Merge pull request #151 from pharmaverse/website_fixes

Inserted CRAN badge.  Moved attribute discussion.  Couple of Typo and…

README.Rmd

@@ -17,12 +17,13 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 [![R build status](https://github.com/pharmaverse/logrx/workflows/R-CMD-check/badge.svg)](https://github.com/pharmaverse/logrx/actions?workflow=R-CMD-check)
+[![CRAN status](https://www.r-pkg.org/badges/version/logrx)](https://CRAN.R-project.org/package=logrx)
 [<img src="https://img.shields.io/codecov/c/github/pharmaverse/logrx">](https://app.codecov.io/gh/pharmaverse/logrx)
 [<img src="https://img.shields.io/badge/License-MIT-blue.svg">](https://github.com/pharmaverse/logrx/blob/master/LICENSE.md)
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental-1)
 <!-- badges: end -->
 
-The goal of logrx is to facilitate logging in a clinical environment with the goal of making code easily traceable and reproducible.
+The goal of `{logrx}` is to facilitate logging in a clinical environment with the goal of making code easily traceable and reproducible.
 
 ## Installation
 
@@ -38,10 +39,10 @@ To get the latest development version use:
 devtools::install_github("pharmaverse/logrx", ref = "dev")
 ```
 
-## What is ```logrx``` ?
+## What is ```{logrx}``` ?
 
-Simple! The logrx package makes a log file for a R script!. Below we have a short gif of
-making a log file for a `adsl.R` script. More details on the parts of the log script
+Simple! The `{logrx}` package makes a log file for a R script!. Below we have a short gif of
+making a log file for a `adsl.R` script using the Addin. More details on the parts of the log script
 are found in [Get Started](https://pharmaverse.github.io/logrx/articles/logrx.html) and we have several vignettes that show specific use cases for using the package.
 
 ```{r img-with-knitr, echo=FALSE, fig.align='center', out.width='100%', fig.cap='logrx Addin in Action'}
@@ -50,7 +51,8 @@ knitr::include_graphics("https://pharmaverse.s3.us-east-2.amazonaws.com/gifs/log
 
 While many packages to facilitate the logging of code already exist in the R ecosystem, it is hard to find a solution that works well for clinical programming applications. Many logging implementations are more implicit and rely on user input to create the log for the execution of a script. While this is useful for logging specific events of an application, in clinical programming a log has a set purpose. 
 
-```logrx``` is built around the concept of creating a log for the execution of an R script that provides an overview of what happened as well as the environment that it happened in. We set out to create a flexible logging utility that could provide the necessary information to anyone reviewing the code execution so they can recreate the execution environment and run the code for themselves. ```logrx``` is purpose-built for the needs of clinical programming to capture necessary elements of the environment and execution to be able to create a complete view of the program execution.
+```{logrx}``` is built around the concept of creating a log for the execution of an R script that provides an overview of what happened as well as the environment that it happened in. We set out to create a flexible logging utility that could provide the necessary information to anyone reviewing the code execution so they can recreate the execution environment and run the code for themselves. ```{logrx}``` is purpose-built for the needs of clinical programming to capture necessary elements of the environment and execution to be able to create a complete view of the program execution.
 
 ## Using logrx
-```logrx``` can be used in a file or through scripting. More information on how to use ```logrx``` can be found in [Get Started](https://pharmaverse.github.io/logrx/articles/logrx.html).
+
+```logrx``` can be used in a file or through scripting. More information on how to use ```{logrx}``` can be found in [Get Started](https://pharmaverse.github.io/logrx/articles/logrx.html) and in our Articles on Execution and Use Cases.

