port over changes from DSC385

Author: clauswilke

_freeze/slides/visualizing-uncertainty/execute-results/html.json

@@ -0,0 +1,49 @@
+library(archdata)
+library(here)
+data('RBPottery')
+
+write_csv(RBPottery, here("datasets", "pottery.csv"))
+
+
+library(tidyverse)
+library(broom)
+
+pca_fit <- RBPottery |> 
+  select(where(is.numeric)) |> # retain only numeric columns
+  scale() |>                   # scale to zero mean and unit variance
+  prcomp() 
+
+pca_fit |>
+  # add PCs to the original dataset
+  augment(RBPottery) |>
+  ggplot(aes(.fittedPC1, .fittedPC2)) +
+  geom_point(aes(color = Region))
+
+arrow_style <- arrow(
+  angle = 20, length = grid::unit(8, "pt"),
+  ends = "first", type = "closed"
+)
+
+pca_fit |>
+  # extract rotation matrix
+  tidy(matrix = "rotation") |>
+  pivot_wider(
+    names_from = "PC", values_from = "value",
+    names_prefix = "PC"
+  ) |>
+  mutate(
+    # order of variables is:
+    # Al2O3, Fe2O3, MgO, CaO, Na2O, K2O, TiO2, MnO, BaO  
+    hjust = c(1.05, -.05, -.05, 0.5, 0.5, -.05, 1.05, -.05, 1.05),
+    vjust = c(0.5, 0.5, 0.5, -.1, -.1, 0.8, 0.5, 0.2, 0)
+  ) |>
+  ggplot(aes(PC1, PC2)) +
+  geom_segment(
+    xend = 0, yend = 0,
+    arrow = arrow_style
+  ) +
+  geom_text(aes(label = column, hjust = hjust, vjust = vjust)) +
+  coord_fixed(
+    xlim = c(-.7, 0.7),
+    ylim = c(-.5, .7) 
+  )

