Learning Curves Behave Data
Russell Chan
23/01/2022
##Set working directory
setwd("C:/Users/ChanRW/OneDrive - Universiteit Twente/2020_MSCA_IF/2_Bachelor_thesis/2022_Joel_Broncho_X/Data")##Packages that are required for the analysis
library(tidyverse)
library(broom.mixed)
library(devtools)
library(brms)
library(mascutils)
library(bayr)
library(readxl)
library(ggplot2)
library(effects)##Import dataset
#dfAcc3<-read.table("Acc_Task3_1.csv", sep = ",", header = T, stringsAsFactors = F)
#dfAcc2<-read.table("Acc_Task1_220124_4.csv", sep = ",", header = T, stringsAsFactors = F)
df1<-read.table("Task1Behav.csv", sep = ",", header = T, stringsAsFactors = F)
df3<-read.table("Task3Behav.csv", sep = ",", header = T, stringsAsFactors = F)##USELESS Free learning curves (ROUGHT AND NOT ACCURATE)
#dfAcc3 %>%
#filter(RT < 10) %>%
#ggplot(aes(x = Time,
#y = DomHandX)) +
#geom_point() +
#geom_smooth(se = F) +
#facet_wrap(~Subject, scales = "free_y")
#dfAcc1 %>%
#filter(RT < 10) %>%
#ggplot(aes(x = Time,
#y = DomHandX,
#group = Part)) +
#facet_grid(~Trial) +
#geom_smooth(se = F)
#dfAcc1 %>%
#filter(RT < 10) %>%
#ggplot(aes(x = Time,
#y = DomHand_X,
#group = Subject)) +
#facet_grid(~Trial) +
#geom_smooth(se = F)
#df %>%
#filter(RT < 10) %>%
#ggplot(aes(x = repetition,
#y = RT,
#group = subject)) +
#geom_smooth(se = F)#Proper
df1$Subject <- factor(df1$Subject)
df3$Subject <- factor(df3$Subject)
mycolors=c("#6b5f3c","#ccc627","#54ab8e","#587ed1","#b04366","#de2d26","#d95f0e", "#a1d99b", "#dd1c77", "#a6bddb")
## FREE LEARNING CURVES ##
# Free learning curve 1
# per subject per sequence
df1 %>%
ggplot(aes(x = Trial,
y = MT,
color=Subject)) +
geom_point() +
geom_smooth(se = F) +
facet_wrap(~Subject, scales = "free_y")+
ylab("MT (s)")+
xlab("Time")+
ylim(0,250)+
theme_classic()+
scale_color_manual(values=mycolors)## `geom_smooth()` using method = 'loess' and formula 'y ~ x'## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 0.98## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 0.98## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 0.98## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 0.98## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 0.98## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 0.98## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 0.98## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 0.98## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 0.98## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 0.98## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804
df3 %>%
ggplot(aes(x = Trial,
y = MT,
color=Subject)) +
geom_point() +
geom_smooth(se = F) +
facet_wrap(~Subject, scales = "free_y")+
ylab("MT (s)")+
xlab("Time")+
ylim(250,1000)+
theme_classic()+
scale_color_manual(values=mycolors)## `geom_smooth()` using method = 'loess' and formula 'y ~ x'## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 0.99## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 0.99## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 0.99## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 0.99## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 0.99## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 0.99## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 0.99## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 0.99## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 0.99## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 0.99## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201
# Free learning curve 2
# Individual learning curves over blocks/reps
df1 %>%
