diff --git a/.Rbuildignore b/.Rbuildignore index dc5886238..8f27db2fa 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -17,8 +17,8 @@ ^R/secure.global.ranking.md$ ^_pkgdown\.yml$ ^docs$ -^dsBase_6.3.1.tar.gz$ -^dsBase_6.3.1-permissive.tar.gz$ +^dsBase_6.3.2.tar.gz$ +^dsBase_6.3.2-permissive.tar.gz$ ^dsDanger_6.3.1.tar.gz$ ^\.circleci$ ^\.circleci/config\.yml$ diff --git a/.circleci/config.yml b/.circleci/config.yml index cff6767a3..c96e0cce7 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -5,7 +5,8 @@ version: 2.1 jobs: dsbaseclient: docker: - - image: cimg/base:current +# - image: cimg/base:current + - image: cimg/base:2024.11 resource_class: small steps: - checkout @@ -18,6 +19,10 @@ jobs: echo " Tag: " $CIRCLE_TAG - run: command: | + sudo apt-get install --no-install-recommends software-properties-common dirmngr + wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc + sudo add-apt-repository -y "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/" + sudo apt-get update -y sudo apt-get install -y r-base-core cmake - run: @@ -33,6 +38,9 @@ jobs: sudo apt-get install -y libjpeg-dev - run: command: | + sudo Rscript -e "install.packages('devtools', dependencies=TRUE)" + sudo Rscript -e "install.packages('covr', dependencies=TRUE)" + sudo Rscript -e "install.packages('fields', dependencies=TRUE)" sudo Rscript -e "install.packages('metafor', dependencies=TRUE)" sudo Rscript -e "install.packages('meta', dependencies=TRUE)" @@ -42,6 +50,15 @@ jobs: sudo Rscript -e "install.packages('panelaggregation', dependencies=TRUE)" sudo Rscript -e "install.packages('methods', dependencies=TRUE)" sudo Rscript -e "install.packages('dplyr', dependencies=TRUE)" + + sudo Rscript -e "install.packages('DSI', dependencies=TRUE)" + sudo Rscript -e "install.packages('DSOpal', dependencies=TRUE)" + sudo Rscript -e "install.packages('DSLite', dependencies=TRUE)" + sudo Rscript -e "install.packages('MolgenisAuth', dependencies=TRUE)" + sudo Rscript -e "install.packages('MolgenisArmadillo', dependencies=TRUE)" + sudo Rscript -e "install.packages('DSMolgenisArmadillo', dependencies=TRUE)" + sudo Rscript -e "install.packages('DescTools', dependencies=TRUE)" + sudo Rscript -e "install.packages('e1071', dependencies=TRUE)" - run: command: | sudo Rscript -e 'library(covr); covr::codecov(token = "'$CODECOV_TOKEN'", quiet=FALSE)' diff --git a/DESCRIPTION b/DESCRIPTION index 60af1d1cf..87814d459 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,42 @@ Package: dsBaseClient Title: DataSHIELD Client Functions -Version: 6.3.1 -Author: DataSHIELD Developers -Maintainer: DataSHIELD Developers +Version: 6.3.2 +Authors@R: c(person(given = "Paul", + family = "Burton", + role = c("aut")), + person(given = "Rebecca", + family = "Wilson", + role = c("aut")), + person(given = "Olly", + family = "Butters", + role = c("aut")), + person(given = "Patricia", + family = "Ryser-Welch", + role = c("aut")), + person(given = "Alex", + family = "Westerberg", + role = c("aut")), + person(given = "Leire", + family = "Abarrategui", + role = c("aut")), + person(given = "Roberto", + family = "Villegas-Diaz", + role = c("aut"), + comment = c(ORCID = "0000-0001-5036-8661")), + person(given = "Demetris", + family = "Avraam", + role = c("aut"), + comment = c(ORCID = "0000-0001-8908-2441")), + person(given = "Yannick", + family = "Marcon", + role = c("aut", "cre"), + email = "yannick.marcon@obiba.org", + comment = c(ORCID = "0000-0003-0138-2023")), + person(given = "Stuart", + family = "Wheater", + role = c("aut", "cre"), + email = "stuart.wheater@arjuna.com", + comment = c(ORCID = "0009-0003-2419-1964"))) Description: DataSHIELD client functions for the client side. License: GPL-3 Depends: @@ -19,6 +53,14 @@ Imports: methods, dplyr Suggests: - testthat + lme4, + httr, + tibble, + testthat, + e1071, + DescTools, + DSOpal, + DSMolgenisArmadillo, + DSLite RoxygenNote: 7.3.2 Encoding: UTF-8 diff --git a/R/ds.glm.R b/R/ds.glm.R index eb5286e99..13cba2d96 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 bbf8b174b..7f3454bc0 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 49d6e282b..8bb8aa36f 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 f964ceb95..b6d05c9bf 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/R/ds.rBinom.R b/R/ds.rBinom.R index ab4472faf..2f39f8b10 100644 --- a/R/ds.rBinom.R +++ b/R/ds.rBinom.R @@ -216,10 +216,11 @@ single.integer.seed<-c(single.integer.seed,seed.as.integer.study.specific) if(seed.as.text=="NULL"){ cat("NO SEED SET IN STUDY",study.id,"\n\n") -} +} else { calltext <- paste0("setSeedDS(", seed.as.text, ")") ssDS.obj[[study.id]] <- DSI::datashield.aggregate(datasources[study.id], as.symbol(calltext)) } +} cat("\n\n") diff --git a/R/ds.rUnif.R b/R/ds.rUnif.R index 936a80709..d98fa28f0 100644 --- a/R/ds.rUnif.R +++ b/R/ds.rUnif.R @@ -234,9 +234,10 @@ single.integer.seed<-c(single.integer.seed,seed.as.integer.study.specific) if(seed.as.text=="NULL"){ cat("NO SEED SET IN STUDY",study.id,"\n") -} +} else { calltext <- paste0("setSeedDS(", seed.as.text, ")") ssDS.obj[[study.id]] <- DSI::datashield.aggregate(datasources[study.id], as.symbol(calltext)) +} } diff --git a/armadillo_azure-pipelines.yml b/armadillo_azure-pipelines.yml index 70788f76b..595258a6e 100644 --- a/armadillo_azure-pipelines.yml +++ b/armadillo_azure-pipelines.yml @@ -58,10 +58,10 @@ schedules: - master always: true - cron: "0 2 * * *" - displayName: Nightly build - v6.3.1-dev + displayName: Nightly build - v6.3.2-dev branches: include: - - v6.3.1-dev + - v6.3.2-dev always: true ######################################################################################### @@ -185,7 +185,7 @@ jobs: # If this step fails still mark as failed, but don't stop the rest of the steps running. - bash: | - R -q -e "library('devtools'); devtools::check(args = c('--no-examples'))" | tee azure-pipelines_check.Rout + R -q -e "library('devtools'); devtools::check(args = c('--no-examples', '--no-tests'))" | tee azure-pipelines_check.Rout grep --quiet "^0 errors" azure-pipelines_check.Rout && grep --quiet " 0 warnings" azure-pipelines_check.Rout && grep --quiet " 0 notes" azure-pipelines_check.Rout workingDirectory: $(Pipeline.Workspace)/dsBaseClient @@ -235,7 +235,7 @@ jobs: curl -u admin:admin -X GET http://localhost:8080/packages - curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.1-permissive.tar.gz" -X POST http://localhost:8080/install-package + curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.2-permissive.tar.gz" -X POST http://localhost:8080/install-package sleep 60 docker container restart dsbaseclient_armadillo_1 @@ -263,7 +263,7 @@ jobs: # best guess is that there is an implicit build or similar that happens. Although # I cannot replicate that directly with build etc directly. - sudo R --verbose -e 'devtools::check()' + sudo R --verbose -e 'devtools::reload()' mkdir $(Pipeline.Workspace)/logs @@ -364,7 +364,7 @@ jobs: - bash: | curl -u admin:admin http://localhost:8080/whitelist - curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.1.tar.gz" -X POST http://localhost:8080/install-package + curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.2.tar.gz" -X POST http://localhost:8080/install-package docker container restart dsbaseclient_armadillo_1 sleep 60 @@ -387,7 +387,7 @@ jobs: - bash: | # See, 'Code coverage and JUnit report output' for issues with the approach and improvement needed. - sudo R --verbose -e 'devtools::check()' + sudo R --verbose -e 'devtools::reload()' pwd mkdir $(Pipeline.Workspace)/logs diff --git a/azure-pipelines.yml b/azure-pipelines.yml index b9811a2ab..691bd140d 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -58,10 +58,10 @@ schedules: - master always: true - cron: "0 2 * * *" - displayName: Nightly build - v6.3.1-dev + displayName: Nightly build - v6.3.2-dev branches: include: - - v6.3.1-dev + - v6.3.2-dev always: true ######################################################################################### @@ -133,13 +133,14 @@ jobs: sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev -y + sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table','panelaggregation'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('DSI','DSOpal','DSLite'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')" - sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)" + sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.2', dependencies = TRUE)" # XML grep for coverage report merging sudo apt-get install -qq xml-twig-tools -y @@ -185,7 +186,7 @@ jobs: # If this step fails still mark as failed, but don't stop the rest of the steps running. - bash: | - R -q -e "library('devtools'); devtools::check(args = c('--no-examples'))" | tee azure-pipelines_check.Rout + R -q -e "library('devtools'); devtools::check(args = c('--no-examples', '--no-tests'))" | tee azure-pipelines_check.Rout grep --quiet "^0 errors" azure-pipelines_check.Rout && grep --quiet " 0 warnings" azure-pipelines_check.Rout && grep --quiet " 0 notes" azure-pipelines_check.Rout workingDirectory: $(Pipeline.Workspace)/dsBaseClient @@ -232,9 +233,11 @@ jobs: # Install dsBase. # If previous steps have failed then don't run. - bash: | - R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.1'); opal.logout(opal)" + R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)" - sleep 120 + R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.2'); opal.logout(opal)" + + sleep 60 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)" @@ -258,7 +261,7 @@ jobs: # best guess is that there is an implicit build or similar that happens. Although # I cannot replicate that directly with build etc directly. - sudo R --verbose -e 'devtools::check()' + sudo R --verbose -e 'devtools::reload()' mkdir $(Pipeline.Workspace)/logs @@ -358,6 +361,8 @@ jobs: # If previous steps have failed then don't run - bash: | + R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)" + R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.1'); opal.logout(opal)" workingDirectory: $(Pipeline.Workspace)/dsBaseClient @@ -374,9 +379,8 @@ jobs: - bash: | # See, 'Code coverage and JUnit report output' for issues with the approach and improvement needed. - sudo R --verbose -e 'devtools::check()' + sudo R --verbose -e 'devtools::reload()' - pwd mkdir $(Pipeline.Workspace)/logs # run the coverage tool and output to coveragelist.csv diff --git a/docker-compose_armadillo.yml b/docker-compose_armadillo.yml index 35b851084..60f33094f 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:5.0.0.2 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-knot-devel-permissive:latest + image: datashield/rserver-neutron:latest environment: DEBUG: "FALSE" diff --git a/docker-compose_opal.yml b/docker-compose_opal.yml index fb233ea4f..a55e8774a 100644 --- a/docker-compose_opal.yml +++ b/docker-compose_opal.yml @@ -1,6 +1,6 @@ services: opal: - image: obiba/opal:5.0.1 + image: obiba/opal:5.1.4 ports: - "8443:8443" links: @@ -20,4 +20,4 @@ services: - MONGO_INITDB_ROOT_USERNAME=root - MONGO_INITDB_ROOT_PASSWORD=foobar rock: - image: datashield/rock-knot-devel-permissive:latest + image: datashield/rock-margin-joule-permissive:latest diff --git a/docs/404.html b/docs/404.html index adefa4804..87a6e3556 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -73,12 +73,12 @@

