#' This function visualizes the result of a single simulation, plotting the original
#' data and the simulated data in one single graph. Data and the simulation settings
#' are taken from the data frame + meta data that is generated by the function
#' 'specify_simulation()'. In this function, a few choices need to be made with regard
#' to the sampling procedure.
#' @df input data: output of any of the 'specify_simulation()' functions
#' @ref_val Any value you want to compare with the distribution of the
#' test-statistic.This simply plots a vertical line at that value. If you don't
#' want to add this line, chose "none" (default)
#' @xdistr Option "as_data' or 'uniform'. The option 'as_data' generates a
#' density curve on the x-values, with densities used as sample weight for all
#' x-values along the observed x-range. This generates distributions of x-values
#' similar to the observed x-value. The option 'uniform' result in a sampling of
#' x-values from a uniform distribution.
#' @sample_size A number that gives the number of data points generated in the
#' simulation. The option 'as_data' returns the same number as in the original
#' data. The latter is default. In the case of categorical variables, the sample
#' size per group will be equal or proportional to the observed sample
#' sizes of the groups. You can set sample_size = "as data" or provide a vector
#' with number of samples per (alphabetic ordered) groups. This allows for setting
#' different sample sizes per group.
#' @import ggplot2
#' @import dplyr
#' @import patchwork
#' @import cowplot
#' @import PupillometryR
#' @import janitor
#' @import ggpubr
#' @export
visualise_simulation <- function(
df,
xdistr = "as data",
sample_size = "as data")
{
#---regression slope------------------------------------------------------------
if(attributes(df)$test == "slope"){
# original data
df <- df %>%
rename(x_obs = attributes(.)$predictor_variable,
y_obs = attributes(.)$response_variable) %>%
mutate(y_pred = predict(lm(y_obs ~ x_obs, data = .)),
orig_res = y_pred-y_obs)
# getting regression statistics of original data
coeff_original <- coefficients(lm(y_obs ~ x_obs, data = df))
# null hypothesis or confidence interval
if(attributes(df)$procedure == "H0"){
coeff_original[1] <- mean(df$y_obs)
coeff_original[2] <- 0
} else {
coeff_original <- coeff_original
}
sd_orig_res <- df %>% summarise(tmp = sd(orig_res)) %>% as.numeric()
if(sample_size == "as data"){nr_data_points = nrow(df)} else {nr_data_points = sample_size}
# Getting predictor values and associated error terms
if(xdistr == "uniform"){
xy_data <- data.frame(sim_x = seq(0.95*min(df$x_obs), 1.05*max(df$x_obs),
length.out = max(1024, nr_data_points)),
heterosc = seq(1, attributes(df)$het_cont1,
length.out = max(1024, nr_data_points))) %>%
mutate(sdx = heterosc * (attributes(df)$error_cont1 * sd_orig_res) / mean(heterosc)) %>%
slice_sample(n=nr_data_points, replace=T) %>% select(-heterosc)
} else if(xdistr == "as data") {
# get coefficients of function of change in error term
tmp <- data.frame(heterosc = seq(1, attributes(df)$het_cont1, length.out = nr_data_points)) %>%
mutate(sim_x = seq(0.95*min(df$x_obs), 1.05*max(df$x_obs), length.out = nr_data_points),
sdx = heterosc * (attributes(df)$error_cont1 * sd_orig_res) / mean(heterosc)) %>%
lm(sdx ~ sim_x, data = .) %>%
coefficients(.)
# get x-value density distribution
dens_distr_x <-density(df$x_obs,
n = max(1024, nr_data_points),
from = 0.95*min(df$x_obs),
to = 1.05*max(df$x_obs))
# Get randomly selected x-values with probabilities given by the x-value density distribution
xy_data <- data.frame(sim_x = sample(dens_distr_x[[1]], nr_data_points,prob = dens_distr_x[[2]], replace=T)) %>%
mutate(sdx = tmp[1] + tmp[2]*sim_x)
} else {stop("xdistr has to be 'as_data' or 'uniform")
}
xy_data <- xy_data %>%
mutate(y_pop = coeff_original[1] + coeff_original[2] * sim_x,
residual = rnorm(nr_data_points, 0, sdx),
sim_y = y_pop + residual) %>%
select(-y_pop, -residual) %>%
mutate(sim_pred = predict(lm(sim_y ~ sim_x, data = .)),
sim_resid = sim_pred - sim_y)
# Use randomly one of these colors in the graphs
kleur <- sample(c('#FFA700', '#FFBD40', '#218359', '#235D79', '#034769',
"#588C7E", "#F2AE72", "#D96459", "#00AFBB",
"#E7B800", "#FC4E07", "#999999", "#E69F00",
"#56B4E9", "#009E73", "#F0E442", "#0072B2",
"#D55E00", "#CC79A7", "#FFDB6D", "#C4961A", "#00AFBB"), 2)
p1 <- ggplot() +
geom_line(data = df,aes(x_obs, y_pred),
color = "lightgrey", alpha = 0.5, size = 0.8) +
geom_line(data = xy_data, aes(sim_x, sim_pred),
color = kleur[1], size = 1.3, alpha = 0.7) +
geom_point(data = xy_data, aes(sim_x, sim_y),
shape = 21, fill = kleur[1], color = kleur[1], size = 4, alpha = 0.4)+
geom_point(data = df,aes(x_obs, y_obs),
shape = 1,color = "lightgrey", alpha = 0.7, size = 4)+
labs(y = attributes(df)$response_variable, x = attributes(df)$predictor_variable) +
