Use rbind() in nested for loop with apply() in r - r

How can you use rbind in a for loop that runs through a list of dataframes? I tried to follow Looping through list of data frames in R but receive the following:
Error in apply(dataFramesList, 2, function(x) { :
dim(X) must have a positive length
I have two dataframes, dfTraining and dfAccuracy (code to reproduce dataframes is below), and need to add a row for any of the crop types missing from either of two columns, CROP or CROP_LABEL. I believe my problem is in my last line of code.
My code block is:
dataFramesList <- list(dfTraining, dfAccuracy)
apply(dataFramesList, 2, function(x){
cropNumbers <- seq(1,23, by = 1)
cropNumbers <- cropNumbers[-c(3)]
cropNumbers <- append(cropNumbers, 34)
listofCROPandCROP_LABELColumns <- list(dataFrameList$CROP, dataFrameList$CROP_LABEL)
missingCROP <- NULL
for (i in listofCROPandCROP_LABELColumns){
for (j in cropNumbers){
if (!j %in% i){
# If crop number is missing from CROP_LABEL, add missingCROP observation (row)
# Make row for missing crop type
missingCrop <- list(FREQUENCY = 0, AA = 1, CROP = j, CROP_LABEL = j, ACRES = 0)
dataFrameList <- rbind(dataFrameList, missingCrop)
}
}
}
})
My dfAccuracy dataframe:
structure(list(FREQUENCY = c(4L, 2L, 1L, 1L, 1L, 1L, 65L, 1L,
1L, 4L, 1L, 5L, 5L, 2L, 4L, 1L, 1L, 1L, 1L, 4L, 9L, 2L, 1L, 1L,
1L, 2L, 4L, 1L, 2L, 18L, 1L, 10L, 3L, 1L, 7L, 1L, 1L, 1L, 3L,
1L, 7L, 1L), AA = c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L),
CROP = c(1L, 4L, 12L, 13L, 14L, 18L, 1L, 1L, 1L, 1L, 1L,
4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 7L, 13L,
13L, 13L, 13L, 14L, 14L, 14L, 18L, 18L, 18L, 18L, 18L, 19L,
19L, 21L, 21L, 21L, 21L), CROP_LABEL = c(1L, 4L, 14L, 13L,
12L, 18L, 1L, 4L, 5L, 6L, 18L, 1L, 4L, 6L, 14L, 18L, 12L,
14L, 18L, 1L, 6L, 14L, 18L, 18L, 4L, 6L, 13L, 21L, 12L, 14L,
18L, 1L, 6L, 14L, 18L, 21L, 1L, 19L, 6L, 13L, 21L, 34L),
ACRES = c(331.737184484, 193.772138572, 26.48543619, 73.2696289437,
112.470306056, 66.6556450342, 3905.71121736, 24.9581079934,
39.9287379709, 259.662359273, 85.2786247851, 306.051491303,
368.342995232, 154.82030835, 265.754349805, 70.3722566979,
35.4066607701, 139.336463432, 58.4307705147, 251.070357093,
471.031628349, 150.965736858, 28.2780117926, 35.3426930108,
34.5730542194, 67.7383953308, 144.442123948, 33.2746560126,
69.4072817311, 1219.65459596, 92.4840910734, 582.983473317,
191.957841327, 35.708775262, 319.638682538, 60.6889287642,
82.6244195055, 36.2898952104, 267.422844756, 72.8352758659,
489.746546145, 65.5392893502)), row.names = c(25L, 26L, 27L,
29L, 30L, 31L, 60L, 61L, 62L, 63L, 64L, 65L, 66L, 67L, 68L, 69L,
70L, 71L, 72L, 73L, 74L, 75L, 76L, 77L, 78L, 79L, 80L, 81L, 82L,
83L, 84L, 85L, 86L, 87L, 88L, 89L, 90L, 91L, 92L, 93L, 94L, 95L
), class = "data.frame")
and my dfTraining dataframe is:
structure(list(FREQUENCY = c(7L, 1L, 1L, 4L, 2L, 6L, 1L, 107L,
1L, 21L, 1L, 1L, 1L, 2L, 1L, 19L, 3L, 1L, 1L, 12L, 1L, 2L, 32L,
2L, 2L, 29L, 2L, 18L, 1L), AA = c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L), CROP = c(1L, 1L, 4L, 4L, 12L, 13L, 21L,
1L, 1L, 4L, 4L, 5L, 5L, 5L, 5L, 6L, 6L, 7L, 12L, 13L, 14L, 14L,
14L, 18L, 18L, 18L, 19L, 21L, 34L), CROP_LABEL = c(1L, 4L, 1L,
4L, 12L, 13L, 21L, 1L, 6L, 4L, 6L, 1L, 5L, 14L, 18L, 6L, 14L,
1L, 12L, 13L, 1L, 6L, 14L, 6L, 14L, 18L, 19L, 21L, 34L), ACRES = c(624.940370218,
26.9188766351, 37.8773839813, 291.79294767, 140.949264214, 391.571023675,
44.5217011939, 6806.02216989, 72.7500299887, 1676.12121152, 14.8739557721,
67.0700291739, 59.7438207953, 82.6713019474, 75.62666152, 1370.78710769,
145.215281276, 41.7380537313, 66.5236760194, 679.91208779, 70.9661875374,
38.8514254734, 1749.63365551, 109.917242057, 79.7758083723, 1660.85759895,
96.8771921798, 1428.71888481, 69.473161379)), row.names = c(18L,
19L, 20L, 21L, 22L, 23L, 24L, 38L, 39L, 40L, 41L, 42L, 43L, 44L,
45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 53L, 54L, 55L, 56L, 57L,
58L, 59L), class = "data.frame")

Related

R plotly multiple plots only show last figure

I would like to make an interactive graphs based on user input. However I'm struggle to make more than one graphs using R plotly. Suppose I have following data and codes,
dput(norwd5)
structure(list(LENGTH_OF_STAY = c(57L, 28L, 15L, 28L, 14L, 49L,
15L, 22L, 17L, 81L, 34L, 24L, 31L, 38L, 33L, 22L, 21L, 49L, 188L,
21L, 21L, 36L, 24L, 23L, 48L, 54L, 42L, 62L, 13L, 139L, 29L,
49L, 15L, 7L, 43L, 28L, 31L, 22L, 23L, 26L, 33L, 30L, 127L, 22L,
22L, 15L, 28L, 26L, 15L, 31L, 22L, 89L, 28L, 60L, 54L, 37L, 20L,
135L, 155L, 51L, 15L, 8L, 38L, 16L, 16L, 22L, 30L, 14L, 16L,
18L, 14L, 272L, 25L, 22L, 18L, 21L, 188L, 264L, 34L, 34L, 136L,
23L, 142L, 25L, 32L, 58L, 163L, 16L, 35L, 23L, 50L, 71L, 10L,
19L, 22L, 24L, 45L, 29L, 15L, 82L), PRE_OPERATIVE_LOS = c(2L,
2L, 3L, 1L, 3L, 6L, 3L, 7L, 2L, 2L, 11L, 2L, 6L, 3L, 6L, 3L,
5L, 3L, 179L, 2L, 5L, 3L, 4L, 2L, 5L, 6L, 2L, 4L, 2L, 6L, 3L,
2L, 2L, 6L, 6L, 1L, 4L, 5L, 6L, 5L, 0L, 4L, 6L, 2L, 4L, 4L, 7L,
4L, 4L, 6L, 2L, 4L, 3L, 3L, 2L, 6L, 4L, 110L, 63L, 6L, 4L, 7L,
5L, 1L, 6L, 1L, 4L, 2L, 6L, 3L, 2L, 8L, 2L, 2L, 4L, 3L, 6L, 171L,
5L, 4L, 116L, 6L, 47L, 3L, 7L, 3L, 60L, 1L, 3L, 20L, 31L, 49L,
9L, 8L, 3L, 4L, 35L, 7L, 4L, 9L), POST_OPERATIVE_LOS = c(55L,
26L, 12L, 27L, 11L, 43L, 12L, 15L, 15L, 79L, 23L, 22L, 25L, 35L,
27L, 19L, 16L, 46L, 9L, 19L, 16L, 33L, 20L, 21L, 43L, 48L, 40L,
58L, 11L, 133L, 26L, 47L, 13L, 1L, 37L, 27L, 27L, 17L, 17L, 21L,
33L, 26L, 121L, 20L, 18L, 11L, 21L, 22L, 11L, 25L, 20L, 85L,
25L, 57L, 52L, 31L, 16L, 25L, 92L, 45L, 11L, 1L, 33L, 15L, 10L,
21L, 26L, 12L, 10L, 15L, 12L, 264L, 23L, 20L, 14L, 18L, 182L,
93L, 29L, 30L, 20L, 17L, 95L, 22L, 25L, 55L, 103L, 15L, 32L,
3L, 19L, 22L, 1L, 11L, 19L, 20L, 10L, 22L, 11L, 73L), digoxin_any = structure(c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L,
2L, 1L, 2L), .Label = c("0:No", "1.Yes"), class = "factor")), row.names = c(NA,
-100L), class = c("data.table", "data.frame"), .internal.selfref = <pointer: 0x0000012f36b61ef0>)
num <- c('PRE_OPERATIVE_LOS','POST_OPERATIVE_LOS')
plist <- scan(text=num,what = "",quiet = T)
groups <- 'digoxin_any'
bygrp <- scan(text=groups,what="",quiet=T)
norwd5[, (bygrp) := lapply(.SD, as.factor), .SDcols = bygrp]
plotList = list()
for(i in length(plist)){
gplot <- ggplot(norwd5,aes_string(x=plist[i],group=bygrp,color=bygrp))+geom_histogram(aes(y=..density..),position = "dodge")+geom_density(alpha=.5) +theme(legend.position = "left")
plotList[[i]] <- plotly_build(gplot)
}
for(i in length(plist)){
print(plotList[[i]])
}
The goal is to show both graphs for PRE_OPERATIVE_LOS and POST_OPERATIVE_LOS. However, the codes above only show histogram for POST_OPERATIVE_LOS.