README.md

@@ -7,13 +7,15 @@
 
 [![R build
 status](https://github.com/pharmaverse/logrx/workflows/R-CMD-check/badge.svg)](https://github.com/pharmaverse/logrx/actions?workflow=R-CMD-check)
+[![CRAN
+status](https://www.r-pkg.org/badges/version/logrx)](https://CRAN.R-project.org/package=logrx)
 [<img src="https://img.shields.io/codecov/c/github/pharmaverse/logrx">](https://app.codecov.io/gh/pharmaverse/logrx)
 [<img src="https://img.shields.io/badge/License-MIT-blue.svg">](https://github.com/pharmaverse/logrx/blob/master/LICENSE.md)
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental-1)
 <!-- badges: end -->
 
-The goal of logrx is to facilitate logging in a clinical environment
+The goal of `{logrx}` is to facilitate logging in a clinical environment
 with the goal of making code easily traceable and reproducible.
 
 ## Installation
@@ -30,23 +32,16 @@ To get the latest development version use:
 devtools::install_github("pharmaverse/logrx", ref = "dev")
 ```
 
-## What is `logrx` ?
+## What is `{logrx}` ?
 
-Simple! The logrx package makes a log file for a R script!. Below we
-have a short gif of making a log file for a `adsl.R` script. More
-details on the parts of the log script are found in [Get
+Simple! The `{logrx}` package makes a log file for a R script!. Below we
+have a short gif of making a log file for a `adsl.R` script using the
+Addin. More details on the parts of the log script are found in [Get
 Started](https://pharmaverse.github.io/logrx/articles/logrx.html) and we
 have several vignettes that show specific use cases for using the
 package.
 
-<div class="figure" style="text-align: center">
-
-<img src="https://pharmaverse.s3.us-east-2.amazonaws.com/gifs/logrx.gif" alt="logrx Addin in Action" width="100%" />
-<p class="caption">
-logrx Addin in Action
-</p>
-
-</div>
+<img src="https://pharmaverse.s3.us-east-2.amazonaws.com/gifs/logrx.gif" alt="logrx Addin in Action" width="100%" style="display: block; margin: auto;" />
 
 While many packages to facilitate the logging of code already exist in
 the R ecosystem, it is hard to find a solution that works well for
@@ -55,18 +50,19 @@ implicit and rely on user input to create the log for the execution of a
 script. While this is useful for logging specific events of an
 application, in clinical programming a log has a set purpose.
 
-`logrx` is built around the concept of creating a log for the execution
-of an R script that provides an overview of what happened as well as the
-environment that it happened in. We set out to create a flexible logging
-utility that could provide the necessary information to anyone reviewing
-the code execution so they can recreate the execution environment and
-run the code for themselves. `logrx` is purpose-built for the needs of
-clinical programming to capture necessary elements of the environment
-and execution to be able to create a complete view of the program
-execution.
+`{logrx}` is built around the concept of creating a log for the
+execution of an R script that provides an overview of what happened as
+well as the environment that it happened in. We set out to create a
+flexible logging utility that could provide the necessary information to
+anyone reviewing the code execution so they can recreate the execution
+environment and run the code for themselves. `{logrx}` is purpose-built
+for the needs of clinical programming to capture necessary elements of
+the environment and execution to be able to create a complete view of
+the program execution.
 
 ## Using logrx
 
 `logrx` can be used in a file or through scripting. More information on
-how to use `logrx` can be found in [Get
-Started](https://pharmaverse.github.io/logrx/articles/logrx.html).
+how to use `{logrx}` can be found in [Get
+Started](https://pharmaverse.github.io/logrx/articles/logrx.html) and in
+our Articles on Execution and Use Cases.

vignettes/logrx.Rmd

@@ -18,41 +18,56 @@ knitr::opts_chunk$set(
 library(logrx)
 ```
 
