Added vignette and updated README

Merge pull request #37 from alwinw/rc0.9.6

.Rbuildignore

@@ -1,26 +1,27 @@
-^renv$
-^renv\.lock$
-^CRAN-RELEASE$
-^Meta$
-^doc$
+.covrignore
+^_pkgdown\.yml$
 ^.*\.Rproj$
-^\.Rproj\.user$
-^packrat/
+^.pytest_cache
+^\.github$
+^\.png$
 ^\.Rprofile$
+^\.Rproj\.user$
 ^\.travis\.yml$
-^README\.Rmd$
-^README\.md$
-^README-.*\.png$
 ^appveyor\.yml$
-^cran-comments.md$
-^\.png$
-^README_cache/
 ^codecov\.yml$
-.covrignore
-^resources$
-^_pkgdown\.yml$
+^cran-comments.md$
+^CRAN-RELEASE$
+^data-raw$
+^doc$
 ^docs$
+^LICENSE\.md$
+^Meta$
+^packrat/
 ^pkgdown$
-^\.github$
-^data-raw$
-^.pytest_cache
+^README_cache/
+^README-.*\.png$
+^README\.md$
+^README\.Rmd$
+^renv\.lock$
+^renv$
+^resources$

.gitignore

@@ -45,3 +45,4 @@ vignettes/*.pdf
 # R Environment Variables
 .Renviron
 .Rproj.user
+inst/doc

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: epocakir
 Title: Clinical Coding of Patients with Kidney Disease using Clinical Practice
     Guidelines
-Version: 0.9.5
+Version: 0.9.6
 Authors@R:
     c(person(given = "Alwin",
              family = "Wang",
@@ -16,7 +16,7 @@ Authors@R:
 Description: Clinical coding and diagnosis of patients with kidney using
     clinical practice guidelines. The guidelines used are the evidence-based
     KDIGO guidelines. This package covers acute kidney injury (AKI), anemia,
-    and chronic liver disease(CKD).
+    and chronic liver disease (CKD).
 License: MIT + file LICENSE
 URL: https://github.com/alwinw/epocakir
 BugReports: https://github.com/alwinw/epocakir/issues
@@ -36,8 +36,12 @@ Imports:
 Suggests:
     usethis,
     testthat,
-    covr
+    covr,
+    knitr,
+    rmarkdown
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.1.1
+VignetteBuilder: knitr
+Language: en-US

LICENSE

@@ -1,21 +1,2 @@
-# MIT License
-
-Copyright (c) 2021 Alwin Wang, Lisa Toh
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2020
+COPYRIGHT HOLDER: Alwin Wang, Lisa Toh

LICENSE.md

@@ -0,0 +1,19 @@
+Copyright (c) 2020 Alwin Wang, Lisa Toh
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -63,6 +63,7 @@ export(as_metric)
 export(binary2factor)
 export(combine_date_time_cols)
 export(combn_changes)
+export(conversion_factors)
 export(dob2age)
 export(eGFR)
 export(eGFR_adult_SCr)