theme_bw() +
theme(axis.title.x = element_text(size=13, colour = kleur[1]),
axis.text.x = element_text(size=13, colour = kleur[1]),
axis.title.y = element_text(size=13, colour = kleur[1]),
axis.text.y = element_text(size=13, colour = kleur[1]),
panel.border = element_rect(colour = kleur[1],
size = 1.1),
axis.ticks = element_blank())
p2 <- ggplot() +
geom_hline(yintercept=0, color = "lightgrey", size = 1)+
geom_point(data = xy_data,aes(sim_pred, sim_resid),
color = kleur[1], fill = kleur[1],
shape = 21, size = 2.5, alpha = 0.7)+
labs(y = "residuals", x = "predicted") +
theme_bw() +
theme(axis.title.x = element_text(size=10, colour = kleur[1]),
axis.text.x = element_text(size=8, colour = kleur[1]),
axis.title.y = element_text(size=10, colour = kleur[1]),
axis.text.y = element_text(size=8, colour = kleur[1]),
panel.border = element_rect(colour = kleur[1],
size = 1.1),
axis.ticks = element_blank(),
legend.position = "none")
mean_resid <- mean(xy_data$sim_resid)
sd_resid <- sd(xy_data$sim_resid)
suppressMessages(
p3 <- ggplot(xy_data, aes(sim_resid)) +
geom_histogram(aes(y = ..density..),
fill = kleur[1],
color = "white",
alpha = 0.5) +
stat_function(fun = dnorm,
args = list(mean = mean_resid,
sd = sd_resid),
color = "black",
lwd = 0.5, linetype = "dashed") +
ylab("density") +
xlab("residuals") +
theme_bw() +
theme(axis.title.x = element_text(size=10, colour = kleur[1]),
axis.text.x = element_text(size=8, colour = kleur[1]),
axis.title.y = element_text(size=10, colour = kleur[1]),
axis.text.y = element_text(size=8, colour = kleur[1]),
panel.border = element_rect(colour = kleur[1],
size = 1.1),
axis.ticks = element_blank(),
legend.position = "none")
)
# Add a residual plot and add histogram of residuals (both with original as well)
p4 = p1 + (p2 / p3) + plot_layout(widths = c(2, 1))
return(p4)
#---difference between regression slopes----------------------------------------
} else if(attributes(df)$test == "diff slopes"){
# original data
df <- df %>%
rename(x_cont = attributes(.)$continuous_predictor,
x_cat = attributes(.)$categorical_predictor,
y_obs = attributes(.)$response_variable) %>%
mutate(y_pred = predict(lm(y_obs ~ x_cont*x_cat, data = .)),
orig_res = y_pred-y_obs)
# Calculate the difference between group sds of residuals and that of the
# overall mean
overall_sd_resid <- sd(df$orig_res)
group_sds <- df %>%
group_by(x_cat) %>%
summarise(sd_resid = sd(orig_res)) %>%
mutate(mf_grp = sd_resid/overall_sd_resid)
# Define the multiplication factors to calculate for each group how much more
# the error term is than the observed overall sd of the residuals
if(length(attributes(df)$error_cat) == 1){
if(attributes(df)$error_cat == "as data"){
mf <- c(group_sds$mf_grp[1], group_sds$mf_grp[2])
} else {
print("error_cat has to be a vector with 2 values, or 'as data'")
}
} else {mf <- c(attributes(df)$error_cat)}
# groups
group_data <- df %>% mutate(overall_sd = sd(orig_res)) %>%
group_by(x_cat) %>%
summarise(nr_original = n(),
overall_sd = mean(overall_sd)) %>%
ungroup() %>%
# calculates the error terms for the two groups by multiplying mf with the
# overall sd of the residuals
mutate(grp_mf = mf,
grp_err = grp_mf*overall_sd) %>%
# Getting proportion of observations (data points) per group
mutate(prop_obs = nr_original / sum(nr_original)) %>%
# define number of observations (= # of data points) per group
# Use ifelse because with case_when all RHSs must evaluate to the same type of vector.
# and when sample_size = "as data", that is not possible
mutate(nr_new = ifelse(sample_size == "as data", nr_original, prop_obs*sample_size))
### Getting x-values
if(xdistr == "uniform"){
# Categorical variable, level 1
grp1_range <- df %>%
filter(x_cat == group_data$x_cat[1]) %>%
summarise(min = 0.95*min(x_cont), max = 1.05*max(x_cont))
grp1 <- data.frame(x_cont = seq(grp1_range$min, grp1_range$max,
length.out = max(1024, group_data$nr_new[1])),
heterosc = seq(1, attributes(df)$het_cont1,
length.out = max(1024, group_data$nr_new[1]))) %>%
mutate(sdx = heterosc * (attributes(df)$error_cont1 * group_data$grp_err[1]) / mean(heterosc)) %>%
slice_sample(n = group_data$nr_new[1], replace=T) %>% select(-heterosc) %>%
mutate(x_cat = group_data$x_cat[1])
# Categorical variable, level 2
grp2_range <- df %>%
filter(x_cat == group_data$x_cat[2]) %>%
summarise(min = 0.95*min(x_cont), max = 1.05*max(x_cont))
grp2 <- data.frame(x_cont = seq(grp2_range$min, grp2_range$max,
length.out = max(1024, group_data$nr_new[2])),
heterosc = seq(1, attributes(df)$het_cont1,
length.out = max(1024, group_data$nr_new[2]))) %>%
mutate(sdx = heterosc * (attributes(df)$error_cont1 * group_data$grp_err[2]) / mean(heterosc)) %>%
slice_sample(n = group_data$nr_new[2], replace=T) %>% select(-heterosc) %>%
mutate(x_cat = group_data$x_cat[2])
# Categorical variable, join two levels
xy_data <- bind_rows(grp1, grp2)
