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Sat, 14 Jul 2018 00:00:00 +0000

Concentration of Senate Representation
https://www.carlbfrederick.com/post/concentrationofsenaterepresentation/
Sat, 14 Jul 2018 00:00:00 +0000
https://www.carlbfrederick.com/post/concentrationofsenaterepresentation/
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<p>Recently saw this tweet <blockquote class="twittertweet"><p lang="en" dir="ltr">I want to repeat a statistic I use in every talk: by 2040 or so, 70 percent of Americans will live in 15 states. Meaning 30 percent will choose 70 senators. And the 30% will be older, whiter, more rural, more male than the 70 percent. Unsettling to say the least <a href="https://t.co/EGPD5nE4qG">https://t.co/EGPD5nE4qG</a></p>— Norman Ornstein (@NormOrnstein) <a href="https://twitter.com/NormOrnstein/status/1016789064379334656?ref_src=twsrc%5Etfw">July 10, 2018</a></blockquote>
<script async src="https://platform.twitter.com/widgets.js" charset="utf8"></script>
and it reminded me of similar discussions I have had in which I was taking a similar position. I know that the point of the Senate was to ensure that states with large and small populations were on equal footing in one of the houses of the legislature. However, it seems to me that at some point the imbalance in population size between states may outweigh the desire for numerical equality. Has the degree of inequality in Senate representation grown over time? <em>I will leave the more intersting question about differential demographics for another post.</em></p>
<p>Since the data are readily available, I decided to look into things to decide how strongly I should argue this point in the future.</p>
<div id="gettingthedata" class="section level1">
<h1>Getting the data</h1>
<p>The <a href="https://www.nhgis.org/">National Historic Geographic Information System</a> contains a wealth of data from the Census over time in a standardized, customizable download extracts. To make things simple, I chose to download total population figures by state from Decennial Censuses back to 1790.</p>
<pre class="r"><code>library(tidyverse)
stpop < read_csv("ExternalData/nhgis0001_ts_nominal_state.csv") %>%
select(year = YEAR, state = STATE, pop = A00AA) %>%
filter(!grepl("Territory", state),
!grepl("District", state),
!grepl("Persons", state),
!grepl("Puerto Rico", state)) %>%
group_by(year) %>%
arrange(pop) %>%
mutate(
cumSen = row_number(pop)/n(),
cumPop = cumsum(pop)/sum(pop)
) %>%
nest %>%
arrange(year)</code></pre>
</div>
<div id="changesovertime" class="section level1">
<h1>Changes over time</h1>
<p>Since the number of Senators per state is constant across states and over time, the question boils down to one of changing population over time. The best way I can think of to answer this question is to look at summary measures of inequality that describe distributions. A suite of these measures are available in the <a href="https://CRAN.Rproject.org/package=ineq"><code>ineq</code> package</a>–instead of income or wealth distributions, we will be looking at population distributions. See the help files (<code>?ineq::ineq</code>) for descriptions of what each of the measures is and for the relevant citations.</p>
<pre class="r"><code>library(ineq)
stpop < stpop %>%
mutate(
nStates = map_dbl(data, nrow),
Gini = map_dbl(data, ~Gini(.$pop)),
RS = map_dbl(data, ~RS(.$pop)),
Atkinson = map_dbl(data, ~Atkinson(.$pop)),
Theil = map_dbl(data, ~Theil(.$pop)),
var.coeff = map_dbl(data, ~var.coeff(.$pop)),
entropy = map_dbl(data, ~entropy(.$pop))
) %>%
unnest
stpop %>%
gather(metric, value, Gini, RS, Atkinson, Theil, var.coeff, entropy) %>%
group_by(year, metric, value) %>%
summarize %>%
ggplot(aes(x = year, y = value, color = metric)) +
geom_point() +
geom_smooth(se=FALSE) +
theme_minimal() +
labs(x = "", y = "") +
facet_wrap(~metric, scales = "free") +
theme(legend.position = "none")</code></pre>
<p><img src="https://www.carlbfrederick.com/post/20180714concentrationofsenaterepresentation_files/figurehtml/calculate%20ineq%20measures%20and%20plot%20trends1.png" width="672" /></p>
<p>The scale of each of the metrics is irrelevant; the point is that each shows a consistent and fairly linear increase over the history of the United States. The obvious conclusion is that as the US has expanded its territory and grown in population, its population has also become relatively more concentrated across states.</p>