Page not found (404)

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 3f1def72b..08411fdbc 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -256,11 +256,11 @@

NA

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/authors.html b/docs/authors.html index feb204c70..22d93a3e4 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -40,7 +40,39 @@

Authors and Citation

@@ -52,15 +84,15 @@

Citation

-

Developers D (2024). +

Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui L, Villegas-Diaz R, Avraam D, Wheater S (2025). dsBaseClient: DataSHIELD Client Functions. -R package version 6.3.1. +R package version 6.3.2.

@Manual{,
   title = {dsBaseClient: DataSHIELD Client Functions},
-  author = {DataSHIELD Developers},
-  year = {2024},
-  note = {R package version 6.3.1},
+  author = {Paul Burton and Rebecca Wilson and Olly Butters and Patricia Ryser-Welch and Alex Westerberg and Leire Abarrategui and Roberto Villegas-Diaz and Demetris Avraam and Stuart Wheater},
+  year = {2025},
+  note = {R package version 6.3.2},
 }
@@ -70,11 +102,11 @@

Citation

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/index.html b/docs/index.html index 94baefd3b..b6b3f2ef2 100644 --- a/docs/index.html +++ b/docs/index.html @@ -33,7 +33,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -117,7 +117,15 @@

Citation

Developers

    -
  • DataSHIELD Developers
    Maintainer
  • +
  • Paul Burton
    Author
  • +
  • Rebecca Wilson
    Author
  • +
  • Olly Butters
    Author
  • +
  • Patricia Ryser-Welch
    Author
  • +
  • Alex Westerberg
    Author
  • +
  • Leire Abarrategui
    Author
  • +
  • Roberto Villegas-Diaz
    Author
  • +
  • Demetris Avraam
    Author
  • +
  • Stuart Wheater
    Author, maintainer
@@ -129,12 +137,12 @@

Developers

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 46a418dac..d0612bd11 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ pandoc: 3.1.3 -pkgdown: 2.1.1 +pkgdown: 2.1.3 pkgdown_sha: ~ articles: {} -last_built: 2024-11-11T14:56Z +last_built: 2025-06-02T10:28Z diff --git a/docs/reference/checkClass.html b/docs/reference/checkClass.html index 8a4483b3b..fdd5d5f4b 100644 --- a/docs/reference/checkClass.html +++ b/docs/reference/checkClass.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -78,11 +78,11 @@