} else if(xdistr == "as data") {
# Categorical variable, level 1
# figure out how to use map() here!
x_dens_distr <- df %>%
filter(x_cat == group_data$x_cat[1])
x_dens_distr = density(x_dens_distr$x_cont,
n = max(1024, group_data$nr_new[1]),
from = 0.95*min(x_dens_distr$x_cont), to = 1.05*max(x_dens_distr$x_cont))
grp1 <- data.frame(x_cont = x_dens_distr$x,
heterosc = seq(1, attributes(df)$het_cont1,
length.out = max(1024, group_data$nr_new[1]))) %>%
mutate(sdx = heterosc * (attributes(df)$error_cont1 * group_data$grp_err[1]) / mean(heterosc)) %>%
slice_sample(n = group_data$nr_new[1], weight_by = x_dens_distr$y, replace=T) %>% select(-heterosc) %>%
mutate(x_cat = group_data$x_cat[1])
# Categorical variable, level 2
x_dens_distr <- df %>%
filter(x_cat == group_data$x_cat[2])
x_dens_distr = density(x_dens_distr$x_cont,
n = max(1024, group_data$nr_new[2]),
from = 0.95*min(x_dens_distr$x_cont), to = 1.05*max(x_dens_distr$x_cont))
grp2 <- data.frame(x_cont = x_dens_distr$x,
heterosc = seq(1, attributes(df)$het_cont1,
length.out = max(1024, group_data$nr_new[2]))) %>%
mutate(sdx = heterosc * (attributes(df)$error_cont1 * group_data$grp_err[2]) / mean(heterosc)) %>%
slice_sample(n = group_data$nr_new[2], weight_by = x_dens_distr$y, replace=T) %>% select(-heterosc) %>%
mutate(x_cat = group_data$x_cat[2])
# Categorical variable, join two levels
xy_data <- bind_rows(grp1, grp2)
} else {stop("xdistr has to be 'as_data' or 'uniform")
}
# When null hypothesis: regression statistics of the model fitted on original
# data with categorical variable but no interaction (i.e., no difference in slope)
if(attributes(df)$procedure == "H0"){
lm.tmp <- lm(y_obs ~ x_cont + x_cat, data = df)
xy_data <- xy_data %>%
mutate(y_pop = predict(lm.tmp, newdata = xy_data)) %>%
rowwise() %>%
mutate(residual = rnorm(1, 0, sdx),
sim_y = y_pop + residual) %>%
ungroup() %>%
select(-y_pop, -residual) %>%
mutate(sim_pred = predict(lm(sim_y ~ x_cont * x_cat, data = .)),
sim_resid = sim_pred - sim_y)
} else {
# When confidence interval: regression statistics of the model fitted on
# original data with the categorical variable
lm.tmp <- lm(y_obs ~ x_cont*x_cat, data = df)
xy_data <- xy_data %>%
mutate(y_pop = predict(lm.tmp, newdata = xy_data)) %>%
rowwise() %>%
mutate(residual = rnorm(1, 0, sdx),
sim_y = y_pop + residual) %>%
ungroup() %>%
select(-y_pop, -residual) %>%
mutate(sim_pred = predict(lm(sim_y ~ x_cont * x_cat, data = .)),
sim_resid = sim_pred - sim_y)
}
# Randomly select a pair of colors for the graph
kleur <- data.frame(kleur1 = c("#2D2926FF", "#FC766AFF", "#5F4B8BFF", "#F95700FF", "#00203FFF", "#2C5F2D", "#EEA47FFF", "#0063B2FF", "#5CC8D7FF", "#101820FF", "#DAA03DFF", "#00539CFF", "#4B878BFF", "#CE4A7EFF", "#00B1D2FF", "#FF7F41FF", "#BD7F37FF"),
kleur2 = c("#E94B3CFF", "#5B84B1FF", "#E69A8DFF", "#00A4CCFF", "#ADEFD1FF", "#97BC62FF", "#00539CFF", "#9CC3D5FF", "#B1624EFF", "#F2AA4CFF", "#616247FF", "#FFD662FF", "#D01C1FFF", "#1C1C1BFF", "#FDDB27FF", "#79C000FF", "#A13941FF")) %>%
slice_sample(n = 1) %>% .[ , sample(1:2)] %>% as.character()
# Create graph
p1 <- ggplot() +
geom_line(data = df,aes(x_cont, y_pred, group = x_cat),
color = "lightgrey", alpha = 0.5, size = 0.8) +
geom_line(data = xy_data, aes(x_cont, sim_pred, group = x_cat, color = x_cat),
size = 1.3, alpha = 0.9) +
geom_point(data = xy_data, aes(x_cont, sim_y, fill = x_cat, color = x_cat),
shape = 21, size = 4, alpha = 0.7)+
geom_point(data = df,aes(x_cont, y_obs),
shape = 1,color = "lightgrey", alpha = 0.7, size = 4)+
scale_colour_manual(values = kleur) +
scale_fill_manual(values = kleur)+
labs(y = attributes(df)$response_variable, x = attributes(df)$continuous_predictor) +
theme_bw() +
theme(axis.title.x = element_text(size=13, colour = kleur[1]),
axis.text.x = element_text(size=13, colour = kleur[1]),
axis.title.y = element_text(size=13, colour = kleur[1]),
axis.text.y = element_text(size=13, colour = kleur[1]),
panel.border = element_rect(colour = kleur[1],
size = 1.1),
axis.ticks = element_blank(),
legend.position = "none")
p2 <- ggplot() +
geom_hline(yintercept=0, color = "lightgrey", size = 1)+
geom_point(data = xy_data,aes(x_cont, sim_resid, fill = x_cat, color = x_cat),
shape = 21, size = 2.5, alpha = 0.7)+
scale_colour_manual(values = kleur) +
scale_fill_manual(values = kleur)+
labs(y = "residuals", x = attributes(df)$continuous_predictor) +
theme_bw() +
theme(axis.title.x = element_text(size=10, colour = kleur[1]),
axis.text.x = element_text(size=8, colour = kleur[1]),
axis.title.y = element_text(size=10, colour = kleur[1]),
axis.text.y = element_text(size=8, colour = kleur[1]),
panel.border = element_rect(colour = kleur[1],
size = 1.1),
axis.ticks = element_blank(),
legend.position = "none")
mean_resid <- mean(xy_data$sim_resid)
sd_resid <- sd(xy_data$sim_resid)
suppressMessages(
p3 <- ggplot(xy_data, aes(sim_resid)) +
geom_histogram(aes(y = ..density..),
fill = kleur[1],
color = "white",
alpha = 0.5) +
stat_function(fun = dnorm,
args = list(mean = mean_resid,
sd = sd_resid),
color = "black",
lwd = 0.5, linetype = "dashed") +
ylab("density") +
xlab("residuals") +
theme_bw() +
theme(axis.title.x = element_text(size=10, colour = kleur[1]),
axis.text.x = element_text(size=8, colour = kleur[1]),