I checked maybe subplot is the way to go but how to make subplot work in a loop? Any hints?
Thanks!
There is an error in your first loop and calling each subplot won't make both appear at the same time.
First-- the issue with your first for call- when you wrote
for(i in length(plist))
You wrote for i in 2 or i == 2, meaning that you never looped. If you modify it to a range of values, now it's written: for i in 1 to 2.
for(i in 1:length(plist))
So you're aware, if you had written for(i in plist) it would have done both loops, but instead of a value, i would be the strings.
Okay, so now there are two graphs. From the plotly library, you can use the function subplot. You will want to turn the legend off for one of them, though.
subplot(plotList[[1]],
style(plotList[[2]], showlegend = FALSE))
If you wanted the outline color, that's more than okay! However, if you wanted to bars to be filled, you need to assign fill instead of color.
If you change color = bygrp to fill = bygrp, this is how this would change:
If you leave the color assignment and add fill = bygrp (so you have both), this is how this would change:

How to fix jagged line from predict_gam in ggplot2?

Data:
structure(list(ID = c(19903L, 28185L, 28207L, 28429L, 28522L,
29092L, 29127L, 29219L, 29304L, 30981L, 31166L, 31411L, 32010L,
33231L, 33640L, 33714L, 34093L, 34193L, 34385L, 35054L, 35337L,
35377L, 35608L, 35881L, 35940L, 37112L, 37122L, 37125L, 37170L,
37198L, 37266L, 37378L, 37589L, 37725L, 37877L, 38519L, 38522L,
38605L, 38623L, 38806L, 39040L, 39083L, 39159L, 39218L, 39593L,
39636L, 39657L, 39686L, 39700L, 39819L, 39820L, 39951L, 40151L,
40152L, 40181L, 40226L, 40248L, 40286L, 40382L, 40556L, 40623L,
40628L, 40798L, 40800L, 40815L, 40915L, 43282L, 43299L, 43450L,
43466L, 43509L, 43677L, 43740L, 43762L, 43998L, 44068L, 44130L,
44131L, 44307L, 44408L, 50679L, 50848L, 51064L, 51455L, 51690L,
51726L, 51727L, 51796L, 52126L, 52183L, 52461L, 52500L, 52502L,
52577L, 52614L, 53202L, 53320L, 53390L, 53456L, 53473L, 53474L,
53475L, 53577L, 53626L, 53851L, 53873L, 54153L, 54206L, 54532L,
54581L, 54913L, 55122L, 55267L, 55332L, 55462L, 55542L, 55612L,
55728L, 55867L, 55903L, 55920L, 55991L, 56022L, 56098L, 56307L,
56420L, 56679L, 56703L, 56746L, 56919L, 57005L, 57035L, 57405L,
57445L, 57480L, 57725L, 57808L, 57809L, 57863L, 58004L, 58060L,
58130L, 58145L, 58215L, 58229L, 58503L, 58515L, 58667L, 58999L,
59326L, 59327L, 59344L, 59361L, 59428L, 59756L, 59865L, 60099L,
60100L, 60169L, 60252L, 60280L, 60306L, 60384L, 60429L, 60472L,
60493L, 60503L, 60575L, 60603L, 60662L, 60664L, 60806L, 60846L,
60925L, 61274L, 61415L, 61727L, 61749L, 61882L, 61883L, 62081L,
62144L, 62210L, 62285L, 62411L, 62809L, 62917L, 62934L, 62937L,
62983L, 62989L, 63327L, 63329L, 63383L, 63458L, 63470L, 63589L,
64081L, 64328L, 64418L, 64507L, 64596L, 65178L, 65250L, 65302L,
65478L, 65480L, 65487L, 65565L, 65572L, 65574L, 65617L, 65802L,
65865L, 65934L, 65935L, 65974L, 65975L, 65978L, 65991L, 65995L,
66013L, 66154L, 66232L, 66237L, 66245L, 66314L, 66389L, 66396L,
66460L, 66572L, 66589L, 66735L, 67174L, 73230L, 73525L, 73539L,
73677L, 73705L, 73942L, 73953L, 74034L, 74113L, 74114L, 74425L,
74427L, 74439L, 74607L, 74618L, 74641L, 74657L, 74794L, 74800L,
74836L, 74942L, 74952L, 74962L, 74969L, 74975L, 74977L, 74985L,
74989L, 75220L, 75229L, 75377L, 75407L, 75432L, 75653L, 75732L,
75735L, 75737L, 75757L, 75895L, 75898L, 76381L, 76559L, 76574L,
76594L, 76595L, 76746L, 76751L, 76755L, 76759L, 76775L, 77088L,
77091L, 77099L, 77109L, 77134L, 77182L, 77188L, 77203L, 77204L,
77252L, 77304L, 77453L, 77528L, 77556L, 77585L, 77668L, 77733L,
77758L, 78262L, 79724L, 79730L, 79747L, 79850L, 79977L, 80052L,
80819L, 80901L, 80932L, 81064L, 81065L, 81071L, 81098L, 81112L,
81142L, 81175L, 81727L, 81938L, 82554L, 83744L, 83949L), Age = c(83L,
26L, 26L, 20L, 84L, 20L, 23L, 77L, 32L, 14L, 21L, 9L, 76L, 18L,
21L, 15L, 75L, 27L, 34L, 81L, 81L, 15L, 24L, 24L, 16L, 35L, 27L,
7L, 30L, 31L, 24L, 24L, 79L, 30L, 19L, 78L, 25L, 20L, 42L, 62L,
83L, 79L, 18L, 26L, 66L, 23L, 83L, 21L, 77L, 24L, 57L, 42L, 32L,
76L, 85L, 29L, 77L, 65L, 79L, 9L, 34L, 20L, 11L, 16L, 9L, 21L,
16L, 34L, 22L, 19L, 23L, 25L, 14L, 53L, 28L, 79L, 22L, 22L, 21L,
82L, 81L, 16L, 19L, 77L, 15L, 18L, 15L, 78L, 24L, 16L, 14L, 29L,
18L, 50L, 17L, 43L, 8L, 14L, 85L, 31L, 20L, 30L, 23L, 78L, 29L,
6L, 61L, 14L, 22L, 10L, 83L, 15L, 13L, 15L, 15L, 29L, 8L, 9L,
15L, 8L, 9L, 15L, 9L, 34L, 8L, 9L, 9L, 16L, 8L, 25L, 21L, 23L,
13L, 56L, 10L, 7L, 27L, 8L, 8L, 8L, 8L, 80L, 80L, 6L, 15L, 42L,
25L, 23L, 21L, 8L, 11L, 43L, 69L, 34L, 34L, 14L, 12L, 10L, 22L,
78L, 16L, 76L, 12L, 10L, 16L, 6L, 13L, 66L, 11L, 26L, 12L, 16L,
13L, 24L, 76L, 10L, 20L, 13L, 25L, 14L, 12L, 15L, 43L, 51L, 27L,
15L, 24L, 34L, 63L, 17L, 15L, 9L, 12L, 17L, 82L, 75L, 24L, 44L,
69L, 11L, 10L, 12L, 10L, 10L, 70L, 54L, 45L, 42L, 84L, 54L, 23L,
23L, 14L, 81L, 17L, 42L, 44L, 16L, 15L, 43L, 45L, 50L, 53L, 23L,
53L, 49L, 13L, 69L, 14L, 65L, 14L, 13L, 22L, 67L, 59L, 52L, 54L,
44L, 78L, 62L, 69L, 10L, 63L, 57L, 22L, 12L, 62L, 9L, 82L, 53L,
54L, 66L, 49L, 63L, 51L, 9L, 45L, 49L, 77L, 49L, 61L, 62L, 57L,
67L, 16L, 65L, 75L, 45L, 16L, 55L, 17L, 64L, 67L, 56L, 52L, 63L,
10L, 62L, 14L, 66L, 68L, 15L, 13L, 43L, 47L, 55L, 69L, 21L, 67L,
34L, 52L, 15L, 31L, 64L, 55L, 13L, 48L, 71L, 64L, 13L, 25L, 34L,
50L, 61L, 70L, 33L, 57L, 51L, 46L, 57L, 69L, 46L, 8L, 11L, 46L,
71L, 33L, 38L, 56L, 17L, 29L, 28L, 6L, 8L), Sex = structure(c(1L,
1L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 1L,
2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 2L,
1L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 2L,
1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L,