<p>Another way to look at this issue is to examine the cumulative distribution of state populations over time, or the Lorenz curves of share of population on the yaxis and share of senators on the xaxis. In lieu of 23 separate plots, an interactive, plotly version is below. For reference, I have also included the value of the popular Gini coefficient for that year. The red line is represents what the distribution would look like if each state had an equal share of the total population. The farther the black curve is from the red line, the more unequally population is distributed across states.</p>
<pre class="r"><code>library(plotly)
out < stpop %>%
ggplot(aes(x = cumSen, y = cumPop)) +
geom_point(aes(frame = year)) +
geom_line(aes(frame = year)) +
geom_text(x = .20, y = .9, vjust = 0, hjust = 0,
aes(label = paste("Year = ", year, "\nGini = ", formatC(Gini, digits = 3, format = "f")),
frame = year)) +
geom_line(data = data.frame(cumSen = c(0,1), cumPop = c(0,1)), color = "red") +
scale_x_continuous(labels = scales::percent) +
scale_y_continuous(labels = scales::percent) +
theme_minimal() +
labs(y = "Cumulative Population", x = "Cumulative Senators")
ggplotly(out, tooltip = NULL)</code></pre>
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/>Gini = 0.505","Year = 1990 <br />Gini = 0.505","Year = 1990 <br />Gini = 0.505","Year = 1990 <br />Gini = 0.505","Year = 1990 <br />Gini = 0.505","Year = 1990 <br />Gini = 0.505","Year = 1990 <br />Gini = 0.505","Year = 1990 <br />Gini = 0.505","Year = 1990 <br />Gini = 0.505","Year = 1990 <br />Gini = 0.505","Year = 1990 <br />Gini = 0.505","Year = 1990 <br />Gini = 0.505","Year = 1990 <br />Gini = 0.505","Year = 1990 <br />Gini = 0.505","Year = 1990 <br />Gini = 0.505","Year = 1990 <br />Gini = 0.505","Year = 1990 <br />Gini = 0.505","Year = 1990 <br />Gini = 0.505","Year = 1990 <br />Gini = 0.505","Year = 1990 <br />Gini = 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= 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 0.503","Year = 2000 <br />Gini = 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= 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503","Year = 2010 <br />Gini = 0.503"],"hovertext":["","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","","",""],"frame":"2010","textfont":{"size":14.6645669291339,"color":"rgba(0,0,0,1)"},"type":"scatter","mode":"text","hoveron":"points","showlegend":false,"xaxis":"x","yaxis":"y","hoverinfo":"text","visible":true}],"traces":[0,1]}],"base_url":"https://plot.ly"},"evals":["config.modeBarButtonsToAdd.0.click"],"jsHooks":{"render":[{"code":"function(el, x) { var ctConfig = crosstalk.var('plotlyCrosstalkOpts').set({\"on\":\"plotly_click\",\"persistent\":false,\"dynamic\":false,\"selectize\":false,\"opacityDim\":0.2,\"selected\":{\"opacity\":1}}); }","data":null}]}}</script>
<p>This post doesn’t fully address the implications of <span class="citation">@NormOrnstein</span>’s point: I don’t do any forecasting and don’t disaggregate anything by race or other predictors of party identification, but I think it is interesting to think about whether and at what point the reality of where people live overcome whatever benefits may have come from a legislative body that divides power equally across arbitrarily chosen geographic divisions. At what point does this violate the basic <strong>one person, one vote</strong> premise of democracy?</p>
</div>

Uncovering the relationships among functions in a package
https://www.carlbfrederick.com/post/uncoveringtherelationshipsamongfunctionsinapackage/
Sat, 03 Mar 2018 00:00:00 +0000
https://www.carlbfrederick.com/post/uncoveringtherelationshipsamongfunctionsinapackage/
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<p>I maintain a few internal R packages that we have at work. Recently, and perhaps foolishly, I decided that I needed to totally refactor one of them to add some more bells and whistles. A substantial part of this task involved simplifying the internal workflow of the package. I needed to be sure not to omit any of the previous functionality, but a simple list of all the exported and unexported functions was not sufficient.<a href="#fn1" class="footnoteRef" id="fnref1"><sup>1</sup></a></p>
<p>So, I decided to map the dependencies between all of the internal functions (e.g. which functions called which). I found it useful, so I thought I’d share a function I wrote that does just that: visualizes the relationships among functions in a package. The functions are available at <a href="https://gist.github.com/carlbfrederick/b30d861ea80a27fad4e44623c41e0170">this gist</a>.</p>
