Merge pull request #99 from ramses-antibiotics/develop

Merge Ramses v0.5.0

.Rbuildignore

@@ -9,7 +9,7 @@
 ^\.idea
 ^_pkgdown\.yml$
 ^pkgdown$
-^.*\.sqlite$
+^.*\.duckdb$
 ^travis$
 ^vignettes/Mechanics-of-entities\.Rmd$
 ^vignettes/.*\.R$

.github/workflows/R-CMD-check.yaml

@@ -5,10 +5,6 @@ on:
       - develop
       - 'feature/**'
       - 'bug_fix/**'
-  pull_request:
-    branches:
-      - master
-      - develop
 
 name: R-CMD-check
 
@@ -50,11 +46,11 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - 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-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -86,23 +82,12 @@ jobs:
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
 
-      # - name: Unit tests
-      #   run: devtools::test()
-      #   shell: Rscript {0}
-
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
         run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
-      # - name: Upload check results
-      #   if: failure()
-      #   uses: actions/upload-artifact@main
-      #   with:
-      #     name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-      #     path: check
-
       - name: Code coverage
         if: github.ref == 'refs/heads/master' && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' &&  matrix.config.r == 'release'
         run: covr::codecov(type = "all", quiet = FALSE, token = Sys.getenv("CODECOVETOKEN"))
@@ -121,3 +106,30 @@ jobs:
         env:
           PROJECT_ID: ramses-antibiotics
           FIREBASE_TOKEN: ${{ secrets.FIREBASE_TOKEN }}
+
+      - uses: r-lib/actions/setup-tinytex@v2
+        if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' &&  matrix.config.r == 'release'
+
+      - name: Install TeX
+        run: tlmgr --version
+        if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' &&  matrix.config.r == 'release'
+
+      - name: Build source and PDF manual
+        if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' &&  matrix.config.r == 'release'
+        run: |
+          devtools::install()
+          devtools::build(".", vignettes = TRUE, path = "~")
+          devtools::build_manual(".", path = "~")
+        shell: Rscript {0}
+
+      - uses: actions/upload-artifact@v3
+        if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' &&  matrix.config.r == 'release'
+        with:
+          name: Ramses package source
+          path: ~/Ramses_[0-9].[0-9].[0-9].tar.gz
+
+      - uses: actions/upload-artifact@v3
+        if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' &&  matrix.config.r == 'release'
+        with:
+          name: Ramses package manual
+          path: ~/Ramses_[0-9].[0-9].[0-9].pdf

.gitignore

@@ -5,6 +5,6 @@
 doc
 Meta
 .idea
-*.sqlite
+*.duckdb
 inst/doc
 docs

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Ramses
 Type: Package
 Title: R Package for Antimicrobial Stewardship & Surveillance 
-Version: 0.4.4
+Version: 0.5.0
 Authors@R: c(
     person(given = "Peter",
            family = "Dutey-Magni",
@@ -14,24 +14,26 @@ Authors@R: c(
            email = "l.shallcross@ucl.ac.uk",
            comment = c(ORCID = "0000-0003-1713-2555")),
     person("University College London", role = c("cph")))
-Description: A one-stop shop for antimicrobial stewardship data warehousing for hospitals. 
-    Ramses supports the modelling and analysis of hospital electronic health records 
-    (episodes of care, drug prescriptions and administrations, microbiology and 
-    investigations results) to help keep antibiotics working for years to come.
+Description: A package for data-driven hospital antimicrobial stewardship and 
+    infection surveillance. Ramses supports the validation and analysis of 
+    routine electronic health records (episodes of care, drug prescriptions and
+    administrations, microbiology and investigations results) to help monitor
+    prescribing and keep antibiotics working for years to come.
 License: GPL-3
 URL: https://github.com/ramses-antibiotics/ramses-package
 BugReports: https://github.com/ramses-antibiotics/ramses-package/issues
 Encoding: UTF-8
 LazyData: true
 Depends: 
-    R (>= 3.2.0),
+    R (>= 3.6.0),
     AMR (>= 1.8.0)
 Imports: 
-    RSQLite (>= 2.1.4),
     DBI,
+    rlang,
     dplyr (>= 1.0.1),
-    dbplyr (>= 2.1.0),
+    dbplyr (>= 2.2.0),
     magrittr,
+    duckdb (>= 0.4.0),
     Rdpack (>= 0.7),
     data.table,
     units (>= 0.7-0),
@@ -55,13 +57,15 @@ Suggests:
     pkgdown (>= 2.0.0),
     R.utils,
     comorbidity,
-    RPostgres
+    RPostgres,
+    gh (>= 1.3.0)
 Remotes: 
     ramses-antibiotics/snomedizer
 RdMacros: Rdpack    
 RoxygenNote: 7.2.0
 VignetteBuilder: knitr,rmarkdown
 Collate: 
+    'Ramses-deprecated.R'
     'Ramses-package.R'
     'objects.R'
     'clinical_features.R'