1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 2L,
1L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L,
2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L,
1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L,
1L, 1L, 1L, 2L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L,
2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L,
1L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 2L,
2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L,
2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L,
2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 2L,
2L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 2L,
2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 2L,
2L, 1L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 1L,
2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 1L,
2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 1L,
1L, 2L, 2L), .Label = c("Male", "Female"), class = "factor"),
mean_FA_scaled = c(-1.52160414281774, -1.30073487609629,
-1.39164271432334, -1.83373601712535, -2.19478262184568,
-0.47769168350816, -1.66624867866514, -0.36061779499817,
-1.10976759821506, -2.01706489349897, -1.21708170925372,
-0.68001882107227, -0.770347444019124, -1.21756680205088,
-1.04908755742334, -0.654272701867476, 0.791455877697352,
0.0263414533200063, -1.48353521852673, -1.48465744813212,
0.885781086077571, 0.937258844105155, -1.76609091258925,
-1.40930154017838, -1.42620014597815, -0.395529996012095,
-1.79188771313106, -1.6968602062236, -1.6213377738768, -1.26578647412735,
-1.3364652186935, -1.52114801078458, 0.587760344033774, -1.4860765255686,
-1.41824317606643, -1.08076339305916, -1.84290933912549,
-1.42950167307528, -0.186882171702826, 0.94192876730175,
-1.96157606965602, -0.668579319288362, -1.2972378638421,
-2.10201405453099, 0.593407693015703, -1.87521507137852,
-0.399874110613579, -2.16173114991939, -1.71213049306692,
-2.03230549555918, 0.864393561856266, 1.66450706953957, -1.76062456838238,
-1.42625806750617, -0.635317881823001, -1.05738481631217,
-0.905876579394418, 0.0731565283419971, -1.15139145628828,
-0.742407546940581, -1.69348627721645, 0.153573329806466,
-1.09929828202549, -0.982123030841461, 0.725678742439884,
-0.850887328730634, -0.99078229928042, 0.215368360012574,
-0.402661584149531, 0.0241114744912448, -0.71105027970887,
0.366463906043185, 0.957024565541906, 0.669292134912623,
1.05465854121026, 1.82844671440856, -0.181835758574102, 0.736386984932541,
-1.09078381740658, 0.0590019549321627, -1.02109697900777,
0.321350275906775, -0.0449237467173357, 0.0239956314352051,
0.117669222625202, -0.725516181331811, 0.387590783388401,
0.829691326381412, 1.37355999410519, -0.459526044282955,
-0.460235583001197, -0.311304854080326, 0.578796987572713,
0.997164184459617, 0.18257029477137, 0.291839257380694, -0.863007408468775,
-1.87780705975741, 2.29568520056216, 0.00319456268509986,
0.881190804982003, 0.930713711438919, -0.525093214001351,
2.54459572703618, 0.166620153992923, 1.20602921449896, -0.289055747129726,
1.46280982859267, -0.391909900510859, 2.11139337878521, 1.59105533181948,
-0.209203680563451, -0.763585105622814, -0.373635658420616,
0.6654186327263, -1.62880965099135, -0.961003393687248, 0.201720599972912,
-0.335957704443747, 0.757593504378786, -0.162251041912412,
0.141221563956246, 0.0760670851249914, -2.24164331007099,
0.424957409152164, -0.0769326311392693, -0.0363368801884033,
0.30505984615121, -0.551628514025415, 0.33740901955026, -0.31017538428394,
0.966704700912213, -1.19032920349958, 0.711567610176064,
0.67279638735782, -0.599819225337876, 0.0996845881750585,
0.656310472445189, -0.0716472917074639, -0.483100106187007,
-0.511691620455773, 2.1239406297925, 1.29844301245453, 0.101559797644699,
-1.35720112572458, 0.307058138867893, -0.0785544339238233,
0.27531714151305, -0.660383423073563, -0.957274695320974,
-1.47069111968835, -0.526229923988739, -0.645664114765535,
-0.887580616731169, 0.119110020634694, -0.368379279752821,
-1.37513507883771, 0.756384392481372, 0.0675019391690662,
1.18129672203451, 0.788168830982229, 0.780204620879509, 0.283447876008828,
0.146224535938955, -0.389296191558966, 0.807326376374772,
0.590410253940679, -0.41226207741881, -1.02024263646948,
0.0042805913354707, -0.217414057160255, 0.302561980255357,
-0.0445038156391923, -0.782909175408415, 0.298159944125853,
0.0170233274998232, -0.0487465675666421, -0.456839933421037,
0.310127979852941, -0.787615299560023, -0.21877521306872,
-0.395986128045251, -0.266386709100983, 0.372589107631277,
-0.47845190356342, 0.546216128061583, -0.483150787524024,
-0.638590448156119, 2.21420409102033, 0.550980173741211,
0.781797462900053, 0.0321553266949922, 0.224223113608598,
0.45913835087484, 0.924827436153908, 2.19646562306427, -0.622017650951458,
0.554498906568413, -0.0470089217260485, -0.401307668432068,
-0.588777934059104, 0.462266113387909, 0.263008816808847,
-0.162403085923465, -0.062640494100388, 0.660965915259779,
0.113397509933743, 0.191685695243484, 1.14629763872856, 0.407899519150338,
0.473039517599588, 0.589070818605222, 1.07992680780889, 0.0233440142449823,
0.303792812725778, 0.560066613449315, -0.401387310533095,
-0.286101749200717, -0.673299923821975, 1.66157479218356,
1.44751130500445, 0.402802424684597, 1.46472123901732, -0.397311082998703,
-0.641768892006205, 0.839031172774602, -0.603272796446055,
1.48020076738061, -0.550643848049078, 0.299513859843316,
0.739782634512702, 0.517841819522891, 0.240976915588321,
0.407841597622318, 1.04632508136641, 0.140700270204069, 0.320249766874399,
-0.0720093012575883, 0.191207842637321, 1.89043722977174,
1.44823532410469, -0.403472485541808, 1.81747058484881, 0.510261339543303,
0.874862878045841, -0.274271277102676, 1.60814942277632,
