manually merge develop -> time_varying

.github/workflows/R_CMD_check_Hades.yaml

@@ -20,12 +20,12 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: 'release'}  # Does not appear to have Java 32-bit, hence the --no-multiarch
+          - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
           - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-#          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:
+      GITHUB_PAT: ${{ secrets.GH_TOKEN }}
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM_SCHEMA }}
@@ -43,75 +43,51 @@ jobs:
       CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }}
       CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }}
       CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }}
+      CDM5_REDSHIFT_CDM_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM_SCHEMA }}
+      CDM5_REDSHIFT_OHDSI_SCHEMA: ${{ secrets.CDM5_REDSHIFT_OHDSI_SCHEMA }}
+      CDM5_REDSHIFT_PASSWORD: ${{ secrets.CDM5_REDSHIFT_PASSWORD }}
+      CDM5_REDSHIFT_SERVER: ${{ secrets.CDM5_REDSHIFT_SERVER }}
+      CDM5_REDSHIFT_USER: ${{ secrets.CDM5_REDSHIFT_USER }}
+      CDM5_SPARK_USER: ${{ secrets.CDM5_SPARK_USER }}
+      CDM5_SPARK_PASSWORD: ${{ secrets.CDM5_SPARK_PASSWORD }}
+      CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }}
+      WEBAPI_TEST_WEBAPI_URL: ${{ secrets.WEBAPI_TEST_WEBAPI_URL }}
+      WEBAPI_TEST_SECURE_WEBAPI_URL: ${{ secrets.WEBAPI_TEST_SECURE_WEBAPI_URL }}
+      WEBAPI_TEST_ADMIN_USER_NAME: ${{ secrets.WEBAPI_TEST_ADMIN_USER_NAME }}
+      WEBAPI_TEST_ADMIN_USER_PASSWORD: ${{ secrets.WEBAPI_TEST_ADMIN_USER_PASSWORD }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-tinytex@v1
+      - uses: r-lib/actions/setup-tinytex@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
+      - name: Install system requirements
         if: runner.os == 'Linux'
         run: |
+          sudo apt-get install -y libssh-dev
+          Rscript -e 'install.packages("remotes")'
           while read -r cmd
           do
             eval sudo $cmd
           done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
 
-      - name: Install libssh
-        if: runner.os == 'Linux'
-        run: |
-          sudo apt-get install libssh-dev
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE, INSTALL_opts=c("--no-multiarch"))
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Install covr
-        if: runner.os == 'macOS'
-        run: |
-          remotes::install_cran("covr")
-        shell: Rscript {0}
-
-      - name: Remove check folder if exists
-        if: runner.os == 'macOS'
-        run: unlink("check", recursive = TRUE)
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-multiarch"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@v2
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          args: 'c("--no-manual", "--as-cran")'
+          build_args: 'c("--compact-vignettes=both")'
+          error-on: '"warning"'
+          check-dir: '"check"'
 
       - name: Upload source package
         if: success() && runner.os == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/main'
@@ -120,6 +96,12 @@ jobs:
           name: package_tarball
           path: check/*.tar.gz
 
+      - name: Install covr
+        if: runner.os == 'macOS'
+        run: |
+          install.packages("covr")
+        shell: Rscript {0}
+
       - name: Test coverage
         if: runner.os == 'macOS'
         run: covr::codecov()
@@ -137,7 +119,7 @@ jobs:
 
     steps:
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
@@ -163,7 +145,7 @@ jobs:
           draft: false
           prerelease: false
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         if: ${{ env.new_version != '' }}
 
       - name: Install drat
@@ -192,3 +174,4 @@ jobs:
         if: ${{ env.new_version != '' }}
         run: |
           curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/broadsea-methodslibrary/trigger/f0b51cec-4027-4781-9383-4b38b42dd4f5/
+

