Ilze risk indicators
knitr::opts_chunk$set(
fig.width = 12,
fig.height = 8,
fig.path = 'Figs/',
echo = FALSE,
include= TRUE, # for the chunks to be displayed
warning = FALSE,
message = FALSE,
out.width = "75%"
)# Use include=TRUE for the chunks to be displayedPackages
Dataset
Change output variable
Combine some variables
EDA
## ecc2 n percent
## 0 115 0.4243542
## 1 156 0.5756458##
## 0 1
## 115 156age
## # A tibble: 1 × 2
## `mean(age)` `sd(age)`
## <dbl> <dbl>
## 1 3.15 1.44
age by ecc
Mark baseline factors
toothbrushing_frequency = Twice daily and more
#Table 1
| No (N=115) |
Yes (N=156) |
Overall (N=271) |
|
|---|---|---|---|
| age | |||
| Mean (SD) | 3.25 (1.15) | 3.08 (1.62) | 3.15 (1.44) |
| Median [Min, Max] | 3.00 [0, 7.00] | 3.00 [0, 6.00] | 3.00 [0, 7.00] |
| gender | |||
| Boy | 59 (51.3%) | 89 (57.1%) | 148 (54.6%) |
| Girl | 56 (48.7%) | 67 (42.9%) | 123 (45.4%) |
| parental_brushing | |||
| Every night | 66 (57.4%) | 39 (25.0%) | 105 (38.7%) |
| Occasionally | 32 (27.8%) | 40 (25.6%) | 72 (26.6%) |
| Seldom or never | 10 (8.7%) | 51 (32.7%) | 61 (22.5%) |
| Missing | 7 (6.1%) | 26 (16.7%) | 33 (12.2%) |
| toothbrushing_frequency | |||
| Twice daily and more | 77 (67.0%) | 49 (31.4%) | 126 (46.5%) |
| In evenings | 27 (23.5%) | 71 (45.5%) | 98 (36.2%) |
| In mornings or less than once | 3 (2.6%) | 35 (22.4%) | 38 (14.0%) |
| Never | 8 (7.0%) | 1 (0.6%) | 9 (3.3%) |
| toothpaste | |||
| Fluoride | 59 (51.3%) | 61 (39.1%) | 120 (44.3%) |
| Low Fluoride | 47 (40.9%) | 90 (57.7%) | 137 (50.6%) |
| Fluoride Free | 9 (7.8%) | 5 (3.2%) | 14 (5.2%) |
| hygiene_combined_foranalysis | |||
| At least once per day F | 32 (27.8%) | 4 (2.6%) | 36 (13.3%) |
| In evenings Fluoride Recently | 8 (7.0%) | 22 (14.1%) | 30 (11.1%) |
| In evenings Low Fluoride | 13 (11.3%) | 44 (28.2%) | 57 (21.0%) |
| Less than once per day and/or no fluoride | 13 (11.3%) | 38 (24.4%) | 51 (18.8%) |
| Twice daily and more low fluoride | 49 (42.6%) | 48 (30.8%) | 97 (35.8%) |
| sugar_liquid | |||
| No | 39 (33.9%) | 47 (30.1%) | 86 (31.7%) |
| Yes | 76 (66.1%) | 109 (69.9%) | 185 (68.3%) |
| sugar_solid | |||
| No | 30 (26.1%) | 26 (16.7%) | 56 (20.7%) |
| Yes | 85 (73.9%) | 130 (83.3%) | 215 (79.3%) |
| imrovement_diet | |||
| No | 81 (70.4%) | 135 (86.5%) | 216 (79.7%) |
| Yes | 34 (29.6%) | 21 (13.5%) | 55 (20.3%) |
| diet_combined_foranalysis | |||
| No sugar Always | 18 (15.7%) | 6 (3.8%) | 24 (8.9%) |
| No sugar Recently | 20 (17.4%) | 37 (23.7%) | 57 (21.0%) |
| Sweet drinks and/or sweets | 77 (67.0%) | 113 (72.4%) | 190 (70.1%) |
| plaque | |||
| No | 85 (73.9%) | 50 (32.1%) | 135 (49.8%) |
| Yes | 30 (26.1%) | 106 (67.9%) | 136 (50.2%) |
| bottle_feeding | |||
| No | 52 (45.2%) | 81 (51.9%) | 133 (49.1%) |
| Yes | 63 (54.8%) | 75 (48.1%) | 138 (50.9%) |
| breastfeeding_code | |||