Details

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/colPercent.html b/docs/reference/colPercent.html index 4f2acdc84..34171191b 100644 --- a/docs/reference/colPercent.html +++ b/docs/reference/colPercent.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -76,11 +76,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.Boole.html b/docs/reference/ds.Boole.html index 2445ed801..d2a72559f 100644 --- a/docs/reference/ds.Boole.html +++ b/docs/reference/ds.Boole.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -200,11 +200,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.abs.html b/docs/reference/ds.abs.html index 65f8640ce..69ac14a93 100644 --- a/docs/reference/ds.abs.html +++ b/docs/reference/ds.abs.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -150,11 +150,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.asCharacter.html b/docs/reference/ds.asCharacter.html index df1c7cb90..8ef088034 100644 --- a/docs/reference/ds.asCharacter.html +++ b/docs/reference/ds.asCharacter.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -132,11 +132,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.asDataMatrix.html b/docs/reference/ds.asDataMatrix.html index b8ceb8706..85eb0d21a 100644 --- a/docs/reference/ds.asDataMatrix.html +++ b/docs/reference/ds.asDataMatrix.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -135,11 +135,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.asFactor.html b/docs/reference/ds.asFactor.html index a75085f91..e60f7ad21 100644 --- a/docs/reference/ds.asFactor.html +++ b/docs/reference/ds.asFactor.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -229,11 +229,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.asFactorSimple.html b/docs/reference/ds.asFactorSimple.html index 2b19b9b3e..2be7e4232 100644 --- a/docs/reference/ds.asFactorSimple.html +++ b/docs/reference/ds.asFactorSimple.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -103,11 +103,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.asInteger.html b/docs/reference/ds.asInteger.html index 76cc6f13c..de40baf5c 100644 --- a/docs/reference/ds.asInteger.html +++ b/docs/reference/ds.asInteger.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -148,11 +148,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.asList.html b/docs/reference/ds.asList.html index d7fe3876f..f2f15875c 100644 --- a/docs/reference/ds.asList.html +++ b/docs/reference/ds.asList.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -133,11 +133,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.asLogical.html b/docs/reference/ds.asLogical.html index e07cc3c30..547791a4f 100644 --- a/docs/reference/ds.asLogical.html +++ b/docs/reference/ds.asLogical.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -134,11 +134,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.asMatrix.html b/docs/reference/ds.asMatrix.html index d3e7a9b37..41cd5d5af 100644 --- a/docs/reference/ds.asMatrix.html +++ b/docs/reference/ds.asMatrix.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -136,11 +136,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.asNumeric.html b/docs/reference/ds.asNumeric.html index 1bcda160d..8b69cd5d1 100644 --- a/docs/reference/ds.asNumeric.html +++ b/docs/reference/ds.asNumeric.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -147,11 +147,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.assign.html b/docs/reference/ds.assign.html index 8057c1a45..d2b20ef5b 100644 --- a/docs/reference/ds.assign.html +++ b/docs/reference/ds.assign.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -131,11 +131,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.auc.html b/docs/reference/ds.auc.html index 28540596e..eaa82ea3f 100644 --- a/docs/reference/ds.auc.html +++ b/docs/reference/ds.auc.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -89,11 +89,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.boxPlot.html b/docs/reference/ds.boxPlot.html index 323aab954..6bfe6f0e8 100644 --- a/docs/reference/ds.boxPlot.html +++ b/docs/reference/ds.boxPlot.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -113,11 +113,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.boxPlotGG.html b/docs/reference/ds.boxPlotGG.html index 4736517a6..05d432795 100644 --- a/docs/reference/ds.boxPlotGG.html +++ b/docs/reference/ds.boxPlotGG.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -108,11 +108,11 @@

Value

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.boxPlotGG_data_Treatment.html b/docs/reference/ds.boxPlotGG_data_Treatment.html index 51205d21f..b5aa6e4d3 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 @@ -95,11 +95,11 @@

Value

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html b/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html index 476f6b4eb..e3b0e9928 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 @@ -75,11 +75,11 @@

Value

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.boxPlotGG_numeric.html b/docs/reference/ds.boxPlotGG_numeric.html index 4b9845e7e..e73616f28 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 @@ -91,11 +91,11 @@

Value

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.boxPlotGG_table.html b/docs/reference/ds.boxPlotGG_table.html index ad10740ac..725db3e72 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 @@ -106,11 +106,11 @@