-0.625188854610541, 0.262176194843562, 0.546426093600656,
-0.0371912227266948, -0.0447861830882888, 1.43379838324576,
-0.0424331210124857, 1.86971580312266, -0.228122299652913,
0.731789463645971, 0.0910470403091081, 0.618791802670374,
0.267229848163289, 0.199251694841068, 0.246957313356364,
1.87125072361518, -1.40312565725327, -0.190900477709198,
0.257180463051856, 1.48421907338698, 0.0556569866890196,
-0.667601893503029, 0.247688572647614, 0.188977863808559,
0.91364858124609, 1.5448556730327, 0.930329981315788, 0.312119032378622,
1.15772266013046, -0.0360834735033167, 1.78212397237474,
-0.861407326257228, 0.476608931763807, 1.38366006055364,
0.803771442592559, 0.145174708243597, -1.13023561817905,
0.570130478942752, 0.862605234678655, -0.328963679935357,
0.654840713671687, 0.852222800781108, 0.304538552399032,
0.652132882236762, -0.639712677761503, 0.046078213992748,
-0.171257839519489, 0.349420496423362, 0.184018332971865,
0.149583984564103, 1.29365724620189, 0.621419992004272, -0.866656464734021,
1.09066401106555, 0.810541021179871, 1.62963106948065, 1.03406743799922,
-0.118969180099629, -0.372665472826285, 1.40028353909531,
0.381002209576151, 0.508378889882659, 0.667424165633985,
0.4092534348678, 0.813183690895774, 1.08099111588625, 0.708867018932142,
0.0693192271106869, 1.26885235182742, -0.117571823236151,
0.174801569825717, 0.584835306868775, -0.84211945742664,
1.05460061968224, 1.61507104537468, -1.62830066556388, 0.0799550676933195
), RAVLT_DELAY = c(NA, 12L, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, 5L, NA, NA, NA, NA, NA, NA, NA,
7L, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 5L, 12L,
NA, NA, NA, NA, 14L, NA, NA, NA, NA, NA, 6L, 7L, NA, NA,
NA, NA, 7L, 1L, 1L, 11L, 4L, 12L, 7L, 9L, 9L, 8L, 14L, 12L,
7L, 12L, 7L, 6L, 13L, 10L, 13L, NA, 11L, 14L, 8L, 0L, 11L,
15L, 13L, 6L, 9L, 9L, 12L, 5L, 14L, 15L, 12L, 4L, 15L, 8L,
15L, 14L, 5L, 12L, 8L, 9L, 9L, 13L, 6L, 4L, 10L, NA, 4L,
13L, 9L, 14L, 8L, 15L, 14L, 9L, 15L, 14L, 11L, 11L, 15L,
12L, 9L, 13L, 14L, 7L, 13L, 9L, 12L, 10L, 6L, 9L, 10L, 11L,
15L, 11L, 11L, NA, 9L, 12L, 10L, 9L, 11L, 2L, 12L, NA, 6L,
12L, 12L, 10L, 11L, 4L, 13L, 4L, 5L, 6L, 12L, 15L, 11L, 11L,
14L, 2L, 11L, 5L, 10L, 12L, 10L, NA, 12L, 8L, 12L, 12L, 8L,
7L, 14L, 14L, 7L, 8L, NA, 9L, 6L, 15L, 7L, 14L, 8L, 14L,
11L, 13L, 6L, 12L, 11L, 14L, 15L, 10L, 6L, 13L, 7L, 4L, 12L,
14L, 7L, 13L, 3L, 13L, 7L, 10L, 6L, 8L, 3L, 15L, 11L, 15L,
11L, 11L, 8L, 4L, 7L, 10L, 5L, 7L, 8L, 9L, 14L, 12L, 14L,
12L, NA, NA, 11L, 10L, 13L, 7L, 12L, 12L, 14L, 8L, 13L, 2L,
11L, 8L, 7L, 4L, 7L, 9L, 4L, 12L, 14L, 15L, 12L, 13L, 9L,
7L, 11L, 10L, 14L, 6L, 5L, 5L, 10L, 8L, 5L, 12L, 2L, 11L,
8L, NA, 9L, 7L, 8L, 12L, 10L, 7L, 13L, 15L, 9L, 6L, 4L, 10L,
8L, 13L, 10L, 9L, 7L, 7L, 15L, 8L, 12L, 9L, 10L, 12L, 6L,
13L, 8L, 11L, 9L, 1L, 13L, 12L, NA, 8L, 2L, 11L, 9L, 7L,
6L, 10L, 13L, 15L, 6L, 5L, 7L, 5L, 5L, 11L, 11L, 13L, 9L,
4L, 10L, 2L, NA, 12L, 10L, 15L, NA, 6L)), row.names = c(NA,
-324L), class = c("tbl_df", "tbl", "data.frame"))
I am using the following model in mgcv::gam:
m1 <- gam(mean_FA_scaled ~ s(Age, bs = 'ad', k = -1) + Sex +
te(Age, by = Sex, bs ='fs') +
te(RAVLT_DELAY, by = Sex, bs = 'fs') + s(RAVLT_DELAY),
data = DF,
method = 'REML', family = gaussian)
I would like to reproduce the gam plot:
But in ggplot. However, When I use predict_gam my plot is very jagged. This doesn't happen when I try to plot the smooth term effect on age.
# Plot
m1_p <- predict_gam(m1)
m1_p %>%
ggplot(aes(x = RAVLT_DELAY, y = fit)) +
geom_line(aes(color = Sex))
geom_smooth_ci(Sex, size = 1, alpha = 1) +
theme_classic(base_size = 24)
Your fit object has predictions for each age and each sex along the length of RAVLY_DELAY. With your existing code, each series tries to plot all the values from these various lines as one series, hence the jaggies.
If we tell ggplot to treat each Age,Sex combination as a different series (aka group), we get:
m1_p %>%
ggplot(aes(x = RAVLT_DELAY, y = fit)) +
geom_line(aes(color = Sex, group = interaction(Age,Sex)))
There are a lot of age groups here, which we could see separately with:
m1_p %>%
mutate(Age = round(Age, 1)) %>%
ggplot(aes(x = RAVLT_DELAY, y = fit)) +
geom_line(aes(color = Sex)) +
facet_wrap(~Age, ncol = 10)
While wrong, I liked the aesthetic qualities that arose when I grouped by Age only:
I had the same problem and I finally managed to fix it, or that's what I think. I am a beginner, not an expert, so sorry for my dummy language in this field.
This is happening because you have more variables in your model, apart from the ones you are plotting, that cause variance.
So, what you have to do is to create a new database with all the variables you are not plotting fixed somehow, the numeric you can use means, the factors, choose one, etc.
Then run the model with the function predict.gam (not "_"), that let you add a new database, that will be the one with your variables fixed.
Then predict.gam has to be turned into a database to plot it, so you bind it (the result) with your new data, and then you can use ggplot2 and geom_smooth_ci with no problem.
EXAMPLE:
model<-x~gam(s(v4, by=v3) + s(v2, by=v1)
#I want to plot the first smooth, first create the data:
new=expand.grid(v1=levels(circ$v1)[1], v2=mean(circ$v2), v3=levels(circ$v3), v4=seq(0,23, 0.1))
# see that I maintain the levels and the numbers of v3 and v4, and I fix the other ones randomly.
predict<-predict.gam(model, newdata = new, se.fit = TRUE)
mew=cbind(new,preddist2n)
mew %>%
ggplot(aes(v4, fit)) +
geom_smooth_ci(v3, ci_z = 1.96, ci_alpha = 0.05 )
If after you need to plot the second smooth, you should create another database to fix the variables out of the second smooth...
