Deploy commit: Proofreading c5 (#1128)

* add first set of reviewer suggestions

* add second set of changes

---------

Co-authored-by: jannes <jannes@cynkra.com> c8635ca

13-transport.md

@@ -511,7 +511,6 @@ This is done using the publicly available OSRM service with the **stplanr** func
 ``` r
 routes_short = route(l = desire_lines_short, route_fun = route_osrm,
                      osrm.profile = "bike")
-#> <simpleError in open.connection(con, "rb"): cannot open the connection to 'https://routing.openstreetmap.de/routed-bike/route/v1/driving/-2.62449584285587,51.5083596238341;-2.66873099020632,51.5135817785512?alternatives=false&geometries=geojson&steps=false&overview=full'>
 ```
 
 The output is `routes_short`, an `sf` object representing routes on the transport network\index{network} that are suitable for cycling (according to the OSRM routing engine at least), one for each desire line.
@@ -570,7 +569,7 @@ routes_short_scenario = routes_short |>
   mutate(bicycle = bicycle + car_driver * uptake,
          car_driver = car_driver * (1 - uptake))
 sum(routes_short_scenario$bicycle) - sum(routes_short$bicycle)
-#> [1] 253
+#> [1] 3850
 ```
 
 Having created a scenario in which approximately 4000 trips have switched from driving to cycling, we can now model where this updated modeled cycling activity will take place.
@@ -584,11 +583,6 @@ route_network_scenario = overline(routes_short_scenario, attrib = "bicycle")
 
 The outputs of the two preceding code chunks are summarized in Figure \@ref(fig:rnetvis) below.
 
-
-```
-#> [plot mode] fit legend/component: Some legend items or map compoments do not fit well, and are therefore rescaled. Set the tmap option 'component.autoscale' to FALSE to disable rescaling.
-```
-
 <div class="figure" style="text-align: center">
 <img src="figures/rnetvis-1.png" alt="Illustration of the percentage of car trips switching to cycling as a function of distance (left) and route network level results of this function (right)." width="49%" /><img src="figures/rnetvis-2.png" alt="Illustration of the percentage of car trips switching to cycling as a function of distance (left) and route network level results of this function (right)." width="49%" />
 <p class="caption">(\#fig:rnetvis)Illustration of the percentage of car trips switching to cycling as a function of distance (left) and route network level results of this function (right).</p>
@@ -648,11 +642,6 @@ ways_centrality = ways_sfn |>
   mutate(betweenness = tidygraph::centrality_edge_betweenness(lengths)) 
 ```
 
-
-```
-#> [plot mode] fit legend/component: Some legend items or map compoments do not fit well, and are therefore rescaled. Set the tmap option 'component.autoscale' to FALSE to disable rescaling.
-```
-
 <div class="figure" style="text-align: center">
 <img src="figures/wayssln-1.png" alt="Illustration of route network datasets. The grey lines represent a simplified road network, with segment thickness proportional to betweenness. The green lines represent potential cycling flows (one way) calculated with the code above." width="100%" />
 <p class="caption">(\#fig:wayssln)Illustration of route network datasets. The grey lines represent a simplified road network, with segment thickness proportional to betweenness. The green lines represent potential cycling flows (one way) calculated with the code above.</p>

404.html

@@ -129,7 +129,7 @@ <h2>Second Edition</h2>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Geocomputation with R</strong>" was written by Robin Lovelace, Jakub Nowosad, Jannes Muenchow. It was last built on 2024-09-26.</p>
+    <p>"<strong>Geocomputation with R</strong>" was written by Robin Lovelace, Jakub Nowosad, Jannes Muenchow. It was last built on 2024-09-28.</p>
   </div>
 
   <div class="col-12 col-md-6 mt-3">

adv-map.html

@@ -1342,7 +1342,7 @@ <h2>Second Edition</h2>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Geocomputation with R</strong>" was written by Robin Lovelace, Jakub Nowosad, Jannes Muenchow. It was last built on 2024-09-26.</p>
+    <p>"<strong>Geocomputation with R</strong>" was written by Robin Lovelace, Jakub Nowosad, Jannes Muenchow. It was last built on 2024-09-28.</p>
   </div>
 
   <div class="col-12 col-md-6 mt-3">

algorithms.html

@@ -529,7 +529,7 @@ <h2>Second Edition</h2>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Geocomputation with R</strong>" was written by Robin Lovelace, Jakub Nowosad, Jannes Muenchow. It was last built on 2024-09-26.</p>
+    <p>"<strong>Geocomputation with R</strong>" was written by Robin Lovelace, Jakub Nowosad, Jannes Muenchow. It was last built on 2024-09-28.</p>
   </div>
 
