Chapter 10 Assignments II

10.1 Andreas Flache

10.1.1 data

flache <- read.csv("https://stulp.gmw.rug.nl/Rworkshop/simulationResultsExpLevelAPolYouGov.csv")

library(skimr)
skim(flache)

10.1.2 visualisations

Andreas wrote: “association across country-elections of sdOpFin with r14Last at parameters sf=1, phi=1, eps=0.25, intergroupDistance=1”

library(tidyverse)
viz1_flache <- flache %>% 
  filter(sF == 0.1 & phi == 1 & eps0 == 0.2)

ggplot(viz1_flache, aes(x = as.numeric(sdOpFin), y = r14Last, fill = factor(intergroupDistance))) +
  geom_point() +
  geom_smooth(method = "lm", colour = "NA") +
  scale_fill_viridis_d() +
  facet_wrap(~intergroupDistance, nrow = 1) +
  theme_minimal() +
  theme(panel.grid.minor = element_blank()) +
  guides(fill = "none")

Andreas wrote: “correlation sdOpFin with r14last by eps0 and intergroupDistance, for SF = 0.5 and phi = 0.5”

viz2_flache <- flache %>% 
  filter(sF == 0.6 & phi == 0.5) %>% # sd = 0.5 does not exist
  select(eps0, intergroupDistance, sdOpFin, r14Last)

corr_flache <- viz2_flache %>% 
  group_by(eps0, intergroupDistance) %>% 
  summarise(cor = cor(as.numeric(sdOpFin), r14Last))

ggplot(corr_flache, aes(x = eps0, y = intergroupDistance, z = cor)) +
  geom_contour_filled() +
  theme_minimal()

10.1.3 running simulations in R

Andreas, people may tell you R is slow for simulations. Maybe, but code is relatively readable. A major benefit to me is that you can store output in the same ‘dataset’ as your parameters. Let’ see an example, a simple one. we’ll simulate from a normal distribution, but we vary the n, mean and sd.

library(tidyverse)
sims_params <- data.frame(n= c(10, 100, 1000), mean = c(0, 10, 100), sd = c(1, 10, 1000)) %>% 
  expand.grid() # this creates a dataframe with all combinations across parameters
head(sims_params)

##      n mean sd
## 1   10    0  1
## 2  100    0  1
## 3 1000    0  1
## 4   10   10  1
## 5  100   10  1
## 6 1000   10  1

sims_params <- sims_params %>% 
  # add new column with list of results in a cell, can also be a dataframe itself
  # mutate creates new column, results = name of column
  # pmap is a function that iterates over multiple lists/columns
  # and applies a function to it
  mutate(results = pmap(list(n, mean, sd), 
                        function(n, m, s) rnorm(n, m, s) ))
head(sims_params)