Tell me if it worked for you :)

Gtsummary output with mgcv gam

I have the following data set:
structure(list(Age = c(83L, 26L, 26L, 20L, 20L, 77L, 32L, 21L,
15L, 75L, 27L, 81L, 81L, 15L, 24L, 16L, 35L, 27L, 30L, 31L, 24L,
24L, 31L, 79L, 30L, 19L, 20L, 42L, 62L, 83L, 79L, 18L, 26L, 66L,
23L, 83L, 77L, 80L, 57L, 42L, 32L, 76L, 85L, 29L, 65L, 79L, 9L,
34L, 20L, 16L, 34L, 22L, 19L, 23L, 25L, 14L, 53L, 28L, 79L, 22L,
22L, 21L, 82L, 81L, 16L, 19L, 77L, 15L, 18L, 15L, 78L, 24L, 16L,
14L, 29L, 18L, 50L, 17L, 43L, 8L, 14L, 85L, 31L, 20L, 30L, 23L,
78L, 29L, 6L, 61L, 14L, 22L, 10L, 83L, 15L, 13L, 15L, 15L, 29L,
8L, 9L, 15L, 8L, 9L, 15L, 9L, 34L, 8L, 9L, 9L, 16L, 8L, 25L,
21L, 23L, 13L, 56L, 10L, 7L, 27L, 8L, 8L, 8L, 8L, 80L, 80L, 6L,
15L, 42L, 25L, 23L, 21L, 8L, 11L, 43L, 69L, 34L, 34L, 14L, 12L,
10L, 22L, 78L, 16L, 76L, 12L, 10L, 16L, 6L, 13L, 66L, 11L, 26L,
12L, 16L, 13L, 24L, 76L, 10L, 65L, 20L, 13L, 25L, 14L, 12L, 15L,
43L, 51L, 27L, 15L, 24L, 34L, 63L, 17L, 15L, 9L, 12L, 17L, 82L,
75L, 24L, 44L, 69L, 11L, 10L, 12L, 10L, 10L, 70L, 54L, 45L, 42L,
84L, 54L, 23L, 23L, 14L, 81L, 17L, 42L, 44L, 16L, 15L, 43L, 45L,
50L, 53L, 23L, 53L, 49L, 13L, 69L, 14L, 65L, 14L, 13L, 22L, 67L,
59L, 52L, 54L, 44L, 78L, 62L, 69L, 10L, 63L, 57L, 22L, 12L, 62L,
9L, 82L, 53L, 54L, 66L, 49L, 63L, 51L, 9L, 45L, 49L, 77L, 49L,
61L, 62L, 57L, 67L, 16L, 65L, 75L, 45L, 16L, 55L, 17L, 64L, 67L,
56L, 52L, 63L, 10L, 62L, 14L, 66L, 68L, 15L, 13L, 43L, 47L, 55L,
69L, 21L, 67L, 34L, 52L, 15L, 31L, 64L, 55L, 13L, 48L, 71L, 64L,
13L, 25L, 34L, 50L, 61L, 70L, 33L, 57L, 51L, 46L, 57L, 69L, 46L,
8L, 11L, 46L, 71L, 33L, 38L, 56L, 17L, 29L, 28L, 6L, 8L), Sex = structure(c(1L,
1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 2L,
1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L,
2L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L,
2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L,
2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L,
2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L,
1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 1L,
1L, 1L, 2L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 2L,
2L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L,
2L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 2L,
2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L,
2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L,
2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 2L,
2L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 2L,
2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 2L,
2L, 1L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 1L,
2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 1L,
2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 1L,
1L, 2L, 2L), .Label = c("Male", "Female"), class = "factor"),
mean_AD_scaled = c(3.15891332561581, -0.0551328105526693,
0.582747640515478, 1.94179165777054, 1.7064645993306, 2.37250948563045,
1.015775832203, 1.36189033704266, -1.05640048650493, 0.184814975542474,
-0.143366705302007, 1.81560178585347, 2.06325078470728, -0.473088628698217,
0.414641167726219, 0.199887349084444, -0.60620959209809,
-0.17879228399189, -1.03483709078065, -1.43497010225613,
-0.958595084469815, 1.0203965598582, -1.44731404613503, -1.17191867788498,
-2.02547709312595, -1.22395687266857, -1.09952727795348,
-1.0830246791849, 1.21072653232248, 1.69997357714829, 1.53648783201423,
0.208688735094353, 0.0862394522314924, 1.08662698958276,
-0.731299290763917, 2.29307697689102, -0.660008064083659,
-1.21425334459264, 1.10191939777498, -2.0957781638801, -1.14947514355972,
0.248845058764562, 2.6526135953958, 0.197907037232212, -0.222469162066061,
1.92880961340592, 1.23328008397287, -1.17288683034607, -0.308282675662673,
-1.02603570477074, -1.32647101621898, -1.58316343919798,
-0.0440210607151585, -0.388375288352846, -0.935491446193807,
-0.63789458173376, 0.454577456746182, -1.77391147749773,
0.709267564407921, 0.125735671950958, -0.821073428064989,
-0.126534054558056, 0.519597695894384, 0.188005477971066,
0.212319306823438, -1.45807374053215, 1.5856655763446, -1.25641198358011,
-0.910847565366061, -1.1191763722206, 0.25300371365424, -0.750772357310844,
0.37932560636146, -0.871791414947088, -1.92771569802088,
-1.1752191976387, 0.210449012296334, -0.347778895382139,
-0.132254955464496, 0.953616043508016, -0.0862677135627232,
0.838977990728951, -1.8993092246739, -0.0254281327692267,
0.298022803094927, -1.21559555595915, 0.0134079829994995,
-0.763094297724715, 0.334768589686298, -1.12568939786794,
-2.11786964276497, -0.0434709740895377, 0.388237009696492,
1.30050066962355, -0.260645173884043, -0.60620959209809,
1.05945271027717, -0.275717547426008, -0.0238878902174922,
0.496604074943496, 0.534009965485611, -0.692903244295693,
-0.566933407028871, 0.125625654625835, -0.518305749324122,
1.79381835547894, -0.790708646330802, -0.227860010997131,
0.347420582075538, 0.784189362817269, -0.660118081408782,
1.29962053102256, -0.561652575422924, -0.710395998990384,
-1.29315777017148, -0.457356151205503, -1.01756437073621,
0.146528946399368, -1.07136284272178, -1.42968927065019,
0.798601632408495, -0.799730066990963, -0.431348055546223,
0.569545561500617, 2.32168148142323, 0.472070211440872, 1.65145593676866,
-0.814142336582189, -0.544489872703603, -0.315433801795725,
0.382626126115175, -0.623812364117908, 0.216279930527897,
-0.606099574772967, -0.367207954999011, 0.719829227619811,
-0.749122097433987, 0.934693063586709, -0.79026857703031,
-0.371872689584264, 0.0769979969210905, -0.793899148759394,
1.50414273842782, 0.730280873506577, -0.290569886317732,
0.303743704001367, 0.390877425499463, -1.00359217044547,
-0.534918365417827, 0.325967203676389, 0.129036191704673,
0.34434009697207, -0.141386393449775, -0.363401355549725,
-0.395416397160769, -0.0235578382421178, -1.13583299524436,
1.16781977552417, -1.31890182425046, 0.139377820266317, 0.0160483988024708,
0.481311666751279, -1.05475022662807, 0.839858129329941,
0.652498624644007, -0.350199276534864, -0.262075399110649,
0.178543988010412, -1.13198238886502, -0.05117218684821,
-1.29678834190056, 0.429603523943066, 1.05098137624263, -0.956504755292464,
0.502765045150433, -0.81678275238516, -1.50263075720731,
-0.826684311646306, 2.40100397283753, 2.06633126981075, -0.470558230220369,
0.484942238480364, 0.822035322659877, 0.143888530596397,
0.384056351341786, -0.63580425255641, 0.358422314587926,
-0.372422776209885, 0.0607154328027556, -0.113221958218067,
1.02710761669075, -0.349649189909243, 2.27195365046724, -0.507634068787109,
-0.326105482332738, -1.0396778530861, 1.06484355920824, 1.32151397872221,
-0.185173288849074, -0.651888785489516, -0.171311105883464,
-0.104200537557911, -0.693673365571561, -1.26609350819101,
0.411230630647381, -0.929770545287362, -0.481009876107135,
0.386146680519137, 0.0482834750637615, -0.198265350538812,
0.790020281048832, 0.926001694901924, -1.08918564939184,
0.50298507980068, -0.0694350628187722, 1.04966116834114,
0.00878725534429612, 1.48742010500899, 0.750194009353997,
0.423772605711498, -0.596418050162068, -0.652636903300361,
-0.308942779613417, 0.314437388003408, 0.679562886624478,
-1.24312189070515, -0.432712270377761, 0.00427654501421597,
-0.197935298563442, 0.228821905592019, 1.06957430418856,
-1.61612462980509, 1.9499329398297, -0.263285589687014, 0.156430505660519,
-0.322254875953402, -0.451085163673446, -0.35526007349056,
0.10780284795577, 0.408700232169533, -0.957604928543701,
-1.05662052115517, 1.00345389178912, -0.238751726184391,
0.300003114947154, -0.397946795638617, -0.0802167606809086,
0.943714484246865, 1.10973062785877, 1.76279346979401, 1.62087112038423,
0.25533608094687, 0.226841593739787, 0.869672824438507, -1.44960240649761,
-0.450315042397579, -0.199629565370345, 0.29813282042005,
0.760425620590513, 1.87391096816911, -0.454275666102039,
-0.0559029318285365, -0.343048150401812, -1.01371376435687,
0.68880434193488, -0.29222014619459, 1.16132875334186, -1.95715633422403,
-0.534368278792206, -0.560112332871189, 1.84508642898666,
-1.19150176175703, -0.772203732244971, -0.3443683583033,
-1.45684154649076, -0.633823940704178, -1.77454957798344,
0.279539892474118, -0.875532004001301, 1.26001429397797,
-0.536590628759707, 2.1869102581465, 0.211109116247078, 0.130246382281038,
-0.355810160116181, -0.898085555651692, -0.429741802599415,
1.13360438741065, 1.61338994227581, 0.588688576072169, 0.454137387445685,
0.747113524250528, 0.460848444278238, -0.38177424884541,
-0.169990897981981, -0.747361820232001, -0.760123829946369,
0.208028631143609, -1.28748087619509, 2.33950428809329, -0.973029357526068,
-1.06091119683501, 0.917530360867389, -0.35041931118511,
-1.90613029883158, -1.15057531681095, 0.65348878057012, 0.43147381847017
)), row.names = c(NA, -308L), class = c("tbl_df", "tbl",
"data.frame"))
I am using this gam model:
m1 <- gam(mean_AD_scaled ~ s(Age, bs = 'ad', k = -1) + Sex + ti(Age, by = Sex, bs ='fs'),
data = DF,
method = 'REML',
family = gaussian)
Output:
Family: gaussian
Link function: identity
Formula:
mean_AD_scaled ~ s(Age, bs = "ad", k = -1) + Sex + ti(Age,
by = Sex, bs = "fs")
Parametric coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 0.04691 0.06976 0.672 0.502
SexFemale -0.12950 0.09428 -1.374 0.171
Approximate significance of smooth terms:
edf Ref.df F p-value
s(Age) 2.980 3.959 8.72 2.24e-06 ***
ti(Age):SexMale 2.391 2.873 23.47 < 2e-16 ***
ti(Age):SexFemale 1.000 1.000 43.40 < 2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Rank: 48/49
R-sq.(adj) = 0.34 Deviance explained = 35.6%
-REML = 375.4 Scale est. = 0.63867 n = 308
But when I use gtsummary, I get a repeated value for each gender 'interaction':
tbl_regression(m1, tidy_fun = tidy_gam)
I see the following in a publication, which I am trying to replicate with gender and age:
I am not sure how to fix this. My goal is to print a table for a manuscript so any other gam-related information that can be added like edf and R^2.