| <6 | 35 (30.4%) | 41 (26.3%) | 76 (28.0%) |
| >6 | 25 (21.7%) | 12 (7.7%) | 37 (13.7%) |
| >12 | 37 (32.2%) | 61 (39.1%) | 98 (36.2%) |
| >24 | 13 (11.3%) | 35 (22.4%) | 48 (17.7%) |
| #N/A | 5 (4.3%) | 7 (4.5%) | 12 (4.4%) |
| mouth_breathing | |||
| No | 97 (84.3%) | 110 (70.5%) | 207 (76.4%) |
| Yes | 18 (15.7%) | 29 (18.6%) | 47 (17.3%) |
| Missing | 0 (0%) | 17 (10.9%) | 17 (6.3%) |
Table 1 gtsummary (sergio)
Modify labels
REMOVE ALL CHILDREN > 6 YEARS OLD
The table one with gtsummary
| Characteristic | Overall, N = 2661 | Caries free, N = 1131 | ECC, N = 1531 |
|---|---|---|---|
| Age | |||
| 0 | 22 (8.3%) | 1 (0.9%) | 21 (14%) |
| 1 | 7 (2.6%) | 3 (2.7%) | 4 (2.6%) |
| 2 | 44 (17%) | 24 (21%) | 20 (13%) |
| 3 | 91 (34%) | 47 (42%) | 44 (29%) |
| 4 | 55 (21%) | 21 (19%) | 34 (22%) |
| 5 | 47 (18%) | 17 (15%) | 30 (20%) |
| Gender | |||
| Boy | 143 (54%) | 57 (50%) | 86 (56%) |
| Girl | 123 (46%) | 56 (50%) | 67 (44%) |
| Parents brush teeth | |||
| Every night | 104 (44%) | 65 (61%) | 39 (30%) |
| Occasionally | 71 (30%) | 31 (29%) | 40 (31%) |
| Seldom or never | 61 (26%) | 10 (9.4%) | 51 (39%) |
| Unknown | 30 | 7 | 23 |
| Tooth brushing frecuency | |||
| Twice daily and more | 124 (47%) | 76 (67%) | 48 (31%) |
| In evenings | 96 (36%) | 27 (24%) | 69 (45%) |
| In mornings or less than once | 37 (14%) | 2 (1.8%) | 35 (23%) |
| Never | 9 (3.4%) | 8 (7.1%) | 1 (0.7%) |
| F Toothpaste use | |||
| Fluoride | 118 (44%) | 59 (52%) | 59 (39%) |
| Low Fluoride | 134 (50%) | 45 (40%) | 89 (58%) |
| Fluoride Free | 14 (5.3%) | 9 (8.0%) | 5 (3.3%) |
| Toothbrushing (Frequency and F) | |||
| At least once per day F | 36 (14%) | 32 (28%) | 4 (2.6%) |
| In evenings Fluoride Recently | 29 (11%) | 8 (7.1%) | 21 (14%) |
| In evenings Low Fluoride | 56 (21%) | 13 (12%) | 43 (28%) |
| Less than once per day and/or no fluoride | 50 (19%) | 12 (11%) | 38 (25%) |
| Twice daily and more low fluoride | 95 (36%) | 48 (42%) | 47 (31%) |
| Consumes sugary liquids | 181 (68%) | 74 (65%) | 107 (70%) |
| Consumes sugary solids | 210 (79%) | 83 (73%) | 127 (83%) |
| Change in the last 12 months towards healthy dietary habits | 53 (20%) | 33 (29%) | 20 (13%) |
| Dietary habits | |||
| No sugar Always | 24 (9.0%) | 18 (16%) | 6 (3.9%) |
| No sugar Recently | 57 (21%) | 20 (18%) | 37 (24%) |
| Sweet drinks and/or sweets | 185 (70%) | 75 (66%) | 110 (72%) |
| Plaque presence | 133 (50%) | 29 (26%) | 104 (68%) |
| Bottle feeding | 135 (51%) | 62 (55%) | 73 (48%) |
| Breastfeeding | |||
| <6 | 75 (28%) | 34 (30%) | 41 (27%) |
| >6 | 36 (14%) | 24 (21%) | 12 (7.8%) |
| >12 | 95 (36%) | 37 (33%) | 58 (38%) |
| >24 | 48 (18%) | 13 (12%) | 35 (23%) |
| #N/A | 12 (4.5%) | 5 (4.4%) | 7 (4.6%) |
| Mouth breathing | 45 (18%) | 17 (15%) | 28 (20%) |
| Unknown | 16 | 0 | 16 |
|
1
n (%)