   <div class="col-12 col-md-6 mt-3">

attr.html

@@ -860,7 +860,7 @@ <h2>Second Edition</h2>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Geocomputation with R</strong>" was written by Robin Lovelace, Jakub Nowosad, Jannes Muenchow. It was last built on 2024-09-26.</p>
+    <p>"<strong>Geocomputation with R</strong>" was written by Robin Lovelace, Jakub Nowosad, Jannes Muenchow. It was last built on 2024-09-28.</p>
   </div>
 
   <div class="col-12 col-md-6 mt-3">

conclusion.html

@@ -132,7 +132,7 @@ <h2>
 </h2>
 <p>A feature of R, and open source software in general, is that there are often multiple ways to achieve the same result.
 The code chunk below illustrates this by using three functions, covered in Chapters <a href="attr.html#attr">3</a> and <a href="geometry-operations.html#geometry-operations">5</a>, to combine the 16 regions of New Zealand into a single geometry:</p>
-<div class="sourceCode" id="cb513"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb511"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://jakubnowosad.com/spData/">spData</a></span><span class="op">)</span></span>
 <span><span class="va">nz_u1</span> <span class="op">=</span> <span class="fu">sf</span><span class="fu">::</span><span class="fu"><a href="https://r-spatial.github.io/sf/reference/geos_combine.html">st_union</a></span><span class="op">(</span><span class="va">nz</span><span class="op">)</span></span>
 <span><span class="va">nz_u2</span> <span class="op">=</span> <span class="fu"><a href="https://rspatial.github.io/terra/reference/aggregate.html">aggregate</a></span><span class="op">(</span><span class="va">nz</span><span class="op">[</span><span class="st">"Population"</span><span class="op">]</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fu"><a href="https://rspatial.github.io/terra/reference/dimensions.html">nrow</a></span><span class="op">(</span><span class="va">nz</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>, <span class="va">sum</span><span class="op">)</span></span>
@@ -154,7 +154,7 @@ <h2>
 The same applies for all packages showcased in this book, although it can be helpful (when not distracting) to be aware of alternatives and being able to justify your choice of software.</p>
 <p>A common choice, for which there is no simple answer, is between <strong>tidyverse</strong> and base R for geocomputation.
 The following code chunk, for example, shows <strong>tidyverse</strong> and base R ways to extract the <code>Name</code> column from the <code>nz</code> object, as described in Chapter <a href="attr.html#attr">3</a>:</p>
-<div class="sourceCode" id="cb514"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb512"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>                          <span class="co"># attach a tidyverse package</span></span>
 <span><span class="va">nz_name1</span> <span class="op">=</span> <span class="va">nz</span><span class="op">[</span><span class="st">"Name"</span><span class="op">]</span>                   <span class="co"># base R approach</span></span>
 <span><span class="va">nz_name2</span> <span class="op">=</span> <span class="va">nz</span> <span class="op">|&gt;</span>                        <span class="co"># tidyverse approach</span></span>
@@ -280,13 +280,13 @@ <h3>
 You could simply ask how to do this in one of the places outlined in the previous section.
 However, it is likely that you will get a better response if you provide a reproducible example of what you have tried so far.
 The following code creates a map of the world with blue sea and green land, but the land is not filled in:</p>
-<div class="sourceCode" id="cb515"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb513"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://r-spatial.github.io/sf/">sf</a></span><span class="op">)</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://jakubnowosad.com/spData/">spData</a></span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rspatial.github.io/terra/reference/plot.html">plot</a></span><span class="op">(</span><span class="fu"><a href="https://r-spatial.github.io/sf/reference/st_geometry.html">st_geometry</a></span><span class="op">(</span><span class="va">world</span><span class="op">)</span>, col <span class="op">=</span> <span class="st">"green"</span><span class="op">)</span></span></code></pre></div>
 <p>If you post this code in a forum, it is likely that you will get a more specific and useful response.
 For example, someone might respond with the following code, which demonstrably solves the problem, as illustrated in Figure <a href="conclusion.html#fig:16-synthesis-reprex">16.1</a>:</p>
-<div class="sourceCode" id="cb516"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb514"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://r-spatial.github.io/sf/">sf</a></span><span class="op">)</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://jakubnowosad.com/spData/">spData</a></span><span class="op">)</span></span>
 <span><span class="co"># use the bg argument to fill in the land</span></span>
@@ -444,7 +444,7 @@ <h2>Second Edition</h2>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Geocomputation with R</strong>" was written by Robin Lovelace, Jakub Nowosad, Jannes Muenchow. It was last built on 2024-09-26.</p>
+    <p>"<strong>Geocomputation with R</strong>" was written by Robin Lovelace, Jakub Nowosad, Jannes Muenchow. It was last built on 2024-09-28.</p>
   </div>
 
   <div class="col-12 col-md-6 mt-3">