ggplot(aes(x = Trial,
y = MT,
group = Subject,
color= Subject)) +
geom_smooth(se = F)+
#scale_x_continuous(limits = c(0,192), expand = c(0, 0))+
theme_classic()+
ylab("MT (s)")+
xlab("Time")+
scale_color_manual(values=mycolors)+
facet_wrap(~Trial)## `geom_smooth()` using method = 'loess' and formula 'y ~ x'
#Over Trials / TimeRepX
df1 %>%
ggplot(aes(x = Rep,
y = MT,
group = Subject,
color=Subject)) +
geom_smooth(se = F)+
#scale_x_continuous(limits = c(0,192), expand = c(0, 0))+
theme_classic()+
ylab("MT (s)")+
xlab("Rep")+
scale_color_manual(values=mycolors)+
facet_wrap(~Subject)## `geom_smooth()` using method = 'loess' and formula 'y ~ x'## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804
df3 %>%
ggplot(aes(x = Rep,
y = MT,
group = Subject,
color=Subject)) +
geom_smooth(se = F)+
#scale_x_continuous(limits = c(0,192), expand = c(0, 0))+
theme_classic()+
ylab("MT (s)")+
xlab("Rep")+
scale_color_manual(values=mycolors)+
facet_wrap(~Subject)## `geom_smooth()` using method = 'loess' and formula 'y ~ x'## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201
#geom_vline(xintercept = c(24,48,72,96,120,144,168),colour="grey”, show.legend=TRUE)+
#geom_text(aes(x=12, label="Trial_1", y=0.1), colour="grey") +
#geom_text(aes(x=36, label="Trial 2", y=0.1), colour="grey") +
#geom_text(aes(x=60, label="Trial 3", y=0.1), colour="grey") +
#geom_text(aes(x=84, label="Trial 4", y=0.1), colour="grey") +
#geom_text(aes(x=108, label="Trial 5", y=0.1), colour="grey")
#geom_vline(xintercept = c(24,48,72,96,120,144,168),colour="grey”, show.legend=TRUE)+
#geom_text(aes(x=12, label="Block 1", y=0.1), colour="grey") +
#geom_text(aes(x=36, label="Block 2", y=0.1), colour="grey") +
#geom_text(aes(x=60, label="Block 3", y=0.1), colour="grey") +
#geom_text(aes(x=84, label="Block 4", y=0.1), colour="grey") +
#geom_text(aes(x=108, label="Block 5", y=0.1), colour="grey") +
#geom_text(aes(x=132, label="Block 6", y=0.1), colour="grey") +
#geom_text(aes(x=156, label="Block 7", y=0.1), colour="grey") +
#geom_text(aes(x=180, label="Block 8", y=0.1), colour="grey") ## NON-LINEAR MULTILEVEL REGRESSION ##
# specify formula, variables and weakly informative priors
F_ary <- formula(MT ~ asym + ampl * exp(-rate * Rep))
F_ary_ef_1 <- list(formula(ampl ~ 1|Subject),
formula(rate ~ 1|Subject),
formula(asym ~ 1|Subject))
F_ary_prior <- c(set_prior("normal(5, 100)", nlpar = "ampl", lb = 0),
set_prior("normal(.5, 3)", nlpar = "rate", lb = 0),
set_prior("normal(3, 20)", nlpar = "asym", lb = 0))
# create model including MCMC sampling
M_1 <-
df1 %>%
brm(bf(F_ary,
flist = F_ary_ef_1,
nl = T),
prior = F_ary_prior,
family = "exgaussian",
data = .,
iter = 10,
warmup = 8,
save_pars=save_pars("Subject"))## Compiling Stan program...## Start sampling##
## SAMPLING FOR MODEL 'cd137cae3425170764c33899873035dd' NOW (CHAIN 1).
## Chain 1: Rejecting initial value:
## Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
## Chain 1: Stan can't start sampling from this initial value.
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## Chain 4:## Warning: There were 6 divergent transitions after warmup. See
## http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
## to find out why this is a problem and how to eliminate them.## Warning: There were 3 chains where the estimated Bayesian Fraction of Missing Information was low. See
## http://mc-stan.org/misc/warnings.html#bfmi-low## Warning: Examine the pairs() plot to diagnose sampling problems## Warning: The largest R-hat is 1.67, indicating chains have not mixed.