##      n mean sd
## 1   10    0  1
## 2  100    0  1
## 3 1000    0  1
## 4   10   10  1
## 5  100   10  1
## 6 1000   10  1
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   results
## 1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 0.08253913, 1.14481207, 0.61831526, 1.18015927, 0.35906253, 0.29999311, 0.08924839, -1.30339310, 0.64521117, 0.00387676
## 2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           -0.12644266, -0.04013385, 0.13424358, 1.20695279, -0.15156935, 1.04678696, 0.50579736, -0.81840117, 0.96306738, -1.17807379, 1.74996793, 0.42864712, -0.36396594, 1.44339283, -1.11322643, 1.12180678, -1.04389519, 0.27865356, -0.85391621, 1.85298574, 1.16956680, 0.53401295, -0.46036706, -0.35324319, -0.32126563, 1.96983864, 2.18008183, 1.23845062, -0.31279422, 0.52552422, -0.64684565, 0.41770540, -0.39400747, 0.14923564, 1.10360119, -1.34003486, 0.19757137, -0.95493648, 0.21989905, -0.50736179, 0.46187524, 0.26324753, 1.10621382, 1.27377736, -0.21249891, -0.31845505, -1.22989788, -0.55419864, 1.05263581, -0.01807382, 0.01833068, 0.89320320, -1.66979955, 1.02548722, -0.74200304, -0.65300053, -2.17902232, -0.91480198, 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## 3 1.284910137, -0.965990664, -0.965915614, 0.422348457, 0.622262678, 0.397786224, 0.583377426, -1.178682323, 0.751745401, 2.868632849, 1.098618573, 0.007233447, 1.081316166, -0.005687142, 0.400639874, -0.458316027, -1.391275001, -1.770166615, -2.220107671, -0.965280351, -1.139785062, -2.131144914, -1.752217516, 0.666518134, -1.036250936, -0.480407953, 1.508379702, 0.858227267, 0.259811847, -0.051592931, -0.092162070, 0.944555400, 1.467954092, -0.384510291, 2.502911605, 1.369809014, -0.657358314, -1.141062069, 0.821721302, -1.165849727, 0.287745011, -0.327174616, -0.968445173, -0.214079444, -0.083389597, -0.359611343, -0.579272353, -0.762652361, -0.590932997, -0.680623358, -1.163207024, 0.288362267, 0.044986007, -0.887025958, -0.391935497, -1.112575585, -0.466624259, 1.406108891, -0.644197845, 0.281443816, 0.143096997, -0.280480017, -0.231191228, 4.023802008, 0.088471252, -0.270096062, -1.718992429, -0.394437777, 1.289285818, 0.462217735, -0.243117770, -0.604123575, 0.573491039, 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0.036871293, -0.512192685, -1.803827500, 2.416741999, -0.556968612, 0.023488620, -1.320678886, 2.300223678, 0.522589182, -0.941667349, -0.887805384, 0.769962636, -0.691727531, -1.743103196, 1.302161095, 0.825048906, -0.140511981, -1.237344624, -1.134202388, -2.109111139, 0.980027556, 1.086644585, -2.150483092, -0.632570975, 0.439631105, 0.570758493, 1.544626307, 0.160542551, 0.630703104, -0.485920466, 0.080173689, 0.644317400, 1.499185400, -1.538209470, 1.087918769, 0.324959213, -1.628941304, 0.703610323, 0.641217981, -0.961973327, 0.372594578, -0.324352064, -3.013590854, -0.945094190, -0.823180018, 0.741222406, 1.678506881, 3.113814262, -1.128127534, 0.003970783, -0.747489626, -0.424140820, -0.548797810, -0.547200981, -0.563407240, -0.156902439, 1.001038897, -0.778908450, 0.893427220, -2.091811048, 0.384655544, 0.837344662, -0.993828280, -0.269044044, 0.430820862, -1.199182146, 0.164437312, 0.592069796, -0.918778854, -0.930030175, 