Merge branch 'dev' into 'default'

1.4.0

See merge request data-analysis5/phenotypes/process.phenotypes!61

CHANGELOG.md

@@ -6,6 +6,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+- nothing for the moment
+
+
+## [1.4.0] - 2022-08-29
+
 ### Added
 - yaml validation as built-in, exported package function
 - SurveyCTO repeat expansion utility function
@@ -14,7 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - unit test coverage now 100%
 - roxygen documentation revised for all functions
 - roxygen documentation CRAN style compliant
-### Deprecated
+- readthedocs and vignettes improved for style
 ### Removed
 - references to python-based yaml validation
   - this was long ago deprecated, but further references to it are removed
@@ -27,7 +32,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - expect there are some hidden functionalities in the package that may yet break due to correction
 - `create.phenotype.report` optional output yaml should now be compatible with reloading output tsv into the package
 - added missing CI dependency
-### Security
 
 
 ## [1.3.0] - 2022-07-12
@@ -88,7 +92,7 @@ system.file("unicode_pattern_replacements.tsv", package = "process.phenotypes"`)
 ## [1.1.2] - 2022-06-09
 
 ### Added
-- entire code base? see [readthedocs](http://54gene-processphenotypes-docs.s3-website.us-east-2.amazonaws.com/index.html) for elaborated feature set
+- entire code base? see [readthedocs](https://54geneprocessphenotypes.readthedocs.io/en/latest/) for elaborated feature set
 
 ## [0.1.0] - 2021-07-12
 ### Added

DESCRIPTION

@@ -2,8 +2,8 @@ Package: process.phenotypes
 Title: automated phenotype standardization and reporting
 Version: 1.4.0
 Authors@R: c(
-    person("Bari", "Ballew", , "bari.ballew@54gene.com", role = "aut"),
-    person("Lightning", "Auriga", , "cameron.palmer@54gene.com", role = c("aut", "cre"))
+    person("Bari", "Ballew", , "bari.ballew@gmail.com", role = "aut"),
+    person("Lightning", "Auriga", , "palmercd5@gmail.com", role = c("aut", "cre"))
   )
 Description: A package for reproducible phenotype data cleaning and
     quality control.

R/create_phenotype_report.R

@@ -71,7 +71,7 @@
 #' The actual functionality and configuration in this package is extensive and frequently
 #' expanding. Full details on exactly what cleaning is performed and available
 #' configuration options for the input data are available at
-#' \url{http://54gene-processphenotypes-docs.s3-website.us-east-2.amazonaws.com/index.html}
+#' \url{https://54geneprocessphenotypes.readthedocs.io/en/latest/}
 #'
 #' @param in.filename Character vector filename of input phenotype data.
 #' @param dataset.yaml character vector filename of the yaml-format configuration

R/process_phenotypes.R

@@ -6,7 +6,7 @@
 #'
 #' @seealso
 #'
-#' - \url{http://54gene-processphenotypes-docs.s3-website.us-east-2.amazonaws.com/index.html}
+#' - \url{https://54geneprocessphenotypes.readthedocs.io/en/latest/}
 #' - \url{https://gitlab.com/data-analysis5/phenotypes/process.phenotypes}
 #'
 #' @docType package

README.md

@@ -1,24 +1,26 @@
 # process.phenotypes: automated phenotype standardization and reporting
 
+[![Documentation Status](https://readthedocs.org/projects/54geneprocessphenotypes/badge/?version=latest)](https://54geneprocessphenotypes.readthedocs.io/en/latest/?badge=latest)
+
 ## Overview
 
 This is an `R` package designed to help the process of phenotype
 dataset cleaning be automated, rigorous, and transparent. The overall
 cleaning process is simplified as follows:
 
-- a phenotype spreadsheet is exported to any of several supported formats:
+- A phenotype spreadsheet is exported to any of several supported formats:
   - .tsv (plaintext, tab-delimited)
   - .dta (STATA format)
   - .sas7bdat (SAS format, with accompanying .sas code for category labels)
   - .zsav (SPSS format)
-- the phenotype dataset is configured in 
+- The phenotype dataset is configured in 
 [YAML](https://docs.ansible.com/ansible/latest/reference_appendices/YAMLSyntax.html)
 format. this allows the user to specify the expected data format
 (binary, categorical, ordinal, numeric, date, blood pressure, string), boundary conditions
 for numeric values, levels and alias for binary/categorical/ordinal variables,
 special values to be encoded as NA (missing) entries, and other restrictions.
-- the entire cleaning process for the file is run with a single R command.
-- after cleaning is complete, an html format report is emitted, reporting 
+- The entire cleaning process for the file is run with a single R command.
+- After cleaning is complete, an html format report is emitted, reporting 
 summary statistics and data cleaning observations (e.g. invalid values detected
 for categorical variables); this file is both for recordkeeping and for helping
 the user improve configuration for more refined cleaning.
@@ -27,7 +29,7 @@ the user improve configuration for more refined cleaning.
 
 Please see any of the following documentation:
 
-- This package's [Read the Docs](http://54gene-processphenotypes-docs.s3-website.us-east-2.amazonaws.com/index.html)
+- This package's [Read the Docs](https://54geneprocessphenotypes.readthedocs.io/en/latest/)
   contains extended documentation about various aspects of the package, including installation, configuration, and use.
 - Once installed, the standard R man pages (accessed, for example, with `?create.phenotype.report`) contain extensive
   function interface documentation and examples.