn{y ~ a + b + (1 + b | c)} +\eqn{y ~ a + b + (1 + b | c)} where the effect of \code{b} can vary randomly between groups defined by \code{c}. Implicit nesting can be specified with formulae such as \eqn{y ~ a + b + (1 | c / d)} or \eqn{y ~ a + b + (1 | c) + (1 | c : d)}. diff --git a/tests/docker/armadillo/standard/config/application.yml b/tests/docker/armadillo/standard/config/application.yml index 7db8b670..87e0fa1f 100644 --- a/tests/docker/armadillo/standard/config/application.yml +++ b/tests/docker/armadillo/standard/config/application.yml @@ -19,12 +19,8 @@ armadillo: host: default package-whitelist: # Packages for 'donkey' - dsBase - - dsMediation - - dsMTLBase - dsSurvival - dsTidyverse - - dsExposome - - dsOmics - resourcer function-blacklist: [ ] options: