tech prep

Author: stevencarlislewalker

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+Workshop on `macpan2` – Technical Preparation
+================
+
+<!-- omit from toc -->
+
+# Technical Preparation for Workshop on `macpan2`
+
+<!-- omit from toc -->
+
+## Table of Contents
+
+-   [The Most Important Things](#the-most-important-things)
+-   [Installing a Sufficiently Recent Version of
+    R](#installing-a-sufficiently-recent-version-of-r)
+-   [Installing Supporting R
+    Packages](#installing-supporting-r-packages)
+-   [Installing `macpan2`](#installing-macpan2)
+-   [Verify that Everything Worked](#verify-that-everything-worked)
+
+This document describes what you will need to do to have your computer
+ready for the [`macpan2`](https://canmod.github.io/macpan2/) workshop.
+
+## The Most Important Things
+
+If you have trouble or questions about any of the technical instructions
+below, please contact [Steve Walker](mailto:swalk@mcmaster.ca) (the
+instructor) as soon as possible so that we can focus on the material
+during the workshop without technical distractions.
+
+Ideally you will be able to install open source software from the
+internet, both before and during the workshop. If this is not possible,
+please contact [Steve](mailto:swalk@mcmaster.ca) as soon as possible.
+
+Everything we do in the workshop will involve
+[R](https://www.r-project.org/). If you do not use R, please email
+[Steve](mailto:swalk@mcmaster.ca) and briefly describe your coding
+background.
+
+## Installing a Sufficiently Recent Version of R
+
+If you are familiar with [R](https://www.r-project.org/) and have it
+installed, you just need to make sure that you have a sufficiently
+recent version. Please start R and print out the R version using the
+following command.
+
+``` r
+print(R.version.string)
+```
+
+    ## [1] "R version 4.4.2 (2024-10-31)"
+
+This shows that I am using version R version 4.4.2 (2024-10-31). The
+version you get will likely be different. You need to have an R version
+greater than or equal to `4.1.0`. If your version is too old, please
+install the most recent version of R following instructions
+[here](https://cran.rstudio.com/).
+
+If you do not have R installed already, I recommend following the
+installation instructions for
+[RStudio](https://posit.co/download/rstudio-desktop/). These
+instructions involve first installing [R](https://cran.rstudio.com/) and
+then RStudio itself, which is the program that I will use to interact
+with R during the workshop.
+
+It is fine if you would rather use R without RStudio, but if you do not
+have a strong preference I recommend using RStudio.
+
+## Installing Supporting R Packages
+
+The [`macpan2`](https://canmod.github.io/macpan2/) package is designed
+to be used with a set of packages known as the
+[tidyverse](https://www.tidyverse.org/). To get these packages, and one
+more that we will also be using, please open R and issue the following
+command.
+
+``` r
+install.packages(c("tidyverse", "broom.mixed"))
+```
+
+## Installing `macpan2`
+
+To install [`macpan2`](https://canmod.github.io/macpan2/) itself, please
+issue the following commands.
+
+``` r
+repos = c('https://canmod.r-universe.dev', 'https://cloud.r-project.org')
+install.packages('macpan2', repos = repos)
+```
+
+## Verify that Everything Worked
+
+A good test of the above instructions is to copy and paste the following
+lines of code, and make sure that you get the same graph printed out
+below.
+
+``` r
+library(macpan2); library(ggplot2); library(dplyr)
+```
+
+    ## 
+    ## Attaching package: 'dplyr'
+
+    ## The following object is masked from 'package:macpan2':
+    ## 
+    ##     all_equal
+
+    ## The following objects are masked from 'package:stats':
+    ## 
+    ##     filter, lag
+
+    ## The following objects are masked from 'package:base':
+    ## 
+    ##     intersect, setdiff, setequal, union
+
+``` r
+("starter_models"
+ |> mp_tmb_library("sir", package = "macpan2")
+ |> mp_simulator(time_steps = 50, outputs = "infection")
+ |> mp_trajectory()
+ |> mutate(incidence = value)
+ |> ggplot() 
+ + geom_line(aes(time, incidence))
+ + theme_bw()
+)
+```
+
+![](technical-preparation_files/figure-gfm/sir-1.png)<!-- -->