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I don't have any 'treatment' except the passage of time (date), and 10 times points. I have a total of 43190 measurements, they are continuous binomial data (0.0 to 1.0) of the percentual response variable (canopycov). In glm logic, this is a quasibinomial case, but I find just only glmmPQL in MASS package for use, but the model is not OK and I have NA for p-values in all the dates. In my case, I try:

#Packages
library(MASS)

# Dataset
ds<-read.csv("https://raw.githubusercontent.com/Leprechault/trash/main/pred_attack_F.csv")
str(ds)
# 'data.frame': 43190 obs. of  3 variables:
#  $ date     : chr  "2021-12-06" "2021-12-06" "2021-12-06" "2021-12-06" ...
#  $ canopycov: int  22 24 24 24 25 25 25 25 26 26 ...
#  $ rep      : chr  "r1" "r1" "r1" "r1" ...
# Binomial Generalized Linear Mixed Models
m.1 <- glmmPQL(canopycov/100~date,random=~1|date,
              family="quasibinomial",data=ds)
summary(m.1)
#Linear mixed-effects model fit by maximum likelihood
#   Data: ds 
#   AIC BIC logLik
#    NA  NA     NA

# Random effects:
#  Formula: ~1 | date
#          (Intercept)  Residual
# StdDev: 1.251838e-06 0.1443305

# Variance function:
#  Structure: fixed weights
#  Formula: ~invwt 
# Fixed effects:  canopycov/100 ~ date 
#                     Value   Std.Error    DF    t-value p-value
# (Intercept)    -0.5955403 0.004589042 43180 -129.77442       0
# date2021-06-14 -0.1249648 0.006555217     0  -19.06341     NaN
# date2021-07-09  0.7661870 0.006363749     0  120.39868     NaN
# date2021-07-24  1.0582366 0.006434893     0  164.45286     NaN
# date2021-08-03  1.0509474 0.006432295     0  163.38607     NaN
# date2021-08-08  1.0794612 0.006442704     0  167.54784     NaN
# date2021-09-02  0.9312346 0.006395722     0  145.60274     NaN
# date2021-09-07  0.9236196 0.006393780     0  144.45595     NaN
# date2021-09-22  0.7268144 0.006359224     0  114.29293     NaN
# date2021-12-06  1.3109809 0.006552314     0  200.07907     NaN
#  Correlation: 
#                (Intr) d2021-06 d2021-07-0 d2021-07-2 d2021-08-03 d2021-08-08
# date2021-06-14 -0.700                                                       
# date2021-07-09 -0.721  0.505                                                
# date2021-07-24 -0.713  0.499    0.514                                       
# date2021-08-03 -0.713  0.499    0.514      0.509                            
# date2021-08-08 -0.712  0.499    0.514      0.508      0.508                 
# date2021-09-02 -0.718  0.502    0.517      0.512      0.512       0.511     
# date2021-09-07 -0.718  0.502    0.518      0.512      0.512       0.511     
# date2021-09-22 -0.722  0.505    0.520      0.515      0.515       0.514     
# date2021-12-06 -0.700  0.490    0.505      0.499      0.500       0.499     
#                d2021-09-02 d2021-09-07 d2021-09-2
# date2021-06-14                                   
# date2021-07-09                                   
# date2021-07-24                                   
# date2021-08-03                                   
# date2021-08-08                                   
# date2021-09-02                                   
# date2021-09-07  0.515                            
# date2021-09-22  0.518       0.518                
# date2021-12-06  0.503       0.503       0.505    

# Standardized Within-Group Residuals:
#         Min          Q1         Med          Q3         Max 
# -6.66259139 -0.47887669  0.09634211  0.54135914  4.32231889 

# Number of Observations: 43190
# Number of Groups: 10

I'd like to correctly specify that my data is temporally pseudo replicated in a mixed-effects, but I don't find another approach for this. Please, I need any help to solve it.

Leprechault
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1 Answers1

2

I don't understand the motivation for a quasi-binomial model here, there's some nice discussion of the binomial and quasi binomial densities here and here that might be worth reading (including applications).

The problem with the code is that you have date as a character, so R doesn't know its a date. You will have to decide the units of measurement for time as well as the reference point, but the model works fine once you fix this.


ds<-read.csv("https://raw.githubusercontent.com/Leprechault/trash/main/pred_attack_F.csv")
str(ds)
head(ds)
class(ds$date)
ds$datex <- as.Date(ds$date)
summary(as.numeric(difftime(ds$datex, as.Date(Sys.Date(), "%d%b%Y"), units = "days")))
ds$date_time <- as.numeric(difftime(ds$datex, as.Date(Sys.Date(), "%d%b%Y"), units = "days"))
# scale for laplace
ds$sdate_time <- scale(ds$date_time)

m1 <-  glmer(cbind(canopycov,100 - canopycov)~ date_time + (1|date_time),
                    family="binomial",data=ds)
summary(m1)
# Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod']
# Family: binomial  ( logit )
# Formula: canopycov/100 ~ date_time + (1 | date_time)
# Data: ds
# 
# AIC      BIC   logLik deviance df.resid 
# 35109.7  35135.7 -17551.9  35103.7    43187 
# 
# Scaled residuals: 
#   Min       1Q   Median       3Q      Max 
# -19.0451  -1.5605  -0.5155  -0.1594   0.8081 
# 
# Random effects:
#   Groups    Name        Variance Std.Dev.
# date_time (Intercept) 0        0       
# Number of obs: 43190, groups:  date_time, 10
# 
# Fixed effects:
#   Estimate Std. Error z value Pr(>|z|)    
# (Intercept) 8.5062394  0.0866696   98.15   <2e-16 ***
#   date_time   0.0399010  0.0004348   91.77   <2e-16 ***
#   ---
#   Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
# 
# Correlation of Fixed Effects:
#   (Intr)
# date_time 0.988 
# optimizer (Nelder_Mead) convergence code: 0 (OK)
# boundary (singular) fit: see ?isSingular

m2 <- MASS::glmmPQL(canopycov/100~ date_time,random=~1|date_time,
               family="quasibinomial",data=ds)

summary(m2)
# Linear mixed-effects model fit by maximum likelihood
# Data: ds 
# AIC BIC logLik
# NA  NA     NA
# 
# Random effects:
#   Formula: ~1 | date_time
# (Intercept)  Residual
# StdDev:   0.3082808 0.1443456
# 
# Variance function:
#   Structure: fixed weights
# Formula: ~invwt 
# Fixed effects:  canopycov/100 ~ date_time 
# Value Std.Error    DF  t-value p-value
# (Intercept) 0.1767127 0.0974997 43180 1.812443  0.0699
# date_time   0.3232878 0.0975013     8 3.315728  0.0106
# Correlation: 
#   (Intr)
# date_time 0     
# 
# Standardized Within-Group Residuals:
#   Min          Q1         Med          Q3         Max 
# -6.66205315 -0.47852364  0.09635514  0.54154467  4.32129236 
# 
# Number of Observations: 43190
# Number of Groups: 10
SushiChef
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