## Running the chains for more iterations may help. See
## http://mc-stan.org/misc/warnings.html#r-hat## Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
## Running the chains for more iterations may help. See
## http://mc-stan.org/misc/warnings.html#bulk-ess## Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
## Running the chains for more iterations may help. See
## http://mc-stan.org/misc/warnings.html#tail-essP_1 <- posterior(M_1) ## Warning: Method 'posterior_samples' is deprecated. Please see ?as_draws for
## recommended alternatives.## Warning: `funs()` was deprecated in dplyr 0.8.0.
## Please use a list of either functions or lambdas:
##
## # Simple named list:
## list(mean = mean, median = median)
##
## # Auto named with `tibble::lst()`:
## tibble::lst(mean, median)
##
## # Using lambdas
## list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))PP_1 <- post_pred(M_1, thin = 10)## Warning: 'nsamples.brmsfit' is deprecated. Please use 'ndraws' instead.## Warning: Argument 'nsamples' is deprecated. Please use argument 'ndraws'
## instead.# save model estimates
save(M_1, P_1, PP_1, df, file = "model_estimates.Rda")
# get parameters for fixed effects, random factor variation and random effects
bayr::fixef(P_1)| nonlin | center | lower | upper |
|---|---|---|---|
| ampl | 1.5372730 | 0.2441283 | 7.532265 |
| rate | 0.9047972 | 0.6752391 | 5.994427 |
| asym | 0.5115005 | 0.2946219 | 89.096451 |
bayr::grpef(P_1)| nonlin | center | lower | upper |
|---|---|---|---|
| ampl | 4.2609141 | 1.5042368 | 13.427043 |
| rate | 0.6306478 | 0.3218369 | 1.849620 |
| asym | 0.7215044 | 0.1628746 | 4.117278 |
P_1 %>% re_scores() %>% bayr::ranef() | nonlin | re_entity | center | lower | upper |
|---|---|---|---|---|
| ampl | 1 | 2.8459440 | -4.0190910 | 6.311818 |
| ampl | 2 | 2.1026237 | -3.3140584 | 5.332197 |
| ampl | 3 | 8.8466523 | 4.9345281 | 26.299112 |
| ampl | 4 | 0.2218807 | -7.9569252 | 5.119654 |
| ampl | 5 | 4.0804121 | -3.8072336 | 20.027441 |
| ampl | 6 | 1.7266856 | -3.0906295 | 16.998520 |
| ampl | 7 | -1.4921182 | -12.0888616 | 9.957731 |
| ampl | 8 | 4.0659946 | -5.9701183 | 9.218559 |
| ampl | 9 | -0.9485475 | -18.1375707 | 15.985171 |
| ampl | 10 | 1.1976497 | -13.7032115 | 11.133031 |
| rate | 1 | 1.4297614 | 0.5545299 | 6.574320 |
| rate | 2 | 1.0628584 | 0.1473731 | 5.893760 |
| rate | 3 | 0.6909012 | -0.2318586 | 7.527884 |
| rate | 4 | 0.8788250 | -0.1372828 | 5.693161 |
| rate | 5 | 0.4432553 | -0.3974981 | 7.021053 |
| rate | 6 | 1.4667947 | 0.9317835 | 8.534708 |
| rate | 7 | 1.6635068 | -0.2545396 | 6.771273 |
| rate | 8 | 0.5969694 | -0.1577749 | 5.854229 |
| rate | 9 | 0.8752235 | -0.3484960 | 5.531201 |
| rate | 10 | 1.3543611 | 1.0857261 | 6.240982 |
| asym | 1 | 0.8224183 | -1.7897847 | 89.182016 |
| asym | 2 | 0.3962197 | -3.5172137 | 88.925652 |