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Regression model
delete the never in toothbrushing frequency
Omit NA in breastfeeding code
Drop levels
Table 1a
| Characteristic | Overall, N = 2541 | Boy, N = 1321 | Girl, N = 1221 |
|---|---|---|---|
| Age | |||
| 0 | 20 (7.9%) | 9 (6.8%) | 11 (9.0%) |
| 1 | 7 (2.8%) | 2 (1.5%) | 5 (4.1%) |
| 2 | 44 (17%) | 23 (17%) | 21 (17%) |
| 3 | 90 (35%) | 41 (31%) | 49 (40%) |
| 4 | 51 (20%) | 34 (26%) | 17 (14%) |
| 5 | 42 (17%) | 23 (17%) | 19 (16%) |
| ecc2 | 146 (57%) | 79 (60%) | 67 (55%) |
| general_health_01 | |||
| 0 | 242 (95%) | 124 (94%) | 118 (97%) |
| 1 | 12 (4.7%) | 8 (6.1%) | 4 (3.3%) |
| Parents brush teeth | |||
| Every night | 101 (45%) | 52 (43%) | 49 (47%) |
| Occasionally | 69 (31%) | 37 (31%) | 32 (30%) |
| Seldom or never | 55 (24%) | 31 (26%) | 24 (23%) |
| Unknown | 29 | 12 | 17 |
| dental_hygienist_attendance | |||
| Regular twice year | 7 (3.5%) | 2 (1.9%) | 5 (5.3%) |
| >2 | 42 (21%) | 26 (25%) | 16 (17%) |
| 1 | 64 (32%) | 39 (37%) | 25 (26%) |
| 0 | 88 (44%) | 39 (37%) | 49 (52%) |
| Unknown | 53 | 26 | 27 |
| dentist_attendance | |||
| Regular twice year | 11 (5.5%) | 3 (2.8%) | 8 (8.4%) |
| >2 | 39 (19%) | 21 (20%) | 18 (19%) |
| 1 | 61 (30%) | 34 (32%) | 27 (28%) |
| 0 | 90 (45%) | 48 (45%) | 42 (44%) |
| Unknown | 53 | 26 | 27 |
| Tooth brushing frecuency | |||
| Twice daily and more | 121 (48%) | 61 (46%) | 60 (49%) |
| In evenings | 92 (36%) | 45 (34%) | 47 (39%) |
| In mornings or less than once | 33 (13%) | 19 (14%) | 14 (11%) |
| Never | 8 (3.1%) | 7 (5.3%) | 1 (0.8%) |
| F Toothpaste use | |||
| Fluoride | 114 (45%) | 61 (46%) | 53 (43%) |
| Low Fluoride | 126 (50%) | 65 (49%) | 61 (50%) |
| Fluoride Free | 14 (5.5%) | 6 (4.5%) | 8 (6.6%) |
| improvement_hygiene | 123 (48%) | 62 (47%) | 61 (50%) |
| Consumes sugary liquids | 170 (67%) | 87 (66%) | 83 (68%) |
| Consumes sugary solids | 199 (78%) | 102 (77%) | 97 (80%) |
| Plaque presence | 124 (49%) | 72 (55%) | 52 (43%) |
| Bottle feeding | 124 (49%) | 66 (50%) | 58 (48%) |
| Breastfeeding | |||
| <6 | 75 (30%) | 38 (29%) | 37 (30%) |
| >6 | 36 (14%) | 17 (13%) | 19 (16%) |
| >12 | 95 (37%) | 56 (42%) | 39 (32%) |
| >24 | 48 (19%) | 21 (16%) | 27 (22%) |
| Mouth breathing | 43 (18%) | 28 (22%) | 15 (13%) |
| Unknown | 16 | 6 | 10 |
|
1
n (%)
|
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Regression table
m1 full
relevel for analysis
Hygienist
| Characteristic | N | OR1 | 95% CI1 | p-value |
|---|---|---|---|---|
| Age | 201 | 0.64 | 0.46, 0.86 | 0.005 |
| Gender | ||||
| Boy | 106 | — | — | |
| Girl | 95 | 0.60 | 0.27, 1.31 | 0.2 |
| Toothbrushing (Frequency and F) | ||||
| At least once per day F | 32 | — | — | |
| Twice daily and more low fluoride | 78 | 4.55 | 1.10, 26.5 | 0.055 |
| In evenings Fluoride Recently | 22 | 7.73 | 1.48, 54.0 | 0.023 |