NAMESPACE

@@ -1,10 +1,14 @@
 # Generated by roxygen2: do not edit by hand
 
+export(Encounter)
 export(MedicationRequest)
 export(Patient)
+export(Patient.DBIConnection)
+export(Patient.RamsesObject)
 export(TherapyEpisode)
 export(TherapyEpisode.DBIConnection)
-export(TherapyEpisode.RamsesObject)
+export(TherapyEpisode.MedicationRequest)
+export(bridge_encounter_therapy_overlap)
 export(bridge_episode_prescription_initiation)
 export(bridge_episode_prescription_overlap)
 export(bridge_spell_therapy_overlap)
@@ -13,7 +17,8 @@ export(clinical_feature_interval)
 export(clinical_feature_last)
 export(clinical_feature_mean)
 export(clinical_feature_ols_trend)
-export(collect_ramses_tbl)
+export(collect)
+export(compute)
 export(compute_DDDs)
 export(connect_local_database)
 export(create_mock_database)
@@ -26,6 +31,7 @@ export(load_inpatient_episodes)
 export(load_inpatient_investigations)
 export(load_inpatient_microbiology)
 export(load_medications)
+export(longitudinal_table)
 export(map_ICD10_CCS)
 export(map_ICD10_CCSR)
 export(map_charlson_comorbidities)
@@ -40,6 +46,7 @@ export(validate_inpatient_episodes)
 export(validate_investigations)
 export(validate_microbiology)
 export(validate_prescriptions)
+exportClasses(Encounter)
 exportClasses(MedicationRequest)
 exportClasses(Patient)
 exportClasses(RamsesObject)
@@ -48,20 +55,22 @@ exportMethods(clinical_feature_interval)
 exportMethods(clinical_feature_last)
 exportMethods(clinical_feature_mean)
 exportMethods(clinical_feature_ols_trend)
-exportMethods(therapy_table)
+exportMethods(collect)
+exportMethods(compute)
+exportMethods(longitudinal_table)
+exportMethods(show)
 exportMethods(therapy_timeline)
-import(methods)
-importClassesFrom(RSQLite,SQLiteConnection)
+importClassesFrom(duckdb,duckdb_connection)
 importFrom(AMR,ab_atc)
-importFrom(DBI,dbConnect)
-importFrom(DBI,dbDisconnect)
 importFrom(Rdpack,reprompt)
 importFrom(data.table,":=")
 importFrom(data.table,data.table)
-importFrom(dbplyr,sql)
 importFrom(dplyr,collect)
 importFrom(dplyr,compute)
 importFrom(dplyr,tbl)
 importFrom(magrittr,"%>%")
+importFrom(methods,is)
+importFrom(methods,show)
+importFrom(rlang,.data)
 importFrom(stats,na.omit)
 importFrom(units,set_units)