<p>For the sake of this post, I will use the <a href="https://cran.rproject.org/web/packages/merTools/index.html"><code>merTools</code></a> package that I have had the pleasure of working on with a great coauthor. The end results are:</p>
<pre class="r"><code>suppressMessages(
devtools::source_gist("b30d861ea80a27fad4e44623c41e0170", filename = "packageFunctionMap.R")
)
fake < plotFcnDependencies("merTools")
fake %>% select_nodes_by_degree(expressions = "deg > 0") %>% transform_to_subgraph_ws %>% render_graph</code></pre>
<div id="htmlwidget1" style="width:672px;height:480px;" class="grViz htmlwidget"></div>
<script type="application/json" datafor="htmlwidget1">{"x":{"diagram":"digraph {\n\ngraph [layout = \"dot\",\n outputorder = \"edgesfirst\",\n bgcolor = \"white\",\n rankdir = \"LR\"]\n\nnode [fontname = \"Helvetica\",\n fontsize = \"10\",\n shape = \"circle\",\n fixedsize = \"false\",\n width = \"0.5\",\n style = \"filled\",\n fillcolor = \"aliceblue\",\n color = \"gray70\",\n fontcolor = \"gray50\"]\n\nedge [fontname = \"Helvetica\",\n fontsize = \"8\",\n len = \"1.5\",\n color = \"gray80\",\n arrowsize = \"0.5\"]\n\n \"1\" [label = \"averageObs\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"4\" [label = \"buildModelMatrix\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"5\" [label = \"collapseFrame\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"7\" [label = \"draw.merMod\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"8\" [label = \"easyVarCorr\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"9\" [label = \"expectedRank\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"10\" [label = \"fastdisp\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"12\" [label = \"findFormFuns\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"18\" [label = \"mkNewReTrms\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"19\" [label = \"modelFixedEff\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"24\" [label = \"predictInterval\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"25\" [label = \"print.merModList\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"26\" [label = \"randomObs\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"29\" [label = \"REimpact\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"30\" [label = \"reOnly\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"31\" [label = \"REquantile\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"33\" [label = \"residDF.merMod\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"37\" [label = \"RHSForm\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"41\" [label = \"setup_parallel\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"44\" [label = \"stripAttributes\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"46\" [label = \"subsetList\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"47\" [label = \"superFactor\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"51\" [label = \"wiggle\", fontsize = \"20\", shape = \"rectangle\", fillcolor = \"#F0F8FF\", fontcolor = \"#000000\"] \n \"1\">\"12\" \n \"1\">\"31\" \n \"1\">\"44\" \n \"1\">\"46\" \n \"1\">\"47\" \n \"4\">\"18\" \n \"4\">\"30\" \n \"4\">\"37\" \n \"7\">\"1\" \n \"7\">\"26\" \n \"10\">\"8\" \n \"12\">\"5\" \n \"24\">\"4\" \n \"24\">\"33\" \n \"24\">\"41\" \n \"25\">\"19\" \n \"26\">\"44\" \n \"26\">\"46\" \n \"26\">\"47\" \n \"29\">\"9\" \n \"29\">\"24\" \n \"51\">\"47\" \n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script>
<p>This diagram shows which of the <code>merTools</code> functions call other <code>merTools</code> functions. Well, technically it shows all of the functions that explicitly call other functions. It does <strong>not</strong> include dependencies that are based on the output of other functions and/or functions that do not call other internal functions. The latter would have degree = 0 in social network terms.</p>
<p>Columns to the left are upstream and columns to the right are downstream. For example <code>REimpact()</code> calls <code>expectedRank()</code> and <code>predictInterval()</code>. <code>predictInterval()</code> then goes on to call three more functions, etc.</p>
<p>The practical value of this exercise comes from the following sorts of insights:</p>