axis.title.y = element_text(size=10, colour = kleur[1]),
axis.text.y = element_text(size=8, colour = kleur[1]),
panel.border = element_rect(colour = kleur[1],
size = 1.1),
axis.ticks = element_blank(),
legend.position = "none")
)
# Add a residual plot and add histogram of residuals (both with original as well)
p4 = p1 + (p2 / p3) + plot_layout(widths = c(2, 1))
return(p4)
#---difference between intercepts (parallel slopes assumed)----------------------------------------
} else if(attributes(df)$test == "diff intercepts"){
# original data
df <- df %>%
rename(x_cont = attributes(.)$continuous_predictor,
x_cat = attributes(.)$categorical_predictor,
y_obs = attributes(.)$response_variable) %>%
mutate(y_pred = predict(lm(y_obs ~ x_cont + x_cat, data = .)),
orig_res = y_pred-y_obs)
# Calculate the difference between group sds of residuals and that of the
# overall mean
overall_sd_resid <- sd(df$orig_res)
group_sds <- df %>%
group_by(x_cat) %>%
summarise(sd_resid = sd(orig_res)) %>%
mutate(mf_grp = sd_resid/overall_sd_resid)
# Define the multiplication factors to calculate for each group how much more
# the error term is than the observed overall sd of the residuals
if(length(attributes(df)$error_cat) == 1){
if(attributes(df)$error_cat == "as data"){
mf <- c(group_sds$mf_grp[1], group_sds$mf_grp[2])
} else {
print("error_cat has to be a vector with 2 values, or 'as data'")
}
} else {mf <- c(attributes(df)$error_cat)}
# groups
group_data <- df %>% mutate(overall_sd = sd(orig_res)) %>%
group_by(x_cat) %>%
summarise(nr_original = n(),
overall_sd = mean(overall_sd)) %>%
ungroup() %>%
# calculates the error terms for the two groups by multiplying mf with the
# overall sd of the residuals
mutate(grp_mf = mf,
grp_err = grp_mf*overall_sd) %>%
# Getting proportion of observations (data points) per group
mutate(prop_obs = nr_original / sum(nr_original)) %>%
# define number of observations (= # of data points) per group
# Use ifelse because with case_when all RHSs must evaluate to the same type of vector.
# and when sample_size = "as data", that is not possible
mutate(nr_new = ifelse(sample_size == "as data", nr_original, prop_obs*sample_size))
### Getting x-values
if(xdistr == "uniform"){
# Categorical variable, level 1
grp1_range <- df %>%
filter(x_cat == group_data$x_cat[1]) %>%
summarise(min = 0.95*min(x_cont), max = 1.05*max(x_cont))
grp1 <- data.frame(x_cont = seq(grp1_range$min, grp1_range$max,
length.out = max(1024, group_data$nr_new[1])),
heterosc = seq(1, attributes(df)$het_cont1,
length.out = max(1024, group_data$nr_new[1]))) %>%
mutate(sdx = heterosc * (attributes(df)$error_cont1 * group_data$grp_err[1]) / mean(heterosc)) %>%
slice_sample(n = group_data$nr_new[1], replace=T) %>% select(-heterosc) %>%
mutate(x_cat = group_data$x_cat[1])
# Categorical variable, level 2
grp2_range <- df %>%
filter(x_cat == group_data$x_cat[2]) %>%
summarise(min = 0.95*min(x_cont), max = 1.05*max(x_cont))
grp2 <- data.frame(x_cont = seq(grp2_range$min, grp2_range$max,
length.out = max(1024, group_data$nr_new[2])),
heterosc = seq(1, attributes(df)$het_cont1,
length.out = max(1024, group_data$nr_new[2]))) %>%
mutate(sdx = heterosc * (attributes(df)$error_cont1 * group_data$grp_err[2]) / mean(heterosc)) %>%
slice_sample(n = group_data$nr_new[2], replace=T) %>% select(-heterosc) %>%
mutate(x_cat = group_data$x_cat[2])
# Categorical variable, join two levels
xy_data <- bind_rows(grp1, grp2)
} else if(xdistr == "as data") {
# Categorical variable, level 1
# figure out how to use map() here!
x_dens_distr <- df %>%
filter(x_cat == group_data$x_cat[1])
x_dens_distr = density(x_dens_distr$x_cont,
n = max(1024, group_data$nr_new[1]),
from = 0.95*min(x_dens_distr$x_cont), to = 1.05*max(x_dens_distr$x_cont))
grp1 <- data.frame(x_cont = x_dens_distr$x,
heterosc = seq(1, attributes(df)$het_cont1,
length.out = max(1024, group_data$nr_new[1]))) %>%
mutate(sdx = heterosc * (attributes(df)$error_cont1 * group_data$grp_err[1]) / mean(heterosc)) %>%
slice_sample(n = group_data$nr_new[1], weight_by = x_dens_distr$y, replace=T) %>% select(-heterosc) %>%
mutate(x_cat = group_data$x_cat[1])
# Categorical variable, level 2
x_dens_distr <- df %>%
filter(x_cat == group_data$x_cat[2])
x_dens_distr = density(x_dens_distr$x_cont,
n = max(1024, group_data$nr_new[2]),
from = 0.95*min(x_dens_distr$x_cont), to = 1.05*max(x_dens_distr$x_cont))
grp2 <- data.frame(x_cont = x_dens_distr$x,
heterosc = seq(1, attributes(df)$het_cont1,
length.out = max(1024, group_data$nr_new[2]))) %>%
mutate(sdx = heterosc * (attributes(df)$error_cont1 * group_data$grp_err[2]) / mean(heterosc)) %>%
slice_sample(n = group_data$nr_new[2], weight_by = x_dens_distr$y, replace=T) %>% select(-heterosc) %>%
mutate(x_cat = group_data$x_cat[2])
# Categorical variable, join two levels
xy_data <- bind_rows(grp1, grp2)
} else {stop("xdistr has to be 'as_data' or 'uniform")
}
# When null hypothesis: regression statistics of the model fitted on original
# data with categorical variable but no interaction (i.e., no difference in
# intercept or slope)
if(attributes(df)$procedure == "H0"){
lm.tmp <- lm(y_obs ~ x_cont, data = df)
xy_data <- xy_data %>%
mutate(y_pop = predict(lm.tmp, newdata = xy_data)) %>%