0.500287015, 0.601695332, -1.501256883, 1.136233004, 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## 4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    8.766951, 9.916208, 10.681969, 10.219824, 9.645698, 8.456056, 9.358497, 9.758353, 8.364799, 9.109842
## 5                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            10.013276, 9.003234, 9.512473, 11.482904, 11.333754, 10.315594, 9.413221, 11.293851, 10.210573, 10.187081, 9.665132, 9.496611, 10.560666, 9.773229, 10.153726, 8.875782, 9.153158, 9.885102, 10.854091, 10.983281, 10.655535, 9.503668, 10.584081, 7.790547, 10.526621, 11.374476, 9.846156, 11.977505, 10.055137, 10.618027, 9.557403, 9.179893, 10.014511, 10.474342, 12.148060, 10.496651, 9.737687, 9.603052, 10.551177, 9.860411, 9.778223, 10.018564, 9.430931, 9.605745, 9.242329, 8.761382, 9.045070, 12.114589, 8.112512, 9.703065, 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## 6                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       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9.108512, 9.735640, 10.505052, 9.381372, 9.556536, 9.318158, 8.893354, 9.819397, 10.220769, 9.338889, 10.909214, 11.341672, 10.554844, 11.340981, 8.065340, 9.712870, 8.956329, 8.628486, 8.589137, 11.424984, 8.921048, 11.948042, 9.974631, 9.918264, 9.721483, 9.414146, 7.735448, 9.481529, 10.385333, 8.394366, 8.703584, 10.337384, 9.363762, 12.030218, 10.002434, 10.033665, 9.079645, 9.251287, 10.380921, 8.910145, 10.520859, 11.088967, 8.801548, 7.865491, 9.731099, 11.071408, 8.361920, 11.007890, 10.855314, 7.983821, 9.647599, 11.357988, 8.604580, 10.485563, 10.618192, 10.516689, 10.398124, 10.101865, 9.890380, 10.676917, 10.417483, 10.629173, 10.854915, 9.353603, 9.756364, 11.078696, 8.957220, 9.464640, 9.866547, 10.621835, 10.160295, 10.865933, 10.438742, 9.473533, 8.547007, 8.743030, 11.406013, 10.000415, 8.737515, 9.483523, 10.053220, 10.218004, 9.373738, 10.245062, 9.829824, 9.804809, 9.139024, 9.720202, 9.481660, 10.374143, 9.828244, 11.030852, 9.509621, 9.899924, 9.058790, 10.616638, 9.087714, 11.369178, 10.886867, 9.530914, 8.655659, 10.709440, 10.214579, 7.496464, 8.099766, 10.303902, 9.851182, 9.924839, 10.359090, 10.188894, 10.317724, 10.532389, 10.096718, 11.224760, 10.715237, 10.376329, 8.629746, 9.779219, 7.587239, 10.337707, 9.335903, 9.540416, 9.809032, 9.191135, 9.664903, 9.822669, 9.664891, 11.746400, 10.931075, 10.559912, 10.713799, 10.929169, 9.200900, 10.533869, 9.444188, 9.601617, 10.152938, 7.996364, 10.363335, 10.527915, 10.200442, 8.753844, 9.921353, 10.498439, 10.614009, 10.731923, 8.207377, 9.596588, 9.892893, 9.564749, 8.304073, 9.995899, 10.342967, 11.603626, 9.900089, 9.326121, 9.486064, 11.761325, 10.264157, 10.320654, 9.345746, 8.885696, 8.203427, 9.347462, 11.504827, 10.832491, 9.133868, 9.993324, 10.004427, 10.607414, 9.559897, 9.174931, 9.832111, 9.717593, 9.788197, 10.201523, 11.164702, 10.575093, 11.419238, 8.906236, 9.112049, 9.696263, 9.770257, 9.496419, 10.625385, 9.425075, 9.386025, 9.757357, 7.737303, 10.799894, 7.913607, 8.862294, 10.219134, 12.092253, 9.311706, 9.305460, 9.463501, 10.525033, 8.881583, 9.667052, 10.316318, 9.571801, 9.140278, 10.174949, 