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
EDA
## ecc2 n percent
## 0 115 0.4243542
## 1 156 0.5756458##
## 0 1
## 115 156age
age by ecc
Mark baseline factors
toothbrushing_frequency = Twice daily and more
Regression model
delete the never in toothbrushing frequency
Omit NA in breastfeeding code
Drop levels
Table 1
| Characteristic | Overall, N = 2591 | Boy, N = 1371 | Girl, N = 1221 |
|---|---|---|---|
| age | |||
| 0 | 20 (7.7%) | 9 (6.6%) | 11 (9.0%) |
| 1 | 7 (2.7%) | 2 (1.5%) | 5 (4.1%) |
| 2 | 44 (17%) | 23 (17%) | 21 (17%) |
| 3 | 90 (35%) | 41 (30%) | 49 (40%) |
| 4 | 51 (20%) | 34 (25%) | 17 (14%) |
| 5 | 42 (16%) | 23 (17%) | 19 (16%) |
| 6 | 4 (1.5%) | 4 (2.9%) | 0 (0%) |
| 7 | 1 (0.4%) | 1 (0.7%) | 0 (0%) |
| ecc2 | 149 (58%) | 82 (60%) | 67 (55%) |
| general_health_01 | |||
| 0 | 247 (95%) | 129 (94%) | 118 (97%) |
| 1 | 12 (4.6%) | 8 (5.8%) | 4 (3.3%) |
| parental_brushing | |||
| Every night | 102 (45%) | 53 (43%) | 49 (47%) |
| Occasionally | 70 (31%) | 38 (31%) | 32 (30%) |
| Seldom or never | 55 (24%) | 31 (25%) | 24 (23%) |
| Unknown | 32 | 15 | 17 |
| dental_hygienist_attendance | |||
| Regular twice year | 7 (3.4%) | 2 (1.9%) | 5 (5.3%) |
| >2 | 43 (21%) | 27 (25%) | 16 (17%) |
| 1 | 65 (32%) | 40 (37%) | 25 (26%) |
| 0 | 88 (43%) | 39 (36%) | 49 (52%) |
| Unknown | 56 | 29 | 27 |
| dentist_attendance | |||
| Regular twice year | 11 (5.4%) | 3 (2.8%) | 8 (8.4%) |
| >2 | 39 (19%) | 21 (19%) | 18 (19%) |
| 1 | 63 (31%) | 36 (33%) | 27 (28%) |
| 0 | 90 (44%) | 48 (44%) | 42 (44%) |
| Unknown | 56 | 29 | 27 |
| toothbrushing_frequency | |||
| Twice daily and more | 123 (47%) | 63 (46%) | 60 (49%) |
| In evenings | 94 (36%) | 47 (34%) | 47 (39%) |
| In mornings or less than once | 34 (13%) | 20 (15%) | 14 (11%) |
| Never | 8 (3.1%) | 7 (5.1%) | 1 (0.8%) |
| toothpaste | |||
| Fluoride | 116 (45%) | 63 (46%) | 53 (43%) |
| Low Fluoride | 129 (50%) | 68 (50%) | 61 (50%) |
| Fluoride Free | 14 (5.4%) | 6 (4.4%) | 8 (6.6%) |
| improvement_hygiene | 127 (49%) | 66 (48%) | 61 (50%) |
| sugar_liquid | 174 (67%) | 91 (66%) | 83 (68%) |
| sugar_solid | 204 (79%) | 107 (78%) | 97 (80%) |
| plaque | 127 (49%) | 75 (55%) | 52 (43%) |
| bottle_feeding | 127 (49%) | 69 (50%) | 58 (48%) |
| breastfeeding_code | |||
| <6 | 76 (29%) | 39 (28%) | 37 (30%) |
| >6 | 37 (14%) | 18 (13%) | 19 (16%) |
| >12 | 98 (38%) | 59 (43%) | 39 (32%) |
| >24 | 48 (19%) | 21 (15%) | 27 (22%) |
| mouth_breathing | 45 (19%) | 30 (23%) | 15 (13%) |
| Unknown | 17 | 7 | 10 |
|
1
n (%)
|
|||
Regression table
m1 full
relevel for analysis
| Characteristic | N | OR1 | 95% CI1 | p-value |
|---|---|---|---|---|
| age | 203 | 0.63 | 0.45, 0.85 | 0.005 |
| gender | ||||
| Boy | 108 | — | — | |
| Girl | 95 | 0.60 | 0.26, 1.37 | 0.2 |