I think you've found a bug in the handling of these types of interactions. While we work on a fix to the bug, this code should get you what you need. Thanks
library(gtsummary)
#> #BlackLivesMatter
library(mgcv)
packageVersion("gtsummary")
#> [1] ‘1.5.2’
m1 <- gam(marker ~ s(age, bs = 'ad', k = -1) + grade + ti(age, by = grade, bs ='fs'),
data = gtsummary::trial,
method = 'REML',
family = gaussian)
tbl_regression(m1, tidy_fun = gtsummary::tidy_gam) %>%
modify_table_body(
~ .x %>%
dplyr::select(-n_obs) %>%
dplyr::distinct()
) %>%
as_kable() # convert to kable to display on SO
Characteristic
Beta
95% CI
p-value
Grade
I
—
—
II
-0.39
-0.70, -0.08
0.014
III
-0.13
-0.43, 0.18
0.4
s(age)
>0.9
ti(age):gradeI
0.6
ti(age):gradeII
>0.9
ti(age):gradeIII
0.6
Created on 2022-02-21 by the reprex package (v2.0.1)

lme4 error: boundary (singular) fit: see ?isSingular

I am trying to run lme4 package in R. I have 10 Lines in total with four plants for each line in each of the two replications. But some of the plants died and there are some missing values. Weight is the response variable. Here are some lines from the data:
Line Rep Weight PLANT
Line 1 1 NA 1
Line 1 1 NA 2
Line 1 1 NA 3
Line 1 1 NA 4
Line 2 1 26 1
Line 2 1 26 2
Line 2 1 26 3
Line 2 1 27 4
Line 1 2 26 1
Line 1 2 28 2
Line 1 2 26 3
Line 1 2 25 4
Line 2 2 24 1
Line 2 2 26 2
Line 2 2 25 3
Line 2 2 NA 4
I want to run linear mixed model using lme4 package so I tried running:
lme4 <- lmer(Weight ~ 1 + (1|Rep:Plant), data=Data)
But I got an error:
boundary (singular) fit: see ?isSingular
> dput(Data)
structure(list(Line = c("Line 1", "Line 1", "Line 1", "Line 1",
"Line 2", "Line 2", "Line 2", "Line 2", "Line 1", "Line 1", "Line 1",
"Line 1", "Line 2", "Line 2", "Line 2", "Line 2"), Rep = c(1,
1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2), Weight = c(NA,
NA, NA, NA, 26, 26, 26, 27, 26, 28, 26, 25, 24, 26, 25, NA),
PLANT = c(1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4)), row.names = c(NA,
-16L), class = c("tbl_df", "tbl", "data.frame"))
I am using it for the first time and I am not sure about the error. I will appreciate any help!
Your model did fit, but it generated that warning because your random effects are very small. You can read more about this in this post or the help page
Let us look at your data:
ggplot(Data,aes(x=PLANT,y=Weight,col=Rep)) + geom_jitter() + geom_boxplot(alpha=0.2) + facet_wrap(~Rep)
The effects of PLANT and in combination with Rep is extremely small. Let's look at the fitted model:
fit = lmer(Weight ~ 1 + (1|PLANT:Rep),data=Data)
boundary (singular) fit: see ?isSingular
ranef(fit)
$`PLANT:Rep`
(Intercept)
1:1 0
1:2 0
2:1 0
2:2 0
3:1 0
3:2 0
4:1 0
4:2 0
This is exactly what happened. So we can try to account for some other effects and we still see very small coefficients:
fit = lmer(Weight ~ Line + (1|Rep:PLANT),data=Data)
ranef(fit)
$`Rep:PLANT`
(Intercept)
1:1 1.397563e-19
1:2 2.811371e-19
1:3 8.112169e-20
1:4 1.813251e-19
2:1 -1.725964e-19
2:2 -2.463986e-20
2:3 -2.027357e-19
2:4 -2.833681e-19
The takehome message is, there's no really systematic effect coming from PLANT, so you don't need to specify a highly complicated model, do something like:
fit = lmer(Weight ~ Line + (1|Rep),data=Data)
The data in case anyone is interested:
Data = structure(list(Line = structure(c(1L, 1L, 1L, 1L, 12L, 12L, 12L,
12L, 23L, 23L, 23L, 23L, 34L, 34L, 34L, 34L, 45L, 45L, 45L, 45L,
56L, 56L, 56L, 56L, 65L, 65L, 65L, 65L, 66L, 66L, 66L, 66L, 67L,
67L, 67L, 67L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L,
5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 8L, 8L, 8L, 8L,
9L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 11L, 11L, 11L, 11L, 13L,
13L, 13L, 13L, 14L, 14L, 14L, 14L, 15L, 15L, 15L, 15L, 16L, 16L,
16L, 16L, 8L, 8L, 8L, 8L, 66L, 66L, 66L, 66L, 17L, 17L, 17L,
17L, 18L, 18L, 18L, 18L, 9L, 9L, 9L, 9L, 19L, 19L, 19L, 19L,
20L, 20L, 20L, 20L, 21L, 21L, 21L, 21L, 22L, 22L, 22L, 22L, 24L,
24L, 24L, 24L, 25L, 25L, 25L, 25L, 2L, 2L, 2L, 2L, 26L, 26L,
26L, 26L, 27L, 27L, 27L, 27L, 10L, 10L, 10L, 10L, 28L, 28L, 28L,
28L, 29L, 29L, 29L, 29L, 30L, 30L, 30L, 30L, 31L, 31L, 31L, 31L,
67L, 67L, 67L, 67L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 33L,
33L, 33L, 33L, 35L, 35L, 35L, 35L, 36L, 36L, 36L, 36L, 37L, 37L,
37L, 37L, 38L, 38L, 38L, 38L, 39L, 39L, 39L, 39L, 40L, 40L, 40L,
40L, 25L, 25L, 25L, 25L, 19L, 19L, 19L, 19L, 24L, 24L, 24L, 24L,
41L, 41L, 41L, 41L, 42L, 42L, 42L, 42L, 30L, 30L, 30L, 30L, 43L,
43L, 43L, 43L, 44L, 44L, 44L, 44L, 22L, 22L, 22L, 22L, 46L, 46L,
46L, 46L, 47L, 47L, 47L, 47L, 17L, 17L, 17L, 17L, 48L, 48L, 48L,
48L, 49L, 49L, 49L, 49L, 27L, 27L, 27L, 27L, 23L, 23L, 23L, 23L,
50L, 50L, 50L, 50L, 51L, 51L, 51L, 51L, 52L, 52L, 52L, 52L, 41L,
41L, 41L, 41L, 7L, 7L, 7L, 7L, 46L, 46L, 46L, 46L, 11L, 11L,
11L, 11L, 33L, 33L, 33L, 33L, 53L, 53L, 53L, 53L, 54L, 54L, 54L,
54L, 13L, 13L, 13L, 13L, 38L, 38L, 38L, 38L, 4L, 4L, 4L, 4L,
37L, 37L, 37L, 37L, 55L, 55L, 55L, 55L, 57L, 57L, 57L, 57L, 44L,
44L, 44L, 44L, 58L, 58L, 58L, 58L, 59L, 59L, 59L, 59L, 12L, 12L,
12L, 12L, 47L, 47L, 47L, 47L, 48L, 48L, 48L, 48L, 60L, 60L, 60L,
60L, 21L, 21L, 21L, 21L, 18L, 18L, 18L, 18L, 28L, 28L, 28L, 28L,
26L, 26L, 26L, 26L, 61L, 61L, 61L, 61L, 31L, 31L, 31L, 31L, 59L,
59L, 59L, 59L, 52L, 52L, 52L, 52L, 29L, 29L, 29L, 29L, 62L, 62L,
62L, 62L, 63L, 63L, 63L, 63L, 54L, 54L, 54L, 54L, 55L, 55L, 55L,
55L, 53L, 53L, 53L, 53L, 51L, 51L, 51L, 51L, 50L, 50L, 50L, 50L,
64L, 64L, 64L, 64L, 20L, 20L, 20L, 20L, 58L, 58L, 58L, 58L, 16L,
16L, 16L, 16L, 57L, 57L, 57L, 57L, 14L, 14L, 14L, 14L, 63L, 63L,
63L, 63L, 64L, 64L, 64L, 64L, 61L, 61L, 61L, 61L, 36L, 36L, 36L,
36L, 40L, 40L, 40L, 40L, 6L, 6L, 6L, 6L, 39L, 39L, 39L, 39L,
45L, 45L, 45L, 45L, 15L, 15L, 15L, 15L, 1L, 1L, 1L, 1L, 42L,
42L, 42L, 42L, 43L, 43L, 43L, 43L, 65L, 65L, 65L, 65L, 49L, 49L,
49L, 49L, 56L, 56L, 56L, 56L, 3L, 3L, 3L, 3L, 62L, 62L, 62L,
62L, 35L, 35L, 35L, 35L, 5L, 5L, 5L, 5L, 60L, 60L, 60L, 60L,
34L, 34L, 34L, 34L), .Label = c("Line1", "Line10", "Line11",
"Line12", "Line13", "Line14", "Line15", "Line16", "Line17", "Line18",
"Line19", "Line2", "Line20", "Line21", "Line22", "Line23", "Line24",
"Line25", "Line26", "Line27", "Line28", "Line29", "Line3", "Line30",
"Line31", "Line32", "Line33", "Line34", "Line35", "Line36", "Line37",
"Line38", "Line39", "Line4", "Line40", "Line41", "Line42", "Line43",
