From 316f2938446456f8aeaa59e70e45c7a9b76da9fa Mon Sep 17 00:00:00 2001 From: LS31 Date: Wed, 11 Nov 2020 18:07:19 +0100 Subject: [PATCH] Build for 2.2. --- NEWS.md | 1 + README.md | 11 ++++++----- docs/index.html | 15 ++++++++------- docs/news/index.html | 1 + docs/pkgdown.yml | 2 +- docs/reference/adjust_calcium_for_albumin.html | 2 +- docs/reference/adjust_sodium_for_glucose.html | 2 +- docs/reference/calculate_bmi.html | 2 +- docs/reference/calculate_pulse_pressure.html | 2 +- docs/reference/calculate_qtc.html | 2 +- docs/reference/estimate_bsa.html | 2 +- docs/reference/estimate_gfr_ckdepi.html | 2 +- docs/reference/estimate_gfr_cockcroft.html | 2 +- docs/reference/estimate_gfr_mdrd.html | 2 +- docs/reference/estimate_gfr_schwartz.html | 2 +- docs/reference/estimate_ibw.html | 2 +- docs/reference/estimate_map.html | 2 +- docs/reference/has_metabolic_syndrome_atpiii.html | 2 +- docs/reference/score_curb65.html | 2 +- docs/reference/score_qsofa.html | 2 +- man/adjust_calcium_for_albumin.Rd | 2 +- man/adjust_sodium_for_glucose.Rd | 2 +- man/calculate_bmi.Rd | 2 +- man/calculate_pulse_pressure.Rd | 2 +- man/calculate_qtc.Rd | 2 +- man/estimate_bsa.Rd | 2 +- man/estimate_gfr_ckdepi.Rd | 2 +- man/estimate_gfr_cockcroft.Rd | 2 +- man/estimate_gfr_mdrd.Rd | 2 +- man/estimate_gfr_schwartz.Rd | 2 +- man/estimate_ibw.Rd | 2 +- man/estimate_map.Rd | 2 +- man/has_metabolic_syndrome_atpiii.Rd | 2 +- man/score_curb65.Rd | 2 +- man/score_qsofa.Rd | 2 +- 35 files changed, 47 insertions(+), 43 deletions(-) diff --git a/NEWS.md b/NEWS.md index 4ef6bc9..2529afb 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,5 +2,6 @@ * Added a `NEWS.md` file to track changes to the package. * Added assertions and testthat tests for existing functions. +* Improved support for `NA` values. * Added new calculations: CURB-65, MAP, pulse pressure, albumin-adjusted calcium, eGFR formula. * Updated documentation. diff --git a/README.md b/README.md index 7a1e93b..fbf5efa 100644 --- a/README.md +++ b/README.md @@ -30,14 +30,14 @@ Help and pull requests are more than welcome. - *Nephrology* - Estimate glomerular filtration rate based on creatinine clearance. -# Design philosophy +# Design ideas **Reliable** - *Explicit units for output* - Numeric output of a function will have a specified unit attribute (if applicable) using the [units](https://r-quantities.github.io/units/) package. - *Fail-fast without assumptions* - - If certain conditions are not explicitly provided, err on the side of caution (e.g. a fasting state has to be provided in order for a glucose to be considered a fasting glucose). + - If certain conditions are not explicitly provided, err on the side of caution (e.g. a fasting state has to be provided in order for a glucose to be considered a fasting glucose). If `NA` values are provided, functions will return `NA` unless otherwise specified. - *Explicit references and caveats* - Every function will have references and a section on caveats. (However, despite our best efforts of quality control, the functions are provided as-is, without any guarantees, and users would be wise to check the output for quality and accuracy in their use case.) @@ -50,7 +50,7 @@ Help and pull requests are more than welcome. # Practical notes on the use of the unit attribute -If applicable, functions will return numeric values with a unit attribute using the [units](https://r-quantities.github.io/units/) package. This is to be as explicit as possible to the end user about the generated data. However, the unit attributes may sometimes be bothersome. Use `units::drop_units(x)` to drop the unit attribute. Load the ggforce package (an extension of ggplot) if you want to incorporate the unit attribute in the scales of a ggplot figure (see [ggforce reference page Position scales for units data](https://ggforce.data-imaginist.com/reference/scale_unit.html)). +If applicable, functions will return numeric values with a unit attribute using the [units](https://r-quantities.github.io/units/) package. The idea is to be as explicit as possible to the end user about the generated data. However, the unit attributes may sometimes be bothersome. Use `units::drop_units(x)` to drop the unit attribute. Load the ggforce package (an extension of ggplot) if you want to incorporate the unit attribute in the scales of a ggplot figure (see [ggforce reference page Position scales for units data](https://ggforce.data-imaginist.com/reference/scale_unit.html)). # How to install @@ -66,7 +66,7 @@ remotes::install_github("ls31/clinicalr") remotes::install_github("lc31/clinicalr") ``` -# To do +# Ideas for the future * effective osmolality? * anion gap? * total body water? @@ -76,4 +76,5 @@ remotes::install_github("lc31/clinicalr") * A-a gradient? * creatinine clearance (using urine)? * Framingham? -* assertion tests +* full SOFA score? +* Calvert formula (AUC) for carboplatin? diff --git a/docs/index.html b/docs/index.html index 70f4853..ccf390d 100644 --- a/docs/index.html +++ b/docs/index.html @@ -126,9 +126,9 @@

-
+

-Design philosophy

+Design ideas

Reliable