-The purpose of the `logrx` package is to generate a log upon execution of 
-an R script which enables traceability and reproducibility of the executed code. 
+# Generating a log
+
+The purpose of the `logrx` package is to generate a log upon execution of an R script which enables traceability and reproducibility of the executed code. Generating a log with `{logrx}` can be as simple as running one line of code as seen in the below example of how to use the `axecute()` function.. However, `{logrx}` has much more advanced capabilities to meet the demands of Clinical Reporting. To learn additional techniques about executing code with ```{logrx}``` please visit our [Execution Vignette](https://pharmaverse.github.io/logrx/articles/execution.html).
+
+## `axecute()`
+
+`axecute()` enables the command line submission of a program. A log is set-up around the program, and its code is run safely and loudly (using `safely()` from the `purrr` package). The log will be generated in the same folder as the script unless you specify differently.
+
+```{r axecute, eval = FALSE}
+axecute("my_script.R")
+```
+
+
+## `logrx` addin:
 
+A log can be generated using the ```{logrx}``` addin, which is a simple point and click interface that allows you to run a single program. The Addin ships with the package and is available once you use install the package. The gif on the [Get Started](https://pharmaverse.github.io/logrx/index.html) page gives a quick snapshot of its intended use. 
 
 # Log attributes
+
+We have compiled a brief overview of the information that we capture in the log file generated by `{logrx}`. We also users to customize sections of the log based on their needs for a log, e.g. you can toggle on/off the messages, outputs, errors and messages. You can also build into your log approved and unapproved packages used in your R script - see [Logging Unapproved Package and Function Use]( https://pharmaverse.github.io/logrx/articles/approved.html) for additional guidance
+
 The following attributes are recorded in the log:
 
-* `metadata`: `logrx` package information
+* **Metadata**: `{logrx}` package information
  + Version of the package
  + Type of build
  + Link to the GitHub repository
-* `user and file information`
+* **User and File Information**
  + User that generated the log
  + Name and path of the script for which the log was generated
  + `hash_sum`: A unique hashsum is created for the log file
-* `session_info`: The R session information
+* **Session Information**: The R session information
  + R version
  + OS and system
  + GUI
  + Language and timezone
-* `packages`: List of all available packages in the environment
-* `external_software`: List of all external software
-* `masked_functions`: List of all functions masked by packages
-* `start_time`, `end_time`, and `run_time`: Start, end, and run times
-* `used_packages_functions`: List of all packages and functions used in the 
+ + Packages - List of all available packages in the environment
+ + External Software - List of all external software
+* **Masked Functions** - List of all functions masked by packages
+* **Program Run Time Information** - Start, end, and run times
+* **Used Package and Functions (optional)** - List of all packages and functions used in the 
 script for which the log was generated
-* `unapproved_packages_functions`: List of all packages and functions used in 
+* **Unapproved Package and Functions (optional)** - List of all packages and functions used in 
 the script for which the log was generated that are not part of the approved 
 list of packages and functions
-* `errors`: Errors generated when running the script
-* `messages`: Messages generated when running the script
-* `warnings`: Warnings generated when running the script
-* `result`: Result generated when running the script
-* `output`: Output generated when running the script
-* `log_name`, `log_path`: Name and path of the log
+* **Errors and Warnings** - List of Errors and Warnings from the Script
+* **Messages, Output and Results (optional)** - List Messages, Outputs and Results
+* **Log Output File** - Name and path of the log
+
+Below we have a scrollabe example of what is included in a log file for an `adsl.R` script. 
 
 
 <style>
@@ -67,16 +82,3 @@ list of packages and functions
  <img src='`r here::here("man/figures/log.png")`'/>
 </div>
 
-# Generating a log
-The log can be generated in a number of ways, below is an example of how to use the `axecute()` function to generate a log. This method is the easiest and most accessible way of creating a log. To learn more about executing code with ```logrx``` please visit our [Execution Vignette](https://pharmaverse.github.io/logrx/articles/execution.html).
-## `axecute()`
-`axecute()` enables the command line submission of a program. A log is 
-set-up around the program, and its code is run safely and loudly (using 
-`safely()` from the `purrr` package).
-```{r axecute, eval = FALSE}
-axecute("my_script.R")
-```
-
-
-## `logrx` addin:
-A log can be generated using the ```logrx``` addin. More information can be found in [logrx](https://pharmaverse.github.io/logrx/index.html).