# note: use library("ggplot") to avoid "ggplot2::" in the following
##################################################################
## 2-factor Within-Subject Design ##
##################################################################
data(md_12.1)
aw <- aov_ez("id", "rt", md_12.1, within = c("angle", "noise"))
##---------------------------------------------------------------
## Basic Interaction Plots -
##---------------------------------------------------------------
## all examples require emmeans and ggplot2:
if (requireNamespace("emmeans") && requireNamespace("ggplot2")) {
afex_plot(aw, x = "angle", trace = "noise")
# or: afex_plot(aw, x = ~angle, trace = ~noise)
afex_plot(aw, x = "noise", trace = "angle")
### For within-subject designs, using within-subject CIs is better:
afex_plot(aw, x = "angle", trace = "noise", error = "within")
(p1 <- afex_plot(aw, x = "noise", trace = "angle", error = "within"))
## use different themes for nicer graphs:
p1 + ggplot2::theme_bw()
}
if (FALSE) {
p1 + ggplot2::theme_light()
p1 + ggplot2::theme_minimal()
p1 + jtools::theme_apa()
p1 + ggpubr::theme_pubr()
### set theme globally for R session:
ggplot2::theme_set(ggplot2::theme_bw())
### There are several ways to deal with overlapping points in the background besides alpha
# Using the default data geom and ggplot2::position_jitterdodge
afex_plot(aw, x = "noise", trace = "angle", error = "within", dodge = 0.3,
data_arg = list(
position =
ggplot2::position_jitterdodge(
jitter.width = 0,
jitter.height = 5,
dodge.width = 0.3 ## needs to be same as dodge
)))
# Overlapping points are shown as larger points using geom_count
afex_plot(aw, x = "noise", trace = "angle", error = "within", dodge = 0.5,
data_geom = ggplot2::geom_count)
# Using ggbeeswarm::geom_quasirandom (overlapping points shown in violin shape)
afex_plot(aw, x = "noise", trace = "angle", error = "within", dodge = 0.5,
data_geom = ggbeeswarm::geom_quasirandom,
data_arg = list(
dodge.width = 0.5, ## needs to be same as dodge
cex = 0.8,
width = 0.05 ## small value ensure data points match means
))
# Using ggbeeswarm::geom_beeswarm (overlapping points are adjacent on y-axis)
afex_plot(aw, x = "noise", trace = "angle", error = "within", dodge = 0.5,
data_geom = ggbeeswarm::geom_beeswarm,
data_arg = list(
dodge.width = 0.5, ## needs to be same as dodge
cex = 0.8))
# Do not display points, but use a violinplot: ggplot2::geom_violin
afex_plot(aw, x = "noise", trace = "angle", error = "within",
data_geom = ggplot2::geom_violin,
data_arg = list(width = 0.5))
# violinplots with color: ggplot2::geom_violin
afex_plot(aw, x = "noise", trace = "angle", error = "within",
mapping = c("linetype", "shape", "fill"),
data_geom = ggplot2::geom_violin,
data_arg = list(width = 0.5))
# do not display points, but use a boxplot: ggplot2::geom_boxplot
afex_plot(aw, x = "noise", trace = "angle", error = "within",
data_geom = ggplot2::geom_boxplot,
data_arg = list(width = 0.3))
# combine points with boxplot: ggpol::geom_boxjitter
afex_plot(aw, x = "noise", trace = "angle", error = "within",
data_geom = ggpol::geom_boxjitter,
data_arg = list(width = 0.3))