Value

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.bp_standards.html b/docs/reference/ds.bp_standards.html index 82247836e..ec66a1884 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 @@ -126,11 +126,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.c.html b/docs/reference/ds.c.html index 7a04d7ddb..9adef3667 100644 --- a/docs/reference/ds.c.html +++ b/docs/reference/ds.c.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -132,11 +132,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.cbind.html b/docs/reference/ds.cbind.html index 7b7718035..4a208bb15 100644 --- a/docs/reference/ds.cbind.html +++ b/docs/reference/ds.cbind.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -206,11 +206,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.changeRefGroup.html b/docs/reference/ds.changeRefGroup.html index 10fb7b255..6c518b3d7 100644 --- a/docs/reference/ds.changeRefGroup.html +++ b/docs/reference/ds.changeRefGroup.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -199,11 +199,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.class.html b/docs/reference/ds.class.html index 4bed09e2b..64262b44d 100644 --- a/docs/reference/ds.class.html +++ b/docs/reference/ds.class.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -130,11 +130,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.colnames.html b/docs/reference/ds.colnames.html index 6dc70fbb8..8a204b118 100644 --- a/docs/reference/ds.colnames.html +++ b/docs/reference/ds.colnames.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -127,11 +127,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.completeCases.html b/docs/reference/ds.completeCases.html index 2e2000092..a4031cb54 100644 --- a/docs/reference/ds.completeCases.html +++ b/docs/reference/ds.completeCases.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -147,11 +147,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.contourPlot.html b/docs/reference/ds.contourPlot.html index 2858a022c..811050d2d 100644 --- a/docs/reference/ds.contourPlot.html +++ b/docs/reference/ds.contourPlot.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -203,11 +203,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.cor.html b/docs/reference/ds.cor.html index f86dd9b9a..a5326e523 100644 --- a/docs/reference/ds.cor.html +++ b/docs/reference/ds.cor.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -156,11 +156,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.corTest.html b/docs/reference/ds.corTest.html index 8190dca4f..3ae065627 100644 --- a/docs/reference/ds.corTest.html +++ b/docs/reference/ds.corTest.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -162,11 +162,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.cov.html b/docs/reference/ds.cov.html index b97c414b6..b0bc95b4f 100644 --- a/docs/reference/ds.cov.html +++ b/docs/reference/ds.cov.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -181,11 +181,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.dataFrame.html b/docs/reference/ds.dataFrame.html index f32cf6bc3..2c2b8b2f9 100644 --- a/docs/reference/ds.dataFrame.html +++ b/docs/reference/ds.dataFrame.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -199,11 +199,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.dataFrameFill.html b/docs/reference/ds.dataFrameFill.html index e6c297958..095bfc7ae 100644 --- a/docs/reference/ds.dataFrameFill.html +++ b/docs/reference/ds.dataFrameFill.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -150,11 +150,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.dataFrameSort.html b/docs/reference/ds.dataFrameSort.html index efa19b70b..74012b6c2 100644 --- a/docs/reference/ds.dataFrameSort.html +++ b/docs/reference/ds.dataFrameSort.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -171,11 +171,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.dataFrameSubset.html b/docs/reference/ds.dataFrameSubset.html index f1559f19a..760ebd05a 100644 --- a/docs/reference/ds.dataFrameSubset.html +++ b/docs/reference/ds.dataFrameSubset.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -216,11 +216,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.densityGrid.html b/docs/reference/ds.densityGrid.html index 03906004a..a4d937384 100644 --- a/docs/reference/ds.densityGrid.html +++ b/docs/reference/ds.densityGrid.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -120,11 +120,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.dim.html b/docs/reference/ds.dim.html index 3469f8ad6..01e9d8cd7 100644 --- a/docs/reference/ds.dim.html +++ b/docs/reference/ds.dim.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -167,11 +167,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.dmtC2S.html b/docs/reference/ds.dmtC2S.html index 3b453ecb3..8a8d9f479 100644 --- a/docs/reference/ds.dmtC2S.html +++ b/docs/reference/ds.dmtC2S.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -120,11 +120,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.elspline.html b/docs/reference/ds.elspline.html index 102add33a..c71f39005 100644 --- a/docs/reference/ds.elspline.html +++ b/docs/reference/ds.elspline.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -119,11 +119,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.exists.html b/docs/reference/ds.exists.html index 08944f12e..e7899ac72 100644 --- a/docs/reference/ds.exists.html +++ b/docs/reference/ds.exists.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -138,11 +138,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.exp.html b/docs/reference/ds.exp.html index 134f9743c..70642f9c9 100644 --- a/docs/reference/ds.exp.html +++ b/docs/reference/ds.exp.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -132,11 +132,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.extractQuantiles.html b/docs/reference/ds.extractQuantiles.html index 8056889b3..9c35bfcdb 100644 --- a/docs/reference/ds.extractQuantiles.html +++ b/docs/reference/ds.extractQuantiles.html @@ -26,7 +26,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -176,11 +176,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.forestplot.html b/docs/reference/ds.forestplot.html index a651872db..4872cf4a3 100644 --- a/docs/reference/ds.forestplot.html +++ b/docs/reference/ds.forestplot.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -118,11 +118,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.gamlss.html b/docs/reference/ds.gamlss.html index 4e92d7c7f..62768da68 100644 --- a/docs/reference/ds.gamlss.html +++ b/docs/reference/ds.gamlss.html @@ -23,7 +23,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -215,11 +215,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.getWGSR.html b/docs/reference/ds.getWGSR.html index 9f647c02b..37e47fb79 100644 --- a/docs/reference/ds.getWGSR.html +++ b/docs/reference/ds.getWGSR.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -204,11 +204,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.glm.html b/docs/reference/ds.glm.html index 097d6a86c..7374ff1f2 100644 --- a/docs/reference/ds.glm.html +++ b/docs/reference/ds.glm.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -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. @@ -427,11 +427,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.glmPredict.html b/docs/reference/ds.glmPredict.html index 228bed889..099a2f76c 100644 --- a/docs/reference/ds.glmPredict.html +++ b/docs/reference/ds.glmPredict.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -227,11 +227,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.glmSLMA.html b/docs/reference/ds.glmSLMA.html index b429327a5..63feddf3d 100644 --- a/docs/reference/ds.glmSLMA.html +++ b/docs/reference/ds.glmSLMA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -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. @@ -493,11 +493,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.glmSummary.html b/docs/reference/ds.glmSummary.html index 327060d84..467d750a8 100644 --- a/docs/reference/ds.glmSummary.html +++ b/docs/reference/ds.glmSummary.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -154,11 +154,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.glmerSLMA.html b/docs/reference/ds.glmerSLMA.html index 8d8a3b6c5..c1c6f9ca9 100644 --- a/docs/reference/ds.glmerSLMA.html +++ b/docs/reference/ds.glmerSLMA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -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. @@ -379,11 +379,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.heatmapPlot.html b/docs/reference/ds.heatmapPlot.html index dd26dbd3f..61fc7624c 100644 --- a/docs/reference/ds.heatmapPlot.html +++ b/docs/reference/ds.heatmapPlot.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -199,11 +199,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.hetcor.html b/docs/reference/ds.hetcor.html index 5373fbaea..81d4bcd47 100644 --- a/docs/reference/ds.hetcor.html +++ b/docs/reference/ds.hetcor.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -124,11 +124,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.histogram.html b/docs/reference/ds.histogram.html index 777c42783..91e6268db 100644 --- a/docs/reference/ds.histogram.html +++ b/docs/reference/ds.histogram.