NEWS.md

@@ -1,4 +1,37 @@
 
+# Ramses 0.5.0
+
+*27 August 2022*
+
+## Improvements
+
+* Local databases (`connect_local_database()` and `create_mock_database()`) 
+are now powered by [DuckDB](https://duckdb.org/) rather than SQLite, bringing support for 
+datetime variable types and increased performance. Ramses now depends on 
+the [`duckdb`](https://CRAN.R-project.org/package=duckdb) library
+* Added new S4 class `Encounter` [#92](https://github.com/ramses-antibiotics/ramses-package/issues/92) 
+to manipulate hospitalisations (admissions)
+with associated methods for `show()`, `compute()`, `collect()`, `Patient()`, 
+`longitudinal_table()`, `clinical_feature_*()`, `therapy_timeline()`
+* `TherapyEpisode()` and `Encounter()` have a new optional `extend_table_start` input
+controlling their longitudinal table's start. This allows the creation of longitudinal
+tables starting before the `therapy_start` or `admission_date`, respectively. More
+detail is available from [`vignette("therapy-episodes")`](https://ramses-antibiotics.web.app/articles/therapy-episodes.html)
+* Added `Patient()` function to create a `Patient` object from any other object
+of class `RamsesObject`
+* Improved documentation and export of S4 methods `compute()` and `collect()`.
+
+## Breaking changes
+
+* `therapy_table()` is now deprecated: use `longitudinal_table()` instead  [#86](https://github.com/ramses-antibiotics/ramses-package/issues/86)
+* `bridge_spell_therapy_overlap()` is now deprecated : use 
+`bridge_encounter_therapy_overlap()` instead  [#86](https://github.com/ramses-antibiotics/ramses-package/issues/86)
+* Database table `inpatient_episodes` and documentation now refer to 'encounters' 
+rather than 'spells'. Variable `spell_id` is now known as `encounter_id` [#86](https://github.com/ramses-antibiotics/ramses-package/issues/86).
+Databases built with previous versions of Ramses will not work with Ramses 0.5.0
+* Function signatures for all methods are standardised: function arguments 
+`object` are now changed to `x`, except for `show(object)`.
+* Support for SQLite databases is withdrawn.
 
 # Ramses 0.4.4
 
@@ -9,6 +42,7 @@
 * `clinical_feature_*()` functions trigger a warning rather than an error if
 no value matching `observation_code` is found in the`inpatient_investigations` table.
 
+
 # Ramses 0.4.3
 
 *2 August 2022*

R/Ramses-deprecated.R

@@ -0,0 +1,56 @@
+
+
+#' Deprecated functions in package \pkg{Ramses}.
+#' 
+#' @description The functions listed below are deprecated and will be defunct in
+#'   the near future. When possible, alternative functions with similar
+#'   functionality are also mentioned. Help pages for deprecated functions are
+#'   available at \code{help("<function>-deprecated")}.
+#'  \itemize{
+#'    \item{\code{\link[Ramses]{therapy_table}()} is now known as
+#'     \code{\link[Ramses]{longitudinal_table}()}}
+#'  }
+#' @name Ramses-deprecated
+#' @keywords internal
+NULL
+
+
+#' Get the therapy table (DEPRECATED)
+#'
+#' @param object an object of class \code{TherapyEpisode}
+#' @param collect if \code{TRUE}, collect the remote \code{tbl_sql} and return a local 
+#' \code{tbl_df}. The default is \code{FALSE}, and simply returns the remote \code{tbl_sql}
+#' @return an object of class \code{tbl}
+#' @rdname therapy_table-deprecated
+#' @description This function is now deprecated. Please use
+#'  \code{\link{longitudinal_table}()}.
+#' @seealso \code{\link{Ramses-deprecated}}
+#' @export
+therapy_table <- function(object, collect = FALSE) {
+  .Deprecated("longitudinal_table")
+  longitudinal_table(
+    x = object, 
+    collect = collect
+  )
+}
+
+
+#' Create database bridge tables
+#'
+#' @param conn a database connection
+#' @param overwrite if \code{TRUE}, will overwrite any existing
+#' database table. The default is \code{FALSE}
+#' @rdname bridge_spell_therapy_overlap-deprecated
+#' @description This function is now deprecated. Please use
+#'  \code{\link{bridge_encounter_therapy_overlap}()}.
+#' @seealso \code{\link{bridge_tables}}, \code{\link{Ramses-deprecated}}
+#' @export
+bridge_spell_therapy_overlap <- function(conn, 
+                                         overwrite = FALSE) {
+  .Deprecated("bridge_encounter_therapy_overlap")
+  bridge_encounter_therapy_overlap(
+    conn = conn, 
+    overwrite = overwrite
+  )
+}
+