Post update

Author: psolymos

README.md

@@ -12,6 +12,8 @@ The course emphasizes critical thinking and active learning through hands on pro
 
 The expected outcome of the course is a solid foundation for further professional development via increased confidence in applying these methods for field observations.
 
+![Qpad overview](https://github.com/psolymos/qpad-workshop/raw/main/images/qpad-sketch.jpg)
+
 ## Instructor
 
 [**Dr. Peter Solymos**](https://peter.solymos.org) \
@@ -20,8 +22,6 @@ The expected outcome of the course is a solid foundation for further professiona
 
 ## Outline
 
-> Note: this outline is preliminary and subject to change.
-
 Each day will consist of 3 sessions, roughly one hour each, with short breaks in between.
 
 | Session | Topic | Files |
@@ -42,7 +42,7 @@ Each day will consist of 3 sessions, roughly one hour each, with short breaks in
 |  |  1. QPAD review  |  [Slides](https://peter.solymos.org/qpad-workshop/day4-1-intro.pdf)  |
 |  |  2. Detectability offsets  |  [Notes](https://peter.solymos.org/qpad-workshop/day4-2-offsets.html)  |
 |  |  3. Recordings  |  [Notes](https://peter.solymos.org/qpad-workshop/day4-3-recordings.html)  |
-|  |  4. Closing remarks  |  See slides  |
+|  |  4. Closing remarks  |    |
 
 
 ## Before the course
@@ -93,7 +93,6 @@ qpad_local(day=1)
 
 LOCAL copies will not be tracked and overwritten by git.
 
-
 ## After the course
 
 Expect some follow up :)

day3-2-detection.Rmd

@@ -727,3 +727,7 @@ res
 plot(diff ~ count, res)
 abline(h=0, lty=2)
 ```
+
+Think about how you'd do leave-one-out cross-validation.
+
+Think about how you would include `HAB` effects on $\tau$ (hint: main effect and interactions).

docs/day1-1-intro.pdf

@@ -375,43 +375,9 @@ <h2>Prerequisites</h2>
 <pre class="r"><code>## update bSims - some issues fixed
 #remotes::install_github(&quot;psolymos/bSims&quot;)
 
-library(bSims)              # simulations</code></pre>
-<pre><code>## Loading required package: intrval</code></pre>
-<pre><code>## Loading required package: mefa4</code></pre>
-<pre><code>## Loading required package: Matrix</code></pre>
-<pre><code>## mefa4 0.3-7   2020-02-28</code></pre>
-<pre><code>## 
-## Attaching package: &#39;mefa4&#39;</code></pre>
-<pre><code>## The following object is masked from &#39;package:intrval&#39;:
-## 
-##     %notin%</code></pre>
-<pre><code>## Loading required package: MASS</code></pre>
-<pre><code>## Loading required package: deldir</code></pre>
-<pre><code>## deldir 0.2-9      Nickname: &quot;Morpheus and Euripides&quot;</code></pre>
-<pre><code>## 
-##      Note 1: As of version 0.2-1, error handling in this 
-##      package was amended to conform to the usual R protocol. 
-##      The deldir() function now actually throws an error 
-##      when one occurs, rather than displaying an error number 
-##      and returning a NULL.
-##  
-##      Note 2:  As of version 0.1-29 the arguments &quot;col&quot; 
-##      and &quot;lty&quot; of plot.deldir() had their names changed to 
-##      &quot;cmpnt_col&quot; and &quot;cmpnt_lty&quot; respectively basically 
-##      to allow &quot;col&quot; and and &quot;lty&quot; to be passed as &quot;...&quot; 
-##      arguments.
-##  
-##      Note 3: As of version 0.1-29 the &quot;plotit&quot; argument 
-##      of deldir() was changed to (simply) &quot;plot&quot;.
-##  
-##      See the help for deldir() and plot.deldir().</code></pre>
-<pre><code>## bSims 0.2-3   2021-03-15      kicky-chew</code></pre>
-<pre class="r"><code>library(detect)             # multinomial models</code></pre>
-<pre><code>## Loading required package: Formula</code></pre>
-<pre><code>## Loading required package: stats4</code></pre>
-<pre><code>## Loading required package: pbapply</code></pre>
-<pre><code>## detect 0.4-4      2020-08-12</code></pre>
-<pre class="r"><code>load(&quot;data/josm-data.rda&quot;)  # JOSM data
+library(bSims)              # simulations
+library(detect)             # multinomial models
+load(&quot;data/josm-data.rda&quot;)  # JOSM data
 set.seed(1)</code></pre>
 <p>Just spend a bit of time admiring the package startup messages…</p>
 </div>

docs/day1-2-data-processing.html

@@ -0,0 +1,18 @@
+## rendering all markdown
+
+library(rmarkdown)
+
+fl <- list.files(".", ".Rmd")
+
+for (i in seq_along(f)) {
+  cat(fl[i], "\n")
+  flush.console()
+  o <- rmarkdown::render(input=fl[i], quiet=TRUE)
+  z <- rev(strsplit(o, "/")[[1]])[1]
+  file.copy(
+    from=o,
+    to=paste0("docs/", z),
+    overwrite=TRUE
+  )
+  unlink(o)
+}