| asym | 3 | 1.6877796 | -1.5135568 | 89.164884 |
| asym | 4 | 0.8901015 | -1.7875809 | 89.126578 |
| asym | 5 | 0.9748117 | -3.9222010 | 89.060216 |
| asym | 6 | -0.0614516 | -5.7202461 | 88.998442 |
| asym | 7 | 0.1393303 | -6.9366189 | 89.225925 |
| asym | 8 | 2.2711239 | -1.2744745 | 89.202639 |
| asym | 9 | 4.8634926 | -1.3297056 | 88.945384 |
| asym | 10 | 2.7202911 | 1.0478260 | 88.950185 |
## LEARNING CURVES BASED ON MODEL ESTIMATES ##
df1$Subject<-df1$Subject
# learning curves per Subject
df1 %>%
mutate(M_1 = predict(PP_1)$center) %>%
ggplot(aes(x = Rep,
y = M_1,
color=Subject)) +
facet_wrap(~Subject, scales = "free_y") +
geom_smooth(se = F) +
geom_point(alpha=0.2, size=1)+
ylim(-100,500)+
labs(x="Rep",y="Model estimates")+
theme_classic()+
scale_color_manual(values=mycolors)## `geom_smooth()` using method = 'loess' and formula 'y ~ x'## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 2.02## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.0804
# crossbar plots for each parameter and Subject
P_1 %>%
re_scores() %>%
bayr::ranef() %>%
ggplot(aes(x = re_entity,
y = center,
ymin = lower,
ymax = upper)) +
facet_grid(nonlin~1, scales = "free_y") +
geom_crossbar(width = .2) +
labs(x = "Subject", y = "Model estimates") +
theme_classic()
## NON-LINEAR MULTILEVEL REGRESSION ##
# specify formula, variables and weakly informative priors
F_ary2 <- formula(MT ~ asym + ampl * exp(-rate * Rep))
F_ary_ef_2 <- list(formula(ampl ~ 1|Subject),
formula(rate ~ 1|Subject),
formula(asym ~ 1|Subject))
F_ary_prior2 <- c(set_prior("normal(5, 100)", nlpar = "ampl", lb = 0),
set_prior("normal(.5, 3)", nlpar = "rate", lb = 0),
set_prior("normal(3, 20)", nlpar = "asym", lb = 0))
# create model including MCMC sampling
M_2 <-
df3 %>%
brm(bf(F_ary2,
flist = F_ary_ef_2,
nl = T),
prior = F_ary_prior2,
family = "exgaussian",
data = .,
iter = 10,
warmup = 8,
save_pars=save_pars("Subject"))## Compiling Stan program...## Start sampling##
## SAMPLING FOR MODEL 'e92e15377b9191dba6fe2a238d4e46dd' NOW (CHAIN 1).
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## Chain 4: Iteration: 8 / 10 [ 80%] (Warmup)
## Chain 4: Iteration: 9 / 10 [ 90%] (Sampling)
## Chain 4: Iteration: 10 / 10 [100%] (Sampling)
## Chain 4:
## Chain 4: Elapsed Time: 0.004 seconds (Warm-up)
## Chain 4: 0.001 seconds (Sampling)
## Chain 4: 0.005 seconds (Total)
## Chain 4:## Warning: There were 6 divergent transitions after warmup. See
## http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
## to find out why this is a problem and how to eliminate them.## Warning: There were 2 chains where the estimated Bayesian Fraction of Missing Information was low. See
## http://mc-stan.org/misc/warnings.html#bfmi-low## Warning: Examine the pairs() plot to diagnose sampling problems## Warning: The largest R-hat is 1.39, indicating chains have not mixed.