NEWS.md

@@ -0,0 +1,141 @@
+# epocakir 0.9.6
+
+Initial CRAN submission
+
+## Improvements
+
+- Added vignette *Introduction to epocakir* with basic usage examples
+- Updated README
+- Added sample `clinical_obvs` to demonstrate utility functions
+
+## Bug fixes
+
+- Exported `conversion_factors`, similar to ordered factors like `aki_stages`
+- Corrected mis-spelled words
+
+# epocakir 0.9.5
+
+Added sample data and better examples
+
+## Improvements
+
+- Added sample data based on test data
+- Cleaned up code comments
+- Added examples to methods
+
+## Breaking Changes
+
+- Renamed `aki()` to `aki_staging()` for more consistent method names
+
+## Bug fixes
+
+- Fixed bug when n < m for combn() in combn_changes()
+- Changed methods from `method.default()` to `method.data.frame()` to prevent infinite recursion on incorrectly specified function arguments
+
+# epocakir 0.9.0
+
+Improved high level API functions
+
+## Improvements
+
+- Wrote new combined `eGFR()` function that automatically selects the appropriate `eGFR_method()` formula to use
+- Wrote new combined `aki()` function that automatically calculates AKI based on all criteria and determines most severe stage
+- Added additional tests including warnings
+
+## Breaking Changes
+
+- Added `No AKI` and `No Albuminuria` to stages ordered factors to prevent users have to handle `NAs` mixed with ordered factors
+
+## Bug fixes
+
+- Fixed bug in `eGFR_internal()` where it was looking for `!is.na(black)` to select `eGFR_adult_SCysC()`, when `black` was not required
+
+# epocakir 0.8.0
+
+Initial full-featured release of epocakir methods
+
+## Improvements
+
+- Wrote `aki_SCr()` function
+- Methods now include `aki_bCr`, `aki_SCr`, `aki_UO`, `anemia`, `eGFR_adult_SCr`, `eGFR_adult_SCysC`, `eGFR_adult_SCr_SCysC`, `eGFR_child_SCr`, `eGFR_child_SCr_BUN`, `eGFR_child_SCysC`, `GFR_staging`, `Albuminuria_staging_AER`, `Albuminuria_staging_ACR` and `combn_changes`
+
+## Bug fixes
+
+- Used `tibble::tibble()` instead of `data.frame()` to prevent issue with `stringsasfactors` difference between R 3.x and R 4.x
+- Fixed sorting error in `aki_UO()
+
+# epocakir 0.7.0
+
+Re-wrote methods for consistency
+
+## Improvements
+
+- Removed duplicate `GFR_staging()` code
+- Stricter `expect_identical()` instead of `expect_equal()` assertions
+- Rewrote `anemia()` to make method selection consistent with other functions
+
+## Bug fixes
+
+- Consistent parameter naming
+
+# epocakir 0.6.0
+
+Re-wrote all eGFR functions as S3 methods
+
+## Improvements
+
+- Wrote `eGFR_adult_SCr`, `eGFR_adult_SCysC`, `eGFR_adult_SCr_SCysC`, `eGFR_child_SCr`, `eGFR_child_SCr_BUN`, `eGFR_child_SCysC` methods
+
+## Breaking changes
+
+- Instead of individual functions, use methods for all low-level functions
+- Renamed functions to snake_case, e.g. `eGFR.adult.SCr_SCysC` to `eGFR_adult_SCr_SCysC`
+
+# epocakir 0.5.0
+
+Improved handling of function arguments
+
+## Improvements
+
+- Changed from `forcats::fct_c` to `vctrs::vec_c` for improved `NA` handling (<https://github.com/tidyverse/forcats/issues/250>)
+- Wrote `aki_bCr()` method
+- Allow symbols to be passed to methods
+
+## Breaking changes
+
+- Added version numbers to dependencies
+
+# epocakir 0.4.0
+
+Added testing and additional utility functions to package
+
+## Improvements
+
+- Testing of edge-cases for `as_metric(NULL)`, `as_metric(1)` and unknown measurements
+- Wrote `as_metric()`
+- Additional KDIGO guidelines (<https://kdigo.org/guidelines/>) added
+- Added Albuminuria levels as an ordered factor
+
+## Bug fix
+
+- Correctly use `pmin` instead of `min` in eGFR calculation
+
+# epocakir 0.1.5
+
+dplyr compatible functions
+
+## Improvements
+
+- Proper handling of column names using dplyr programming (<https://dplyr.tidyverse.org/articles/programming.html>)
+- Wrote `aki_bCr` calculation as part of `aki()` staging
+- Wrote `.dob2age()` function to calculate a patient's age
+
+# epocakir 0.1.0
+
+Initial release
+
+## Improvements
+
+- Wrote `combn_changes()`
+- Wrote `conversion_factors()`
+- Wrote initial functions based on KDIGO guidelines (<https://kdigo.org/guidelines/>)

R/aki.R

@@ -24,7 +24,7 @@ aki_stages <- factor(
 #' The staging (1, 2, 3) of AKI is returned.
 #'
 #' When multiple columns are provided, `aki_staging()` will automatically
-#' calculate whether or not AKI has occurred using each KDIGIO definition.
+#' calculate whether or not AKI has occurred using each KDIGO definition.
 #'
 #' \itemize{
 #'   \item{[`aki_bCr()`]: Staging of AKI based on baseline serum creatinine}

R/anemia.R

@@ -17,7 +17,7 @@
 #' See <https://kdigo.org/guidelines/anemia-in-ckd/> for more details.
 #'
 #' @param .data (data.frame) A data.frame, optional
-#' @param Hb Hemoglobin concenration
+#' @param Hb Hemoglobin concentration
 #'   column name, or vector of units or numeric if `.data` is not provided
 #' @param age Age of patient
 #'   column name, or vector of units or numeric if `.data` is not provided

R/ckd.R

@@ -33,7 +33,7 @@
 #'   column name, or vector of logical (TRUE/FALSE) if `.data` is not provided
 #' @param black Black race or not
 #'   column name, or vector of logical (TRUE/FALSE) if `.data` is not provided
-#' @param pediatric (logical) Paediatric or not
+#' @param pediatric (logical) Pediatric or not
 #'   column name, or vector of logical (TRUE/FALSE) if `.data` is not provided
 #' @param ... Further optional arguments
 #'

R/data-clinical_obs.R

@@ -0,0 +1,7 @@
+#' Clinical Patient Data
+#'
+#' A sample dataset to demonstrate utility functions in `epocakir`
+#'
+#' @examples
+#' clinical_obvs
+"clinical_obvs"

R/utils.R

@@ -22,8 +22,9 @@ NULL
 #' \item{mol_weight}{Molecular weight (where required)}
 #' \item{description}{Full name}
 #' }
+#' @export
 #' @examples
-#' epocakir:::conversion_factors
+#' conversion_factors
 conversion_factors <- tibble::tribble(
   ~parameter, ~metric_units, ~mol_weight, ~description,
   # General
@@ -60,6 +61,8 @@ conversion_factors <- tibble::tribble(
 
 #' Convert a measured value to metric units
 #'
+#' Refer to [`conversion_factors`] for a full list of available conversions
+#'
 #' @param param (character) Name of measurement, e.g. param = "SCr"
 #' @param meas (units) Measurement or vector of measurements
 #' @param ... (units) One of conversion_factors$parameter,