10.087803, 9.112264, 9.101806, 10.979977, 10.623635, 9.968905, 10.216783, 11.197280, 10.317132, 10.605772, 10.319681, 9.766572, 10.563078, 9.203115, 10.750117, 10.298165, 12.072843, 11.060393, 10.299479, 9.491145, 8.029435, 10.809034, 10.373499, 11.190284, 10.426747, 10.684293, 8.837594, 10.813157, 10.226372, 9.031395, 10.152485, 8.951677, 10.944782, 9.601706, 7.974729, 10.681787, 10.166822, 10.008238, 8.442486, 8.756618, 10.455850, 10.771917, 11.395517, 9.901488, 10.734908, 9.151000, 10.474453, 10.315320, 9.423482, 11.235143, 9.973593, 9.581985, 10.805422, 12.951618, 11.222901, 11.398180, 12.305573, 10.084300, 11.163184, 8.060712, 8.273327, 9.722170, 11.868268, 10.381129, 10.352963, 9.652463, 9.063947, 9.999939, 7.745706, 11.439191, 11.421585, 10.669235, 10.231542, 11.555473, 9.290163, 9.781588, 10.641631, 8.870737, 9.961228, 10.152471, 10.701095, 9.639386, 9.704847, 8.386438, 9.691039, 9.438302, 8.536975, 10.906786, 10.331116, 10.154511, 10.270707, 9.894782, 8.825470, 9.255693, 9.376458, 10.090437, 10.873842, 10.040061, 9.124264, 9.896380, 9.561775, 10.300410, 11.182623, 9.645314, 9.351918, 10.330386, 8.953582, 11.008343, 10.041948, 10.033368, 9.465004, 11.628076, 8.932290, 9.738400, 10.904389, 11.735299, 8.935832, 11.498027, 8.665653, 10.428195, 9.138071, 9.790693, 8.903969, 8.541032, 9.621205, 10.250937, 9.508771, 9.691424, 10.625531, 10.400719, 9.986159, 11.507922, 9.741586, 9.992386, 9.086492, 11.473888, 10.591698, 11.612968, 10.445655, 9.798401, 7.816810, 9.942985, 8.956580, 12.240080, 10.313457, 8.634876, 7.862968, 9.488418, 10.373834, 10.828103, 10.791451, 10.223457, 9.524728, 9.679661, 10.033102, 9.302010, 11.536446, 12.405076, 9.773102, 11.309863, 9.993004, 11.655022, 7.520774, 10.562319, 9.882691, 9.605436, 10.646069, 10.575667, 10.922361, 8.153279, 9.519408, 9.468581, 11.826312, 10.380124, 8.934935, 10.841604, 9.829076, 10.211765, 10.069486, 11.048851, 10.397219, 10.662034, 9.872268, 10.480888, 8.696845, 10.026067, 8.651362, 10.423995, 9.405661, 10.099827, 11.009172, 10.084169, 11.182502, 12.687428, 9.190498, 10.309547, 9.957170, 8.638909, 10.191562, 10.485705, 9.704820, 9.184108, 9.722958, 10.790946, 11.816174, 9.590653, 11.683918, 11.470011, 9.364330, 10.839935, 10.518452, 9.779177, 8.702325, 8.601475, 9.243668, 11.130121, 11.072347, 10.042778, 9.050042, 9.956540, 9.363137, 9.126041, 10.585496, 8.711752, 9.802268, 10.947973, 8.113576, 10.716731, 10.240010, 11.140043, 8.682857, 10.659638, 9.287213, 8.874848, 9.758189, 10.730460, 10.648399, 9.869584, 11.398486, 9.528981, 9.786899, 10.365807, 10.503342, 10.650460, 10.021140, 8.420704, 10.262457, 9.414031, 10.192640, 11.216565, 11.489888, 8.178023, 9.675902, 9.976851, 10.497954, 10.281422, 10.105191, 10.877848, 9.124498, 8.974505, 9.916633, 8.549409, 7.325130, 10.092245, 9.448228, 10.186502, 9.103377, 9.651142, 8.683039, 9.143402, 9.667670, 9.637887, 10.816128, 8.562564, 8.427163, 9.674526, 9.859896, 9.093664, 10.838368, 7.628519, 9.601675, 9.702483, 10.275522, 11.018597, 9.792508, 8.248438, 9.142949, 10.974740, 11.884209, 10.666975, 9.749937, 10.134521, 12.280345, 8.581153, 10.410645, 10.363688, 11.417167, 9.072678, 8.687405, 10.412317, 8.300738, 9.599063, 10.825961, 10.764990, 10.657208, 