## Running the chains for more iterations may help. See
## http://mc-stan.org/misc/warnings.html#r-hat## Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
## Running the chains for more iterations may help. See
## http://mc-stan.org/misc/warnings.html#bulk-ess## Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
## Running the chains for more iterations may help. See
## http://mc-stan.org/misc/warnings.html#tail-essP_2 <- posterior(M_2) ## Warning: Method 'posterior_samples' is deprecated. Please see ?as_draws for
## recommended alternatives.PP_2 <- post_pred(M_2, thin = 10)## Warning: 'nsamples.brmsfit' is deprecated. Please use 'ndraws' instead.## Warning: Argument 'nsamples' is deprecated. Please use argument 'ndraws'
## instead.# save model estimates
save(M_2, P_2, PP_2, df, file = "model_estimates2.Rda")
# get parameters for fixed effects, random factor variation and random effects
bayr::fixef(P_2)| nonlin | center | lower | upper |
|---|---|---|---|
| ampl | 2.217012 | 0.5119803 | 24.779228 |
| rate | 3.956863 | 0.4145142 | 6.454642 |
| asym | 6.109056 | 0.7827957 | 22.210695 |
bayr::grpef(P_2)| nonlin | center | lower | upper |
|---|---|---|---|
| ampl | 1.2876692 | 0.2697084 | 3.184098 |
| rate | 0.5482723 | 0.1011188 | 1.255198 |
| asym | 1.2282076 | 0.0985602 | 13.334264 |
P_2 %>% re_scores() %>% bayr::ranef() | nonlin | re_entity | center | lower | upper |
|---|---|---|---|---|
| ampl | 1 | 2.520021 | 0.5933774 | 20.895040 |
| ampl | 2 | 2.743138 | 0.8504929 | 25.153398 |
| ampl | 3 | 3.010682 | -0.1947308 | 24.804242 |
| ampl | 4 | 2.251460 | 0.4408577 | 21.751716 |
| ampl | 5 | 3.265185 | -1.4391451 | 23.096544 |
| ampl | 6 | 2.009275 | -0.3846950 | 25.612125 |
| ampl | 7 | 2.281924 | 0.5345588 | 27.873327 |
| ampl | 8 | 3.061369 | 0.6124279 | 26.926629 |
| ampl | 9 | 2.578767 | -9.0206021 | 21.354280 |
| ampl | 10 | 3.784110 | 0.8083094 | 25.035000 |
| rate | 1 | 4.182387 | -0.3153740 | 6.372929 |
| rate | 2 | 3.523668 | 1.2422143 | 6.806751 |
| rate | 3 | 4.313452 | -0.5138478 | 7.050187 |
| rate | 4 | 4.508422 | -1.3744200 | 7.515303 |
| rate | 5 | 3.788438 | -0.0356767 | 6.241064 |
| rate | 6 | 3.625326 | 1.0719685 | 6.453255 |
| rate | 7 | 3.148713 | -0.1200784 | 5.938351 |
| rate | 8 | 3.250953 | 0.7751837 | 6.206078 |
| rate | 9 | 3.610666 | 0.6568504 | 5.973544 |
| rate | 10 | 4.446138 | 1.0639951 | 7.975844 |
| asym | 1 | 2.917321 | 0.5679055 | 14.149390 |
| asym | 2 | 5.503346 | 0.6218894 | 24.101602 |
| asym | 3 | 4.883594 | 0.2545269 | 21.813136 |
| asym | 4 | 5.839893 | 0.8644056 | 36.366124 |
| asym | 5 | 3.682677 | 0.8159019 | 18.837016 |
| asym | 6 | 6.153524 | 0.3633338 | 16.280428 |
| asym | 7 | 3.008648 | 0.7916115 | 17.441304 |
| asym | 8 | 6.108018 | 0.8848794 | 23.359119 |
| asym | 9 | 6.207769 | 0.2081330 | 23.266166 |
| asym | 10 | 3.494624 | -5.5384711 | 27.583948 |
## LEARNING CURVES BASED ON MODEL ESTIMATES ##
df3$Subject<-df3$Subject
# learning curves per Subject
df3 %>%
mutate(M_2 = predict(PP_2)$center) %>%
ggplot(aes(x = Rep,
y = M_2,
color=Subject)) +
facet_wrap(~Subject, scales = "free_y") +
geom_smooth(se = F) +
geom_point(alpha=0.2, size=1)+
ylim(-500,1500)+
labs(x="Rep",y="Model estimates")+
theme_classic()+
scale_color_manual(values=mycolors)## `geom_smooth()` using method = 'loess' and formula 'y ~ x'## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1.01## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0201
# crossbar plots for each parameter and Subject
P_2 %>%
re_scores() %>%
bayr::ranef() %>%
ggplot(aes(x = re_entity,
y = center,
ymin = lower,
ymax = upper)) +
facet_grid(nonlin~1, scales = "free_y") +
geom_crossbar(width = .2) +
labs(x = "Subject", y = "Model estimates") +
theme_classic()