| In evenings Low Fluoride | 32 | 9.32 | 1.86, 62.6 | 0.011 |
| Less than once per day and/or no fluoride | 37 | 7.05 | 1.39, 48.1 | 0.027 |
| Parents brush teeth | ||||
| Every night | 95 | — | — | |
| Occasionally | 62 | 1.23 | 0.51, 2.89 | 0.6 |
| Seldom or never | 44 | 6.09 | 2.05, 20.2 | 0.002 |
| Plaque presence | ||||
| No | 104 | — | — | |
| Yes | 97 | 4.92 | 2.21, 11.5 | <0.001 |
| dental_hygienist_attendance | ||||
| Regular | 49 | — | — | |
| 1 | 64 | 1.21 | 0.41, 3.55 | 0.7 |
| 0 | 88 | 0.61 | 0.21, 1.69 | 0.3 |
| Bottle feeding | ||||
| No | 104 | — | — | |
| Yes | 97 | 0.92 | 0.37, 2.31 | 0.9 |
| Breastfeeding | ||||
| <6 | 59 | — | — | |
| >6 | 29 | 0.84 | 0.21, 3.20 | 0.8 |
| >12 | 78 | 1.77 | 0.62, 5.16 | 0.3 |
| >24 | 35 | 3.53 | 0.98, 13.8 | 0.059 |
| Dietary habits | ||||
| No sugar Always | 19 | — | — | |
| No sugar Recently | 46 | 8.19 | 1.69, 51.4 | 0.014 |
| Sweet drinks and/or sweets | 136 | 3.64 | 0.83, 20.7 | 0.11 |
| Mouth breathing | ||||
| No | 167 | — | — | |
| Yes | 34 | 0.73 | 0.26, 2.01 | 0.5 |
|
1
OR = Odds Ratio, CI = Confidence Interval
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Check model
m1
## We fitted a logistic model (estimated using ML) to predict ecc2 with age, gender, hygiene_combined_foranalysis, parental_brushing, plaque, dental_hygienist_attendance, bottle_feeding, breastfeeding_code, diet_combined_foranalysis and mouth_breathing (formula: ecc2 ~ age + gender + hygiene_combined_foranalysis + parental_brushing + plaque + dental_hygienist_attendance + bottle_feeding + breastfeeding_code + diet_combined_foranalysis + mouth_breathing). The model's explanatory power is substantial (Tjur's R2 = 0.42). The model's intercept, corresponding to age = 0, gender = Boy, hygiene_combined_foranalysis = At least once per day F, parental_brushing = Every night, plaque = No, dental_hygienist_attendance = Regular, bottle_feeding = No, breastfeeding_code = <6, diet_combined_foranalysis = No sugar Always and mouth_breathing = No, is at -2.80 (95% CI [-5.53, -0.33], p = 0.034). Within this model:
##
## - The effect of age is statistically significant and negative (beta = -0.45, 95% CI [-0.77, -0.15], p = 0.005; Std. beta = -0.61, 95% CI [-1.06, -0.20])
## - The effect of gender [Girl] is statistically non-significant and negative (beta = -0.52, 95% CI [-1.32, 0.27], p = 0.200; Std. beta = -0.52, 95% CI [-1.32, 0.27])
## - The effect of hygiene combined foranalysis [Twice daily and more low fluoride] is statistically non-significant and positive (beta = 1.52, 95% CI [0.10, 3.28], p = 0.055; Std. beta = 1.52, 95% CI [0.10, 3.28])
## - The effect of hygiene combined foranalysis [In evenings Fluoride Recently] is statistically significant and positive (beta = 2.04, 95% CI [0.39, 3.99], p = 