Cyclops.Rproj

@@ -1,7 +1,7 @@
 Version: 1.0
 
-RestoreWorkspace: Default
-SaveWorkspace: Default
+RestoreWorkspace: No
+SaveWorkspace: No
 AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Cyclops
 Type: Package
 Title: Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis
-Version: 3.3.1.99
+Version: 3.3.1.999
 Authors@R: c(
     person("Marc A.", "Suchard", email = "[email protected]", role = c("aut","cre")),
     person("Martijn J.", "Schuemie", role = "aut"),
@@ -30,7 +30,7 @@ Biarch: true
 URL: https://github.com/ohdsi/cyclops
 BugReports: https://github.com/ohdsi/cyclops/issues
 Depends:
-    R (>= 3.1.0)
+    R (>= 3.5.0)
 Imports:
     rlang,
     Matrix,
@@ -41,7 +41,6 @@ Imports:
     survival,
     bit64
 LinkingTo: Rcpp,
-    BH (>= 1.51.0),
     RcppEigen (>= 0.3.2),
     RcppParallel
 Suggests:

NEWS.md

@@ -1,19 +1,22 @@
-develop
+Cyclops v3.4.0
 ==============
 
 Changes:
 
-1. improvements on adaptive likelihood profiling
-2. add `auto` option to `cvRepetitions`
-3. bumped explicit C++11 requirement up to R v4.1
+1. remove dependence on `BH`
+2. improvements on adaptive likelihood profiling
+3. add `auto` option to `cvRepetitions`
+4. bumped explicit C++11 requirement up to R v4.1
+5. removed deprecated use of `dbplyr:::$.tbl_lazy`
+   a. breaking change in `dbplyr v2.4.0`
 
 Cyclops v3.3.1
 ==============
 
 Changes:
 
-1. fix uninitialized value in detected in computeAsymptoticPrecisionMatrix(); value was priorType
-2. fix memory leak caused by call to ::Rf_error()
+1. fix uninitialized value in detected in `computeAsymptoticPrecisionMatrix()`; value was priorType
+2. fix memory leak caused by call to `::Rf_error()`
 3. fix line-endings on Makevar on windows
 
 Cyclops v3.3.0

R/DataManagement.R

@@ -634,8 +634,8 @@ reduce <- function(object, covariates, groupBy, power = 1) {
 #' \code{appendSqlCyclopsData} appends data to an OHDSI data object.
 #'
 #' @details Append data using two tables.  The outcomes table is dense and contains ...  The covariates table is sparse and contains ...
-#' All entries in the outcome table must be sorted in increasing order by {oStratumId, oRowId}.  All entries in the covariate table
-#' must be sorted in increasing order by {cRowId}. Each cRowId value must match exactly one oRowId value.
+#' All entries in the outcome table must be sorted in increasing order by (oStratumId, oRowId).  All entries in the covariate table
+#' must be sorted in increasing order by (cRowId). Each cRowId value must match exactly one oRowId value.
 #'
 #' @param object    OHDSI Cyclops data object to append entries
 #' @param oStratumId    Integer vector (optional): non-unique stratum identifier for each row in outcomes table

R/NewDataConversion.R

@@ -323,7 +323,7 @@ convertToCyclopsData.tbl_dbi <- function(outcomes,
     }
 
     if (modelType == "pr" | modelType == "cpr") {
-        if (any((select(outcomes, time) %>% pull()) <= 0)) {
+        if (any(pull(outcomes, .data$time) <= 0)) {
             stop("time cannot be non-positive", call. = FALSE)
         }
     }

R/TimeEffects.R

@@ -22,8 +22,8 @@ splitTime <- function(shortOut, cut) {
     if (!"y" %in% colnames(shortOut)) stop("Must provide observed event status.")
     if ("rowId" %in% colnames(shortOut)) {
         shortOut <- shortOut %>%
-            rename(subjectId = rowId) %>%
-            arrange(subjectId)
+            rename(subjectId = .data$rowId) %>%
+            arrange(.data$subjectId)
     } else {
         shortOut <- shortOut %>%
             mutate(subjectId = row_number())
@@ -36,10 +36,10 @@ splitTime <- function(shortOut, cut) {
                                          episode = "stratumId",
                                          id = "newSubjectId"))
     longOut <- longOut %>%
-        rename(y = event) %>%
-        mutate(time = tstop - tstart) %>%
-        select(-c(newSubjectId, tstart, tstop)) %>%
-        arrange(stratumId, subjectId)
+        rename(y = .data$event) %>%
+        mutate(time = .data$tstop - .data$tstart) %>%
+        select(-c(.data$newSubjectId, .data$tstart, .data$tstop)) %>%
+        arrange(.data$stratumId, .data$subjectId)
 
