Fixed broken links to script files

04-viz.Rmd

@@ -700,10 +700,10 @@ In addition, we've created a mind map to help you remember which types of plots
 ### Script of R code
 
 ```{r include=FALSE, eval=FALSE}
-knitr::purl("04-viz.Rmd", "docs/04-viz.R")
+knitr::purl("04-viz.Rmd", "docs/scripts/04-viz.R")
 ```
 
-An R script file of all R code used in this chapter is available [here](http://ismayc.github.io/moderndiver-book/04-viz.R).
+An R script file of all R code used in this chapter is available [here](http://ismayc.github.io/moderndiver-book/scripts/04-viz.R).
 
 
 ### What's to come?

05-manip.Rmd

@@ -645,10 +645,10 @@ We will focus only on the `dplyr` functions in this book, but you are encouraged
 ### Script of R code
 
 ```{r include=FALSE, eval=FALSE}
-knitr::purl("05-manip.Rmd", "docs/05-manip.R")
+knitr::purl("05-manip.Rmd", "docs/scripts/05-manip.R")
 ```
 
-An R script file of all R code used in this chapter is available [here](http://ismayc.github.io/moderndiver-book/05-manip.R).
+An R script file of all R code used in this chapter is available [here](http://ismayc.github.io/moderndiver-book/scripts/05-manip.R).
 
 
 

06-sim.Rmd

@@ -464,10 +464,10 @@ In this chapter, we've discussed three functions in the `mosaic` package useful
 ### Script of R code
 
 ```{r include=FALSE, eval=FALSE}
-knitr::purl("06-sim.Rmd", "docs/06-sim.R")
+knitr::purl("06-sim.Rmd", "docs/scripts/06-sim.R")
 ```
 
-An R script file of all R code used in this chapter is available [here](http://ismayc.github.io/moderndiver-book/06-sim.R).
+An R script file of all R code used in this chapter is available [here](http://ismayc.github.io/moderndiver-book/scripts/06-sim.R).
 
 
 ### What's to come?

07-hypo.Rmd

@@ -753,10 +753,10 @@ Since all three conditions are met, we can be reasonably certain that the theory
 ### Script of R code
 
 ```{r include=FALSE, eval=FALSE}
-knitr::purl("07-hypo.Rmd", "docs/07-hypo.R")
+knitr::purl("07-hypo.Rmd", "docs/scripts/07-hypo.R")
 ```
 
-An R script file of all R code used in this chapter is available [here](http://ismayc.github.io/moderndiver-book/07-hypo.R).
+An R script file of all R code used in this chapter is available [here](http://ismayc.github.io/moderndiver-book/scripts/07-hypo.R).
 
 
 ### What's to come?

08-ci.Rmd

@@ -310,10 +310,10 @@ Describe how $s / \sqrt{n}$ does in approximating the standard error for these t
 ### Script of R code
 
 ```{r include=FALSE, eval=FALSE}
-knitr::purl("08-ci.Rmd", "docs/08-ci.R")
+knitr::purl("08-ci.Rmd", "docs/scripts/08-ci.R")
 ```
 
-An R script file of all R code used in this chapter is available [here](http://ismayc.github.io/moderndiver-book/08-ci.R).
+An R script file of all R code used in this chapter is available [here](http://ismayc.github.io/moderndiver-book/scripts/08-ci.R).
 
 ### What's to come? 
 

09-regress.Rmd

@@ -460,10 +460,10 @@ We have reason to doubt whether a linear regression is valid here.  Unfortunatel
 ### Script of R code
 
 ```{r include=FALSE, eval=FALSE}
-knitr::purl("09-regress.Rmd", "docs/09-regress.R")
+knitr::purl("09-regress.Rmd", "docs/scripts/09-regress.R")
 ```
 
-An R script file of all R code used in this chapter is available [here](http://ismayc.github.io/moderndiver-book/09-regress.R).
+An R script file of all R code used in this chapter is available [here](http://ismayc.github.io/moderndiver-book/scripts/09-regress.R).
 