## hides error bars!
# nicer variant of ggpol::geom_boxjitter
afex_plot(aw, x = "noise", trace = "angle", error = "within",
mapping = c("shape", "fill"),
data_geom = ggpol::geom_boxjitter,
data_arg = list(
width = 0.3,
jitter.params = list(width = 0, height = 10),
outlier.intersect = TRUE),
point_arg = list(size = 2.5),
error_arg = list(linewidth = 1.5, width = 0))
# nicer variant of ggpol::geom_boxjitter without lines
afex_plot(aw, x = "noise", trace = "angle", error = "within", dodge = 0.7,
mapping = c("shape", "fill"),
data_geom = ggpol::geom_boxjitter,
data_arg = list(
width = 0.5,
jitter.params = list(width = 0, height = 10),
outlier.intersect = TRUE),
point_arg = list(size = 2.5),
line_arg = list(linetype = 0),
error_arg = list(linewidth = 1.5, width = 0))
### we can also use multiple geoms for the background by passing a list of geoms
afex_plot(aw, x = "noise", trace = "angle", error = "within",
data_geom = list(
ggplot2::geom_violin,
ggplot2::geom_point
))
## with separate extra arguments:
afex_plot(aw, x = "noise", trace = "angle", error = "within",
dodge = 0.5,
data_geom = list(
ggplot2::geom_violin,
ggplot2::geom_point
),
data_arg = list(
list(width = 0.4),
list(position =
ggplot2::position_jitterdodge(
jitter.width = 0,
jitter.height = 5,
dodge.width = 0.5 ## needs to be same as dodge
)))
)
}
##---------------------------------------------------------------
## One-Way Plots -
##---------------------------------------------------------------
if (FALSE) {
afex_plot(aw, x = "angle", error = "within") ## default
## with color we need larger points
afex_plot(aw, x = "angle", mapping = "color", error = "within",
point_arg = list(size = 2.5),
error_arg = list(linewidth = 1.5, width = 0.05))
afex_plot(aw, x = "angle", error = "within", data_geom = ggpol::geom_boxjitter)
## nicer
afex_plot(aw, x = "angle", error = "within", data_geom = ggpol::geom_boxjitter,
mapping = "fill", data_alpha = 0.7,
data_arg = list(
width = 0.6,
jitter.params = list(width = 0.07, height = 10),
outlier.intersect = TRUE
),
point_arg = list(size = 2.5),
error_arg = list(linewidth = 1.5, width = 0.05))
## we can use multiple geoms with separate argument lists:
afex_plot(aw, x = "angle", error = "within",
data_geom =
list(ggplot2::geom_violin, ggplot2::geom_boxplot),
data_arg =
list(list(width = 0.7), list(width = 0.1)))
## we can add a line connecting the means using geom_point(aes(group = 1)):
afex_plot(aw, x = "angle", error = "within") +
ggplot2::geom_line(ggplot2::aes(group = 1))
## we can also add lines connecting the individual data-point in the bg.
# to deal with overlapping points, we use geom_count and make means larger
afex_plot(aw, x = "angle", error = "within",
data_geom = list(ggplot2::geom_count, ggplot2::geom_line),
data_arg = list(list(), list(mapping = ggplot2::aes(group = id))),
point_arg = list(size = 2.5),
error_arg = list(width = 0, linewidth = 1.5)) +
ggplot2::geom_line(ggplot2::aes(group = 1), linewidth = 1.5)
## One-way plots also supports panels:
afex_plot(aw, x = "angle", panel = "noise", error = "within")
## And panels with lines:
afex_plot(aw, x = "angle", panel = "noise", error = "within") +
ggplot2::geom_line(ggplot2::aes(group = 1))
## For more complicated plots it is easier to attach ggplot2:
library("ggplot2")
## We can hide geoms by plotting them in transparent colour and add them
## afterward to use a mapping not directly supported.
## For example, the next plot adds a line to a one-way plot with panels, but
## with all geoms in the foreground having a colour conditional on the panel.
afex_plot(aw, x = "angle", panel = "noise", error = "within",
point_arg = list(color = "transparent"),
error_arg = list(color = "transparent")) +
geom_point(aes(color = panel)) +
geom_linerange(aes(color = panel, ymin = lower, ymax = upper)) +
geom_line(aes(group = 1, color = panel)) +
guides(color = guide_legend(title = "NOISE"))