9.734481, 12.979993, 10.298546, 10.531114, 10.923880, 9.977144, 10.200539, 11.881036, 8.644229, 9.094089, 9.832888, 9.355230, 9.279063, 10.812236, 10.676737, 10.927068, 10.397510, 9.024753, 9.811172, 9.975316, 8.659678, 9.442479, 10.249591, 11.253545, 10.902825, 9.415690, 9.634740, 9.684527, 10.735558, 9.743835, 9.921465, 11.782390, 10.903383, 9.969399, 9.156814, 10.780347, 7.337662, 10.778125, 9.949904, 8.578268, 10.985283, 10.429938, 10.406474, 11.369870, 9.229029, 10.558955, 9.572663, 10.498102, 10.660994, 10.045021, 10.416994, 9.012258, 11.532279, 9.923012, 9.392907, 9.268365, 7.560612, 9.928200, 9.816891, 9.860343, 11.235790, 10.908594, 8.222334, 9.511190, 12.003088, 10.091970, 10.331374, 9.823783, 10.683826, 10.024939, 9.224565, 9.837166, 10.671292, 11.425289, 10.713830, 12.579985, 9.545282, 9.716812, 8.313902, 10.825890, 11.161697, 10.220967, 9.470631, 9.947429, 8.411280, 10.770040, 9.383231, 9.092753, 8.809386, 10.467792, 9.727430, 8.349651, 11.305646, 11.391385, 10.493144, 9.845840, 9.063731, 9.861723, 9.767982, 11.091891, 8.712233, 8.042582, 10.743650, 9.503386, 9.963313, 9.593963, 10.732379, 9.246339, 10.623622, 8.008479, 10.608146, 11.060495, 9.660293, 9.181529, 9.990229, 10.006011, 10.716400, 11.374642, 8.699556, 9.429442, 9.818635, 9.177998, 10.625990, 11.779092, 10.772575, 8.789054, 10.124886, 10.447428, 9.158372, 10.297997, 9.746652, 9.194531, 9.898574, 11.858540, 10.354109, 10.337246, 9.537548, 10.080415, 8.941232, 9.243643, 9.216450, 9.601460, 10.705705, 11.495498, 8.021209, 9.158023, 10.049786, 10.206002, 9.840382, 10.511339, 9.808722, 11.863674, 9.851566, 11.984424, 10.493033, 10.675728, 10.967017, 11.181461, 9.747133, 10.370004, 9.544052, 9.266302, 8.167258, 10.631599, 9.849817, 9.868850, 10.728361, 9.354710, 9.377939, 9.746100, 10.747862, 8.989380, 8.827305, 8.801978, 8.741015, 9.664542, 9.901717, 10.263631, 8.744049, 10.478964, 10.073194, 9.711056, 9.535023, 9.083965, 10.719378, 10.296844, 9.908362, 11.610282, 11.501248, 10.353716, 9.060216, 9.125652, 8.508152, 9.665984, 10.560817, 10.389446, 10.203933, 8.585846, 9.693076, 7.806456, 9.228678, 11.206045, 10.004210, 10.685133, 9.748971, 9.791968, 9.124395, 10.691426, 9.306298, 8.556914, 10.978633, 9.896028, 9.410492, 9.842168, 10.518184, 11.587089, 9.659977, 10.336470, 9.374351, 9.564199, 11.336254, 8.955792, 10.069912, 10.463644, 9.205037, 9.419180, 13.292354, 9.610713, 11.908050, 9.764769, 9.553787, 9.374184, 11.168603, 10.753956, 10.773290, 11.030094, 10.064411, 11.533500, 10.279346, 9.003859, 9.223373, 9.322732, 11.003284, 8.708577, 10.406839, 8.904925, 9.654805, 10.380845, 9.686316, 9.462291, 10.772549, 10.241606, 9.285133, 8.187873, 11.320723, 9.729517, 9.495353, 10.425702, 10.051868, 10.073336, 8.943924, 9.461441, 9.502669, 10.456348, 9.804450, 10.214987, 9.282813, 9.017329, 10.041324, 10.057059, 9.969523, 8.797695, 10.320788, 9.092741, 11.278159, 8.739611, 9.243788, 10.262926, 8.625632, 11.958114, 10.113955, 9.505054, 9.376113, 12.324662, 9.860883, 11.368752, 8.683030, 10.769603, 9.829992, 9.413043, 9.627115, 11.885099, 10.511566, 9.654177, 9.146754, 10.104255, 10.237020, 9.180521, 10.166853, 10.734459, 8.077281, 10.786672, 10.074116, 9.709398, 11.252524, 8.617186

