[R-sig-ME] Representation model problem with standardized variables

Mon Apr 4 13:57:35 CEST 2022

Dear Daniel,

Thank you so much and my problem was solved.

The hard to me is to retrieve the center and scale from standardization and after calculating back, but now with your answer looks easy!

Best wishes,

Alexandre

 --Alexandre dos Santos
Geotechnologies and Spatial Statistics applied to Forest Entomology
Instituto Federal de Mato Grosso (IFMT) - Campus Caceres
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Em segunda-feira, 4 de abril de 2022 06:26:04 AMT, Daniel Lüdecke <d.luedecke using uke.de> escreveu: 

Dear Alexandre,
this one might solve your issue. I use the plot() method from ggeffects, but you can of course use ggplot2 as well, to build your own plot from scratch. The basic idea is to map the values of the range from the unstandardized variable with those from the standardized one, and then use "scale_x_...()" from ggplot to change the labels. At the bottom, you find the two plots when you use the unstandardized data in your model, and you can see, that the axis labels (range) represents the original scale.

Best
Daniel

library(datawizard)
library(lme4)
library(ggeffects)
library(ggplot2)

myds <- read.csv("https://raw.githubusercontent.com/Leprechault/trash/main/ds.desenvol.csv")
d.scale <- standardize(myds, select = c("temp", "storage"))
m_6 <- glmer.nb(development ~ poly(temp,2) + poly(storage,2) + (1 | storage ), data = d.scale)

# for temp
mydf <- ggpredict(m_6, terms = "temp [all]")

# retrieve center and scale from standardization
center_temp <- attributes(d.scale)$center["temp"]
scale_temp <- attributes(d.scale)$scale["temp"]

# scaled range, calculate back to range of unstandardized
scaled_range <- c(-1, 0, 1, 2)
new_range <- round(scaled_range * scale_temp + center_temp)

# scaled range
plot(mydf, add.data = TRUE)

# original range
plot(mydf, add.data = TRUE) + 
  scale_x_continuous(
    breaks = scaled_range, 
    labels = new_range
  )

# for storage
mydf <- ggpredict(m_6, terms = "storage [all]")

# retrieve center and scale from standardization
center_storage <- attributes(d.scale)$center["storage"]
scale_storage <- attributes(d.scale)$scale["storage"]

# scaled range, calculate back to range of unstandardized
scaled_range <- c(-1, 0, 1)
new_range <- round(scaled_range * scale_storage + center_storage)

# scaled range
plot(mydf, add.data = TRUE)

# original range
plot(mydf, add.data = TRUE) + 
  scale_x_continuous(
    breaks = scaled_range, 
    labels = new_range
  )

# compare to plots w/o standardization
m_7 <- glmer.nb(development ~ poly(temp,2) + poly(storage,2) + (1 | storage ), data = myds)
ggpredict(m_7, terms = "temp [all]") |> plot(add.data = TRUE)
ggpredict(m_7, terms = "storage [all]") |> plot(add.data = TRUE)

-----Ursprüngliche Nachricht-----
Von: R-sig-mixed-models <r-sig-mixed-models-bounces using r-project.org> Im Auftrag von Alexandre Santos via R-sig-mixed-models
Gesendet: Mittwoch, 30. März 2022 13:34
An: r-sig-mixed-models using r-project.org
Betreff: [R-sig-ME] Representation model problem with standardized variables

Hi Everyone!!

I standardized my input variables (ds.scale) before glmm adjustments but in the final plot, I have a problem with the real-world scale of my variables and the predicted values by model (m_6). I´d like the original scale of my temp and storage variables represented in my better model (m_6). What is the correct approach for this? Do not standardise my input variables, despite I lot of warmings? Some data transformation at the end? I make:

#Packages
library(lme4)
library(ggplot2)
library(ggeffects)
library(tidyverse)
library(bbmle) 
library(broom)

#Open my dataset
myds<-read.csv("https://raw.githubusercontent.com/Leprechault/trash/main/ds.desenvol.csv")
str(myds)
# 'data.frame': 400 obs. of  4 variables:
#  $ temp      : num  0 0 0 0 0 0 0 0 0 0 ...
#  $ storage    : int  5 5 5 5 5 5 5 5 5 5 ...
#  $ rep        : chr  "r1" "r2" "r3" "r4" ...
#  $ development: int  0 23 22 27 24 25 24 22 0 22 ...

# Storage (days) is temporally correlated with temperature then mixed model
ds.scale<- myds %>%
  mutate(across(c(temp, storage), ~ drop(scale(.))))

# Models creation Poisson/Negative binomial
m_1 <- glmer(development ~ temp + storage +
              (1 | storage ), data = ds.scale, 
                family = "poisson")
m_2 <- glmer(development ~ poly(temp,2) + storage +
              (1 | storage ), data = ds.scale, 
                family = "poisson")  
m_3 <- glmer(development ~ poly(temp,2) + poly(storage,2) +
              (1 | storage ), data = ds.scale, 
                family = "poisson")  
m_4 <- glmer.nb(development ~ temp + storage +
              (1 | storage ), data = ds.scale)
m_5 <- glmer.nb(development ~ poly(temp,2) + storage +
              (1 | storage ), data = ds.scale)  
m_6 <- glmer.nb(development ~ poly(temp,2) + poly(storage,2) +
              (1 | storage ), data = ds.scale)  
modList <- tibble::lst(m_1,m_2,m_3,m_4,m_5,m_6)
bbmle::AICtab(modList)

#    dAIC df
# m_6  0.0 7 
# m_3  1.0 6 
# m_5  3.3 6 
# m_2  5.0 5 
# m_4 17.9 5 
# m_1 21.0 4

# Plot the results for my better model (m_6)
mydf <- ggpredict(m_6, terms = c("temp [all]", "storage[all]"))

# For temp
ggplot(mydf, aes(x, predicted)) +
  geom_point(data=myds, aes(temp, development), alpha = 0.5) + 
  geom_line() +
  labs(x = "temp", y = "development")

# For storage
ggplot(mydf, aes(x, predicted)) +
  geom_point(data=myds, aes(storage, development), alpha = 0.5) + 
  geom_line() +
  labs(x = "storage", y = "development")
# -------------------------------------------------------------------------------------------  

Please, any help with it?
--
Alexandre dos Santos
Geotechnologies and Spatial Statistics applied to Forest Entomology

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