From 05088e736172351b9fcbe72f07f41545943e8e00 Mon Sep 17 00:00:00 2001
From: Andrew Bruce <andrewbruce.himni@gmail.com>
Date: Sun, 5 Nov 2023 03:12:09 -0500
Subject: [PATCH] cleanup part deux

---
 R/globals.R                        | 10 +++++-----
 man/ndc_lookup.Rd                  | 16 +++++++++++++++-
 man/open_payments.Rd               |  2 +-
 man/opt_out.Rd                     |  2 +-
 vignettes/articles/partb-stats.Rmd | 16 +++++++++++++++-
 5 files changed, 37 insertions(+), 9 deletions(-)

diff --git a/R/globals.R b/R/globals.R
index 85e5ad96..786fbe0f 100644
--- a/R/globals.R
+++ b/R/globals.R
@@ -7,6 +7,11 @@ utils::globalVariables(c(
   "y", # <beneficiaries>
   "y", # <betos>
   "rbcs_major_ind", # <betos>
+  "hcpcs", # <rbcs_util>
+  "category", # <rbcs_util>
+  "subcategory", # <rbcs_util>
+  "family", # <rbcs_util>
+  "procedure", # <rbcs_util>
   "copy", # <ror>
   ":=", # <ror>
   "lg", # <ror>
@@ -197,11 +202,6 @@ utils::globalVariables(c(
   "address", # <tidyup_service>
   "specialty", # <tidyup_service>
   "place_of_srvc", # <tidyup_geography>
-  "hcpcs", # <rbcs_util>
-  "category", # <rbcs_util>
-  "subcategory", # <rbcs_util>
-  "family", # <rbcs_util>
-  "procedure", # <rbcs_util>
   "title", # <cms_update>
   "modified", # <cms_update>
   "distribution", # <cms_update>
diff --git a/man/ndc_lookup.Rd b/man/ndc_lookup.Rd
index 57af7ac7..ed1cfdf2 100644
--- a/man/ndc_lookup.Rd
+++ b/man/ndc_lookup.Rd
@@ -10,7 +10,21 @@ ndc_lookup(ndc)
 \item{ndc}{< \emph{character} > // \strong{required} 10- to 11-digit National Drug Code}
 }
 \value{
-A \link[tibble:tibble-package]{tibble} with the columns:
+A \link[tibble:tibble-package]{tibble} with the columns:\tabular{ll}{
+   \strong{Field} \tab \strong{Description} \cr
+   \code{ndc} \tab National Drug Code \cr
+   \code{rxcui} \tab RxNorm Identifier \cr
+   \code{atc} \tab ATC Identifier \cr
+   \code{status} \tab Status (NDC) \cr
+   \code{brand_name} \tab Brand Name (RxCUI) \cr
+   \code{drug_name} \tab Drug Name (RxCUI) \cr
+   \code{atc_first} \tab ATC I: Anatomical, Pharmacological \cr
+   \code{atc_first} \tab ATC II: Pharmacological, Therapeutic \cr
+   \code{atc_first} \tab ATC III: Chemical, Pharmacological, Therapeutic \cr
+   \code{atc_first} \tab ATC IV: Chemical, Pharmacological, Therapeutic \cr
+   \code{subject} \tab Medline Plus: Subject \cr
+   \code{summary} \tab Medline Plus: Summary \cr
+}
 }
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}
diff --git a/man/open_payments.Rd b/man/open_payments.Rd
index 925e92dc..de43344b 100644
--- a/man/open_payments.Rd
+++ b/man/open_payments.Rd
@@ -203,7 +203,7 @@ open_payments(year = 2021, pay_form = "Stock option")
 open_payments(year = 2021, payer = "Adaptive Biotechnologies Corporation")
 open_payments(year = 2021, teaching_hospital = "Nyu Langone Hospitals")
 
-# Use the years helper function to retrieve results for all avaliable years:
+# Use the years helper function to retrieve results for all available years:
 open_years() |>
 map(\(x) open_payments(year = x, npi = 1043477615)) |>
 list_rbind()
diff --git a/man/opt_out.Rd b/man/opt_out.Rd
index 79dbd555..1f545621 100644
--- a/man/opt_out.Rd
+++ b/man/opt_out.Rd
@@ -103,9 +103,9 @@ fee-for-service (Part B).
 }
 
 \examples{
+\dontshow{if ( interactive()) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
 opt_out(npi = 1043522824)
 
-\dontshow{if ( interactive()) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
 # For opt-out providers eligible
 # to order and refer, use [order_refer()]
 # to look up their eligibility status:
diff --git a/vignettes/articles/partb-stats.Rmd b/vignettes/articles/partb-stats.Rmd
index 647cb76e..73bcf5bb 100644
--- a/vignettes/articles/partb-stats.Rmd
+++ b/vignettes/articles/partb-stats.Rmd
@@ -26,6 +26,7 @@ library(tidyr)
 library(dplyr)
 library(purrr)
 library(furrr)
+library(ggplot2)
 library(gt)
 library(gtExtras)
 ```
@@ -53,12 +54,25 @@ plan(sequential)
 ## Overall Performance
 
 ```{r}
-ind |> 
+performance <- ind |> 
   unnest(performance) |> 
+  mutate(year = as.integer(year)) |> 
   select(year, tot_hcpcs:.pymt_per_srvc)
+performance
 ```
 
 
+```{r}
+lm.performance <- lm(tot_payment ~ .srvcs_per_bene + tot_benes + .pymt_per_srvc, data = performance)
+summary(lm.performance)
+```
+
+
+```{r}
+ggplot(performance, aes(x = tot_payment, y = .srvcs_per_bene, fill = year, group = year)) +
+  geom_point(shape = 21, size = 4, alpha = 0.75) +
+  theme_minimal()
+```
 
 
 ```{r}