<ul>
<li><code>stripAttributes()</code> is called by both <code>averageObs()</code> and <code>randomObs()</code>, don’t forget to include that functionality in whatever function(s) replace those two; and</li>
<li><code>fastdisp()</code> is the only function that calls <code>easyVarCorr()</code>, perhaps <code>easyVarCorr()</code> is a good candidate to be rolled into <code>fastdisp()</code> if there are no other use cases for this function.</li>
</ul>
<div id="steppingthroughthefunctions" class="section level2">
<h2>Stepping through the functions</h2>
<p>The first function, <code>ls_fcns()</code>, retrieves the names of the functions from a namespace (using <code>lsf.str</code>) and returns it as a character vector.</p>
<pre class="r"><code>ls_fcns < function(pkg) {
fcns < unclass(lsf.str(envir = asNamespace(pkg), all = TRUE))
return(as.character(fcns))
}
ls_fcns("merTools")</code></pre>
<pre><code>## [1] "averageObs" "bglmerModList" "blmerModList"
## [4] "buildModelMatrix" "collapseFrame" "draw"
## [7] "draw.merMod" "easyVarCorr" "expectedRank"
## [10] "fastdisp" "FEsim" "findFormFuns"
## [13] "formulaBuild" "glmerModList" "ICC"
## [16] "levelfun" "lmerModList" "mkNewReTrms"
## [19] "modelFixedEff" "modelInfo" "modelRandEffStats"
## [22] "plotFEsim" "plotREsim" "predictInterval"
## [25] "print.merModList" "randomObs" "REcorrExtract"
## [28] "REextract" "REimpact" "reOnly"
## [31] "REquantile" "REsdExtract" "residDF.merMod"
## [34] "REsim" "reTermCount" "reTermNames"
## [37] "RHSForm" "RMSE.merMod" "safeDeparse"
## [40] "sanitizeNames" "setup_parallel" "shinyMer"
## [43] "shuffle" "stripAttributes" "subBoot"
## [46] "subsetList" "superFactor" "thetaExtract"
## [49] "trimModelFrame" "VarCorr.merModList" "wiggle"
## [52] "zzz"</code></pre>
<p>The second function, <code>fcn_deps()</code>, cycles through each function to and does a regular expression search to see which, if any, of the other functions from that namespace are called. This part could be written more efficiently, I’m sure, but I was starting to feel bad about procrastinating too much. Feel free to suggest improvements in the comments or via twitter – <a href="https://twitter.com/carlbfrederick">@carlbfrederick</a>.</p>
<pre class="r"><code>fcn_deps < function(pkg) {
fcns < ls_fcns(pkg)
out < data.frame(Function = as.character(),
Dependency_Function = as.character(),
Number_Calls = as.integer())
for (i in fcns) {
this_fcn < capture.output(getAnywhere(i))
for (j in fcns[grep(i, fcns)]) {
dep_fcns < grep(paste(j, "\\(", sep=""), this_fcn)
if (length(dep_fcns > 0)) {
out < rbind(out,
data.frame(Function = i,
Dependency_Function = j,
Number_Calls = length(dep_fcns)))
}
}
}
return(out)
}
fcn_deps("merTools") %>% as_data_frame</code></pre>
<pre><code>## # A tibble: 22 x 3
## Function Dependency_Function Number_Calls
## * <fct> <fct> <int>
## 1 averageObs findFormFuns 1
## 2 averageObs REquantile 1
## 3 averageObs stripAttributes 1
## 4 averageObs subsetList 2
## 5 averageObs superFactor 1
## 6 buildModelMatrix mkNewReTrms 1
## 7 buildModelMatrix reOnly 1
## 8 buildModelMatrix RHSForm 1
## 9 draw.merMod averageObs 1
## 10 draw.merMod randomObs 1
## # ... with 12 more rows</code></pre>
<p>As you can see, <code>fcn_deps()</code> returns a data.frame with three columns: Function, Dependency_Function and Number_Calls. The first two are used to create the diagram. I don’t recall what I originally intended to do with Number_Calls, but it is still there.</p>
<p>The third function, <code>plotFcnDependencies()</code>, produces the <a href="https://cran.rstudio.com/web/packages/DiagrammeR/index.html"><code>DiagrammeR</code></a> <span class="citation">[@Ianone]</span><br />
object that can be plotted. It is definitely “hacky” and will throw some errors that I haven’t quite ironed out yet, hence the <code>try()</code> in there.</p>
<p>The for loop is used to place the functions horizontally in the diagram above by calculating the longest of the shortest paths from each function to all the others. For example, the longest shortest paths between <code>draw.MerMod()</code> and the rest of the functions is 4. I call this quantity depth in the function.</p>
<p>Using this depth quantity, the rest of the function just creates the node and edge data.frames and then creates the diagram using the <code>DiagrammeR</code> package … and voila!</p>
<pre class="r"><code>plotFcnDependencies < function(pkg) {
fcns < ls_fcns(pkg)