rowwise() %>%
mutate(residual = rnorm(1, 0, sdx),
sim_y = y_pop + residual) %>%
ungroup() %>%
select(-y_pop, -residual) %>%
mutate(sim_pred = predict(lm(sim_y ~ x_cont + x_cat, data = .)),
sim_resid = sim_pred - sim_y)
} else {
# When confidence interval: regression statistics of the model fitted on
# original data with the categorical variable
lm.tmp <- lm(y_obs ~ x_cont + x_cat, data = df)
xy_data <- xy_data %>%
mutate(y_pop = predict(lm.tmp, newdata = xy_data)) %>%
rowwise() %>%
mutate(residual = rnorm(1, 0, sdx),
sim_y = y_pop + residual) %>%
ungroup() %>%
select(-y_pop, -residual) %>%
mutate(sim_pred = predict(lm(sim_y ~ x_cont + x_cat, data = .)),
sim_resid = sim_pred - sim_y)
}
# Randomly select a pair of colors for the graph
kleur <- data.frame(kleur1 = c("#2D2926FF", "#FC766AFF", "#5F4B8BFF", "#F95700FF", "#00203FFF", "#2C5F2D", "#EEA47FFF", "#0063B2FF", "#5CC8D7FF", "#101820FF", "#DAA03DFF", "#00539CFF", "#4B878BFF", "#CE4A7EFF", "#00B1D2FF", "#FF7F41FF", "#BD7F37FF"),
kleur2 = c("#E94B3CFF", "#5B84B1FF", "#E69A8DFF", "#00A4CCFF", "#ADEFD1FF", "#97BC62FF", "#00539CFF", "#9CC3D5FF", "#B1624EFF", "#F2AA4CFF", "#616247FF", "#FFD662FF", "#D01C1FFF", "#1C1C1BFF", "#FDDB27FF", "#79C000FF", "#A13941FF")) %>%
slice_sample(n = 1) %>% .[ , sample(1:2)] %>% as.character()
# Create graph
p1 <- ggplot() +
geom_line(data = df,aes(x_cont, y_pred, group = x_cat),
color = "lightgrey", alpha = 0.5, size = 0.8) +
geom_line(data = xy_data, aes(x_cont, sim_pred, group = x_cat, color = x_cat),
size = 1.3, alpha = 0.9) +
geom_point(data = xy_data, aes(x_cont, sim_y, fill = x_cat, color = x_cat),
shape = 21, size = 4, alpha = 0.7)+
geom_point(data = df,aes(x_cont, y_obs),
shape = 1,color = "lightgrey", alpha = 0.7, size = 4)+
scale_colour_manual(values = kleur) +
scale_fill_manual(values = kleur)+
labs(y = attributes(df)$response_variable, x = attributes(df)$continuous_predictor) +
theme_bw() +
theme(axis.title.x = element_text(size=13, colour = kleur[1]),
axis.text.x = element_text(size=13, colour = kleur[1]),
axis.title.y = element_text(size=13, colour = kleur[1]),
axis.text.y = element_text(size=13, colour = kleur[1]),
panel.border = element_rect(colour = kleur[1],
size = 1.1),
axis.ticks = element_blank(),
legend.position = "none")
p2 <- ggplot() +
geom_hline(yintercept=0, color = "lightgrey", size = 1)+
geom_point(data = xy_data,aes(x_cont, sim_resid, fill = x_cat, color = x_cat),
shape = 21, size = 2.5, alpha = 0.7)+
scale_colour_manual(values = kleur) +
scale_fill_manual(values = kleur)+
labs(y = "residuals", x = attributes(df)$continuous_predictor) +
theme_bw() +
theme(axis.title.x = element_text(size=10, colour = kleur[1]),
axis.text.x = element_text(size=8, colour = kleur[1]),
axis.title.y = element_text(size=10, colour = kleur[1]),
axis.text.y = element_text(size=8, colour = kleur[1]),
panel.border = element_rect(colour = kleur[1],
size = 1.1),
axis.ticks = element_blank(),
legend.position = "none")
mean_resid <- mean(xy_data$sim_resid)
sd_resid <- sd(xy_data$sim_resid)
suppressMessages(
p3 <- ggplot(xy_data, aes(sim_resid)) +
geom_histogram(aes(y = ..density..),
fill = kleur[1],
color = "white",
alpha = 0.5) +
stat_function(fun = dnorm,
args = list(mean = mean_resid,
sd = sd_resid),
color = "black",
lwd = 0.5, linetype = "dashed") +
ylab("density") +
xlab("residuals") +
theme_bw() +
theme(axis.title.x = element_text(size=10, colour = kleur[1]),
axis.text.x = element_text(size=8, colour = kleur[1]),
axis.title.y = element_text(size=10, colour = kleur[1]),
axis.text.y = element_text(size=8, colour = kleur[1]),
panel.border = element_rect(colour = kleur[1],
size = 1.1),
axis.ticks = element_blank(),
legend.position = "none")
)
# Add a residual plot and add histogram of residuals (both with original as well)
p4 = p1 + (p2 / p3) + plot_layout(widths = c(2, 1))
return(p4)
#---difference between sample means---------------------------------------------
} else if(attributes(df)$test == "diff means"){
# original data
df <- df %>%
rename(x_obs = attributes(.)$predictor_variable,
y_obs = attributes(.)$response_variable)
# get the means of the levels of the categorical variable and the difference
# between these means
model_stats <- df %>%
group_by(x_obs) %>%
summarise(means = mean(y_obs)) %>%
ungroup() %>%
pivot_wider(names_from = x_obs, values_from = means) %>%
mutate(diff_means= .[[1,1]]-.[[1,2]])
# Get the overall mean plus the mean of the residuals (difference between
# group mean and observed values).
model_stats <- df %>%
group_by(x_obs) %>%
# the residuals are calculated as the difference between observed y and
# the group mean of the observed Y
mutate(residual = y_obs - mean(y_obs)) %>%
# the following two lines mean that we calculate a single sd of the errors
# (observed - mean), i.e., we assume the same error term across groups. That
# might not be true (it is not true for the example data!). If you want to
# use the observed difference in error term, use 'error_cat', based on
# values calculated prior to using this function.
ungroup() %>%
mutate(sd_resid = sd(residual)) %>%
summarise(mean_y_obs = mean(y_obs),
sd_resid = mean(sd_resid)) %>%
# multiply the error term with user-provided factor
bind_cols(model_stats, .)