 
 ### What's to come?  

NEWS.md

@@ -2,6 +2,7 @@
 
 * Converted last updated in index.Rmd to inline instead of R chunk
 * Fixed edit link to point to moderndive-book GitHub repo instead of moderndive-source repo
+* Fixed broken links to script files at the end of Chapters 4-9
 * Attempting to fix Shiny app in Figure 6.2 appearing as white box in published site noted [here](https://github.com/ismayc/moderndiver-book/issues/2)
 
 # ModernDive 0.1.1

docs/scripts/04-viz.R

@@ -0,0 +1,200 @@
+## ----setup_viz, include=FALSE--------------------------------------------
+chap <- 4
+lc <- 0
+rq <- 0
+# **`r paste0("(LC", chap, ".", (lc <- lc + 1), ")")`**
+# **`r paste0("(RQ", chap, ".", (rq <- rq + 1), ")")`**
+knitr::opts_chunk$set(
+  tidy = FALSE, 
+  out.width = '\\textwidth', 
+  fig.height = 4,
+  warning = FALSE
+  )
+
+## ----warning=FALSE-------------------------------------------------------
+library(ggplot2)
+library(nycflights13)
+library(knitr)
+library(dplyr)
+
+## ----minard, echo=FALSE, fig.cap="Minard's Visualization of Napolean's March"----
+knitr::include_graphics("images/Minard.png")
+
+## ---- echo=FALSE---------------------------------------------------------
+map <- data_frame(
+  data = c("longitude", "latitude", "army size", "army direction"),
+  aes = c("x", "y", "size", "color"),
+  geom = c("point", "point", "path", "path")
+)
+line_graph <- data_frame(
+  data = c("date", "temperature"),
+  aes = c("x", "y"),
+  geom = c("line & text", "line & text") 
+)
+
+knitr::kable(
+  list(
+    map,
+    line_graph
+  ),
+  caption = "Grammar of Map (Top) and Line-Graph (Bottom) in Minard's Graphic of Napolean's March", booktabs = TRUE
+)
+
+## ----viz_review, type='review', engine="block"---------------------------
+**_Review questions_**
+
+## ------------------------------------------------------------------------
+data(flights)
+all_alaska_flights <- flights %>% 
+  filter(carrier == "AS")
+
+## ----lc-all_alaska_flights, type='learncheck', engine="block"------------
+**_Learning check_**
+
+## ----noalpha, fig.cap="Arrival Delays vs Departure Delays for Alaska Airlines flights from NYC in 2013"----
+ggplot(data = all_alaska_flights, aes(x = dep_delay, y = arr_delay)) + 
+  geom_point()
+
+## ----lc-scatter-plots, type='learncheck', engine="block"-----------------
+**_Learning check_**
+
+## ----alpha, fig.cap="Delay scatterplot with alpha=0.2"-------------------
+ggplot(data = all_alaska_flights, aes(x = dep_delay, y = arr_delay)) + 
+  geom_point(alpha = 0.2)
+
+## ----jitter, fig.cap="Jittered delay scatterplot"------------------------
+ggplot(data = all_alaska_flights, aes(x = dep_delay, y = arr_delay)) + 
+  geom_jitter(width = 30, height = 30)
+
+## ----lc-overplotting, type='learncheck', engine="block"------------------
+**_Learning check_**
+
+## ------------------------------------------------------------------------
+data(weather)
+early_january_weather <- weather %>% 
+  filter(origin == "EWR" & month == 1 & day <= 15)
+
+## ----lc-early_january_weather, type='learncheck', engine="block"---------
+**_Learning check_**
+
+## ----hourlytemp, fig.cap="Hourly Temperature in Newark for Jan 1-15 2013"----
+ggplot(data = early_january_weather, aes(x = time_hour, y = temp)) +
+  geom_line()
+
+## ----lc-line-graph, type='learncheck', engine="block"--------------------
+**_Learning check_**
+
+## ----echo=FALSE, fig.height=0.8, fig.cap="Strip Plot of Hourly Temperature Recordings from NYC in 2013"----
+ggplot(data = weather, mapping = aes(x = temp, y = factor("A"))) +
+  geom_point() +
+  theme(axis.ticks.y = element_blank(), 
+        axis.title.y = element_blank(),
+        axis.text.y = element_blank())
+hist_title <- "Histogram of Hourly Temperature Recordings from NYC in 2013"
+
+## ---- warning=TRUE, fig.cap=hist_title-----------------------------------
+ggplot(data = weather, mapping = aes(x = temp)) +
+  geom_histogram()
+
+## ----fig.cap=paste(hist_title, "- 60 Bins")------------------------------