10.2 Marieke de Haan

10.2.1 data

library(haven)
haan <- read_sav("https://stulp.gmw.rug.nl/Rworkshop/haan.sav")

library(skimr)
skim(haan)

10.2.2 accessing the labels from SPSS

This turns most variables into factors, also the ones you may not want to (likert scales)

haan <- as_factor(haan)

skim(haan)

library(tidyverse)
haan_summ <- haan %>% 
  group_by(Q8) %>% 
  # calculate sample size of each group
  summarise(n = n()) %>% 
  # calculate total n + percentages per group
  mutate(tot_n = sum(n),
         perc = round(100 * n / tot_n)) %>% 
  # remove na
  filter(!is.na(Q8))

ggplot(haan_summ, aes(x = Q8, y = n, fill = Q8)) +
  geom_bar(stat = "identity") +
  geom_text(aes(label = paste0(perc, "%")), hjust = 1, colour = "white", size = 8) +
  theme_linedraw() +
  scale_fill_viridis_d() +
  coord_flip() +
  guides(fill = "none") +
  labs(x = NULL, title = "Vul jij meestal cursusevaluaties in?") +
  theme(panel.grid.minor = element_blank(),
        panel.grid.major.y = element_blank())

10.2.3 reshaping data

# select three variables with same measurement
haan_sel <- haan %>% 
  select(Q13, Q14, Q15)

# go from wide to long
haan_long <- haan_sel %>% 
  pivot_longer(cols = c(Q13, Q14, Q15), names_to = "question", values_to = "answer") %>% 
  filter(!is.na(answer)) # exclude NA

ggplot(haan_long, aes(y = answer)) +
  geom_bar(fill = "grey") +
  theme_classic() +
  facet_wrap(~question)

ggplot(haan_long, aes(x = question, fill = answer)) +
  geom_bar(position = "fill") +
  theme_classic() +
  scale_fill_viridis_d() +
  coord_flip()

10.3 Wietske de Vries

10.3.1 data

vries <- read_sav("https://stulp.gmw.rug.nl/Rworkshop/vries.sav") %>% 
  as_factor()

library(skimr)
skim(vries)

library(lme4)
# empty model, random intercept
null_mod <- lmer(Self_efficacy ~ 1 + (1 | sub_ID), data = vries)
summary(null_mod)

## Linear mixed model fit by REML ['lmerMod']
## Formula: Self_efficacy ~ 1 + (1 | sub_ID)
##    Data: vries
## 
## REML criterion at convergence: 1762.5
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -5.5184 -0.3095  0.0804  0.4563  2.8046 
## 
## Random effects:
##  Groups   Name        Variance Std.Dev.
##  sub_ID   (Intercept) 8.170    2.858   
##  Residual             4.561    2.136   
## Number of obs: 352, groups:  sub_ID, 133
## 
## Fixed effects:
##             Estimate Std. Error t value
## (Intercept)  35.2133     0.2742   128.4

# List of fitted intercepts (estimate average self_efficacy for each respondent)
head(coef(null_mod)$sub_ID) # alternatively:  ranef(null_mod)[["sub_ID"]]

##   (Intercept)
## 1    38.40594
## 2    37.84386
## 3    32.50941
## 4    37.56282
## 5    31.66100
## 6    39.24905

# all fixed effectsl, random intercept
mod_fe <- lmer(Self_efficacy ~ 1 + time + Group + Biomed_beliefs + (1 | sub_ID), data = vries)
summary(mod_fe)

