formula cleaning

nicholasjclark · web-flow · commit a508e2f78182 · 2024-11-30T09:25:46.000+10:00
diff --git a/ESA_slidedeck.Rmd b/ESA_slidedeck.Rmd
@@ -1,5 +1,5 @@
 ---
-title: "Ecological Time Series Analysis and Forecasting in R"
+title: "Ecological Time Series Analysis and Forecasting"
 institute: "School of Veterinary Science, University of Queensland, Australia"
 author: "Nicholas Clark"
 date: "Friday 13th December, 2024"
@@ -231,7 +231,7 @@ myscatter = function(x,
 Press the "o" key on your keyboard to navigate among html slides
 
 Access the [workshop materials here](https://github.com/nicholasjclark/ESA_2024_timeseries)
-- View the sample `R` scripts in [live_code_examples](https://github.com/nicholasjclark/ESA_2024_timeseries/tree/main/live_code_examples)
+- View the sample `r fontawesome::fa("r-project", fill = "steelblue")` scripts in [live_code_examples](https://github.com/nicholasjclark/ESA_2024_timeseries/tree/main/live_code_examples)
 - Use the [Google Doc](https://docs.google.com/document/d/1xd3icf1wxGxO3SVt2AmKO8CkeKv1QpsxgqK7rR15U08/edit?tab=t.0#heading=h.ds87nag4ykyb) to ask questions
 
 Relevant open-source materials include:
@@ -616,7 +616,7 @@ background-image: url('./resources/SS_model.svg')
 
 \begin{align*}
 Y_t & \sim Normal(\alpha + \sum_{j=1}^{J}(\beta_j x_{jt}) + Zz_t, \sigma_y) \\
-z_t & \sim Normal(\sum_{k=1}^{K}(\beta_k q_{kt}), \sigma_z) 
+z_t & \sim Normal(f(z_{t-lag}) + \sum_{k=1}^{K}(\beta_k q_{kt}), \sigma_z) 
 \end{align*}
 
 
@@ -770,7 +770,7 @@ background-image: url('./ESA_slidedeck_files/figure-html/complexity-1.svg')
 
 \begin{align*}
 \mathbb{E}(\boldsymbol{Y_t}|\boldsymbol{X_t}, \boldsymbol{Q_t}) & = g^{-1}(\alpha + \sum_{j=1}^{J}f(x_{jt}) + Zz_t) \\
-z_t & \sim Normal(\sum_{k=1}^{K}f(q_{kt}), \sigma_z) 
+z_t & \sim Normal(f(z_{t-lag}) + \sum_{k=1}^{K}f(q_{kt}), \sigma_z) 
 \end{align*}
 
 
@@ -833,7 +833,7 @@ model <- mvgam(
 
 ## Produce all `Stan` code and objects
 ```{r eval=FALSE}
-code(model)
+stancode(model)
 ```
 .small[
 ```{r echo=FALSE}
@@ -889,4 +889,4 @@ background-size: contain
 
 class: inverse middle center big-subsection
 
-# Live code example
+# Live code examples
diff --git a/ESA_slidedeck.html b/ESA_slidedeck.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <html lang="" xml:lang="">
   <head>
-    <title>Ecological Time Series Analysis and Forecasting in R</title>
+    <title>Ecological Time Series Analysis and Forecasting</title>
     <meta charset="utf-8" />
     <meta name="author" content="Nicholas Clark" />
     <script src="libs/header-attrs/header-attrs.js"></script>
@@ -23,7 +23,7 @@
 class: inverse, middle, left, my-title-slide, title-slide
 
 .title[
-# Ecological Time Series Analysis and Forecasting in R
+# Ecological Time Series Analysis and Forecasting
 ]
 .author[
 ### Nicholas Clark
@@ -61,7 +61,7 @@
 Press the "o" key on your keyboard to navigate among html slides
 
 Access the [workshop materials here](https://github.com/nicholasjclark/ESA_2024_timeseries)
-- View the sample `R` scripts in [live_code_examples](https://github.com/nicholasjclark/ESA_2024_timeseries/tree/main/live_code_examples)
+- View the sample <svg aria-hidden="true" role="img" viewBox="0 0 581 512" style="height:1em;width:1.13em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:steelblue;overflow:visible;position:relative;"><path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"/></svg> scripts in [live_code_examples](https://github.com/nicholasjclark/ESA_2024_timeseries/tree/main/live_code_examples)
 - Use the [Google Doc](https://docs.google.com/document/d/1xd3icf1wxGxO3SVt2AmKO8CkeKv1QpsxgqK7rR15U08/edit?tab=t.0#heading=h.ds87nag4ykyb) to ask questions
 
 Relevant open-source materials include:
@@ -336,7 +336,7 @@
 
 `\begin{align*}
 Y_t &amp; \sim Normal(\alpha + \sum_{j=1}^{J}(\beta_j x_{jt}) + Zz_t, \sigma_y) \\
-z_t &amp; \sim Normal(\sum_{k=1}^{K}(\beta_k q_{kt}), \sigma_z) 
+z_t &amp; \sim Normal(f(z_{t-lag}) + \sum_{k=1}^{K}(\beta_k q_{kt}), \sigma_z) 
 \end{align*}`
 
 
@@ -424,7 +424,7 @@
 
 `\begin{align*}
 \mathbb{E}(\boldsymbol{Y_t}|\boldsymbol{X_t}, \boldsymbol{Q_t}) &amp; = g^{-1}(\alpha + \sum_{j=1}^{J}f(x_{jt}) + Zz_t) \\
-z_t &amp; \sim Normal(\sum_{k=1}^{K}f(q_{kt}), \sigma_z) 
+z_t &amp; \sim Normal(f(z_{t-lag}) + \sum_{k=1}^{K}f(q_{kt}), \sigma_z) 
 \end{align*}`
 
 
@@ -489,7 +489,7 @@
 ## Produce all `Stan` code and objects
 
 ```r
-code(model)
+stancode(model)
 ```
 .small[
 
@@ -757,7 +757,7 @@
 
 class: inverse middle center big-subsection
 
-# Live code example
+# Live code examples
     </textarea>
 <style data-target="print-only">@media screen {.remark-slide-container{display:block;}.remark-slide-scaler{box-shadow:none;}}</style>
 <script src="https://remarkjs.com/downloads/remark-latest.min.js"></script>
