Nothing
## ----setup--------------------------------------------------------------------
library(archetyper)
## ---- eval=TRUE, include=FALSE, message=FALSE, warning=FALSE------------------
if(dir.exists("majestic_12")){
unlink("majestic_12", recursive=TRUE)
}
## ---- eval=FALSE, include=TRUE, message=FALSE, warning=FALSE------------------
# generate("majestic_12")
#
# list.files("majestic_12")
# [1] "data_input" "data_output" "data_working" "docs" "majestic_12.Rproj"
# [6] "models" "R" "readme.md" ".gitignore"
## ---- eval=FALSE, include=TRUE, message=FALSE, warning=FALSE------------------
# list.files("majestic_12/R/")
#
# [1] "0_test.R" "1_integrate.R" "2_enrich.R" "3_model.R"
# [5] "4_evaluate.R" "5_present.Rmd" "api.R" "common.R"
# [9] "explore.R" "lint.R" "mediator.R" "utilities.R"
## ---- eval=FALSE, include=TRUE, message=FALSE, warning=FALSE------------------
# library(odbc)
# con <- dbConnect(odbc::odbc(), "dev_database")
# sql <- "select my_value from my_table"
# result_df <- dbGetQuery(con, sql)
## ---- eval=FALSE, include=TRUE, message=FALSE, warning=FALSE------------------
# library(RJDBC)
# db_credentials <- config::get("dev_database")
# drv <- RJDBC::JDBC(driverClass = db_credentials$driver_class, classPath = Sys.glob("drivers/*"))
# con <- dbConnect(drv,db_credentials$connection_string, db_credentials$username, db_credentials$password)
# sql <- "select my_value from my_table"
# result_df <- dbGetQuery(con, sql)
## ---- eval=TRUE, include=FALSE, message=FALSE, warning=FALSE------------------
if(dir.exists("majestic_12")){
unlink("majestic_12", recursive=TRUE)
}
## ---- eval=FALSE, include=TRUE, message=FALSE, warning=FALSE------------------
# generate("majestic_12", db_connection_type = 'jdbc')
# list.files(project_path)
#
# [1] "config.yml" "data_input" "data_output"
# [4] "data_working" "docs" "drivers"
# [7] "majestic_12.Rproj" "models" "R"
# [10] "readme.md" ".gitignore" "dml_ddl.sql"
#
## ---- eval=TRUE, include=FALSE, message=FALSE, warning=FALSE------------------
if(dir.exists("majestic_12")){
unlink("majestic_12", recursive=TRUE)
}
## ---- eval=FALSE, include=TRUE------------------------------------------------
# generate(project_name = project_name, path = project_directory, exclude = c("api.R", "utilities.R", "readme.md", "lint.R", ".gitignore"))
#
# list.files(project_path)
# [1] "data_input" "data_output" "data_working" "docs" "majestic_12.Rproj"
# [6] "models" "R"
# list.files(project_path_r)
# [1] "0_test.R" "1_integrate.R" "2_enrich.R" "3_model.R" "4_evaluate.R" "5_present.Rmd"
# [7] "common.R" "explore.R" "mediator.R"
## ---- eval=TRUE, include=FALSE, message=FALSE, warning=FALSE------------------
if(dir.exists("majestic_12")){
unlink("majestic_12", recursive=TRUE)
}
if(dir.exists("hospital_readmissions_demo")){
unlink("hospital_readmissions_demo", recursive=TRUE)
}
## ---- eval=FALSE, include=TRUE------------------------------------------------
# archetyper::generate_demo()
# list.files("hospital_readmissions_demo/")
# [1] "data_input" "data_output" "data_working" "docs" "hospital_readmissions_demo.Rproj"
# [6] "models" "R" "readme.md" ".gitignore"
## ---- eval=FALSE, include=TRUE, message=FALSE, warning=FALSE------------------
# cat(readChar("hospital_readmissions_demo/R/mediator.R"), 1e5))
#
# ##--------------------------------------------------------------------------
# ## The mediator file will execute the linear data processing work-flow. -
# ##--------------------------------------------------------------------------
#
# source("R/common.R")
# tryCatch({
# info(logger, "running tests...")
# source("R/0_test.R")
# info(logger, "gathering and integrating data...")
# source("R/1_integrate.R")
# info(logger, "enriching base data...")
# source("R/2_enrich.R")
# info(logger, "building model(s)...")
# source("R/3_model.R")
# info(logger, "applying model(s) to test partitions...")
# source("R/4_evaluate.R")
# info(logger, "building presentation materials...")
# rmarkdown::render("R/5_present.Rmd", "pdf_document", output_dir = "docs")
# info(logger, "workflow is complete.")
#
# },
# error = function(cond) {
# log4r::error(logger, str_c("Script error: ", cond))
# }
# )
## ---- eval=FALSE, message=FALSE, warning=FALSE, include=T---------------------
# > list.files("data_working/")
# [1] "hospital_readmissions_integrated_2021-02-25.feather"
## ---- eval=FALSE, message=FALSE, warning=FALSE, include=T---------------------
# > list.files("data_working/")
# [1] "hospital_readmissions_enriched_2021-02-25.feather" "hospital_readmissions_integrated_2021-02-25.feather"
## ---- eval=FALSE, message=FALSE, warning=FALSE, include=T---------------------
# > list.files("data_ouput/")
# [1] "hospital_readmissions_feature_dtl_2021-02-25.csv" "hospital_readmissions_perf_2021-02-25.csv"
#
# > list.files("mod/")
# [1] "hospital_readmissions_readmissions_2021-02-23.mod"
## ---- eval=FALSE, message=FALSE, warning=FALSE, include=T---------------------
# > list.files("data_ouput/")
# [1] "hospital_readmissions_feature_dtl_2021-02-25.csv" "hospital_readmissions_holdout_perf_stats_2021-02-25.csv"
# [3] "hospital_readmissions_perf_2021-02-25.csv" "hospital_readmissions_testing_w_predictions_2021-02-25.csv"
## ---- eval=FALSE, message=FALSE, warning=FALSE, include=T---------------------
# #Present
# > list.files("hospital_readmissions_demo/docs/")
# [1] "5_present.pdf"
## ---- eval=F, message=FALSE, warning=FALSE, include=T-------------------------
# {
# "dt": {"state": "AL",
# "hospital_type": "acute_care_hospitals",
# "hospital_ownership": "government_hospital_district_or_authority",
# "emergency_services": "Yes",
# "ehr_interop": "Y",
# "denominator": 1.4791,
# "PSI_10": -1.3895,
# "PSI_11": 0.597,
# "PSI_12": -0.9487,
# "PSI_13": -0.102,
# "PSI_14": -1.1131,
# "PSI_15": -0.9439,
# "PSI_3": 0.029,
# "PSI_6": -0.5752,
# "PSI_8": -1.4081,
# "PSI_9": -0.3028,
# "denominator_ln": 1.3489}
# }
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