     # Restore rowIds
     SubjectIds <- shortOut$subjectId
@@ -49,9 +49,10 @@ splitTime <- function(shortOut, cut) {
 
     # Reorder columns
     longOut <- longOut %>%
-        select(rowId, everything()) %>%
-        select(subjectId, everything()) %>%
-        select(stratumId, everything())
+        select(.data$stratumId, .data$subjectId, .data$rowId, everything())
+        # select(.data$rowId, everything()) %>%
+        # select(.data$subjectId, everything()) %>%
+        # select(.data$stratumId, everything())
 
     return(longOut)
 }

src/cyclops/CcdInterface.cpp

@@ -29,7 +29,7 @@
 #include "CyclicCoordinateDescent.h"
 #include "ModelData.h"
 
-#include "boost/iterator/counting_iterator.hpp"
+//#include "boost/iterator/counting_iterator.hpp"
 #include "Thread.h"
 
 // #include "io/InputReader.h"
@@ -373,9 +373,9 @@ double CcdInterface::profileModel(CyclicCoordinateDescent *ccd, AbstractModelDat
                       }
                     );
     } else {
-        auto scheduler = TaskScheduler<boost::counting_iterator<int> >(
-            boost::make_counting_iterator(0),
-            boost::make_counting_iterator(static_cast<int>(bounds.size())),
+        auto scheduler = TaskScheduler<IncrementableIterator<size_t>>(
+            IncrementableIterator<size_t>(0), // boost::make_counting_iterator(0),
+            IncrementableIterator<size_t>(bounds.size()), //boost::make_counting_iterator(static_cast<int>(bounds.size())),
             nThreads);
 
         auto oneTask = [&getBound, &scheduler, &ccdPool, &bounds](unsigned long task) {
@@ -587,8 +587,10 @@ double CcdInterface::evaluateProfileModel(CyclicCoordinateDescent *ccd, Abstract
             values[i] = evaluate(points[i], ccd);
         }
     } else {
-        auto scheduler = TaskScheduler<boost::counting_iterator<int>>(
-            boost::make_counting_iterator(0), boost::make_counting_iterator(static_cast<int>(points.size())), nThreads);
+        auto scheduler = TaskScheduler<IncrementableIterator<size_t>>(
+            IncrementableIterator<size_t>(0), //boost::make_counting_iterator(0),
+            IncrementableIterator<size_t>(points.size()), //boost::make_counting_iterator(static_cast<int>(points.size())),
+            nThreads);
 
         auto oneTask = [&evaluate, &scheduler, &ccdPool, &points, &values](unsigned long task) {
             values[task] = evaluate(points[task], ccdPool[scheduler.getThreadIndex(task)]);

src/cyclops/CyclicCoordinateDescent.cpp

@@ -208,12 +208,12 @@ void CyclicCoordinateDescent::init(bool offset) {
 
 	// initialize starting betas to default value 0.0
 	startingBeta.resize(J, static_cast<double>(0.0));
-	
+
 // 	hXBeta.resize(K, static_cast<double>(0.0));
 // 	hXBetaSave.resize(K, static_cast<double>(0.0));
 
 	fixBeta.resize(J, false);
-	
+
 	hWeights.resize(0);
     cWeights.resize(0); // ESK: For censor weights
 
@@ -757,7 +757,7 @@ void CyclicCoordinateDescent::kktSwindle(const ModeFindingArguments& arguments)
 	int swindleIterationCount = 1;
 
 //	int initialActiveSize = activeSet.size();
-	int perPassSize = arguments.swindleMultipler;
+	// int perPassSize = arguments.swindleMultipler;
 
 	while (!done) {
 
@@ -885,7 +885,7 @@ void CyclicCoordinateDescent::kktSwindle(const ModeFindingArguments& arguments)
 			}
 		}
 		++swindleIterationCount;
-		perPassSize *= 2;
+		// perPassSize *= 2;
 
 		logger->yield();			// This is not re-entrant safe
 	}