+ggplot(data = weather, mapping = aes(x = temp)) +
+  geom_histogram(bins = 60, color = "white")
+
+## ----fig.cap=paste(hist_title, "- Binwidth = 10"), fig.height=5----------
+ggplot(data = weather, mapping = aes(x = temp)) +
+  geom_histogram(binwidth = 10, color = "white")
+
+## ----lc-histogram, type='learncheck', engine="block"---------------------
+**_Learning check_**
+
+## ----facethistogram, fig.cap="Faceted histogram"-------------------------
+ggplot(data = weather, aes(x = temp)) +
+  geom_histogram(binwidth = 5, color = "white") +
+  facet_wrap(~ month, nrow = 4)
+
+## ----lc-facet, type='learncheck', engine="block"-------------------------
+**_Learning check_**
+
+## ----badbox, fig.cap="Invalid boxplot specification", fig.height=3.5-----
+ggplot(data = weather, aes(x = month, y = temp)) +
+  geom_boxplot()
+
+## ----monthtempbox, fig.cap="Month by temp boxplot", fig.height=3.7-------
+ggplot(data = weather, mapping = aes(x = factor(month), y = temp)) +
+  geom_boxplot()
+
+## ----lc-boxplot, type='learncheck', engine="block"-----------------------
+**_Learning check_**
+
+## ----flightsbar, fig.cap="Number of flights departing NYC in 2013 by airline", fig.height=2.5----
+ggplot(data = flights, mapping = aes(x = carrier)) +
+  geom_bar()
+
+## ------------------------------------------------------------------------
+data(airlines)
+kable(airlines)
+
+## ----message=FALSE-------------------------------------------------------
+flights_table <- flights %>% dplyr::count(carrier)
+knitr::kable(flights_table)
+
+## ----lc-barplot, type='learncheck', engine="block"-----------------------
+**_Learning check_**
+
+## ----carrierpie, echo=FALSE, fig.cap="The dreaded pie chart", fig.height=5----
+ggplot(flights, aes(x = factor(1), fill = carrier)) +
+  geom_bar(width = 1) +
+  coord_polar(theta = "y") +
+  theme(axis.title.x = element_blank(), 
+    axis.title.y = element_blank(),
+    axis.ticks = element_blank(),
+    axis.text.y = element_blank(),
+    axis.text.x = element_blank(),
+    panel.grid.major = element_blank(),
+    panel.grid.minor = element_blank()) +
+  guides(fill = guide_legend(keywidth = 0.8, keyheight = 0.8))
+
+## ----echo=FALSE, fig.align='center', fig.cap="The only good pie chart", out.height=if(knitr:::is_latex_output()) '2.5in'----
+knitr::include_graphics("images/Pie-I-have-Eaten.jpg")
+
+## ----lc-pie-charts, type='learncheck', engine="block"--------------------
+**_Learning check_**
+
+## ----message=FALSE-------------------------------------------------------
+flights_namedports <- flights %>% 
+  inner_join(airports, by = c("origin" = "faa"))
+
+## ---- fig.cap="Stacked barplot comparing the number of flights by carrier and airport", fig.height=3.5----
+ggplot(data = flights_namedports, mapping = aes(x = carrier, fill = name)) +
+  geom_bar()
+
+## ----lc-barplot-two-var, type='learncheck', engine="block"---------------
+**_Learning check_**
+
+## ---- fig.cap="Side-by-side barplot comparing the number of flights by carrier and airport", fig.height=5----
+ggplot(data = flights_namedports, mapping = aes(x = carrier, fill = name)) +
+  geom_bar(position = "dodge")
+
+## ----lc-barplot-stacked, type='learncheck', engine="block"---------------
+**_Learning check_**
+
+## ---- fig.cap="Faceted barplot comparing the number of flights by carrier and airport", fig.height=7.5----
+ggplot(data = flights_namedports, mapping = aes(x = carrier, fill = name)) +
+  geom_bar() +
+  facet_grid(name ~ .)
+
+## ----lc-barplot-facet, type='learncheck', engine="block"-----------------
+**_Learning check_**
+
+## ----viz-map, echo=FALSE, fig.cap="Mind map for Data Visualization", out.width="200%"----
+#library(knitr)
+#if(knitr:::is_html_output()){
+#  include_url("https://coggle.it/diagram/V_G2gzukTDoQ-aZt-", 
+#              height = "1000px")
+#} else {
+  include_graphics("images/coggleviz.png", dpi = 300)
+#}
+
+## ----include=FALSE, eval=FALSE-------------------------------------------
+## knitr::purl("04-viz.Rmd", "docs/scripts/04-viz.R")
+