hi there.
I am trying to fit a general mixed model with negative binomial error distribution.
I am familiar with the model and have used it before.
However this time I am getting a strange error, noting that my random effect would "not be found" though it is defined in my df.
first I load the packages
library(lme4)
install.packages("Matrix")
library(Matrix)
df <- read.csv("C:/Users/example/results.csv")
This is how sed looks like
"ID1" , "sample.ID" , "ID" , "type" , "date" , "weight", "MP", "non_fl_fibres", "total.MP", "Mp.Kg", "flow" "pH" , "EC" , "Alkalinity", "DOC" |
"MB1", "MBC-CR 1" , "MB1L" , "sediment", "18-10-19", 35.89 , 8L , 0L , 8L , 222.9 , 292.2 , 7.75 , 58L , 18.07 , 2.233 |
"MB1", "MBC-CR 2" , "MB1R" , "sediment", "18-10-19", 35.27 , 4L , 1L , 5L , 141.8 , 292.2 , 7.75 , 58L , 18.07 , 2.233 |
"MB2", "MBC-ANBC 1" , "MB2L" , "sediment", "18-10-19", 35.6 , 4L , 0L , 4L , 112.4 , 229.7 , 7.71 , 72L , 20.51 , 2.199 |
"MB2", "MBC-ANBC 2" , "MB2R" , "sediment", "18-10-19", 35.9 , 2L , 1L , 3L , 83.58 , 229.7 , 7.71 , 72L , 20.51 , 2.199 |
"B1" , "BC-O 3" , "B1L" , "sediment", "14-10-19", 36.05 , 2L , 1L , 3L , 83.22 , NA_real_, NA_real_, NA_integer_, NA_real_ , NA_real_ |
"B1" , "BC-O 4" , "B1R" , "sediment", "14-10-19", 36.28 , 3L , 1L , 4L , 110.3 , NA_real_, NA_real_, NA_integer_, NA_real_ , NA_real_ |
"B2" , "BC-AFM 1" , "B2L" , "sediment", "18-10-19", 35.44 , 4L , 0L , 4L , 112.9 , 452.8 , 7.77 , 89L , 24.92 , 2.012 |
"B2" , "BC-AFM 2" , "B2R" , "sediment", "18-10-19", 35.36 , 5L , 1L , 6L , 169.7 , 452.8 , 7.77 , 89L , 24.92 , 2.012 |
"B3" , "BC-100 1" , "B3L" , "sediment", "18-10-19", 35.2 , 6L , 0L , 6L , 170.4 , 499.6 , 7.78 , 102L , 26.56 , 2.018 |
"B3" , "BC-100 2" , "B3R" , "sediment", "18-10-19", 35.7 , 12L , 0L , 12L , 336.2 , 499.6 , 7.78 , 102L , 26.56 , 2.018 |
"B4" , "BC-AFB 2" , "B4L" , "sediment", "17-10-19", 35.27 , 8L , 2L , 10L , 283.6 , 399.7 , 7.79 , 106L , 26.86 , 1.927 |
"B4" , "BC-AFB 1" , "B4R" , "sediment", "17-10-19", 36.92 , 5L , 0L , 5L , 135.4 , 399.7 , 7.79 , 106L , 26.86 , 1.927 |
"B5" , "BC-9TH 2" , "B5L" , "sediment", "17-10-19", 35.32 , 3L , 1L , 4L , 113.3 , 463.3 , 7.68 , 117L , 30.04 , 2.116 |
"B5" , "BC-9TH 1" , "B5R" , "sediment", "17-10-19", 35.22 , 6L , 2L , 8L , 227.2 , 463.3 , 7.68 , 117L , 30.04 , 2.116 |
"B6" , "BC-BRO 2" , "B6L" , "sediment", "17-10-19", 35.75 , 8L , 3L , 11L , 307.7 , 490.6 , 7.81 , 142L , 35.25 , 1.917 |
"B6" , "BC-BRO 1" , "B6R" , "sediment", "17-10-19", 36 , 8L , 1L , 9L , 250 , 490.6 , 7.81 , 142L , 35.25 , 1.917 |
"B7" , "BC-AF 2" , "B7L" , "sediment", "17-10-19", 35.18 , 7L , 1L , 8L , 227.4 , 119.4 , 8.16 , 260L , 45.62 , 1.949 |
"B7" , "BC-AF 1" , "B7R" , "sediment", "17-10-19", 33.31 , 11L , 2L , 13L , 390.3 , 119.4 , 8.16 , 260L , 45.62 , 1.949 |
"B8" , "BC-30 2" , "B8L" , "sediment", "17-10-19", 35.35 , 5L , 0L , 5L , 141.4 , 140.1 , 7.97 , 264L , 50.12 , 1.855 |
"B8" , "BC-30 1" , "B8R" , "sediment", "17-10-19", 35.88 , 4L , 1L , 5L , 139.4 , 140.1 , 7.97 , 264L , 50.12 , 1.855 |
"B9" , "BC-FOOT 1(b)" , "B9L" , "sediment", "16-10-19", 35.87 , 8L , 2L , 10L , 278.8 , NA_real_, NA_real_, NA_integer_, NA_real_ , NA_real_ |
"B9" , "BC-FOOT 2" , "B9R" , "sediment", "16-10-19", 36.11 , 4L , 0L , 4L , 110.8 , NA_real_, NA_real_, NA_integer_, NA_real_ , NA_real_ |
"B10", "BC-61ST 2" , "B10L" , "sediment", "16-10-19", 35.8 , 5L , 1L , 6L , 167.6 , 244.5 , 8.29 , 449L , 92.17 , 3.147 |
"B10", "BC-61ST 1(b)" , "B10R" , "sediment", "16-10-19", 35.28 , 5L , 2L , 7L , 198.4 , 244.5 , 8.29 , 449L , 92.17 , 3.147 |
"B11", "BC-75 1(b)" , "B11L" , "sediment", "14-10-19", 34.9 , 7L , 0L , 7L , 200.6 , NA_real
There is 6 NA rows, but these should not have any effect on the model
When I try to fit the glmer this is what I do
md1 <- glmer.nb(total.MP ~ EC + flow +DOC + Alkalinity + pH, (1|ID1), data = sed)
And I receive an error:
Error in glmer(total.MP ~ EC + flow + DOC + Alkalinity + pH, (1 | ID), :
object 'ID' not found
I have defined ID1 and loaded packages that I need (or is there something i have missed?)
Any help with this would be highly appreciated
Thanks