"Line44", "Line45", "Line46", "Line47", "Line48", "Line49", "Line5",
"Line50", "Line51", "Line52", "Line53", "Line54", "Line55", "Line56",
"Line57", "Line58", "Line59", "Line6", "Line60", "Line61", "Line62",
"Line63", "Line64", "Line65", "Line66", "Line67", "Line7", "Line8",
"Line9"), class = "factor"), Rep = structure(c(1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L), .Label = c("1", "2"), class = "factor"), Weight = c(NA,
NA, NA, NA, 26L, 26L, 26L, 27L, NA, NA, NA, NA, 26L, 28L, 26L,
25L, 22L, 17L, 20L, 20L, 28L, 20L, 27L, 26L, 22L, 25L, 21L, 25L,
18L, 18L, 19L, 18L, 24L, 28L, 23L, 30L, 29L, 25L, 26L, 27L, NA,
NA, NA, NA, 29L, 30L, 29L, 30L, NA, NA, NA, NA, 33L, NA, NA,
NA, 21L, 23L, 18L, 23L, 32L, 29L, 30L, 30L, 18L, 19L, 21L, 21L,
25L, 25L, 25L, 26L, 26L, 27L, NA, NA, 29L, 29L, 27L, 29L, 26L,
NA, NA, NA, 26L, 20L, 23L, 27L, NA, NA, NA, NA, 32L, 32L, 30L,
30L, 20L, 20L, 20L, 19L, 22L, 21L, 22L, 22L, 24L, 23L, 23L, 25L,
20L, 25L, NA, NA, 27L, 26L, NA, NA, NA, NA, NA, NA, 30L, 28L,
NA, NA, 25L, 26L, 27L, 26L, NA, NA, NA, NA, 20L, 19L, NA, NA,
19L, 27L, 26L, 29L, 26L, 29L, 31L, 29L, 25L, 25L, 24L, 25L, 26L,
25L, 26L, 26L, 25L, 24L, 24L, 28L, 22L, 26L, 24L, 28L, 29L, 30L,
26L, NA, NA, NA, NA, NA, 26L, 24L, 24L, 24L, NA, NA, NA, NA,
NA, NA, NA, NA, 30L, 30L, 30L, 31L, 24L, 25L, 28L, 22L, 28L,
31L, 30L, NA, 31L, 30L, 29L, 25L, 25L, 22L, 24L, 20L, 30L, 30L,
30L, 29L, 26L, 32L, 28L, 29L, 20L, 15L, 15L, 11L, 25L, 24L, 24L,
24L, 26L, 29L, 31L, 30L, 24L, 28L, 20L, 22L, 29L, 26L, 26L, 28L,
27L, 27L, 27L, 26L, 21L, 22L, 21L, NA, 28L, 29L, 24L, 24L, 28L,
29L, 28L, 27L, 28L, 29L, 27L, 29L, NA, NA, NA, NA, 22L, 26L,
21L, 21L, 26L, 30L, 28L, 30L, 27L, 26L, 28L, 26L, 25L, 25L, 26L,
26L, 27L, 26L, 23L, 29L, NA, NA, NA, NA, 27L, 23L, 29L, 23L,
28L, 29L, 28L, 26L, 20L, NA, NA, NA, 28L, 23L, 26L, 21L, 28L,
26L, 26L, 29L, 20L, 27L, 20L, 26L, 29L, 26L, 28L, 28L, 30L, 27L,
NA, NA, 26L, 21L, 26L, 25L, 27L, 26L, 27L, 24L, 25L, 20L, 21L,
20L, 25L, 25L, 31L, 24L, 29L, 28L, 31L, 27L, 25L, 28L, 26L, 26L,
NA, NA, NA, NA, 24L, 25L, 23L, 27L, 20L, 26L, 25L, 25L, 29L,
28L, 29L, 29L, 26L, 27L, 25L, 28L, NA, NA, NA, NA, 26L, 28L,
NA, NA, 21L, 20L, 31L, 25L, 31L, 28L, 30L, 29L, 23L, 25L, 24L,
28L, 25L, 22L, 25L, 25L, 28L, 29L, 28L, 29L, 26L, 24L, 25L, 26L,
29L, 27L, NA, NA, 26L, 29L, 29L, 30L, 25L, 24L, 25L, 24L, 28L,
25L, 29L, 28L, 24L, 24L, 24L, 24L, 28L, 30L, 27L, 27L, 26L, 25L,
25L, 25L, 25L, 25L, 28L, 25L, 25L, 30L, 28L, 25L, 22L, 24L, 25L,
24L, NA, NA, NA, NA, 5L, 7L, 4L, 5L, 21L, 20L, 22L, 24L, 25L,
27L, 25L, 28L, 32L, 31L, NA, NA, 19L, 26L, 20L, NA, 26L, 26L,
30L, 25L, 28L, 31L, 30L, 26L, 5L, 8L, 4L, 8L, 25L, 25L, 28L,
25L, 28L, 28L, 27L, 26L, 30L, 27L, 27L, 24L, 32L, 29L, 31L, 25L,
30L, 30L, 27L, 28L, 16L, 20L, 16L, 21L, 25L, 22L, 25L, 20L, 24L,
25L, 18L, 25L, 25L, 26L, 29L, 29L, 21L, 20L, 22L, 21L, 19L, 22L,
19L, 21L, 28L, 25L, 26L, 24L, 28L, 26L, 24L, 25L, NA, NA, NA,
NA, 25L, NA, NA, NA, 23L, 21L, 19L, 23L, 25L, 24L, 25L, NA, 22L,
30L, 29L, 26L, 25L, 25L, 24L, 24L), PLANT = structure(c(1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L,
3L, 4L, 1L, 2L, 3L, 4L), .Label = c("1", "2", "3", "4"), class = "factor"),
X = structure(c(4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L,
6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L,
5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L,
2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L,
4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L,
6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L,
5L, 6L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L,
7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L,
3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L,
1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L,
8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L,
7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L,
4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L,
6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L,
5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L,
2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L,
4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L,
6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L,
5L, 6L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L,
7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L,
3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L,
1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L,
8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L,
7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L,
3L, 7L, 8L, 1L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L,
6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L,
5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L,
2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L,
4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L,
6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L, 5L, 6L, 4L, 2L,
5L, 6L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L,
7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L,
3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L,
1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L,
8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L,
7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L, 3L, 7L, 8L, 1L
), .Label = c("24", "12", "21", "11", "13", "14", "22", "23"
), class = "factor")), row.names = c(NA, -536L), class = "data.frame")

Undesired error in length() when running a glmer() model in R

My dataset looks like this:
> head(GLM_df)
hour Feeding Foraging Standing ID Area Feeding_Foraging
1 0 0.119 0.789 0.0339 41361 Seronera 0.908
2 1 0.0920 0.819 0.0339 41361 Seronera 0.911
3 2 0.0847 0.824 0.0678 41361 Seronera 0.909
4 3 0.233 0.632 0.132 41361 Seronera 0.866
5 4 0.254 0.597 0.124 41361 Seronera 0.852
6 5 0.245 0.664 0.0832 41361 Seronera 0.909
And I'm trying to run a glmer() model as such to verify an interaction, the error associated is found below:
> m <- glmer(cbind(Feeding_Foraging,Standing) ~ poly(hour,2)*Area+(1|ID) , data=GLM_df , family=binomial)
Error in length(value <- as.numeric(value)) == 1L :
(maxstephalfit) PIRLS step-halvings failed to reduce deviance in pwrssUpdate
In addition: Warning message:
In eval(family$initialize, rho) : non-integer counts in a binomial glm!