# Define the size of the sample
if(length(sample_size) == 1){
if(sample_size == "as data"){
nr_samples <- df %>% group_by(x_obs) %>% summarise(nr = n())
} else {
nr_samples <- data.frame(nr = c(sample_size, sample_size))
}
} else if(length(sample_size) == 2){
nr_samples <- data.frame(nr = sample_size)
}
# Calculate the difference between group sds of residuals and that of the
# overall mean
group_sds <- df %>%
group_by(x_obs) %>%
mutate(means = mean(y_obs),
resid = mean(y_obs)-y_obs) %>%
summarise(mean = mean(means),
sd_resid = sd(resid)) %>%
mutate(mf_grp = sd_resid/model_stats$sd_resid[1])
# extract the error_cat values from the attributes of the original data
if(attributes(df)$error_cat == "as data"){
mf <- c(group_sds$mf_grp[1], group_sds$mf_grp[2])
} else{
mf <- c(attributes(df)$error_cat)
}
# Get a random sample
if(attributes(df)$procedure == "CI"){
# sample error term and add group means
new_sample <- data.frame(new_sample =
purrr::modify(rnorm(nr_samples$nr[1],
0, mf[1]*model_stats$sd_resid),
~ .x + model_stats[[1]]),
x_obs = rep(unique(df$x_obs)[1], nr_samples$nr[1])
)
new_sample <- data.frame(new_sample =
purrr::modify(rnorm(nr_samples$nr[2],
0, mf[2]*model_stats$sd_resid),
~ .x + model_stats[[2]]),
x_obs = rep(unique(df$x_obs)[2], nr_samples$nr[2])
) %>%
bind_rows(new_sample, .)
} else if(attributes(df)$procedure == "H0"){
# sample error term and add mean_y_obs
new_sample <- data.frame(new_sample =
purrr::modify(rnorm(nr_samples$nr[1],
0, mf[1]*model_stats$sd_resid),
~ .x + model_stats$mean_y_obs),
x_obs = rep(unique(df$x_obs)[1], nr_samples$nr[1])
)
new_sample <- data.frame(new_sample =
purrr::modify(rnorm(nr_samples$nr[2],
0, mf[2]*model_stats$sd_resid),
~ .x + model_stats$mean_y_obs),
x_obs = rep(unique(df$x_obs)[2], nr_samples$nr[2])
) %>%
bind_rows(new_sample, .)
}
# Randomly select a pair of colors for the graph
kleur <- data.frame(kleur1 = c("#2D2926FF", "#FC766AFF", "#5F4B8BFF", "#F95700FF", "#00203FFF", "#2C5F2D", "#EEA47FFF", "#0063B2FF", "#5CC8D7FF", "#101820FF", "#DAA03DFF", "#00539CFF", "#4B878BFF", "#CE4A7EFF", "#00B1D2FF", "#FF7F41FF", "#BD7F37FF"),
kleur2 = c("#E94B3CFF", "#5B84B1FF", "#E69A8DFF", "#00A4CCFF", "#ADEFD1FF", "#97BC62FF", "#00539CFF", "#9CC3D5FF", "#B1624EFF", "#F2AA4CFF", "#616247FF", "#FFD662FF", "#D01C1FFF", "#1C1C1BFF", "#FDDB27FF", "#79C000FF", "#A13941FF")) %>%
slice_sample(n = 1) %>% .[ , sample(1:2)] %>% as.character()
# overall y limits
overall_y_min <- min(min(density(df$y_obs)$x), min(density(new_sample$new_sample)$x))
overall_y_max <- max(max(density(df$y_obs)$x), max(density(new_sample$new_sample)$x))
# create first graph with original data
p1 <- ggplot(df, aes(x = x_obs, y = y_obs)) +
geom_hline(yintercept = model_stats[[1]], color = "grey", linetype = "dashed")+
geom_hline(yintercept = model_stats[[2]], color = "grey", linetype = "dashed")+
geom_flat_violin(fill = "grey", alpha = .5, colour = NA,
position = position_nudge(x = 0, y = 0),
adjust = 1.5, trim = FALSE)+
geom_point(aes(x = as.numeric(as.factor(x_obs)),
y = y_obs),
fill = "grey",
position = position_jitter(width = .05),
size = 3, shape = 21, color = "white")+
geom_boxplot(aes(x = x_obs, y = y_obs),
color = "grey", fill = "grey",
outlier.shape = NA,
alpha = .5, width = .1,
position = position_nudge(x = -.2, y = 0))+
ylim(overall_y_min, overall_y_max)+
labs(y = attributes(df)$response_variable) +
theme_bw() +
theme(axis.title.x = element_blank(),
axis.text.x = element_text(size=12, colour = "darkgrey"),
axis.title.y = element_text(size=12, colour = "darkgrey"),
axis.text.y = element_text(size=12, colour = "darkgrey"),
panel.border = element_rect(colour = "darkgrey",
size = 1.1),
axis.ticks = element_blank(),
legend.position = "none")+
ggtitle("Original sample") +
theme(plot.title = element_text(color = "darkgrey"))
# create second graph with new sample data
mean_new <- new_sample %>% group_by(x_obs) %>%
summarise(means = mean(new_sample))
p2 <- ggplot(new_sample, aes(x = x_obs, y = new_sample, fill = x_obs)) +
geom_hline(yintercept = mean_new[[1,2]], color = kleur[1], linetype = "dashed")+
geom_hline(yintercept = mean_new[[2,2]], color = kleur[2], linetype = "dashed")+
geom_flat_violin(aes(fill = x_obs),
position = position_nudge(x = 0, y = 0),
adjust = 1.5,
trim = FALSE,
alpha = .5, colour = NA)+
geom_point(aes(x = as.numeric(as.factor(x_obs)),
y = new_sample,
fill = x_obs),
position = position_jitter(width = .05),
size = 3, shape = 21, color = "white")+
geom_boxplot(aes(x = x_obs, y = new_sample, color = x_obs, fill = x_obs),
outlier.shape = NA,
alpha = .5, width = .1,
position = position_nudge(x = -.2, y = 0))+
scale_colour_manual(values = kleur) +
scale_fill_manual(values = kleur)+