| hygiene_combined_foranalysis | ||||
| Twice daily and more Fluoride Always | 28 | — | — | |
| Twice daily and more Fluoride Recently | 74 | 9.75 | 1.62, 190 | 0.039 |
| Twice daily and more Fluoride Free | 5 | 0.52 | 0.01, 22.6 | 0.7 |
| In evenings Fluoride Always | 4 | 11.8 | 0.44, 428 | 0.13 |
| In evenings Fluoride Recently | 22 | 15.5 | 2.06, 333 | 0.022 |
| In evenings Low Fluoride | 32 | 16.5 | 2.28, 347 | 0.017 |
| Less than once per day and/or no fluoride | 38 | 11.9 | 1.64, 249 | 0.035 |
| parental_brushing | ||||
| Every night | 96 | — | — | |
| Occasionally | 63 | 1.38 | 0.57, 3.33 | 0.5 |
| Seldom or never | 44 | 9.33 | 2.80, 36.9 | <0.001 |
| plaque | ||||
| No | 105 | — | — | |
| Yes | 98 | 5.40 | 2.35, 13.1 | <0.001 |
| dental_hygienist_attendance | ||||
| Regular twice year | 7 | — | — | |
| >2 | 43 | 0.54 | 0.05, 4.76 | 0.6 |
| 1 | 65 | 0.72 | 0.07, 6.01 | 0.8 |
| 0 | 88 | 0.43 | 0.04, 3.45 | 0.4 |
| bottle_feeding | ||||
| No | 105 | — | — | |
| Yes | 98 | 0.99 | 0.39, 2.59 | >0.9 |
| breastfeeding_code | ||||
| <6 | 60 | — | — | |
| >6 | 30 | 0.70 | 0.17, 2.79 | 0.6 |
| >12 | 78 | 1.71 | 0.58, 5.15 | 0.3 |
| >24 | 35 | 3.68 | 0.97, 15.2 | 0.062 |
| diet_combined_foranalysis | ||||
| No sugar Always | 19 | — | — | |
| No sugar Recently | 46 | 6.53 | 1.33, 41.6 | 0.029 |
| Sweet drinks and/or sweets | 138 | 2.42 | 0.54, 14.1 | 0.3 |
| mouth_breathing | ||||
| No | 168 | — | — | |
| Yes | 35 | 0.72 | 0.26, 2.00 | 0.5 |
|
1
OR = Odds Ratio, CI = Confidence Interval
|
||||
| Characteristic | N | OR1 | 95% CI1 | p-value |
|---|---|---|---|---|
| parental_brushing | ||||
| Every night | 96 | — | — | |
| Occasionally | 63 | 1.25 | 0.39, 3.99 | 0.7 |
| Seldom or never | 44 | 6.25 | 1.33, 35.1 | 0.027 |
| dental_hygienist_attendance | ||||
| Regular twice year | 7 | — | — | |
| >2 | 43 | 0.45 | 0.02, 9.51 | 0.6 |
| 1 | 65 | 5.65 | 0.37, 140 | 0.2 |
| 0 | 88 | 2.43 | 0.14, 62.3 | 0.6 |
| dentist_attendance | ||||
| Regular twice year | 11 | — | — | |
| >2 | 39 | 0.40 | 0.01, 16.7 | 0.7 |
| 1 | 63 | 0.01 | 0.00, 0.54 | 0.055 |
| 0 | 90 | 0.01 | 0.00, 0.29 | 0.027 |
| age | 203 | 0.65 | 0.43, 0.94 | 0.032 |
| gender | ||||
| Boy | 108 | — | — | |
| Girl | 95 | 0.32 | 0.10, 0.92 | 0.040 |
| general_health_01 | ||||
| 0 | 193 | — | — | |
| 1 | 10 | 11.2 | 1.00, 152 | 0.055 |
| toothbrushing_frequency | ||||
| Twice daily and more | 107 | — | — | |
| In evenings | 61 | 13.1 | 2.23, 97.1 | 0.007 |
| In mornings or less than once | 27 | 4.62 | 0.41, 75.1 | 0.2 |
| Never | 8 | 0.06 | 0.00, 3.11 | 0.14 |
| toothpaste | ||||
| Fluoride | 102 | — | — | |
| Low Fluoride | 91 | 13.4 | 1.75, 167 | 0.022 |
| Fluoride Free | 10 | 0.31 | 0.01, 14.6 | 0.6 |
| improvement_hygiene | ||||
| No | 100 | — | — | |
