Merge pull request #8 from kristinawlai/installation_instructions

Installation instructions

.gitignore

@@ -2,6 +2,7 @@
 .Rhistory
 .RData
 .Ruserdata
+.html
 inst/doc
 /doc/
 /Meta/

README.md

@@ -21,7 +21,7 @@ the longitudinal response of the selected serum antibodies.
 ## Installation
 
 You can install the development version from
-[GitHub](https://github.com/) with:
+[GitHub](https://github.com/) with the following code:
 
 ``` r
 install.packages("devtools")
@@ -30,16 +30,26 @@ devtools::install_github("ucd-serg/serocalculator")
 
 **A Note for Windows Users**
 
-Windows users will need to install Rtools, which contains a collection of tools for building and employing R packages that are still in development. 
+  Windows users will need to install Rtools, which contains a collection of tools for building    and employing R packages that are still in development. This can be done either during the      *devtools* package installation, or independently if *devtools* is already installed. 
+
+
+|  *During devtools installation:*
+|    When prompted to install additional build tools, select "Yes" and Rtools will be installed. |
+
+!(Click Yes to install Rtools along with the *devtools* package)[\vignettes\fig\Rtools1.png]
+|
+
+|  *Independently:*
 
 1. Download Rtools from https://cran.r-project.org/bin/windows/Rtools/
 2. Run the installer
 
-During the Rtools installation you may see a window asking you to “Select Additional Tasks”.
 
-Do *not* select the box for “Edit the system PATH”. devtools and RStudio should put Rtools on the PATH automatically when it is needed.
-Do select the box for “Save version information to registry”. It should be selected by default.
 
+    * During the Rtools installation you may see a window asking you to “Select Additional Tasks”.
+    * Do **not** select the box for “Edit the system PATH”. devtools and RStudio should put Rtools on the PATH automatically when it is needed.
+    * **Do** select the box for “Save version information to registry”. It should be selected by default.
+|
 ## Getting Help
 
 If you need assistance or encounter a clear bug, please file an issue with a minimal reproducible example on [GitHub](https://github.com/UCD-SERG/serocalculator/issues). 

vignettes/installation.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "Serocalculator package installation manual"
-author: "European Centre for Disease Prevention and Control (ECDC)"
+author: "UC Davis Seroepidemiology Research Group (SERG)"
 date: "`r Sys.Date()`"
 output: 
   rmarkdown::html_vignette:
@@ -23,7 +23,7 @@ pkgVersion <- packageDescription(pkgName)$Version
 pkgDate <- packageDescription(pkgName)$Date
 pkgBaseFileName <- paste(pkgName, pkgVersion, sep = "_")
 pkgUrl <- gsub("\n", "", packageDescription(pkgName)$URL)
-pkgPath <- "http://ecdc.europa.eu/en/data-tools/seroincidence-calculator-tool/Documents"
+pkgPath <- "https://ucd-serg.github.io/serocalculator/"
 library("knitr")
 ```
 
@@ -34,13 +34,13 @@ library("knitr")
 Package **`r pkgName`** is written in programming language R and end user must have access to a 
 working installation of R engine. This document describes the most common setup with R installed 
 locally on the user's computer. The screenshots refer to the classical R interface, but the package 
-can also be opened in other Graphical User Interfaces fo R like e.g. 
+can also be opened in other Graphical User Interfaces for R like e.g. 
 [RStudio](http://www.rstudio.com/products/RStudio/).
 
 # 2. Installation steps
 
 R is a free software and can be downloaded from [http://cran.r-project.org/](http://cran.r-project.org/).
-Latest version as of writing this document is **R 3.5.0**. Once the appropriate, operating system 
+Latest version as of writing this document is **R 4.3.1**. Once the appropriate, operating system 
 dependent, version is downloaded, install it on your computer following the standard procedure 
 applicable to the operating system. For Windows the file to be downloaded is the so-called *base* 
 distribution: [http://cran.r-project.org/bin/windows/base/](http://cran.r-project.org/bin/windows/base/).
@@ -85,74 +85,13 @@ include_graphics("fig/RGui1.png")
 
 ## 2.2. Installing *serocalculator* package
 
-Since this is a new installation of R, the **serocalculator** package must be installed before first 
-use. The package can be installed either through a menu option in the graphical user interface (GUI) 
-or with a command executed in the R console. Both options are presented:
+Since this is a new installation of R, the **serocalculator** package must be installed before first use. As of 09/20/2023, **serocalculator** is still in development. To install the development version, you must install the **devtools** package and then download **serocalculator** from GitHub. 
 
-### 2.2.1. Package installation from the graphical user interface
-
-Download the serocalculator package from ECDC website: [`r pkgUrl`](`r pkgUrl`). 
-Two versions of the package are made available:
-
-* binary package (serocalculator_[version].zip) - Microsoft Windows compatible
-* Source package (serocalculator_[version].tar.gz) - cross-platform compatible (MS Windows, Linux, 
-  MacOS)
-
-If your operating system is Windows then it is best to download the Windows binary package.
-
-Go to menu *Packages* and select command *Install package(s) from local files...*:
-
-```{r echo=FALSE, fig.pos="!h", fig.align='center'}
-include_graphics("fig/RGui2.png")
+```r
+install.packages("devtools")
+devtools::install_github("ucd-serg/serocalculator")
 ```
 
-Select the package file and click "Open":
-
-```{r echo=FALSE, fig.pos="!h", fig.align='center'}
-include_graphics("fig/RGui3.png")
-```
-
-Post-installation message should appear:
-
-```{r echo=FALSE, fig.pos="!h", fig.align='center'}
-include_graphics("fig/RGui4.png")
-```
-
-The package is now installed in R. 
-
-### 2.2.2. Package installation from R console
-
-Alternatively, installation of the package can also be performed 
-by executing one of the following commands in the *R console*:
-```{r, include=FALSE, tidy=FALSE}
-chunkTemplate <- "```{r, eval = FALSE}
-# OPTION A
-# Install Windows binary package \"serocalculator\" directly from internet ECDC website:
-install.packages(
-    pkgs = \"{{pkgPath}}/
-                {{pkgBaseFileName}}.zip\",
-    repos = NULL, type = \"win.binary\")
-
-# OPTION B
-# Install source package directly from internet CRAN repository:
-install.packages(\"serocalculator\")
-
-# OPTION C
-# Install Windows binary package from a local file:
-#   install.packages(\"[PATH/TO/FILE/]serocalculator_[version].zip\", 
-#                       repos = NULL, type = \"win.binary\")
-# For instance:
-install.packages(pkgs = \"C:/{{pkgBaseFileName}}.zip\", repos = NULL, type = \"win.binary\")
-
-# OPTION D
-# Install source package from a local file:
-install.packages(pkgs = \"C:/{{pkgBaseFileName}}.tar.gz\", repos = NULL, type = \"source\")
-```"
-chunkSource <- knit_expand(text = chunkTemplate, pkgBaseFileName = pkgBaseFileName)
-```
-
-`r knit(text = chunkSource)`
-
 # 3. Post-installation
 
 Successful installation can be confirmed by loading the package into the workspace