## Note that we need to use guides explicitly, otherwise the legend title would
## be "panel". legend_title does not work in this case.
##---------------------------------------------------------------
## Other Basic Options -
##---------------------------------------------------------------
## relabel factor levels via factor_levels (with message)
afex_plot(aw, x = "noise", trace = "angle",
factor_levels = list(angle = c("0°", "4°", "8°"),
noise = c("Absent", "Present")))
## factor_levels allows named vectors which enable reordering the factor levels
### and renaming subsets of levels:
afex_plot(aw, x = "noise", trace = "angle",
factor_levels = list(
angle = c(X8 = "8°", X4 = "4°", X0 = "0°"),
noise = c(present = "Present")
)
)
## Change title of legend
afex_plot(aw, x = "noise", trace = "angle",
legend_title = "Noise Condition")
## Add reference line in the background
afex_plot(aw, x = "noise", trace = "angle",
plot_first = ggplot2::geom_hline(yintercept = 450,
colour = "darkgrey"))
## for plots with few factor levels, smaller dodge might be better:
afex_plot(aw, x = "angle", trace = "noise", dodge = 0.25)
#################################################################
## 4-factor Mixed Design ##
#################################################################
data(obk.long, package = "afex")
a1 <- aov_car(value ~ treatment * gender + Error(id/(phase*hour)),
data = obk.long, observed = "gender")
## too difficult to see anything
afex_plot(a1, ~phase*hour, ~treatment) +
ggplot2::theme_light()
## better
afex_plot(a1, ~hour, ~treatment, ~phase) +
ggplot2::theme_light()
## even better
afex_plot(a1, ~hour, ~treatment, ~phase,
dodge = 0.65,
data_arg = list(
position =
ggplot2::position_jitterdodge(
jitter.width = 0,
jitter.height = 0.2,
dodge.width = 0.65 ## needs to be same as dodge
),
color = "darkgrey")) +
ggplot2::theme_classic()
# with color instead of linetype to separate trace factor
afex_plot(a1, ~hour, ~treatment, ~phase,
mapping = c("shape", "color"),
dodge = 0.65,
data_arg = list(
position =
ggplot2::position_jitterdodge(
jitter.width = 0,
jitter.height = 0.2,
dodge.width = 0.65 ## needs to be same as dodge
))) +
ggplot2::theme_light()
# only color to separate trace factor
afex_plot(a1, ~hour, ~treatment, ~phase,
mapping = c("color"),
dodge = 0.65,
data_color = NULL, ## needs to be set to NULL to avoid error
data_arg = list(
position =
ggplot2::position_jitterdodge(
jitter.width = 0,
jitter.height = 0.2,
dodge.width = 0.65 ## needs to be same as dodge
))) +
ggplot2::theme_classic()
## plot involving all 4 factors:
afex_plot(a1, ~hour, ~treatment, ~gender+phase,
dodge = 0.65,
data_arg = list(
position =
ggplot2::position_jitterdodge(
jitter.width = 0,
jitter.height = 0.2,
dodge.width = 0.65 ## needs to be same as dodge
),
color = "darkgrey")) +
ggplot2::theme_bw()
##---------------------------------------------------------------
## Different Standard Errors Available -
##---------------------------------------------------------------
## purely within-design
cbind(
afex_plot(a1, ~phase, ~hour,
error = "model", return = "data")$means[,c("phase", "hour", "y", "SE")],
multivariate = afex_plot(a1, ~phase, ~hour,
error = "model", return = "data")$means$error,
mean = afex_plot(a1, ~phase, ~hour,
error = "mean", return = "data")$means$error,
within = afex_plot(a1, ~phase, ~hour,
error = "within", return = "data")$means$error,
between = afex_plot(a1, ~phase, ~hour,
error = "between", return = "data")$means$error)
## mixed design
cbind(
afex_plot(a1, ~phase, ~treatment,
error = "model", return = "data")$means[,c("phase", "treatment", "y", "SE")],
multivariate = afex_plot(a1, ~phase, ~treatment,
error = "model", return = "data")$means$error,
mean = afex_plot(a1, ~phase, ~treatment,
error = "mean", return = "data")$means$error,
within = afex_plot(a1, ~phase, ~treatment,
error = "within", return = "data")$means$error,
between = afex_plot(a1, ~phase, ~treatment,
error = "between", return = "data")$means$error)
}
##################################################################
## Mixed Models ##
##################################################################
if (requireNamespace("MEMSS") &&
requireNamespace("emmeans") &&
requireNamespace("ggplot2")) {
data("Machines", package = "MEMSS")
m1 <- mixed(score ~ Machine + (Machine|Worker), data=Machines)
pairs(emmeans::emmeans(m1, "Machine"))
# contrast estimate SE df t.ratio p.value
# A - B -7.966667 2.420850 5 -3.291 0.0481
# A - C -13.916667 1.540100 5 -9.036 0.0007
# B - C -5.950000 2.446475 5 -2.432 0.1253
## Default (i.e., model-based) error bars suggest no difference between Machines.
## This contrasts with pairwise comparisons above.
afex_plot(m1, "Machine")
## Impression from within-subject error bars is more in line with pattern of differences.
afex_plot(m1, "Machine", error = "within")
}
if (FALSE) {
data("fhch2010") # load
fhch <- droplevels(fhch2010[ fhch2010$correct,]) # remove errors
### following model should take less than a minute to fit:
mrt <- mixed(log_rt ~ task*stimulus*frequency + (stimulus*frequency||id)+
(task||item), fhch, method = "S", expand_re = TRUE)
## way too many points in background:
afex_plot(mrt, "stimulus", "frequency", "task")
## better to restrict plot of data to one random-effects grouping variable
afex_plot(mrt, "stimulus", "frequency", "task", id = "id")
## when plotting data from a single random effect, different error bars are possible:
afex_plot(mrt, "stimulus", "frequency", "task", id = "id", error = "within")
afex_plot(mrt, "stimulus", "frequency", "task", id = "id", error = "mean")
## compare visual impression with:
pairs(emmeans::emmeans(mrt, c("stimulus", "frequency"), by = "task"))
## same logic also possible for other random-effects grouping factor
afex_plot(mrt, "stimulus", "frequency", "task", id = "item")