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -190,11 +190,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.igb_standards.html b/docs/reference/ds.igb_standards.html index e59a54133..bf14f06e3 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 @@ -135,11 +135,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.isNA.html b/docs/reference/ds.isNA.html index 9f81d8063..7cc1b8f9a 100644 --- a/docs/reference/ds.isNA.html +++ b/docs/reference/ds.isNA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -131,11 +131,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.isValid.html b/docs/reference/ds.isValid.html index d34ddbd66..f491d8b89 100644 --- a/docs/reference/ds.isValid.html +++ b/docs/reference/ds.isValid.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -131,11 +131,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.kurtosis.html b/docs/reference/ds.kurtosis.html index 896113ff1..c42e001d7 100644 --- a/docs/reference/ds.kurtosis.html +++ b/docs/reference/ds.kurtosis.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -103,11 +103,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.length.html b/docs/reference/ds.length.html index fa6be2081..03f616933 100644 --- a/docs/reference/ds.length.html +++ b/docs/reference/ds.length.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -157,11 +157,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.levels.html b/docs/reference/ds.levels.html index d4eda89f0..6679271f9 100644 --- a/docs/reference/ds.levels.html +++ b/docs/reference/ds.levels.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -133,11 +133,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.lexis.html b/docs/reference/ds.lexis.html index 72b4fc787..35c03b5c3 100644 --- a/docs/reference/ds.lexis.html +++ b/docs/reference/ds.lexis.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -298,11 +298,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.list.html b/docs/reference/ds.list.html index 209dcb5b5..85fb1820b 100644 --- a/docs/reference/ds.list.html +++ b/docs/reference/ds.list.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -129,11 +129,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.listClientsideFunctions.html b/docs/reference/ds.listClientsideFunctions.html index 6f6570e6b..a28aeec06 100644 --- a/docs/reference/ds.listClientsideFunctions.html +++ b/docs/reference/ds.listClientsideFunctions.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -86,11 +86,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.listDisclosureSettings.html b/docs/reference/ds.listDisclosureSettings.html index 459697065..364d8890c 100644 --- a/docs/reference/ds.listDisclosureSettings.html +++ b/docs/reference/ds.listDisclosureSettings.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -162,11 +162,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.listOpals.html b/docs/reference/ds.listOpals.html index 5ab10679e..3f00c1d25 100644 --- a/docs/reference/ds.listOpals.html +++ b/docs/reference/ds.listOpals.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -80,11 +80,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.listServersideFunctions.html b/docs/reference/ds.listServersideFunctions.html index 757fbc036..aa0096749 100644 --- a/docs/reference/ds.listServersideFunctions.html +++ b/docs/reference/ds.listServersideFunctions.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -124,11 +124,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.lmerSLMA.html b/docs/reference/ds.lmerSLMA.html index efd0e6f9e..fd5f3682f 100644 --- a/docs/reference/ds.lmerSLMA.html +++ b/docs/reference/ds.lmerSLMA.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -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. @@ -328,11 +328,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.log.html b/docs/reference/ds.log.html index 30f10ae26..59dd2f799 100644 --- a/docs/reference/ds.log.html +++ b/docs/reference/ds.log.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -138,11 +138,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.look.html b/docs/reference/ds.look.html index ae0d0cc76..2c9c80b5c 100644 --- a/docs/reference/ds.look.html +++ b/docs/reference/ds.look.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -147,11 +147,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.ls.html b/docs/reference/ds.ls.html index e00868318..749fcb671 100644 --- a/docs/reference/ds.ls.html +++ b/docs/reference/ds.ls.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -198,11 +198,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.lspline.html b/docs/reference/ds.lspline.html index 188e46324..6aa7384d5 100644 --- a/docs/reference/ds.lspline.html +++ b/docs/reference/ds.lspline.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -116,11 +116,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.make.html b/docs/reference/ds.make.html index 7d4ae3e28..d6914e5ea 100644 --- a/docs/reference/ds.make.html +++ b/docs/reference/ds.make.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -201,11 +201,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.matrix.html b/docs/reference/ds.matrix.html index 0b7c0d61b..26ddf4f22 100644 --- a/docs/reference/ds.matrix.html +++ b/docs/reference/ds.matrix.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -246,11 +246,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.matrixDet.html b/docs/reference/ds.matrixDet.html index 8d94a581b..c8c19e2ee 100644 --- a/docs/reference/ds.matrixDet.html +++ b/docs/reference/ds.matrixDet.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -164,11 +164,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.matrixDet.report.html b/docs/reference/ds.matrixDet.report.html index f216c8517..e7e79f0f5 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 @@ -152,11 +152,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.matrixDiag.html b/docs/reference/ds.matrixDiag.html index 66e8c6c4c..df72afa91 100644 --- a/docs/reference/ds.matrixDiag.html +++ b/docs/reference/ds.matrixDiag.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -155,11 +155,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.matrixDimnames.html b/docs/reference/ds.matrixDimnames.html index 24230307d..5af5b7599 100644 --- a/docs/reference/ds.matrixDimnames.html +++ b/docs/reference/ds.matrixDimnames.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -170,11 +170,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.matrixInvert.html b/docs/reference/ds.matrixInvert.html index 07f7e00c4..91f588bd6 100644 --- a/docs/reference/ds.matrixInvert.html +++ b/docs/reference/ds.matrixInvert.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -157,11 +157,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.matrixMult.html b/docs/reference/ds.matrixMult.html index 55623b506..58b496541 100644 --- a/docs/reference/ds.matrixMult.html +++ b/docs/reference/ds.matrixMult.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -174,11 +174,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.matrixTranspose.html b/docs/reference/ds.matrixTranspose.html index 524e75313..298fb9935 100644 --- a/docs/reference/ds.matrixTranspose.html +++ b/docs/reference/ds.matrixTranspose.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -159,11 +159,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.mean.html b/docs/reference/ds.mean.html index 301e391e7..b9247e706 100644 --- a/docs/reference/ds.mean.html +++ b/docs/reference/ds.mean.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -185,11 +185,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.meanByClass.html b/docs/reference/ds.meanByClass.html index 8b081930b..60c915b08 100644 --- a/docs/reference/ds.meanByClass.html +++ b/docs/reference/ds.meanByClass.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -169,11 +169,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.meanSdGp.html b/docs/reference/ds.meanSdGp.html index 51702b221..f2eea8808 100644 --- a/docs/reference/ds.meanSdGp.html +++ b/docs/reference/ds.meanSdGp.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -214,11 +214,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.merge.html b/docs/reference/ds.merge.html index 877676384..1dfe61146 100644 --- a/docs/reference/ds.merge.html +++ b/docs/reference/ds.merge.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -232,11 +232,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.message.html b/docs/reference/ds.message.html index 7c94b88ef..1e4bc6709 100644 --- a/docs/reference/ds.message.html +++ b/docs/reference/ds.message.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -144,11 +144,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.metadata.html b/docs/reference/ds.metadata.html index 0d8070901..9be4695a7 100644 --- a/docs/reference/ds.metadata.html +++ b/docs/reference/ds.metadata.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -122,11 +122,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.mice.html b/docs/reference/ds.mice.html index 871cd3c20..20dfeb42e 100644 --- a/docs/reference/ds.mice.html +++ b/docs/reference/ds.mice.html @@ -25,7 +25,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -160,11 +160,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.names.html b/docs/reference/ds.names.html index 69c83c369..9e2b8756c 100644 --- a/docs/reference/ds.names.html +++ b/docs/reference/ds.names.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -142,11 +142,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.ns.html b/docs/reference/ds.ns.html index 4cb30d135..aadd01685 100644 --- a/docs/reference/ds.ns.html +++ b/docs/reference/ds.ns.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -129,11 +129,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.numNA.html b/docs/reference/ds.numNA.html index 2bb4270f1..1676928bb 100644 --- a/docs/reference/ds.numNA.html +++ b/docs/reference/ds.numNA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -127,11 +127,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.qlspline.html b/docs/reference/ds.qlspline.html index d1a702dda..5a131ae60 100644 --- a/docs/reference/ds.qlspline.html +++ b/docs/reference/ds.qlspline.