| Yes | 103 | 13.0 | 1.54, 188 | 0.032 |
| sugar_liquid | ||||
| No | 68 | — | — | |
| Yes | 135 | 1.90 | 0.53, 7.31 | 0.3 |
| sugar_solid | ||||
| No | 43 | — | — | |
| Yes | 160 | 0.41 | 0.09, 1.70 | 0.2 |
| plaque | ||||
| No | 105 | — | — | |
| Yes | 98 | 16.4 | 4.90, 69.3 | <0.001 |
| bottle_feeding | ||||
| No | 105 | — | — | |
| Yes | 98 | 0.96 | 0.30, 3.08 | >0.9 |
| breastfeeding_code | ||||
| <6 | 60 | — | — | |
| >6 | 30 | 1.14 | 0.13, 8.56 | >0.9 |
| >12 | 78 | 1.67 | 0.39, 7.38 | 0.5 |
| >24 | 35 | 6.98 | 1.26, 43.1 | 0.030 |
| mouth_breathing | ||||
| No | 168 | — | — | |
| Yes | 35 | 0.89 | 0.19, 3.88 | 0.9 |
| toothbrushing_frequency * improvement_hygiene | 203 | |||
| In evenings * Yes | 36 | 0.15 | 0.01, 1.33 | 0.095 |
| In mornings or less than once * Yes | 13 | 13.8 | 0.30, 1,031 | 0.2 |
| Never * Yes | 6 | 0.00 | 0.00, 1,099,462,362,098,545,590,272 | >0.9 |
| toothpaste * improvement_hygiene | 203 | |||
| Low Fluoride * Yes | 30 | 0.01 | 0.00, 0.16 | 0.002 |
| Fluoride Free * Yes | 4 | 0.00 | >0.9 | |
|
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 = 0.45). The model's intercept, corresponding to age = 0, gender = Boy, hygiene_combined_foranalysis = Twice daily and more Fluoride Always, parental_brushing = Every night, plaque = No, dental_hygienist_attendance = Regular twice year, bottle_feeding = No, breastfeeding_code = <6, diet_combined_foranalysis = No sugar Always and mouth_breathing = No, is at -2.71 (95% CI [-6.70, 0.81], p = 0.144). Within this model:
##
## - The effect of age is statistically significant and negative (beta = -0.47, 95% CI [-0.81, -0.16], p = 0.005; Std. beta = -0.66, 95% CI [-1.15, -0.22])
## - The effect of gender [Girl] is statistically non-significant and negative (beta = -0.51, 95% CI [-1.35, 0.32], p = 0.229; Std. beta = -0.51, 95% CI [-1.35, 0.32])
## - The effect of hygiene combined foranalysis [Twice daily and more Fluoride Recently] is statistically significant and positive (beta = 2.28, 95% CI [0.48, 5.25], p = 0.039; Std. beta = 2.28, 95% CI [0.48, 5.25])
## - The effect of hygiene combined foranalysis [Twice daily and more Fluoride Free] is statistically non-significant and negative (beta = -0.65, 95% CI [-4.49, 3.12], p = 0.719; Std. beta = -0.65, 95% CI [-4.49, 3.12])
## - The effect of hygiene combined foranalysis [In evenings Fluoride Always] is statistically non-significant and positive (beta = 2.47, 95% CI [-0.81, 6.06], p = 0.129; Std. beta = 2.47, 95% CI [-0.81, 6.06])
## - The effect of hygiene combined foranalysis [In evenings Fluoride Recently] is statistically significant and positive (beta = 2.74, 95% CI [0.72, 5.81], p = 0.022; Std. beta = 2.74, 95% CI [0.72, 5.81])
## - The effect of hygiene combined foranalysis [In evenings Low Fluoride] is