depFcn < fcn_deps(pkg)
depth < NULL
for (i in fcns) {
try(suppressWarnings(dist < max(sapply(igraph::shortest_paths(igraph::graph_from_data_frame(depFcn[,1:2]), from = i)$vpath, length))))
depth < c(depth, dist)
dist < 0
}
nodes < data.frame(nodes = fcns,
type = "",
label = htmltools::htmlEscape(fcns),
depth = depth)
nodes < dplyr::arrange(nodes, desc(depth))
out < DiagrammeR::create_graph(
nodes_df = nodes,
edges_df = DiagrammeR::create_edges(
from = depFcn$Function,
to = depFcn$Dependency_Function,
rel = "leading_to"
),
graph_name = paste(pkg, " (version ", packageVersion(pkg), ") Function Map", sep=""),
graph_attrs = c("layout = dot", "rankdir = LR"),
node_attrs = "fontsize = 20"
)
return(out)
}</code></pre>
</div>
<div id="advice" class="section level2">
<h2>Advice</h2>
<p>Many packages have <em>a lot</em> of functions. Mapping an entire package often results in an unreadable network diagram. Go ahead an make a diagram of <code>dplyr</code> once and you will see what I mean.</p>
</div>
<div id="ideasforfurtherenhancements" class="section level2">
<h2>Ideas for further enhancements</h2>
<ol style="liststyletype: decimal">
<li>Differentiate exported functions from unexported functions.</li>
<li>Add an argument to focus on certain function(s) to focus the diagram on the area of interest.</li>
</ol>
<p>Thanks for reading! Feel free to join the discussion below.</p>
<pre class="r"><code>devtools::session_info()</code></pre>
<pre><code>## Session info </code></pre>
<pre><code>## setting value
## version R version 3.3.2 (20161031)
## system x86_64, darwin13.4.0
## ui X11
## language (EN)
## collate en_US.UTF8
## tz <NA>
## date 20180303</code></pre>
<pre><code>## Packages </code></pre>
<pre><code>## package * version date
## abind 1.45 20160721
## arm 1.93 20161127
## assertthat 0.2.0 20170411
## backports 1.1.2 20171213
## bindr 0.1 20161113
## bindrcpp * 0.2 20170617
## blme 1.04 20150614
## blogdown 0.5 20180128
## bookdown 0.5 20170820
## brew 1.06 20110413
## broom 0.4.2 20170213
## cellranger 1.1.0 20160727
## cli 1.0.0 20171105
## coda 0.191 20161208
## colorspace 1.32 20161214
## crayon 1.3.4 20170916
## curl 3.1 20180130
## devtools 1.12.0 20160624
## DiagrammeR * 0.9.3 20180130
## digest 0.6.12 20170127
## downloader 0.4 20150709
## dplyr * 0.7.4 20170928
## DT 0.2 20160809
## evaluate 0.10.1 20170624
## forcats * 0.2.0 20170123
## foreign 0.867 20160913
## ggplot2 * 2.2.1 20161230
## glue 1.2.0 20171029
## gridExtra 2.3 20170909
## gtable 0.2.0 20160226
## haven 1.1.0 20170709
## hms 0.3 20161122
## htmltools 0.3.6 20170428
## htmlwidgets 1.0 20180120
## httpuv 1.3.5 20170704
## httr 1.3.1 20170820
## igraph 1.1.2 20170721
## influenceR 0.1.0 20150903
## jsonlite 1.5 20170601
## knitr 1.18.10 20180128
## lattice 0.2034 20160906
## lazyeval 0.2.0 20160612
## lme4 1.112 20160416
## lubridate 1.7.1 20171103
## magrittr 1.5 20141122
## MASS 7.345 20160421
## Matrix 1.27.1 20160901
## memoise 1.0.0 20160129
## merTools 0.3.0 20161212
## mime 0.5 20160707
## minqa 1.2.4 20141009
## mnormt 1.55 20161015
## modelr 0.1.1 20170724
## munsell 0.4.3 20160213
## mvtnorm 1.05 20160202
## nlme 3.1128 20160510
## nloptr 1.0.4 20140804
## pillar 1.1.0 20180114
## pkgconfig 2.0.1 20170321
## plyr 1.8.4 20160608
## psych 1.7.3.21 20170322
## purrr * 0.2.4 20171018
## R6 2.2.2 20170617
## RColorBrewer 1.12 20141207
## Rcpp 0.12.13 20170928
## readr * 1.1.1 20170516
## readxl 1.0.0 20170418
## reshape2 1.4.2 20161022
## rgexf 0.15.3 20150324
## rlang 0.1.6 20171221
## rmarkdown 1.8 20171117
## Rook 1.11 20141020
## rprojroot 1.32 20180103
## rstudioapi 0.7 20170907
## rvest 0.3.2 20160617
## scales 0.5.0 20170824
## shiny 1.0.5 20170823
## stringi 1.1.5 20170407
## stringr * 1.2.0 20170218
## tibble * 1.4.1 20171225
## tidyr * 0.7.2 20171016
## tidyverse * 1.2.1 20171114
## utf8 1.1.3 20180103
## viridis 0.4.1 20180108
## viridisLite 0.2.0 20170324
## visNetwork 2.0.3 20180109
## withr 1.0.2 20160620
## xfun 0.1 20180122
## XML 3.981.5 20161110
## xml2 1.1.1 20170124
## xtable 1.82 20160205
## yaml 2.1.16 20171212
## source
## CRAN (R 3.3.0)
## CRAN (R 3.3.2)
## cran (@0.2.0)
## cran (@1.1.2)
## cran (@0.1)
## cran (@0.2)
## CRAN (R 3.3.0)
## Github (rstudio/blogdown@aa98b32)
## cran (@0.5)
## CRAN (R 3.3.0)
## cran (@0.4.2)
## CRAN (R 3.3.0)
## CRAN (R 3.3.2)
## CRAN (R 3.3.2)
## CRAN (R 3.3.2)
## CRAN (R 3.3.2)
## local
## CRAN (R 3.3.0)
## Github (richiannone/DiagrammeR@9d6a8e2)