_site/datasets/pottery.R

@@ -0,0 +1,49 @@
+ID,Kiln,Region,Al2O3,Fe2O3,MgO,CaO,Na2O,K2O,TiO2,MnO,BaO
+GA1,Gloucester,Gloucester,18.8,9.52,2,0.79,0.4,3.2,1.01,0.077,0.015
+GA2,Gloucester,Gloucester,16.9,7.33,1.65,0.84,0.4,3.05,0.99,0.067,0.018
+GA3,Gloucester,Gloucester,18.2,7.64,1.82,0.77,0.4,3.07,0.98,0.087,0.014
+GA4,Gloucester,Gloucester,17.4,7.48,1.71,1.01,0.4,3.16,0.03,0.084,0.017
+GA5,Gloucester,Gloucester,16.9,7.29,1.56,0.76,0.4,3.05,1,0.063,0.019
+GB1,Gloucester,Gloucester,17.8,7.24,1.83,0.92,0.43,3.12,0.93,0.061,0.019
+GB2,Gloucester,Gloucester,18.8,7.45,2.06,0.87,0.25,3.26,0.98,0.072,0.017
+GB3,Gloucester,Gloucester,16.5,7.05,1.81,1.73,0.33,3.2,0.95,0.066,0.019
+GB4,Gloucester,Gloucester,18,7.42,2.06,1,0.28,3.37,0.96,0.072,0.017
+GB5,Gloucester,Gloucester,15.8,7.15,1.62,0.71,0.38,3.25,0.93,0.062,0.017
+GC1,Gloucester,Gloucester,14.6,6.87,1.67,0.76,0.33,3.06,0.91,0.055,0.012
+GC2,Gloucester,Gloucester,13.7,5.83,1.5,0.66,0.13,2.25,0.75,0.034,0.012
+GC3,Gloucester,Gloucester,14.6,6.76,1.63,1.48,0.2,3.02,0.87,0.055,0.016
+GC4,Gloucester,Gloucester,14.8,7.07,1.62,1.44,0.24,3.03,0.86,0.08,0.016
+GD1,Gloucester,Gloucester,17.1,7.79,1.99,0.83,0.46,3.13,0.93,0.09,0.02
+GD2,Gloucester,Gloucester,16.8,7.86,1.86,0.84,0.46,2.93,0.94,0.094,0.02
+GD3,Gloucester,Gloucester,15.8,7.65,1.94,0.81,0.83,3.33,0.96,0.112,0.019
+GD4,Gloucester,Gloucester,18.6,7.85,2.33,0.87,0.38,3.17,0.98,0.081,0.018
+GD5,Gloucester,Gloucester,16.9,7.87,1.83,1.31,0.53,3.09,0.95,0.092,0.023
+GE1,Gloucester,Gloucester,18.9,7.58,2.05,0.83,0.13,3.29,0.98,0.072,0.015
+GE2,Gloucester,Gloucester,18,7.5,1.94,0.69,0.12,3.14,0.93,0.035,0.017
+GE3,Gloucester,Gloucester,17.8,7.28,1.92,0.81,0.18,3.15,0.9,0.067,0.017
+C01,Llanedeyrn,Wales,14.4,7,4.3,0.15,0.51,4.25,0.79,0.16,0.019
+CO2,Llanedeyrn,Wales,13.8,7.08,3.43,0.12,0.17,4.14,0.77,0.144,0.02
+CO3,Llanedeyrn,Wales,14.6,7.09,3.88,0.13,0.2,4.36,0.81,0.124,0.019
+C04,Llanedeyrn,Wales,11.5,6.37,5.64,0.16,0.14,3.89,0.69,0.087,0.009
+CO5,Llanedeyrn,Wales,13.8,7.06,5.34,0.2,0.2,4.31,0.71,0.101,0.021
+C06,Llanedeyrn,Wales,10.9,6.26,3.47,0.17,0.22,3.4,0.66,0.109,0.01
+C07,Llanedeyrn,Wales,10.1,4.26,4.26,0.2,0.18,3.32,0.59,0.149,0.017
+C08,Llanedeyrn,Wales,11.6,5.78,5.91,0.18,0.16,3.7,0.65,0.082,0.015
+C09,Llanedeyrn,Wales,11.1,5.49,4.52,0.29,0.3,4.03,0.63,0.08,0.016
+C10,Llanedeyrn,Wales,13.4,6.92,7.23,0.28,0.2,4.54,0.69,0.163,0.017
+C11,Llanedeyrn,Wales,12.4,6.13,5.69,0.22,0.54,4.65,0.7,0.159,0.015
+C12,Llanedeyrn,Wales,13.1,6.64,5.51,0.31,0.24,4.89,0.72,0.094,0.017
+C13,Llanedeyrn,Wales,12.7,6.69,4.45,0.2,0.22,4.7,0.73,0.394,0.024
+C14,Llanedeyrn,Wales,12.5,6.44,3.94,0.22,0.23,0.81,0.75,0.177,0.019
+GO1,Caldicot,Wales,11.6,5.39,3.77,0.29,0.06,4.51,0.56,0.11,0.015
+G02,Caldicot,Wales,11.8,5.44,3.94,0.3,0.04,4.64,0.59,0.085,0.013
+T11,Islands Thorns,New Forest,18.3,1.28,0.67,0.03,0.03,1.96,0.65,0.001,0.014
+T12,Islands Thorns,New Forest,15.8,2.39,0.63,0.01,0.04,1.94,1.29,0.001,0.014
+T13,Islands Thorns,New Forest,18,1.5,0.67,0.01,0.06,2.11,0.92,0.001,0.016
+T14,Islands Thorns,New Forest,18,1.88,0.68,0.01,0.04,2,1.11,0.006,0.022
+T16,Islands Thorns,New Forest,20.8,1.51,0.72,0.07,0.1,2.37,1.26,0.002,0.016
+A11,Ashley Rails,New Forest,17.7,1.12,0.56,0.06,0.06,2.06,0.79,0.001,0.013
+Al2,Ashley Rails,New Forest,18.3,1.14,0.67,0.06,0.05,2.11,0.89,0.006,0.019
+A16,Ashley Rails,New Forest,16.7,0.92,0.53,0.01,0.05,1.76,0.91,0.004,0.013
+A18,Ashley Rails,New Forest,14.8,2.74,0.67,0.03,0.05,2.15,1.34,0.003,0.015
+A26,Ashley Rails,New Forest,19.1,1.64,0.6,0.1,0.03,1.75,1.04,0.007,0.018

_site/datasets/pottery.csv

@@ -6957,6 +6957,13 @@
     "section": "Hypothetical Outcome Plots again help develop intuition",
     "text": "Hypothetical Outcome Plots again help develop intuition\n\n\n\n\n\n\nFuel efficiency versus displacement, for 32 cars (1973–74 models). Source: Motor Trend, 1974"
   },
+  {
+    "objectID": "slides/visualizing-uncertainty.html#getting-the-data",
+    "href": "slides/visualizing-uncertainty.html#getting-the-data",
+    "title": "Visualizing Uncertainty",
+    "section": "Getting the data",
+    "text": "Getting the data\n\nThe gapminder dataset:\n\n\n\nlibrary(gapminder)\n\ngapminder\n\n# A tibble: 1,704 × 6\n   country     continent  year lifeExp      pop gdpPercap\n   <fct>       <fct>     <int>   <dbl>    <int>     <dbl>\n 1 Afghanistan Asia       1952    28.8  8425333      779.\n 2 Afghanistan Asia       1957    30.3  9240934      821.\n 3 Afghanistan Asia       1962    32.0 10267083      853.\n 4 Afghanistan Asia       1967    34.0 11537966      836.\n 5 Afghanistan Asia       1972    36.1 13079460      740.\n 6 Afghanistan Asia       1977    38.4 14880372      786.\n 7 Afghanistan Asia       1982    39.9 12881816      978.\n 8 Afghanistan Asia       1987    40.8 13867957      852.\n 9 Afghanistan Asia       1992    41.7 16317921      649.\n10 Afghanistan Asia       1997    41.8 22227415      635.\n# ℹ 1,694 more rows"
+  },
   {
     "objectID": "slides/visualizing-uncertainty.html#making-a-plot-with-error-bars",
     "href": "slides/visualizing-uncertainty.html#making-a-plot-with-error-bars",