diff --git a/DESCRIPTION b/DESCRIPTION index 8654937..37d3830 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -12,18 +12,18 @@ Authors@R: role="cph", email="xxx@xxx.org")) Maintainer: Guillaume Fabre -Description: This package provides functions to assign standardized diagnosis - using the Banff Classification (Category 1 to 6 diagnoses, including Acute - and Chronic active T-cell mediated rejection as well as Active, - Chronic active, and Chronic antibody mediated rejection). The main function - considers a minimal dataset containing biopsies information in a specific - format (described by a data dictionary), verifies its content and format - (based on the data dictionary), assign diagnoses, and create a summary - report. +Description: The goal of this package is to provide functions to assign + standardized diagnosis using the Banff Classification (Category 1 to 6 + diagnoses, including Acute and Chronic active T-cell mediated rejection as + well as Active, Chronic active, and Chronic antibody mediated rejection). + The main function considers a minimal dataset containing biopsies + information in a specific format (described by a data dictionary), verifies + its content and format (based on the data dictionary), assign diagnoses, and + create a summary report. License: GPL-3 Depends: R (>= 3.4) -URL: https://github.com/maelstrom-research/banffIT -BugReports: https://github.com/maelstrom-research/banffIT/issues +URL: https://github.com/PersonalizedTransplantCare/banffIT +BugReports: https://github.com/PersonalizedTransplantCare/banffIT/issues Roxygen: list(markdown = TRUE) Imports: dplyr (>= 1.1.0), rlang, diff --git a/NEWS.md b/NEWS.md index c0c08f9..485d10e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -5,12 +5,10 @@ The banffIT package provides provides functions to assign standardized diagnosis using the Banff Classification (Category 1 to 6 diagnoses, including Acute and Chronic active T-cell mediated rejection as well as Active, Chronic active, and Chronic antibody mediated rejection). The -main function -[banff_launcher()](https://PersonalizedTransplantCare.github.io/banffIT-documentation/reference/banff_launcher.html) -considers a minimal dataset containing biopsies information in a -specific format (described by a data dictionary), verifies its content -and format (based on the data dictionary), assign diagnoses, and create -a summary report. +main function `banff_launcher()`considers a minimal dataset containing +biopsies information in a specific format (described by a data +dictionary), verifies its content and format (based on the data +dictionary), assign diagnoses, and create a summary report. ## Main functionality @@ -20,12 +18,12 @@ a summary report. the user gets information allowing them to correct the input dataset and rerun the process. Once all tests pass, the dataset is given as an output with a diagnosis for each observation (using the function - [add_diagnosis()](https://PersonalizedTransplantCare.github.io/banffIT-documentation/reference/add_diagnosis.html) - internally). The output dataset, along with its associated labels - (“label:en” by default) are provided to the user in an Excel format - file accessible in the output_folder specified (the working directory - by default). The output dataset comes with a report that summarizes - information about variable distributions and descriptive statistics. + `add_diagnosis()` internally). The output dataset, along with its + associated labels (“label:en” by default) are provided to the user in + an Excel format file accessible in the output_folder specified (the + working directory by default). The output dataset comes with a report + that summarizes information about variable distributions and + descriptive statistics. ## additional functions (used in the main function, but can be used separately) @@ -43,10 +41,9 @@ a summary report. - function `add_diagnosis()` This function takes a dataset and returns a diagnosis for each observation. For the function to run, the dataset - must not contain any errors that - [banff_launcher()](https://PersonalizedTransplantCare.github.io/banffIT-documentation/reference/banff_launcher.html) - would have detected. Please prefer using `banff_launcher()` to run - additional tests. + must not contain any errors that `banff_launcher()`would have + detected. Please prefer using `banff_launcher()` to run additional + tests. - function `dataset_summarize()` [Function](https://maelstrom-research.github.io/madshapR-documentation/reference/summarize.html) diff --git a/README.md b/README.md index 3d06ebd..b48db3e 100644 --- a/README.md +++ b/README.md @@ -12,12 +12,10 @@ The banffIT package provides provides functions to assign standardized diagnosis using the Banff Classification (Category 1 to 6 diagnoses, including Acute and Chronic active T-cell mediated rejection as well as Active, Chronic active, and Chronic antibody mediated rejection). The -main function -[banff_launcher()](https://PersonalizedTransplantCare.github.io/banffIT-documentation/reference/banff_launcher.html) -considers a minimal dataset containing biopsies information in a -specific format (described by a data dictionary), verifies its content -and format (based on the data dictionary), assign diagnoses, and create -a summary report. +main function `banff_launcher()`considers a minimal dataset containing +biopsies information in a specific format (described by a data +dictionary), verifies its content and format (based on the data +dictionary), assign diagnoses, and create a summary report. # Get started diff --git a/inst/WORDLIST b/inst/WORDLIST new file mode 100644 index 0000000..7656032 --- /dev/null +++ b/inst/WORDLIST @@ -0,0 +1,12 @@ +Banff +CMD +banff +bookdown +de +glomeruli +jp +madshapR +nl +sp +tibble +tibbles diff --git a/vignettes/banffIT-vignette.Rmd b/vignettes/banffIT-vignette.Rmd index 6a008af..2a14691 100644 --- a/vignettes/banffIT-vignette.Rmd +++ b/vignettes/banffIT-vignette.Rmd @@ -18,10 +18,9 @@ The banffIT package provides provides functions to assign standardized diagnosis using the Banff Classification (Category 1 to 6 diagnoses, including Acute and Chronic active T-cell mediated rejection as well as Active, Chronic active, and Chronic antibody mediated rejection). The main function -[banff_launcher()](https://PersonalizedTransplantCare.github.io/banffIT-documentation/reference/banff_launcher.html) -considers a minimal dataset containing biopsies information in a specific -format (described by a data dictionary), verifies its content and format -(based on the data dictionary), assign diagnoses, and create a summary +`banff_launcher()`considers a minimal dataset containing biopsies information +in a specific format (described by a data dictionary), verifies its content and +format (based on the data dictionary), assign diagnoses, and create a summary report. # Get started