## cran (@0.6.12)
## CRAN (R 3.3.0)
## cran (@0.7.4)
## CRAN (R 3.3.0)
## cran (@0.10.1)
## CRAN (R 3.3.2)
## CRAN (R 3.3.2)
## cran (@2.2.1)
## CRAN (R 3.3.2)
## cran (@2.3)
## CRAN (R 3.3.0)
## CRAN (R 3.3.2)
## CRAN (R 3.3.2)
## cran (@0.3.6)
## CRAN (R 3.3.2)
## cran (@1.3.5)
## CRAN (R 3.3.2)
## CRAN (R 3.3.2)
## CRAN (R 3.3.0)
## cran (@1.5)
## Github (yihui/knitr@1bdaf39)
## CRAN (R 3.3.2)
## CRAN (R 3.3.0)
## CRAN (R 3.3.0)
## CRAN (R 3.3.2)
## CRAN (R 3.3.0)
## CRAN (R 3.3.2)
## CRAN (R 3.3.2)
## CRAN (R 3.3.0)
## CRAN (R 3.3.2)
## CRAN (R 3.3.0)
## CRAN (R 3.3.0)
## CRAN (R 3.3.0)
## CRAN (R 3.3.2)
## CRAN (R 3.3.0)
## CRAN (R 3.3.0)
## CRAN (R 3.3.2)
## CRAN (R 3.3.0)
## CRAN (R 3.3.2)
## cran (@2.0.1)
## CRAN (R 3.3.0)
## cran (@1.7.3.2)
## CRAN (R 3.3.2)
## cran (@2.2.2)
## CRAN (R 3.3.0)
## cran (@0.12.13)
## CRAN (R 3.3.2)
## CRAN (R 3.3.2)
## CRAN (R 3.3.0)
## CRAN (R 3.3.0)
## CRAN (R 3.3.2)
## cran (@1.8)
## CRAN (R 3.3.0)
## cran (@1.32)
## CRAN (R 3.3.2)
## CRAN (R 3.3.0)
## cran (@0.5.0)
## cran (@1.0.5)
## cran (@1.1.5)
## cran (@1.2.0)
## CRAN (R 3.3.2)
## CRAN (R 3.3.2)
## CRAN (R 3.3.2)
## CRAN (R 3.3.2)
## CRAN (R 3.3.2)
## cran (@0.2.0)
## CRAN (R 3.3.2)
## CRAN (R 3.3.0)
## CRAN (R 3.3.2)
## CRAN (R 3.3.2)
## CRAN (R 3.3.2)
## CRAN (R 3.3.0)
## cran (@2.1.16)</code></pre>
</div>
<div class="footnotes">
<hr />
<ol>
<li id="fn1"><p>Also developing this function was a fun way to put off doing the hard work.<a href="#fnref1">↩</a></p></li>
</ol>
</div>

Using R to Create Google Maps
https://www.carlbfrederick.com/post/usingrtocreategooglemaps/
Fri, 09 Feb 2018 00:00:00 +0000
https://www.carlbfrederick.com/post/usingrtocreategooglemaps/
<p>Google maps are a great way to share maps that users can interact with and customize for their own purposes. The <a href="https://cran.rproject.org/web/packages/RgoogleMaps/"><code>RgoogleMaps</code></a> <span class="citation">(Loecher and Ropkins 2015)</span> and <a href="https://cran.rproject.org/web/packages/ggmap/"><code>ggmap</code></a> <span class="citation">(Kahle and Wickham 2013)</span> packages are great tools to download static map queries from Google maps and plot over them. There are some helpful tutorials on using <code>ggmap</code> <a href="https://rpubs.com/nickbearman/rgooglemapmaking">here</a> and <a href="https://www.youtube.com/watch?v=qSVwTj60di8">a video here</a>.</p>
<p>This post illustrates how I have implemented the reverse process: creating maps in R and embedding them in Google Maps using the awesome <a href="https://cran.rstudio.com/web/packages/plotKML/index.html"><code>plotKML</code></a> <span class="citation">(Hengl et al. 2015)</span> and <a href="https://cran.rstudio.com/web/packages/rmapshaper/index.html"><code>rmapshaper</code></a> <span class="citation">(Teucher and Russell 2017)</span> packages. Specifically, I wanted to create a shareable map that overlaid Wisconsin school district boundaries onto the regular Google Maps interface to share with users who are not R users.</p>
<div id="createspatialpolygondataframeinr" class="section level2">
<h2>Create SpatialPolygonDataFrame in R</h2>
<p>Wisconsin’s Department of Public Instruction has <a href="https://dpi.wi.gov/gis/schooldistrictboundaries/data">published shapefiles for district boundaries and school locations</a>. This post will use the elementary school boundary shapefile. After downloading the file, we need to read the file into R using the <a href="https://cran.rstudio.com/web/packages/rgdal/"><code>rgdal</code></a> package:<a href="#fn1" class="footnoteRef" id="fnref1"><sup>1</sup></a></p>
<pre class="r"><code>library(sp)
library(rgdal)
library(tidyverse)
#Download files to temporary directory
fname < tempfile(fileext = ".zip")
dname < tempdir()
curl::curl_download("https://dpi.wi.gov/sites/default/files/imce/gis/spatialdata/tl_2013_55_unsd_elsd_harn.zip",
destfile = fname)
unzip(fname, exdir = dname)
#Read data into R
widists < readOGR(dname, layer="tl_2013_55_unsd_elsd_harn", verbose = FALSE, stringsAsFactors = FALSE)
plot(widists)</code></pre>
<p><img src="https://www.carlbfrederick.com/post/20180206usingrtocreategooglemaps_files/figurehtml/unnamedchunk11.png" width="672" /></p>
</div>
<div id="exportto.kmlformat" class="section level2">
<h2>Export to .kml format</h2>