labs(y = attributes(df)$response_variable) +
ylim(overall_y_min, overall_y_max)+
theme_bw() +
theme(axis.title.x = element_blank(),
axis.text.x = element_text(size=12, colour = "darkgrey"),
axis.title.y = element_blank(),
axis.text.y = element_blank(),
panel.border = element_rect(colour = "darkgrey",
size = 1.1),
axis.ticks = element_blank(),
legend.position = "none")+
ggtitle("New sample") +
theme(plot.title = element_text(color = "darkgrey"))
p3 <- p1+p2
return(p3)
#---difference between sample proportions---------------------------------------------
} else if(attributes(df)$test == "diff props"){
# original data
df <- df %>%
rename(x_obs = attributes(.)$predictor_variable,
y_obs = attributes(.)$response_variable)
# get the proportions of success for both groups separately and overall
proportion_success <- df %>%
group_by(x_obs) %>%
mutate(nr_samples = n()) %>%
# Keep only the successes
filter(y_obs == attributes(df)$success) %>%
# Successes as proportion of total number (per group)
group_by(x_obs, nr_samples) %>%
summarise(prop_grp = n() / mean(nr_samples)) %>%
# code within mutate yields a single value (overall proportion of success)
# and the column with new variable is thus 'filled' with this value
mutate(
(df %>%
mutate(nr_samples = n()) %>%
filter(y_obs == attributes(df)$success) %>%
summarise(prop_all = n() / mean(nr_samples))
)
)
# Define the size of the sample
if(length(sample_size) == 1){
if(sample_size == "as data"){
proportion_success$nr_samples <- proportion_success$nr_samples
} else {
proportion_success$nr_samples <- data.frame(nr = c(sample_size, sample_size))
}
} else if(length(sample_size) == 2){
proportion_success$nr_samples <- c(sample_size)
}
# Get a random sample
if(attributes(df)$procedure == "CI"){
proportion_success %<>%
mutate(new_prop =
list(sample(x = unique(df$y_obs),
size = nr_samples,
replace = TRUE,
prob = c(prop_grp,
1-prop_grp)))) %>%
unnest(cols = c(new_prop)) %>%
filter(new_prop == attributes(df)$success) %>%
group_by(x_obs, nr_samples, prop_grp, prop_all) %>%
summarise(new_prop = n()/mean(nr_samples)) %>%
ungroup()
} else if(attributes(df)$procedure == "H0"){
proportion_success %<>%
mutate(new_prop =
list(sample(x = unique(df$y_obs),
size = nr_samples,
replace = TRUE,
prob = c(prop_all,
1-prop_all)))) %>%
unnest(cols = c(new_prop)) %>%
filter(new_prop == attributes(df)$success) %>%
group_by(x_obs, nr_samples, prop_grp, prop_all) %>%
summarise(new_prop = n()/mean(nr_samples)) %>%
ungroup()
}
# Randomly select a pair of colors for the graph
kleur <- data.frame(kleur1 = c("#2D2926FF", "#FC766AFF", "#5F4B8BFF", "#F95700FF", "#00203FFF", "#2C5F2D", "#EEA47FFF", "#0063B2FF", "#5CC8D7FF", "#101820FF", "#DAA03DFF", "#00539CFF", "#4B878BFF", "#CE4A7EFF", "#00B1D2FF", "#FF7F41FF", "#BD7F37FF"),
kleur2 = c("#E94B3CFF", "#5B84B1FF", "#E69A8DFF", "#00A4CCFF", "#ADEFD1FF", "#97BC62FF", "#00539CFF", "#9CC3D5FF", "#B1624EFF", "#F2AA4CFF", "#616247FF", "#FFD662FF", "#D01C1FFF", "#1C1C1BFF", "#FDDB27FF", "#79C000FF", "#A13941FF")) %>%
slice_sample(n = 1) %>% .[ , sample(1:2)] %>% as.character()
# overall y limits
overall_y_min <- min(min(proportion_success$prop_grp, min(proportion_success$new_prop)))
overall_y_max <- max(max(proportion_success$prop_grp, max(proportion_success$new_prop)))
if(attributes(df)$procedure == "CI"){
ggplot(proportion_success) +
geom_hline(aes(yintercept = prop_grp, color = x_obs), linetype = "dotted", size = 1.5)+
geom_bar(aes(x = x_obs, y = new_prop, fill = x_obs),
stat = "identity")+
scale_colour_manual(values = kleur) +
scale_fill_manual(values = kleur)+
ylim(0, overall_y_max + (overall_y_max-overall_y_min))+
labs(y = "proportion") +
theme_bw() +
theme(axis.title.x = element_blank(),
axis.text.x = element_text(size=15, colour = "darkgrey"),
axis.title.y = element_text(size=14, colour = "darkgrey"),
axis.text.y = element_text(size=14, colour = "darkgrey"),
panel.border = element_rect(colour = "darkgrey",
size = 1.1),
axis.ticks = element_blank(),
legend.position = "none")+
ggtitle("Difference between sample proportions (Confidence Interval)") +
theme(plot.title = element_text(color = "darkgrey"))
} else if(attributes(df)$procedure == "H0"){
ggplot(proportion_success) +
geom_hline(aes(yintercept = prop_grp, color = x_obs), linetype = "dotted", size = 1.5)+
geom_bar(aes(x = x_obs, y = new_prop, fill = x_obs),
stat = "identity")+
scale_colour_manual(values = kleur) +
scale_fill_manual(values = kleur)+
ylim(0, overall_y_max + (overall_y_max-overall_y_min))+
labs(y = "proportion") +
theme_bw() +
theme(axis.title.x = element_blank(),
axis.text.x = element_text(size=15, colour = "darkgrey"),
axis.title.y = element_text(size=14, colour = "darkgrey"),