## within-item error bars are misleading here. task is sole within-items factor.
afex_plot(mrt, "stimulus", "frequency", "task", id = "item", error = "within")
## CIs based on standard error of mean look small, but not unreasonable given results.
afex_plot(mrt, "stimulus", "frequency", "task", id = "item", error = "mean")
### compare distribution of individual data for different random effects:
## requires package cowplot
p_id <- afex_plot(mrt, "stimulus", "frequency", "task", id = "id",
error = "within", dodge = 0.7,
data_geom = ggplot2::geom_violin,
mapping = c("shape", "fill"),
data_arg = list(width = 0.7)) +
ggplot2::scale_shape_manual(values = c(4, 17)) +
ggplot2::labs(title = "ID")
p_item <- afex_plot(mrt, "stimulus", "frequency", "task", id = "item",
error = "within", dodge = 0.7,
data_geom = ggplot2::geom_violin,
mapping = c("shape", "fill"),
data_arg = list(width = 0.7)) +
ggplot2::scale_shape_manual(values = c(4, 17)) +
ggplot2::labs(title = "Item")
### see: https://cran.r-project.org/package=cowplot/vignettes/shared_legends.html
p_comb <- cowplot::plot_grid(
p_id + ggplot2::theme_light() + ggplot2::theme(legend.position="none"),
p_item + ggplot2::theme_light() + ggplot2::theme(legend.position="none")
)
legend <- cowplot::get_legend(p_id + ggplot2::theme(legend.position="bottom"))
cowplot::plot_grid(p_comb, legend,
ncol = 1,
rel_heights = c(1, 0.1))
##----------------------------------------------------------------
## Support for lme4::lmer -
##----------------------------------------------------------------
Oats <- nlme::Oats
## afex_plot does currently not support implicit nesting: (1|Block/Variety)
## Instead, we need to create the factor explicitly
Oats$VarBlock <- Oats$Variety:Oats$Block
Oats.lmer <- lmer(yield ~ Variety * factor(nitro) + (1|VarBlock) + (1|Block),
data = Oats)
afex_plot(Oats.lmer, "nitro", "Variety")
afex_plot(Oats.lmer, "nitro", panel = "Variety")
##################################################################
## Default Method works for Models Supported by emmeans ##
##################################################################
## lm
warp.lm <- lm(breaks ~ wool * tension, data = warpbreaks)
afex_plot(warp.lm, "tension")
afex_plot(warp.lm, "tension", "wool")
## poisson glm
ins <- data.frame(
n = c(500, 1200, 100, 400, 500, 300),
size = factor(rep(1:3,2), labels = c("S","M","L")),
age = factor(rep(1:2, each = 3)),
claims = c(42, 37, 1, 101, 73, 14))
ins.glm <- glm(claims ~ size + age + offset(log(n)),
data = ins, family = "poisson")
afex_plot(ins.glm, "size", "age")
## binomial glm adapted from ?predict.glm
ldose <- factor(rep(0:5, 2))
numdead <- c(1, 4, 9, 13, 18, 20, 0, 2, 6, 10, 12, 16)
sex <- factor(rep(c("M", "F"), c(6, 6)))
SF <- numdead/20 ## dv should be a vector, no matrix
budworm.lg <- glm(SF ~ sex*ldose, family = binomial,
weights = rep(20, length(numdead)))
afex_plot(budworm.lg, "ldose")
afex_plot(budworm.lg, "ldose", "sex") ## data point is hidden behind mean!
afex_plot(budworm.lg, "ldose", "sex",
data_arg = list(size = 4, color = "red"))
## nlme mixed model
data(Oats, package = "nlme")
Oats$nitro <- factor(Oats$nitro)
oats.1 <- nlme::lme(yield ~ nitro * Variety,
random = ~ 1 | Block / Variety,
data = Oats)
afex_plot(oats.1, "nitro", "Variety", data = Oats)
afex_plot(oats.1, "nitro", "Variety", data = Oats, id = "Block")
afex_plot(oats.1, "nitro", data = Oats)
afex_plot(oats.1, "nitro", data = Oats, id = c("Block", "Variety"))
afex_plot(oats.1, "nitro", data = Oats, id = "Block")
}
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