<p>This looks about right. The <code>plotKML</code> package writes geographic objects to <strong>K</strong>eyhole <strong>M</strong>arkup <strong>L</strong>anguage the format used by Google Maps, among others. The package comes with a handy vignette that I was able to use to do everything that follows.</p>
<pre class="r"><code>library(plotKML)
#Write the district boundaries to a KML file to the working directory
kml_open("mapdata/widists_sm.kml")
kml_layer.SpatialPolygons(widists,
subfolder.name = "Elementary District Boundaries",
labels = widists@data$NAME,
outline = TRUE,
alpha = 0,
width = 2,
colour = "yellow")
kml_close("mapdata/widists_sm.kml")</code></pre>
<p>Now, this file will open just fine in Google Earth, but unfortunately it is too large for sharing via Google Maps because, at 1.6 MB, it is over the 5 MB limit. Luckily, <code>rmapshaper</code> provides</p>
<blockquote>
<p>“a wrapper around the ‘mapshaper’ ‘JavaScript’ library by Matthew Bloch <a href="https://github.com/mbloch/mapshaper/" class="uri">https://github.com/mbloch/mapshaper/</a> to perform topologicallyaware polygon simplification.”</p>
</blockquote>
<p>via the <code>ms_simplify()</code> (among other) function.</p>
<pre class="r"><code>library(rmapshaper)
widists_sm < ms_simplify(widists)
#Write the district boundaries to a KML file to the working directory
kml_open("mapdata/widists_sm.kml")
kml_layer.SpatialPolygons(widists_sm,
subfolder.name = "Elementary District Boundaries",
labels = widists_sm@data$NAME,
outline = TRUE,
alpha = 0,
width = 3,
colour = "yellow")
kml_close("mapdata/widists_sm.kml")</code></pre>
<p>Voila! The new file is only 1.6 MB. Now, all that is left to do is to login to Google Maps, import the widists_sm.kml file and share it. The results are below:</p>
<iframe src="https://www.google.com/maps/d/u/3/embed?mid=1xFVB_OuvZYaQonABVCeEh0yJbte3BO" width="640" height="480">
</iframe>
</div>
<div id="myunresolvedissues" class="section level2">
<h2>(My) Unresolved issues</h2>
<p>Observant readers will notice that I specified many options in the <code>kml_layer.SpatialPolygons()</code> function including alpha, color and (perhaps?) width that do not appear to have translated to the shared Google map above. As far as I can tell, this happens upon importing the file into Google Maps. Opening either file in Google Earth will show yellow lines and transparent polygons.</p>
<p>I am sure there are more, so please reach out in the <a href = ".#commentsection">comments below</a>.</p>
</div>
<div id="sessioninfo" class="section level2">
<h2>Session Info</h2>
<pre class="r"><code>devtools::session_info()</code></pre>
<pre><code>## setting value
## version R version 3.3.2 (20161031)
## system x86_64, darwin13.4.0
## ui X11
## language (EN)
## collate en_US.UTF8
## tz <NA>
## date 20180209
##
## package * version date source
## acepack 1.4.1 20161029 CRAN (R 3.3.0)
## aqp 1.15 20171112 CRAN (R 3.3.2)
## assertthat 0.2.0 20170411 cran (@0.2.0)
## backports 1.1.2 20171213 cran (@1.1.2)
## base64 2.0 20160510 CRAN (R 3.3.0)
## bindr 0.1 20161113 cran (@0.1)
## bindrcpp 0.2 20170617 cran (@0.2)
## blogdown 0.5 20180128 Github (rstudio/blogdown@aa98b32)
## bookdown 0.5 20170820 cran (@0.5)
## broom 0.4.2 20170213 cran (@0.4.2)
## cellranger 1.1.0 20160727 CRAN (R 3.3.0)
## class 7.314 20150830 CRAN (R 3.3.2)
## classInt 0.124 20170416 CRAN (R 3.3.2)
## cli 1.0.0 20171105 CRAN (R 3.3.2)
## cluster 2.0.5 20161008 CRAN (R 3.3.2)
## codetools 0.215 20161005 CRAN (R 3.3.2)
## colorRamps 2.3 20121029 CRAN (R 3.3.0)
## colorspace 1.32 20161214 CRAN (R 3.3.2)
## crayon 1.3.4 20170916 CRAN (R 3.3.2)
## curl 3.1 20180130 local
## data.table 1.10.0 20161203 CRAN (R 3.3.2)
## devtools 1.12.0 20160624 CRAN (R 3.3.0)
## digest 0.6.12 20170127 cran (@0.6.12)
## dismo 1.14 20170109 CRAN (R 3.3.2)
## dplyr * 0.7.4 20170928 cran (@0.7.4)
## e1071 1.67 20150805 CRAN (R 3.3.0)
## evaluate 0.10.1 20170624 cran (@0.10.1)
## FNN 1.1 20130731 CRAN (R 3.3.0)
## forcats * 0.2.0 20170123 CRAN (R 3.3.2)
## foreign 0.867 20160913 CRAN (R 3.3.2)
## Formula 1.21 20150407 CRAN (R 3.3.0)
## geojson 0.2.0 20171108 CRAN (R 3.3.2)
## geojsonio 0.5.0 20171110 CRAN (R 3.3.2)
## geojsonlint 0.2.0 20161103 CRAN (R 3.3.0)
## ggplot2 * 2.2.1 20161230 cran (@2.2.1)
## glue 1.2.0 20171029 CRAN (R 3.3.2)
## gridExtra 2.3 20170909 cran (@2.3)
## gstat 1.15 20170312 CRAN (R 3.3.2)
## gtable 0.2.0 20160226 CRAN (R 3.3.0)
## haven 1.1.0 20170709 CRAN (R 3.3.2)
## Hmisc 4.01 20161208 CRAN (R 3.3.2)
## hms 0.3 20161122 CRAN (R 3.3.2)
## htmlTable 1.7 20161019 