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -128,11 +128,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.quantileMean.html b/docs/reference/ds.quantileMean.html index bcc80bc55..ef54c5e93 100644 --- a/docs/reference/ds.quantileMean.html +++ b/docs/reference/ds.quantileMean.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -146,11 +146,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.rBinom.html b/docs/reference/ds.rBinom.html index 63e174a89..207bc8ad4 100644 --- a/docs/reference/ds.rBinom.html +++ b/docs/reference/ds.rBinom.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -198,11 +198,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.rNorm.html b/docs/reference/ds.rNorm.html index 164ac7084..c547e5f10 100644 --- a/docs/reference/ds.rNorm.html +++ b/docs/reference/ds.rNorm.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -213,11 +213,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.rPois.html b/docs/reference/ds.rPois.html index aaacd484a..c670ad7bf 100644 --- a/docs/reference/ds.rPois.html +++ b/docs/reference/ds.rPois.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -188,11 +188,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.rUnif.html b/docs/reference/ds.rUnif.html index a9c582ced..9990bb91c 100644 --- a/docs/reference/ds.rUnif.html +++ b/docs/reference/ds.rUnif.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -219,11 +219,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.ranksSecure.html b/docs/reference/ds.ranksSecure.html index f29d764c9..a3115eaea 100644 --- a/docs/reference/ds.ranksSecure.html +++ b/docs/reference/ds.ranksSecure.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -278,11 +278,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.rbind.html b/docs/reference/ds.rbind.html index 30de91059..1af221f32 100644 --- a/docs/reference/ds.rbind.html +++ b/docs/reference/ds.rbind.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -171,11 +171,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.reShape.html b/docs/reference/ds.reShape.html index cbd97a295..0f9a83541 100644 --- a/docs/reference/ds.reShape.html +++ b/docs/reference/ds.reShape.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -194,11 +194,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.recodeLevels.html b/docs/reference/ds.recodeLevels.html index 008e50144..4f331bfed 100644 --- a/docs/reference/ds.recodeLevels.html +++ b/docs/reference/ds.recodeLevels.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -144,11 +144,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.recodeValues.html b/docs/reference/ds.recodeValues.html index 80bff4117..0c5023bce 100644 --- a/docs/reference/ds.recodeValues.html +++ b/docs/reference/ds.recodeValues.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -132,11 +132,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.rep.html b/docs/reference/ds.rep.html index 564136428..c469ef707 100644 --- a/docs/reference/ds.rep.html +++ b/docs/reference/ds.rep.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -206,11 +206,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.replaceNA.html b/docs/reference/ds.replaceNA.html index 144448a8e..b01dfb2db 100644 --- a/docs/reference/ds.replaceNA.html +++ b/docs/reference/ds.replaceNA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -170,11 +170,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.rm.html b/docs/reference/ds.rm.html index 47cbcb7a9..b344db54f 100644 --- a/docs/reference/ds.rm.html +++ b/docs/reference/ds.rm.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -140,11 +140,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.rowColCalc.html b/docs/reference/ds.rowColCalc.html index 595600728..2654f6432 100644 --- a/docs/reference/ds.rowColCalc.html +++ b/docs/reference/ds.rowColCalc.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -143,11 +143,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.sample.html b/docs/reference/ds.sample.html index 8ebc307c1..6a957360e 100644 --- a/docs/reference/ds.sample.html +++ b/docs/reference/ds.sample.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -234,11 +234,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.scatterPlot.html b/docs/reference/ds.scatterPlot.html index 5c792f451..d01dd6b96 100644 --- a/docs/reference/ds.scatterPlot.html +++ b/docs/reference/ds.scatterPlot.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -222,11 +222,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.seq.html b/docs/reference/ds.seq.html index 2235f6106..0d888dc03 100644 --- a/docs/reference/ds.seq.html +++ b/docs/reference/ds.seq.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -213,11 +213,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.setDefaultOpals.html b/docs/reference/ds.setDefaultOpals.html index 2753f52af..0dec6a327 100644 --- a/docs/reference/ds.setDefaultOpals.html +++ b/docs/reference/ds.setDefaultOpals.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -93,11 +93,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.setSeed.html b/docs/reference/ds.setSeed.html index f20baffa9..4e2e76404 100644 --- a/docs/reference/ds.setSeed.html +++ b/docs/reference/ds.setSeed.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -156,11 +156,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.skewness.html b/docs/reference/ds.skewness.html index 86ff4c8ca..e46e99f86 100644 --- a/docs/reference/ds.skewness.html +++ b/docs/reference/ds.skewness.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -154,11 +154,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.sqrt.html b/docs/reference/ds.sqrt.html index 46c711cb1..2ba54df03 100644 --- a/docs/reference/ds.sqrt.html +++ b/docs/reference/ds.sqrt.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -146,11 +146,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.subset.html b/docs/reference/ds.subset.html index 69240cf02..5eef31eb5 100644 --- a/docs/reference/ds.subset.html +++ b/docs/reference/ds.subset.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -180,11 +180,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.subsetByClass.html b/docs/reference/ds.subsetByClass.html index 8a8fad3bd..375848264 100644 --- a/docs/reference/ds.subsetByClass.html +++ b/docs/reference/ds.subsetByClass.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -142,11 +142,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.summary.html b/docs/reference/ds.summary.html index 309c6a0dd..a5585a615 100644 --- a/docs/reference/ds.summary.html +++ b/docs/reference/ds.summary.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -139,11 +139,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.table.html b/docs/reference/ds.table.html index 4c524ddda..c56501bff 100644 --- a/docs/reference/ds.table.html +++ b/docs/reference/ds.table.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -284,11 +284,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.table1D.html b/docs/reference/ds.table1D.html index cd8e6c28c..b4ce1e1c7 100644 --- a/docs/reference/ds.table1D.html +++ b/docs/reference/ds.table1D.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -160,11 +160,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.table2D.html b/docs/reference/ds.table2D.html index 962708391..7a9da43b8 100644 --- a/docs/reference/ds.table2D.html +++ b/docs/reference/ds.table2D.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -139,11 +139,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.tapply.assign.html b/docs/reference/ds.tapply.assign.html index c65eeacf4..8b4c14786 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 @@ -212,11 +212,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.tapply.html b/docs/reference/ds.tapply.html index d1d6d8d8c..6cff11737 100644 --- a/docs/reference/ds.tapply.html +++ b/docs/reference/ds.tapply.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -203,11 +203,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.testObjExists.html b/docs/reference/ds.testObjExists.html index 2dc6b97d5..e09821106 100644 --- a/docs/reference/ds.testObjExists.html +++ b/docs/reference/ds.testObjExists.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -131,11 +131,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.unList.html b/docs/reference/ds.unList.html index 1a0b9c559..74f4e795c 100644 --- a/docs/reference/ds.unList.html +++ b/docs/reference/ds.unList.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -149,11 +149,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.unique.html b/docs/reference/ds.unique.html index 5d1cd79b6..f78956888 100644 --- a/docs/reference/ds.unique.html +++ b/docs/reference/ds.unique.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -122,11 +122,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.var.html b/docs/reference/ds.var.html index 030dc4cd2..b690b6ef7 100644 --- a/docs/reference/ds.var.html +++ b/docs/reference/ds.var.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -153,11 +153,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.vectorCalc.html b/docs/reference/ds.vectorCalc.html index 43e81df9a..fb2642a3b 100644 --- a/docs/reference/ds.vectorCalc.html +++ b/docs/reference/ds.vectorCalc.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -120,11 +120,11 @@

