Enhance dataset splitting functions, add new mortality prediction tas…

.Rbuildignore

@@ -1,17 +1,21 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^\.git$
-^\.gitignore$
-^\.gitattributes$
+^\.Rhistory$
+^\.RData$
+^\.RDataTmp$
+^output$
+^\.renv$
 ^renv$
 ^renv\.lock$
+# Ignore vignettes and tests for CRAN
+#^vignettes$
+#^tests$
 ^01dev_config.R$
 ^02document_genera.R$
 ^README\.Rmd$
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
-# 你特定的Demo文件
 ^RHealth---medcode Module Demo\.html$
 ^RHealth---medcode Module Demo\.qmd$
 ^LICENSE\.md$

DESCRIPTION

@@ -1,8 +1,13 @@
 Package: RHealth
 Type: Package
 Title: A Deep Learning Toolkit for Healthcare Predictive Modeling
-Version: 0.1.0
+Version: 0.2.0
 Authors@R: c(
+    person(
+      "Junyi", "Gao",
+      email = "junyii.gao@gmail.com",
+      role = c("aut", "cre")
+    ),
     person(
       "Ji", "Song",
       email = "eaad0907@163.com",
@@ -42,31 +47,18 @@ Authors@R: c(
       "Ewen", "Harrison",
       email = "ewen.harrison@ed.ac.uk",
       role = c("aut")
-    ),
-    person(
-      "Junyi", "Gao",
-      email = "junyii.gao@gmail.com",
-      role = c("aut", "cre")
     )
   )
 Description: RHealth is an open-source R package specifically designed to bring comprehensive deep learning toolkits to the R community for healthcare predictive modeling.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-URL: https://v1xerunt.github.io/dev/RHealth, https://github.com/v1xerunt/RHealth
+URL: https://v1xerunt.github.io/RHealth/dev, https://github.com/v1xerunt/RHealth
 BugReports: https://github.com/v1xerunt/RHealth/issues
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 Depends: R (>= 4.1.0)
-Suggests:
-    devtools (>= 2.4.5),
-    usethis,
-    testthat (>= 3.0.0),
-    lintr (>= 3.2.0),
-    styler (>= 1.10.3),
-    pkgdown (>= 2.1.1),
-    roxygen2 (>= 7.3.2)
-Imports:
+Imports: 
     R6,
     httr,
     readr,
@@ -78,18 +70,29 @@ Imports:
     yaml,
     psych,
     progressr,
-    polars,
-    pROC,
+    DBI,
     metrica,
     lubridate,
     future,
     future.apply,
     futile.logger,
-    PRROC,
     MLmetrics,
     tidyr,
     checkmate,
     fs,
-    duckdb
-Additional_repositories: https://community.r-multiverse.org, https://rpolars.r-universe.dev/
+    duckdb,
+    stringr
+Suggests:
+    devtools (>= 2.4.5),
+    usethis,
+    testthat (>= 3.0.0),
+    lintr (>= 3.2.0),
+    styler (>= 1.10.3),
+    pkgdown (>= 2.1.1),
+    roxygen2 (>= 7.3.2),
+    knitr,
+    rmarkdown,
+    ps
+VignetteBuilder: knitr
+Additional_repositories: https://community.r-multiverse.org
 Config/testthat/edition: 3

NAMESPACE

@@ -8,13 +8,16 @@ export(DatasetProcessor)
 export(EmbeddingModel)
 export(Event)
 export(FeatureProcessor)
+export(InHospitalMortalityMIMIC3)
 export(InHospitalMortalityMIMIC4)
 export(JoinConfig)
 export(MIMIC3Dataset)
 export(MIMIC4EHRDataset)
 export(MIMIC4NoteDataset)
 export(MultiClassLabelProcessor)
 export(MultiLabelProcessor)
+export(NextMortalityMIMIC3)
+export(NextMortalityMIMIC4)
 export(Patient)
 export(Processor)
 export(RNN)
@@ -41,6 +44,7 @@ export(get_descendants)
 export(get_metrics_fn)
 export(get_processor)
 export(is_best)
+export(load_sample_dataset)
 export(load_yaml_config)
 export(lookup_code)
 export(map_code)
@@ -54,16 +58,32 @@ import(R6)
 import(checkmate)
 import(dplyr)
 import(lubridate)
-import(polars)
 import(tidyr)
 import(torch)
 import(yaml)
+importFrom(DBI,dbConnect)
+importFrom(DBI,dbDisconnect)
+importFrom(DBI,dbExecute)
+importFrom(DBI,dbExistsTable)
+importFrom(DBI,dbListTables)
+importFrom(DBI,dbRemoveTable)
 importFrom(MLmetrics,Accuracy)
 importFrom(MLmetrics,F1_Score)
 importFrom(MLmetrics,Precision)
 importFrom(MLmetrics,Recall)
-importFrom(PRROC,pr.curve)
 importFrom(R6,R6Class)
+importFrom(dplyr,collect)
+importFrom(dplyr,distinct)
+importFrom(dplyr,filter)
+importFrom(dplyr,left_join)
+importFrom(dplyr,mutate)
+importFrom(dplyr,pull)
+importFrom(dplyr,rename)
+importFrom(dplyr,rename_with)
+importFrom(dplyr,select)
+importFrom(dplyr,tbl)
+importFrom(dplyr,union_all)
+importFrom(duckdb,duckdb)
 importFrom(fs,dir_create)
 importFrom(fs,file_exists)
 importFrom(fs,path)
@@ -82,8 +102,6 @@ importFrom(lubridate,as.duration)
 importFrom(lubridate,dhours)
 importFrom(metrica,balacc)
 importFrom(metrica,jaccardindex)
-importFrom(pROC,auc)
-importFrom(polars,pl)
 importFrom(progressr,handlers)
 importFrom(progressr,progressor)
 importFrom(psych,cohen.kappa)
@@ -92,6 +110,9 @@ importFrom(purrr,map)
 importFrom(rappdirs,user_cache_dir)
 importFrom(readr,cols)
 importFrom(readr,read_csv)
+importFrom(stats,aggregate)
+importFrom(stats,setNames)
+importFrom(stringr,str_pad)
 importFrom(torch,nn_dropout)
 importFrom(torch,nn_linear)
 importFrom(torch,nn_module)