CRAN (R 3.3.0)
## htmltools 0.3.6 20170428 cran (@0.3.6)
## httr 1.3.1 20170820 CRAN (R 3.3.2)
## intervals 0.15.1 20150827 CRAN (R 3.3.0)
## jqr 1.0.0 20170928 CRAN (R 3.3.2)
## jsonlite 1.5 20170601 cran (@1.5)
## jsonvalidate 1.0.0 20160613 CRAN (R 3.3.0)
## knitr 1.18.10 20180128 Github (yihui/knitr@1bdaf39)
## lattice 0.2034 20160906 CRAN (R 3.3.2)
## latticeExtra 0.628 20160209 CRAN (R 3.3.0)
## lazyeval 0.2.0 20160612 CRAN (R 3.3.0)
## lubridate 1.7.1 20171103 CRAN (R 3.3.2)
## magrittr 1.5 20141122 CRAN (R 3.3.0)
## maptools 0.840 20161115 CRAN (R 3.3.2)
## MASS 7.345 20160421 CRAN (R 3.3.2)
## Matrix 1.27.1 20160901 CRAN (R 3.3.2)
## memoise 1.0.0 20160129 CRAN (R 3.3.0)
## mnormt 1.55 20161015 CRAN (R 3.3.0)
## modelr 0.1.1 20170724 CRAN (R 3.3.2)
## munsell 0.4.3 20160213 CRAN (R 3.3.0)
## nlme 3.1128 20160510 CRAN (R 3.3.2)
## nnet 7.312 20160202 CRAN (R 3.3.2)
## openssl 0.9.5 20161028 CRAN (R 3.3.0)
## pillar 1.1.0 20180114 CRAN (R 3.3.2)
## pixmap 0.411 20110719 CRAN (R 3.3.0)
## pkgconfig 2.0.1 20170321 cran (@2.0.1)
## plotKML * 0.58 20170514 CRAN (R 3.3.2)
## plotrix 3.7 20171207 CRAN (R 3.3.2)
## plyr 1.8.4 20160608 CRAN (R 3.3.0)
## psych 1.7.3.21 20170322 cran (@1.7.3.2)
## purrr * 0.2.4 20171018 CRAN (R 3.3.2)
## R6 2.2.2 20170617 cran (@2.2.2)
## raster 2.58 20160602 CRAN (R 3.3.0)
## RColorBrewer 1.12 20141207 CRAN (R 3.3.0)
## Rcpp 0.12.13 20170928 cran (@0.12.13)
## readr * 1.1.1 20170516 CRAN (R 3.3.2)
## readxl 1.0.0 20170418 CRAN (R 3.3.2)
## reshape 0.8.6 20161021 CRAN (R 3.3.0)
## reshape2 1.4.2 20161022 CRAN (R 3.3.0)
## rgdal * 1.25 20161215 CRAN (R 3.3.2)
## rgeos 0.321 20161020 CRAN (R 3.3.0)
## rlang 0.1.6 20171221 CRAN (R 3.3.2)
## rmapshaper * 0.3.0 20170816 CRAN (R 3.3.2)
## rmarkdown 1.8 20171117 cran (@1.8)
## rpart 4.110 20150629 CRAN (R 3.3.2)
## rprojroot 1.32 20180103 cran (@1.32)
## RSAGA 0.945 20160105 CRAN (R 3.3.0)
## rstudioapi 0.7 20170907 CRAN (R 3.3.2)
## rvest 0.3.2 20160617 CRAN (R 3.3.0)
## scales 0.5.0 20170824 cran (@0.5.0)
## shapefiles 0.7 20130126 CRAN (R 3.3.0)
## sp * 1.24 20161222 CRAN (R 3.3.2)
## spacetime 1.21 20170924 CRAN (R 3.3.2)
## stringi 1.1.5 20170407 cran (@1.1.5)
## stringr * 1.2.0 20170218 cran (@1.2.0)
## survival 2.401 20161030 CRAN (R 3.3.0)
## tibble * 1.4.1 20171225 CRAN (R 3.3.2)
## tidyr * 0.7.2 20171016 CRAN (R 3.3.2)
## tidyverse * 1.2.1 20171114 CRAN (R 3.3.2)
## V8 1.5 20170425 CRAN (R 3.3.2)
## withr 1.0.2 20160620 CRAN (R 3.3.0)
## xfun 0.1 20180122 CRAN (R 3.3.2)
## XML 3.981.5 20161110 CRAN (R 3.3.2)
## xml2 1.1.1 20170124 CRAN (R 3.3.2)
## xts 0.97 20140102 CRAN (R 3.3.0)
## yaml 2.1.16 20171212 cran (@2.1.16)
## zoo 1.714 20161216 CRAN (R 3.3.2)</code></pre>
</div>
<div id="references" class="section level2 unnumbered">
<h2>References</h2>
<div id="refs" class="references">
<div id="refHenglRoudieretal2015">
<p>Hengl, Tomislav, Pierre Roudier, Dylan Beaudette, and Edzer Pebesma. 2015. “plotKML: Scientific Visualization of SpatioTemporal Data.” <em>Journal of Statistical Software</em> 63 (5): 1–25. <a href="http://www.jstatsoft.org/v63/i05/" class="uri">http://www.jstatsoft.org/v63/i05/</a>.</p>
</div>
<div id="refKahleWickham2013">
<p>Kahle, David, and Hadley Wickham. 2013. “ggmap: Spatial Visualization with ggplot2.” <em>The R Journal</em> 5 (1): 144–61. <a href="http://journal.rproject.org/archive/20131/kahlewickham.pdf" class="uri">http://journal.rproject.org/archive/20131/kahlewickham.pdf</a>.</p>
</div>
<div id="refLoecherRopkins2015">
<p>Loecher, Markus, and Karl Ropkins. 2015. “RgoogleMaps and loa: Unleashing R Graphics Power on Map Tiles.” <em>Journal of Statistical Software</em> 63 (4): 1–18. <a href="http://www.jstatsoft.org/v63/i04/" class="uri">http://www.jstatsoft.org/v63/i04/</a>.</p>
</div>
<div id="refTeucherRussell2017">
<p>Teucher, Andy, and Kenton Russell. 2017. <em>rmapshaper: Client for ’mapshaper’ for ’Geospatial’ Operations</em>. <a href="https://CRAN.Rproject.org/package=rmapshaper" class="uri">https://CRAN.Rproject.org/package=rmapshaper</a>.</p>
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<div class="footnotes">
<hr />
<ol>
<li id="fn1"><p>I choose to use <code>rgdal</code> instead of the <a href="https://cran.rstudio.com/web/packages/sf/"><code>sf</code></a> (simple features) package because <code>plotKML</code> plays better with spclass objects.<a href="#fnref1">↩</a></p></li>
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