Examples

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/extract.html b/docs/reference/extract.html index eacb3fcfc..64577154d 100644 --- a/docs/reference/extract.html +++ b/docs/reference/extract.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -72,11 +72,11 @@

Details

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/getPooledMean.html b/docs/reference/getPooledMean.html index 4986842d0..9cb08c8ad 100644 --- a/docs/reference/getPooledMean.html +++ b/docs/reference/getPooledMean.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -79,11 +79,11 @@

Details

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/getPooledVar.html b/docs/reference/getPooledVar.html index 0286fd8ed..741009762 100644 --- a/docs/reference/getPooledVar.html +++ b/docs/reference/getPooledVar.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -79,11 +79,11 @@

Details

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/glmChecks.html b/docs/reference/glmChecks.html index 5a944f9ef..d2873ca02 100644 --- a/docs/reference/glmChecks.html +++ b/docs/reference/glmChecks.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -100,11 +100,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/index.html b/docs/reference/index.html index 0ceeb7bf8..692761d7b 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -534,11 +534,11 @@

All functions
-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/isAssigned.html b/docs/reference/isAssigned.html index b3d66e75a..ad2d88ba7 100644 --- a/docs/reference/isAssigned.html +++ b/docs/reference/isAssigned.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -80,11 +80,11 @@

Details

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/isDefined.html b/docs/reference/isDefined.html index 54184020b..5a5a61453 100644 --- a/docs/reference/isDefined.html +++ b/docs/reference/isDefined.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -91,11 +91,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/logical2int.html b/docs/reference/logical2int.html index ac52dac10..cfd5fccfd 100644 --- a/docs/reference/logical2int.html +++ b/docs/reference/logical2int.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -74,11 +74,11 @@

Details

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/meanByClassHelper0a.html b/docs/reference/meanByClassHelper0a.html index 8d6cfebeb..bbb31b260 100644 --- a/docs/reference/meanByClassHelper0a.html +++ b/docs/reference/meanByClassHelper0a.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -93,11 +93,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/meanByClassHelper0b.html b/docs/reference/meanByClassHelper0b.html index f35054efb..b9b4a5ecb 100644 --- a/docs/reference/meanByClassHelper0b.html +++ b/docs/reference/meanByClassHelper0b.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -97,11 +97,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/meanByClassHelper1.html b/docs/reference/meanByClassHelper1.html index 810f46d76..c6ba0f25f 100644 --- a/docs/reference/meanByClassHelper1.html +++ b/docs/reference/meanByClassHelper1.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -90,11 +90,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/meanByClassHelper2.html b/docs/reference/meanByClassHelper2.html index 7540f66fc..526cb8dbc 100644 --- a/docs/reference/meanByClassHelper2.html +++ b/docs/reference/meanByClassHelper2.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -91,11 +91,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/meanByClassHelper3.html b/docs/reference/meanByClassHelper3.html index c5eb79f5a..b60233440 100644 --- a/docs/reference/meanByClassHelper3.html +++ b/docs/reference/meanByClassHelper3.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -90,11 +90,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/meanByClassHelper4.html b/docs/reference/meanByClassHelper4.html index ef479e862..90cb78b87 100644 --- a/docs/reference/meanByClassHelper4.html +++ b/docs/reference/meanByClassHelper4.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -100,11 +100,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/rowPercent.html b/docs/reference/rowPercent.html index da5df3fd6..f6a60e159 100644 --- a/docs/reference/rowPercent.html +++ b/docs/reference/rowPercent.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -76,11 +76,11 @@