## Linear mixed model fit by REML ['lmerMod']
## Formula: Self_efficacy ~ 1 + time + Group + Biomed_beliefs + (1 | sub_ID)
##    Data: vries
## 
## REML criterion at convergence: 1749.7
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -5.1893 -0.3698  0.0683  0.4544  2.5142 
## 
## Random effects:
##  Groups   Name        Variance Std.Dev.
##  sub_ID   (Intercept) 9.022    3.004   
##  Residual             4.095    2.024   
## Number of obs: 352, groups:  sub_ID, 133
## 
## Fixed effects:
##                         Estimate Std. Error t value
## (Intercept)             33.71864    0.64287  52.450
## timepost-measure         0.34428    0.26948   1.278
## timefollow-up           -0.49680    0.28350  -1.752
## Groupexperimental group -0.34269    0.58499  -0.586
## Biomed_beliefs           0.08559    0.03067   2.791
## 
## Correlation of Fixed Effects:
##             (Intr) tmpst- tmfll- Grpxpg
## timepst-msr  0.062                     
## timefollw-p -0.093  0.452              
## Grpxprmntlg -0.235  0.082  0.040       
## Biomed_blfs -0.755 -0.319 -0.108 -0.249

# all fixed effectsl, random intercept, random slope of Biomed_beliefs
mod_rs <- lmer(Self_efficacy ~ 1 + time + Group + Biomed_beliefs + (1 + Biomed_beliefs | sub_ID), data = vries)
summary(mod_rs)

## Linear mixed model fit by REML ['lmerMod']
## Formula: 
## Self_efficacy ~ 1 + time + Group + Biomed_beliefs + (1 + Biomed_beliefs |  
##     sub_ID)
##    Data: vries
## 
## REML criterion at convergence: 1711.3
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -3.8355 -0.3406  0.0413  0.4184  2.7887 
## 
## Random effects:
##  Groups   Name           Variance Std.Dev. Corr 
##  sub_ID   (Intercept)    35.90404 5.9920        
##           Biomed_beliefs  0.05607 0.2368   -0.88
##  Residual                 2.78444 1.6687        
## Number of obs: 352, groups:  sub_ID, 133
## 
## Fixed effects:
##                         Estimate Std. Error t value
## (Intercept)             34.51437    0.78502  43.966
## timepost-measure         0.25599    0.23798   1.076
## timefollow-up           -0.41104    0.25026  -1.642
## Groupexperimental group -0.05147    0.57267  -0.090
## Biomed_beliefs           0.03278    0.03723   0.880
## 
## Correlation of Fixed Effects:
##             (Intr) tmpst- tmfll- Grpxpg
## timepst-msr  0.032                     
## timefollw-p -0.085  0.477              
## Grpxprmntlg -0.163  0.024 -0.001       
## Biomed_blfs -0.848 -0.177 -0.034 -0.230

# save estimates per respondent of intercept and slope of Biomed_beliefs into dataframe
df <- ranef(mod_rs)[["sub_ID"]]

ggplot(df, aes(x = `(Intercept)`, y = Biomed_beliefs)) +
  geom_point() +
  geom_smooth(method = "lm") +
  theme_minimal() +
  labs(
    x = "per respondent fitted intercept of self-efficacy",
    y = "per respondent fitted slope of\nbiomedical beliefs on self-efficacy",
    title = "respondents that had higher levels of self-efficacy,\nhad lower effects of biomedical beliefs on self-efficacy"
  )

10.4 Goda Perlaviciute

library(haven)
goda <- read_sav("https://stulp.gmw.rug.nl/Rworkshop/goda.sav") %>% 
  as_factor()

library(skimr)
skim(goda)

10.4.1 visualisation

library(tidyverse)
goda_sel <- goda %>% 
  select(Q1, Q9) %>% 
  rename(pre = "Q1",
         post = "Q9") %>% 
  filter(!is.na(pre) & !is.na(post))

10.4.1.1 option 1

goda_sel_summ <- goda_sel %>% 
  group_by(pre, post) %>% 
  summarise(n = n()) %>%
  group_by(pre) %>%
  mutate(n_tot = sum(n),
         prop = n / n_tot)

ggplot(goda_sel_summ, aes(x = pre, y = post, fill = prop)) +
  geom_tile() +
  geom_text(aes(label = paste0(round(100 * prop), "%")), colour = "white", size = 5 ) +
  scale_fill_viridis_c() +
  coord_fixed() +
  scale_x_discrete(expand = c(0, 0)) +
  labs(
    x = "opinion prior to intervention",
    y = "opinion post intervention"
  ) + 
  theme_minimal() +
  theme(axis.text.x = element_text(angle = 25, hjust = 1),
        panel.grid.major = element_blank())