statistically significant and positive (beta = 2.80, 95% CI [0.82, 5.85], p = 0.017; Std. beta = 2.80, 95% CI [0.82, 5.85])
## - The effect of hygiene combined foranalysis [Less than once per day and/or no fluoride] is statistically significant and positive (beta = 2.48, 95% CI [0.49, 5.52], p = 0.035; Std. beta = 2.48, 95% CI [0.49, 5.52])
## - The effect of parental brushing [Occasionally] is statistically non-significant and positive (beta = 0.32, 95% CI [-0.57, 1.20], p = 0.475; Std. beta = 0.32, 95% CI [-0.57, 1.20])
## - The effect of parental brushing [Seldom or never] is statistically significant and positive (beta = 2.23, 95% CI [1.03, 3.61], p < .001; Std. beta = 2.23, 95% CI [1.03, 3.61])
## - The effect of plaque [Yes] is statistically significant and positive (beta = 1.69, 95% CI [0.86, 2.58], p < .001; Std. beta = 1.69, 95% CI [0.86, 2.58])
## - The effect of dental hygienist attendance [>2] is statistically non-significant and negative (beta = -0.62, 95% CI [-2.99, 1.56], p = 0.583; Std. beta = -0.62, 95% CI [-2.99, 1.56])
## - The effect of dental hygienist attendance [1] is statistically non-significant and negative (beta = -0.33, 95% CI [-2.64, 1.79], p = 0.765; Std. beta = -0.33, 95% CI [-2.64, 1.79])
## - The effect of dental hygienist attendance [0] is statistically non-significant and negative (beta = -0.85, 95% CI [-3.16, 1.24], p = 0.435; Std. beta = -0.85, 95% CI [-3.16, 1.24])
## - The effect of bottle feeding [Yes] is statistically non-significant and negative (beta = -7.73e-03, 95% CI [-0.95, 0.95], p = 0.987; Std. beta = -7.73e-03, 95% CI [-0.95, 0.95])
## - The effect of breastfeeding code [>6] is statistically non-significant and negative (beta = -0.35, 95% CI [-1.79, 1.03], p = 0.621; Std. beta = -0.35, 95% CI [-1.79, 1.03])
## - The effect of breastfeeding code [>12] is statistically non-significant and positive (beta = 0.53, 95% CI [-0.54, 1.64], p = 0.334; Std. beta = 0.53, 95% CI [-0.54, 1.64])
## - The effect of breastfeeding code [>24] is statistically non-significant and positive (beta = 1.30, 95% CI [-0.03, 2.72], p = 0.062; Std. beta = 1.30, 95% CI [-0.03, 2.72])
## - The effect of diet combined foranalysis [No sugar Recently] is statistically significant and positive (beta = 1.88, 95% CI [0.29, 3.73], p = 0.029; Std. beta = 1.88, 95% CI [0.29, 3.73])
## - The effect of diet combined foranalysis [Sweet drinks and/or sweets] is statistically non-significant and positive (beta = 0.88, 95% CI [-0.63, 2.65], p = 0.280; Std. beta = 0.88, 95% CI [-0.63, 2.65])
## - The effect of mouth breathing [Yes] is statistically non-significant and negative (beta = -0.33, 95% CI [-1.36, 0.70], p = 0.527; Std. beta = -0.33, 95% CI [-1.36, 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