update documentation, ready to CRAN

DESCRIPTION

@@ -12,18 +12,18 @@ Authors@R:
              role="cph",
              email="xxx@xxx.org"))
 Maintainer: Guillaume Fabre <gfabre@maelstrom-research.org>
-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,

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)

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
 

inst/WORDLIST

@@ -0,0 +1,12 @@
+Banff
+CMD
+banff
+bookdown
+de
+glomeruli
+jp
+madshapR
+nl
+sp
+tibble
+tibbles

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