#### option 2 See https://ggforce.data-imaginist.com/reference/geom_parallel_sets.html

library(ggforce)
temp <- reshape2::melt(Titanic)
temp <- gather_set_data(temp, 1:4)

# select only relevant variables
goda_sankey <- goda_sel_summ %>% 
  select(pre, post, n) 

# code from ggforce package
goda_sankey <- gather_set_data(goda_sankey, 1:2)


ggplot(goda_sankey, aes(x, id = id, split = y, value = n)) +
  geom_parallel_sets(aes(fill = pre), alpha = 0.3, axis.width = 0.1) +
  geom_parallel_sets_axes(axis.width = 0.1) +
  geom_parallel_sets_labels(colour = 'white', angle = 0, nudge_x = 0, hjust = 0.5) +
  scale_fill_brewer(palette = "Set1") +
  scale_x_continuous(limits = c(0.8, 2.2), expand = c(0, 0)) +
  coord_cartesian(clip = "off") +
  theme_void() +
  guides(fill = "none") +
  theme(panel.background = element_rect(colour = "grey77", fill = "grey77"))

10.5 Thomas de Lang

[I am absolutely not knowledgeable about structure equation modelling or confirmatory factor analyses. This was helpful to me: https://lavaan.ugent.be/tutorial/tutorial.pdf]

library(lavaan)

There is this dataset mpg on cars in the ggplot package, let’s use it for a confirmatory factor analysis. There are three variables that measure efficiency of the car, hwy, cty, and displ

library(ggplot2)
data <- mpg

# model specifications
cars_model_spec <- ' efficiency =~ hwy + cty + displ'

# fit model
fit <- cfa(cars_model_spec, data = data)
summary(fit, fit.measures = TRUE)

## lavaan 0.6-12 ended normally after 82 iterations
## 
##   Estimator                                         ML
##   Optimization method                           NLMINB
##   Number of model parameters                         6
## 
##   Number of observations                           234
## 
## Model Test User Model:
##                                                       
##   Test statistic                                 0.000
##   Degrees of freedom                                 0
## 
## Model Test Baseline Model:
## 
##   Test statistic                               811.079
##   Degrees of freedom                                 3
##   P-value                                        0.000
## 
## User Model versus Baseline Model:
## 
##   Comparative Fit Index (CFI)                    1.000
##   Tucker-Lewis Index (TLI)                       1.000
## 
## Loglikelihood and Information Criteria:
## 
##   Loglikelihood user model (H0)              -1405.396
##   Loglikelihood unrestricted model (H1)      -1405.396
##                                                       
##   Akaike (AIC)                                2822.792
##   Bayesian (BIC)                              2843.524
##   Sample-size adjusted Bayesian (BIC)         2824.506
## 
## Root Mean Square Error of Approximation:
## 
##   RMSEA                                          0.000
##   90 Percent confidence interval - lower         0.000
##   90 Percent confidence interval - upper         0.000
##   P-value RMSEA <= 0.05                             NA
## 
## Standardized Root Mean Square Residual:
## 
##   SRMR                                           0.000
## 
## Parameter Estimates:
## 
##   Standard errors                             Standard
##   Information                                 Expected
##   Information saturated (h1) model          Structured
## 
## Latent Variables:
##                    Estimate  Std.Err  z-value  P(>|z|)
##   efficiency =~                                       
##     hwy               1.000                           
##     cty               0.745    0.019   39.903    0.000
##     displ            -0.181    0.010  -18.893    0.000
## 
## Variances:
##                    Estimate  Std.Err  z-value  P(>|z|)
##    .hwy               2.930    0.558    5.247    0.000
##    .cty               0.064    0.271    0.234    0.815
##    .displ             0.599    0.058   10.389    0.000
##     efficiency       32.376    3.289    9.843    0.000