0.023; Std. beta = 2.04, 95% CI [0.39, 3.99])
## - The effect of hygiene combined foranalysis [In evenings Low Fluoride] is statistically significant and positive (beta = 2.23, 95% CI [0.62, 4.14], p = 0.011; Std. beta = 2.23, 95% CI [0.62, 4.14])
## - The effect of hygiene combined foranalysis [Less than once per day and/or no fluoride] is statistically significant and positive (beta = 1.95, 95% CI [0.33, 3.87], p = 0.027; Std. beta = 1.95, 95% CI [0.33, 3.87])
## - The effect of parental brushing [Occasionally] is statistically non-significant and positive (beta = 0.20, 95% CI [-0.66, 1.06], p = 0.640; Std. beta = 0.20, 95% CI [-0.66, 1.06])
## - The effect of parental brushing [Seldom or never] is statistically significant and positive (beta = 1.81, 95% CI [0.72, 3.01], p = 0.002; Std. beta = 1.81, 95% CI [0.72, 3.01])
## - The effect of plaque [Yes] is statistically significant and positive (beta = 1.59, 95% CI [0.79, 2.44], p < .001; Std. beta = 1.59, 95% CI [0.79, 2.44])
## - The effect of dental hygienist attendance [1] is statistically non-significant and positive (beta = 0.19, 95% CI [-0.88, 1.27], p = 0.729; Std. beta = 0.19, 95% CI [-0.88, 1.27])
## - The effect of dental hygienist attendance [0] is statistically non-significant and negative (beta = -0.49, 95% CI [-1.54, 0.53], p = 0.347; Std. beta = -0.49, 95% CI [-1.54, 0.53])
## - The effect of bottle feeding [Yes] is statistically non-significant and negative (beta = -0.09, 95% CI [-0.99, 0.84], p = 0.854; Std. beta = -0.09, 95% CI [-0.99, 0.84])
## - The effect of breastfeeding code [>6] is statistically non-significant and negative (beta = -0.18, 95% CI [-1.56, 1.16], p = 0.798; Std. beta = -0.18, 95% CI [-1.56, 1.16])
## - The effect of breastfeeding code [>12] is statistically non-significant and positive (beta = 0.57, 95% CI [-0.47, 1.64], p = 0.286; Std. beta = 0.57, 95% CI [-0.47, 1.64])
## - The effect of breastfeeding code [>24] is statistically non-significant and positive (beta = 1.26, 95% CI [-0.02, 2.62], p = 0.059; Std. beta = 1.26, 95% CI [-0.02, 2.62])
## - The effect of diet combined foranalysis [No sugar Recently] is statistically significant and positive (beta = 2.10, 95% CI [0.52, 3.94], p = 0.014; Std. beta = 2.10, 95% CI [0.52, 3.94])
## - The effect of diet combined foranalysis [Sweet drinks and/or sweets] is statistically non-significant and positive (beta = 1.29, 95% CI [-0.19, 3.03], p = 0.108; Std. beta = 1.29, 95% CI [-0.19, 3.03])
## - The effect of mouth breathing [Yes] is statistically non-significant and negative (beta = -0.31, 95% CI [-1.33, 0.70], p = 0.542; Std. beta = -0.31, 95% CI [-1.33, 0.70])
##
## Standardized parameters were obtained by fitting the model on a standardized version of the dataset. 95% Confidence Intervals (CIs) and p-values were computed using