I apologize if I'm not asking on the right forum, but does somebody know what is the cause of this error? I've been using this dataset to run other glmer() models not having such issue, so I hope somebody can help me.
I can provide a dput() sample of the data below:
> dput(GLM_df)
structure(list(hour = c(0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L,
10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L,
23L, 0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L,
14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 0L, 1L, 2L,
3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L,
17L, 18L, 19L, 20L, 21L, 22L, 23L, 0L, 1L, 2L, 3L, 4L, 5L, 6L,
7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L,
20L, 21L, 22L, 23L, 0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L,
11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L,
0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L,
15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L), Feeding = c(0.118579234700529,
0.0919594065024507, 0.0846994533575204, 0.233092895639896, 0.254098360072561,
0.244523639258233, 0.238513660654777, 0.245289616923379, 0.211748633393801,
0.253514225911475, 0.275555554923133, 0.222477230819087, 0.232641165221989,
0.238368461591879, 0.30265937999754, 0.433661201190504, 0.178745053292422,
0.12125395428024, 0.10605844594333, 0.163238946470857, 0.174611180767811,
0.22483854891269, 0.177868852050793, 0.183918813004901, 0.241998438164344,
0.161698956409812, 0.158105646267371, 0.36138433432542, 0.468670308578279,
0.333151183206247, 0.32072859671381, 0.301413227120555, 0.295571885509692,
0.313952640445209, 0.343315117609149, 0.309435336266141, 0.345573769698683,
0.307176684176607, 0.322987248803344, 0.303788706042306, 0.266520946564997,
0.179710144515087, 0.151781420416677, 0.272293057460473, 0.384777516681307,
0.358157688483229, 0.370418942683556, 0.295571885509692, 0.194038747691774,
0.0980730512560762, 0.104719324151116, 0.287394007254483, 0.360255008280653,
0.356867030146353, 0.303788706042306, 0.297908422154037, 0.295883423728938,
0.309435336266141, 0.335409835295781, 0.294754097684171, 0.329763205071946,
0.311693988355675, 0.252969034027794, 0.320554854245385, 0.269908924699298,
0.114670029160951, 0.145400728263743, 0.208925318281884, 0.252065573191981,
0.343637782193368, 0.234552332374672, 0.25071038193826, 0.139938227286338,
0.127049180036281, 0.0779234970889187, 0.271038250744065, 0.37923497180722,
0.365027321566604, 0.313661201465914, 0.342076501947147, 0.292896174191167,
0.283060108639971, 0.271038250744065, 0.238251365573412, 0.196721311023918,
0.191256830162143, 0.16601092858074, 0.0626775954845651, 0.134426229199678,
0.105704917790185, 0.11195058182907, 0.140192198660723, 0.14806719253611,
0.21262483463543, 0.226733921295516, 0.21891551021636, 0.120612021581109,
0.140939890386914, 0.0931693986932724, 0.2142076497816, 0.228415300022216,
0.194244079699913, 0.181821493207477, 0.186922931547631, 0.153588342088304,
0.15187488188245, 0.135519125372033, 0.171657558804575, 0.144302772386887,
0.113322027250751, 0.0931693986932724, 0.0657666343717217, 0.126775955993192,
0.0912147959234835, 0.0966201171633936, 0.143219075677262, 0.127049180036281,
0.145683059774935, 0.171657558804575, 0.140731399424803, 0.238570126957016,
0.109339294334254, 0.14013909555517, 0.190856101565613, 0.175240248325904,
0.217486338298665, 0.251366119641673, 0.295081966535877, 0.278688523950551,
0.268852458399355, 0.349726775153633, 0.328961747878886, 0.351912567498343,
0.284153004812326, 0.220218578729553, 0.179437360446302, 0.283460837236502,
0.156693988711413, 0.114187411193102, 0.207187893597627, 0.198761383878981,
0.22134790477432, 0.199890709923748, 0.218466176246294), Foraging = c(0.78939890529209,
0.81876138245603, 0.824408012679865, 0.632422585069486, 0.59741347768171,
0.66404371432296, 0.599672129771244, 0.632422585069486, 0.629034606935185,
0.575956282831139, 0.525136610816626, 0.588378869323575, 0.577085608875906,
0.574826956786372, 0.482222221115483, 0.336377829048438, 0.677595626860163,
0.811985426187429, 0.797304187605459, 0.744225863501412, 0.727285972829908,
0.702440799845036, 0.721639342606074, 0.744225863501412, 0.593480307663729,
0.692276865442133, 0.705828777979336, 0.29136611954987, 0.178520386307389,
0.320647930567756, 0.343470886718772, 0.422913132626516, 0.393706424572198,
0.350480496651808, 0.350091073877751, 0.339966081752254, 0.289107467460336,
0.294403617187519, 0.226644054501503, 0.185602280400827, 0.465282330443979,
0.671948996636328, 0.677595626860163, 0.525136610816626, 0.359125682235886,
0.398652093802729, 0.407725644438271, 0.496903459697453, 0.519489980592792,
0.647103823651456, 0.618870672532282, 0.247583017506598, 0.159987856341983,
0.170810564270999, 0.290898812221001, 0.315807961804469, 0.2952380945605,
0.274543055710583, 0.21405861848537, 0.274947456283643, 0.241067674940635,
0.254098360072561, 0.192437158028286, 0.1589743586095, 0.334732239668921,
0.591766847457876, 0.587638966052866, 0.500018841889913, 0.436807180886641,
0.401884302827407, 0.44922080447396, 0.438017173077463, 0.748633878063245,
0.820765025438681, 0.896174861331183, 0.336612021085371, 0.116546447819948,
0.204633879311769, 0.282720933965792, 0.313952640445209, 0.293235348865346,
0.217959926640019, 0.244687309699503, 0.267759562227, 0.256357012162095,
0.20666666619235, 0.110109289364776, 0.0532396563961557, 0.284590163281268,
0.810928959887485, 0.790163932612739, 0.619999998577049, 0.523384208333367,
0.47682655223493, 0.493009231956877, 0.637874503906291, 0.632422585069486,
0.726775954616143, 0.817486336921616, 0.340983605774792, 0.142779078516963,
0.193598750531475, 0.256357012162095, 0.254682494233647, 0.206783493024567,
0.19198542761038, 0.221428570920375, 0.213793102957603, 0.203278688058049,
0.194157208465701, 0.112932604476694, 0.0948633877604228, 0.380582877086458,
0.787978140268028, 0.810928959887485, 0.719125681409657, 0.625136610587118,
0.562404370293935, 0.366120217738959, 0.535519124454, 0.655009105964824,
0.782513659406253, 0.757377047442085, 0.18996877395901, 0.158105646267371,
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6L, 6L, 6L), biggest_group_size = 6L, labels = structure(list(
hour = 0:23), row.names = c(NA, -24L), class = "data.frame", vars = "hour"), class = c("grouped_df",
"tbl_df", "tbl", "data.frame"))
Any input is appreciated!

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