axis.text.y = element_text(size=14, colour = "darkgrey"),
panel.border = element_rect(colour = "darkgrey",
size = 1.1),
axis.ticks = element_blank(),
legend.position = "none")+
ggtitle("Difference between sample proportions (Null hypothesis)") +
theme(plot.title = element_text(color = "darkgrey"))
}
#---Chi-square test ---------------------------------------------
} else if(attributes(df)$test == "Chi-sqr"){
# original data
df <- df %>%
rename(x_cat1 = attributes(.)$categorical_variable_1,
x_cat2 = attributes(.)$categorical_variable_2,
y_obs = attributes(.)$response_variable)
# get Chi-square
obs_chi_sqr <-df %>% tabyl(y_obs, x_cat1) %>%
chisq.test() %>% .$statistic
# Define the size of the sample
if(length(sample_size) == 1){
if(sample_size == "as data"){
cat1_info <- df %>%
group_by(x_cat1) %>%
summarise(nr_obs = n()) %>%
ungroup()
} else {
nr_levels <- df %>% distinct(x_cat1) %>% nrow()
cat1_info <-
data.frame(x_cat1 = sort(unique(df$x_cat1)),
nr_obs = rep(sample_size, nr_levels))
}
} else {
cat1_info <-
data.frame(x_cat1 = sort(unique(df$x_cat1)),
nr_obs = sample_size)
}
# Observed probability per categorical level
cat1_info <- df %>%
group_by(x_cat1,y_obs) %>%
summarise(probs = n()) %>%
group_by(x_cat1) %>%
mutate(probs = probs/sum(probs)) %>%
pivot_wider(names_from = y_obs, values_from = probs) %>%
left_join(cat1_info) %>%
ungroup()
# Null hypothesis probabilities per categorical level
probs_overall <- df %>%
group_by(y_obs) %>%
summarise(probs = n()) %>%
ungroup() %>%
mutate(probs = probs / sum(probs)) %>%
pivot_wider(names_from = y_obs, values_from = probs)
# Randomly select a pair of colors for the graph
kleur <- data.frame(kleur1 = c("#2D2926FF", "#FC766AFF", "#5F4B8BFF", "#F95700FF", "#00203FFF", "#2C5F2D", "#EEA47FFF", "#0063B2FF", "#5CC8D7FF", "#101820FF", "#DAA03DFF", "#00539CFF", "#4B878BFF", "#CE4A7EFF", "#00B1D2FF", "#FF7F41FF", "#BD7F37FF"),
kleur2 = c("#E94B3CFF", "#5B84B1FF", "#E69A8DFF", "#00A4CCFF", "#ADEFD1FF", "#97BC62FF", "#00539CFF", "#9CC3D5FF", "#B1624EFF", "#F2AA4CFF", "#616247FF", "#FFD662FF", "#D01C1FFF", "#1C1C1BFF", "#FDDB27FF", "#79C000FF", "#A13941FF")) %>%
slice_sample(n = 1) %>% .[ , sample(1)] %>% as.character()
# Get a random sample
cat_levels <- sort(unique(df$y_obs))
if(attributes(df)$procedure == "CI"){
p2 <- cat1_info %>%
group_split(x_cat1) %>%
map_dfr( ~ data.frame(
category = .$x_cat1,
y_sim = sample(x = cat_levels,
size = .$nr_obs,
replace = TRUE,
prob = .[cat_levels]))) %>%
group_by(category,y_sim) %>%
summarise(probs = n()) %>%
group_by(category) %>%
mutate(probs = 100*probs/sum(probs)) %>%
pivot_wider(names_from = y_sim, values_from = probs) %>%
column_to_rownames("category") %>%
ggballoonplot(fill = kleur, color = "white")+
scale_size(range = c(5, 27))+
theme_bw() +
theme(axis.title.x = element_blank(),
axis.text.x = element_text(size=14, colour = "darkgrey"),
axis.title.y = element_blank(),
axis.text.y = element_blank(),
panel.border = element_rect(colour = kleur,
size = 1.1),
axis.ticks = element_blank(),
legend.position = "none")
} else if(attributes(df)$procedure == "H0"){
p2 <- cat1_info %>%
group_split(x_cat1) %>%
map_dfr( ~ data.frame(
category = .$x_cat1,
y_sim = sample(x = cat_levels,
size = .$nr_obs,
replace = TRUE,
prob = as.vector(as.matrix(probs_overall))))) %>%
group_by(category,y_sim) %>%
summarise(probs = n()) %>%
group_by(category) %>%
mutate(probs = 100*probs/sum(probs)) %>%
pivot_wider(names_from = y_sim, values_from = probs) %>%
column_to_rownames("category") %>%
ggballoonplot(fill = kleur, color = "white")+
scale_size(range = c(5, 27))+
theme_bw() +
theme(axis.title.x = element_blank(),
axis.text.x = element_text(size=14, colour = "darkgrey"),
axis.title.y = element_blank(),
axis.text.y = element_blank(),
panel.border = element_rect(colour = kleur,
size = 1.1),
axis.ticks = element_blank(),
legend.position = "none")+
ggtitle("New sample") +
theme(plot.title = element_text(color = kleur))
}
# original data
p1 <- df %>%
group_by(x_cat1,y_obs) %>%
summarise(probs = n()) %>%
group_by(x_cat1) %>%
mutate(probs = 100*probs/sum(probs)) %>%
pivot_wider(names_from = y_obs, values_from = probs) %>%
column_to_rownames("x_cat1") %>%
ggballoonplot(color = "darkgrey")+
scale_size(range = c(5, 20))+
theme_bw() +
theme(axis.title.x = element_blank(),
axis.text.x = element_text(size=14, colour = "darkgrey"),
axis.title.y = element_blank(),
axis.text.y = element_text(size=13, colour = "darkgrey"),
panel.border = element_rect(colour = "darkgrey",
size = 1.1),
axis.ticks = element_blank(),
legend.position = "none")+
ggtitle("Original data") +
theme(plot.title = element_text(color = "darkgrey"))
p3 <- p1+p2
return(p3)
}
}
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