Author

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/subsetHelper.html b/docs/reference/subsetHelper.html index 33f96c87d..740cb6d56 100644 --- a/docs/reference/subsetHelper.html +++ b/docs/reference/subsetHelper.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.2 @@ -131,11 +131,11 @@

Examples

diff --git a/dsBase_6.3.1-permissive.tar.gz b/dsBase_6.3.2-permissive.tar.gz similarity index 53% rename from dsBase_6.3.1-permissive.tar.gz rename to dsBase_6.3.2-permissive.tar.gz index 4acec10b7..0d70f01c6 100644 Binary files a/dsBase_6.3.1-permissive.tar.gz and b/dsBase_6.3.2-permissive.tar.gz differ diff --git a/dsBase_6.3.1.tar.gz b/dsBase_6.3.2.tar.gz similarity index 50% rename from dsBase_6.3.1.tar.gz rename to dsBase_6.3.2.tar.gz index 042b8a372..5d93ba950 100644 Binary files a/dsBase_6.3.1.tar.gz and b/dsBase_6.3.2.tar.gz differ diff --git a/man/ds.glm.Rd b/man/ds.glm.Rd index 4746ce2c7..67728e009 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 f2e7fdefb..f0a9863d4 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 19d5a55ad..8ad49c3ae 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 3ea75c10a..dbd9b7fbe 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/opal_azure-pipelines.yml b/opal_azure-pipelines.yml index 06fdade52..684052d9f 100644 --- a/opal_azure-pipelines.yml +++ b/opal_azure-pipelines.yml @@ -58,10 +58,10 @@ schedules: - master always: true - cron: "0 2 * * *" - displayName: Nightly build - v6.3.1-dev + displayName: Nightly build - v6.3.2-dev branches: include: - - v6.3.1-dev + - v6.3.2-dev always: true ######################################################################################### @@ -132,7 +132,7 @@ jobs: sudo apt-get upgrade -y sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y - sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev -y + sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table','panelaggregation'), dependencies=TRUE, repos='https://cloud.r-project.org')" @@ -186,7 +186,7 @@ jobs: # If this step fails still mark as failed, but don't stop the rest of the steps running. - bash: | - R -q -e "library('devtools'); devtools::check(args = c('--no-examples'))" | tee azure-pipelines_check.Rout + R -q -e "library('devtools'); devtools::check(args = c('--no-examples', '--no-tests'))" | tee azure-pipelines_check.Rout grep --quiet "^0 errors" azure-pipelines_check.Rout && grep --quiet " 0 warnings" azure-pipelines_check.Rout && grep --quiet " 0 notes" azure-pipelines_check.Rout workingDirectory: $(Pipeline.Workspace)/dsBaseClient @@ -235,7 +235,7 @@ jobs: - bash: | R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)" - R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.1'); opal.logout(opal)" + R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.2'); opal.logout(opal)" sleep 60 @@ -261,7 +261,7 @@ jobs: # best guess is that there is an implicit build or similar that happens. Although # I cannot replicate that directly with build etc directly. - sudo R --verbose -e 'devtools::check()' + sudo R --verbose -e 'devtools::reload()' mkdir $(Pipeline.Workspace)/logs @@ -379,9 +379,8 @@ jobs: - bash: | # See, 'Code coverage and JUnit report output' for issues with the approach and improvement needed. - sudo R --verbose -e 'devtools::check()' + sudo R --verbose -e 'devtools::reload()' - pwd mkdir $(Pipeline.Workspace)/logs # run the coverage tool and output to coveragelist.csv diff --git a/tests/docker/armadillo/standard/config/application.yml b/tests/docker/armadillo/standard/config/application.yml index c38ba2795..87e0fa1fb 100644 --- a/tests/docker/armadillo/standard/config/application.yml +++ b/tests/docker/armadillo/standard/config/application.yml @@ -14,11 +14,13 @@ armadillo: # oidc-admin-user: user@yourdomain.org profiles: - name: default - image: datashield/rock-knot-devel-permissive:latest + image: datashield/rock-lemon-donkey-permissive:latest port: 8085 host: default - package-whitelist: + package-whitelist: # Packages for 'donkey' - dsBase + - dsSurvival + - dsTidyverse - resourcer function-blacklist: [ ] options: diff --git a/tests/testthat.R b/tests/testthat.R new file mode 100644 index 000000000..3e6bbe151 --- /dev/null +++ b/tests/testthat.R @@ -0,0 +1,12 @@ +# This file is part of the standard setup for testthat. +# It is recommended that you do not modify it. +# +# Where should you do additional test configuration? +# Learn more about the roles of various files in: +# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview +# * https://testthat.r-lib.org/articles/special-files.html + +library(testthat) +library(dsBaseClient) + +test_check("dsBaseClient") diff --git a/tests/testthat/perf_files/armadillo_azure-pipeline.csv b/tests/testthat/perf_files/armadillo_azure-pipeline.csv index 5fd247c97..186e1d583 100644 --- a/tests/testthat/perf_files/armadillo_azure-pipeline.csv +++ b/tests/testthat/perf_files/armadillo_azure-pipeline.csv @@ -1,14 +1,14 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"conndisconn::perf::simple0","0.1050","0.5","2" -"ds.abs::perf::0","3.896","0.5","2" -"ds.asInteger::perf:0","3.550","0.5","2" -"ds.asList::perf:0","8.040","0.5","2" -"ds.asNumeric::perf:0","3.577","0.5","2" -"ds.assign::perf::0","6.739","0.5","2" -"ds.class::perf::combine:0","8.171","0.5","2" -"ds.colnames::perf:0","6.292","0.5","2" -"ds.exists::perf::combine:0","16.33","0.5","2" -"ds.length::perf::combine:0","16.08","0.5","2" -"ds.mean::perf::combine:0","16.08","0.5","2" -"ds.mean::perf::split:0","15.83","0.5","2" -"void::perf::void::0","36510.0","0.5","2" +"conndisconn::perf::simple0","0.1275","0.5","2" +"ds.abs::perf::0","4.824","0.5","2" +"ds.asInteger::perf:0","4.366","0.5","2" +"ds.asList::perf:0","9.787","0.5","2" +"ds.asNumeric::perf:0","4.316","0.5","2" +"ds.assign::perf::0","8.055","0.5","2" +"ds.class::perf::combine:0","9.847","0.5","2" +"ds.colnames::perf:0","7.574","0.5","2" +"ds.exists::perf::combine:0","19.84","0.5","2" +"ds.length::perf::combine:0","19.58","0.5","2" +"ds.mean::perf::combine:0","19.66","0.5","2" +"ds.mean::perf::split:0","19.21","0.5","2" +"void::perf::void::0","41810.0","0.5","2" diff --git a/tests/testthat/perf_files/default_perf_profile.csv b/tests/testthat/perf_files/default_perf_profile.csv index 9d5c755f1..cff242360 100644 --- a/tests/testthat/perf_files/default_perf_profile.csv +++ b/tests/testthat/perf_files/default_perf_profile.csv @@ -1,14 +1,14 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"conndisconn::perf::simple0","0.229","0.5","2" -"ds.abs::perf::0","1.796","0.5","2" -"ds.asInteger::perf:0","1.538","0.5","2" -"ds.asList::perf:0","3.061","0.5","2" -"ds.asNumeric::perf:0","1.548","0.5","2" -"ds.assign::perf::0","3.556","0.5","2" -"ds.class::perf::combine:0","3.149","0.5","2" -"ds.colnames::perf:0","2.584","0.5","2" -"ds.exists::perf::combine:0","7.138","0.5","2" -"ds.length::perf::combine:0","6.385","0.5","2" -"ds.mean::perf::combine:0","5.982","0.5","2" -"ds.mean::perf::split:0","6.923","0.5","2" -"void::perf::void::0","41810.0","0.5","2" +"conndisconn::perf::simple0","0.2118","0.5","2" +"ds.abs::perf::0","1.718","0.5","2" +"ds.asInteger::perf:0","1.484","0.5","2" +"ds.asList::perf:0","3.050","0.5","2" +"ds.asNumeric::perf:0","1.508","0.5","2" +"ds.assign::perf::0","3.547","0.5","2" +"ds.class::perf::combine:0","3.061","0.5","2" +"ds.colnames::perf:0","2.456","0.5","2" +"ds.exists::perf::combine:0","6.904","0.5","2" +"ds.length::perf::combine:0","6.058","0.5","2" +"ds.mean::perf::combine:0","5.892","0.5","2" +"ds.mean::perf::split:0","6.881","0.5","2" +"void::perf::void::0","27070.0","0.5","2" diff --git a/tests/testthat/perf_files/dslite_hp-laptop_quay.csv b/tests/testthat/perf_files/dslite_hp-laptop_quay.csv new file mode 100644 index 000000000..5d552ae05 --- /dev/null +++ b/tests/testthat/perf_files/dslite_hp-laptop_quay.csv @@ -0,0 +1,14 @@ +"refer_name","rate","lower_tolerance","upper_tolerance" +"conndisconn::perf::simple0","1.28701068653782","0.5","2" +"ds.abs::perf::0","9.58736733800142","0.5","2" +"ds.asInteger::perf:0","8.50891366904172","0.5","2" +"ds.asList::perf:0","16.5820946915488","0.5","2" +"ds.asNumeric::perf:0","9.11018116242571","0.5","2" +"ds.assign::perf::0","20.7627800741047","0.5","2" +"ds.class::perf::combine:0","16.4968034024194","0.5","2" +"ds.colnames::perf:0","12.2919611789594","0.5","2" +"ds.exists::perf::combine:0","41.3622556042039","0.5","2" +"ds.length::perf::combine:0","41.0818690662793","0.5","2" +"ds.mean::perf::combine:0","40.9888639028757","0.5","2" +"ds.mean::perf::split:0","41.2851424288384","0.5","2" +"void::perf::void::0","24346.5613457168","0.5","2" diff --git a/tests/testthat/perf_files/opal_azure-pipeline.csv b/tests/testthat/perf_files/opal_azure-pipeline.csv index 9d5c755f1..cff242360 100644 --- a/tests/testthat/perf_files/opal_azure-pipeline.csv +++ b/tests/testthat/perf_files/opal_azure-pipeline.csv @@ -1,14 +1,14 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"conndisconn::perf::simple0","0.229","0.5","2" -"ds.abs::perf::0","1.796","0.5","2" -"ds.asInteger::perf:0","1.538","0.5","2" -"ds.asList::perf:0","3.061","0.5","2" -"ds.asNumeric::perf:0","1.548","0.5","2" -"ds.assign::perf::0","3.556","0.5","2" -"ds.class::perf::combine:0","3.149","0.5","2" -"ds.colnames::perf:0","2.584","0.5","2" -"ds.exists::perf::combine:0","7.138","0.5","2" -"ds.length::perf::combine:0","6.385","0.5","2" -"ds.mean::perf::combine:0","5.982","0.5","2" -"ds.mean::perf::split:0","6.923","0.5","2" -"void::perf::void::0","41810.0","0.5","2" +"conndisconn::perf::simple0","0.2118","0.5","2" +"ds.abs::perf::0","1.718","0.5","2" +"ds.asInteger::perf:0","1.484","0.5","2" +"ds.asList::perf:0","3.050","0.5","2" +"ds.asNumeric::perf:0","1.508","0.5","2" +"ds.assign::perf::0","3.547","0.5","2" +"ds.class::perf::combine:0","3.061","0.5","2" +"ds.colnames::perf:0","2.456","0.5","2" +"ds.exists::perf::combine:0","6.904","0.5","2" +"ds.length::perf::combine:0","6.058","0.5","2" +"ds.mean::perf::combine:0","5.892","0.5","2" +"ds.mean::perf::split:0","6.881","0.5","2" +"void::perf::void::0","27070.0","0.5","2" diff --git a/tests/testthat/perf_files/opal_hp-laptop_quay.csv b/tests/testthat/perf_files/opal_hp-laptop_quay.csv index da068a01d..a6e5e655a 100644 --- a/tests/testthat/perf_files/opal_hp-laptop_quay.csv +++ b/tests/testthat/perf_files/opal_hp-laptop_quay.csv @@ -1,14 +1,14 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"conndisconn::perf::simple0","0.145258829974366","0.5","2" -"ds.abs::perf::0","0.685354162883962","0.5","2" -"ds.asInteger::perf:0","0.757343916339244","0.5","2" -"ds.asList::perf:0","1.39411478465579","0.5","2" -"ds.asNumeric::perf:0","0.695929483688074","0.5","2" -"ds.assign::perf::0","1.98579096107968","0.5","2" -"ds.class::perf::combine:0","1.83959664387857","0.5","2" -"ds.colnames::perf:0","1.38390626627527","0.5","2" -"ds.exists::perf::combine:0","4.37111331491725","0.5","2" -"ds.length::perf::combine:0","2.99769707214692","0.5","2" -"ds.mean::perf::combine:0","3.14458208946095","0.5","2" -"ds.mean::perf::split:0","4.258064355457","0.5","2" -"void::perf::void::0","20588.7831697084","0.5","2" +"conndisconn::perf::simple0","0.163258942292474","0.5","2" +"ds.abs::perf::0","0.855013692368105","0.5","2" +"ds.asInteger::perf:0","0.788986058823576","0.5","2" +"ds.asList::perf:0","1.77505549252221","0.5","2" +"ds.asNumeric::perf:0","0.877591207737289","0.5","2" +"ds.assign::perf::0","2.08707546713196","0.5","2" +"ds.class::perf::combine:0","1.65635603819885","0.5","2" +"ds.colnames::perf:0","1.33221754701434","0.5","2" +"ds.exists::perf::combine:0","4.18346517297051","0.5","2" +"ds.length::perf::combine:0","3.45700158311582","0.5","2" +"ds.mean::perf::combine:0","3.36796688580702","0.5","2" +"ds.mean::perf::split:0","4.11472547478384","0.5","2" +"void::perf::void::0","23198.7075219865","0.5","2" diff --git a/tests/testthat/perf_files/template_perf_profile.csv b/tests/testthat/perf_files/template_perf_profile.csv new file mode 100644 index 000000000..c01b6fec1 --- /dev/null +++ b/tests/testthat/perf_files/template_perf_profile.csv @@ -0,0 +1 @@ +"refer_name","rate","lower_tolerance","upper_tolerance" diff --git a/tests/testthat/perf_tests/perf_rate.R b/tests/testthat/perf_tests/perf_rate.R index 1884cda89..0384bf637 100644 --- a/tests/testthat/perf_tests/perf_rate.R +++ b/tests/testthat/perf_tests/perf_rate.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2024-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -47,4 +47,3 @@ perf.reference.tolerance.upper <- function(perf.ref.name) { return(as.numeric(.perf.reference[which(.perf.reference$refer_name == perf.ref.name),]$upper_tolerance)) } -