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jadebc committed Jul 19, 2021
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273 changes: 125 additions & 148 deletions bookdown-demo.log
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2 changes: 1 addition & 1 deletion docs/01-quality-assurance.md
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\raggedright

To check for outliers in length measurements, we plotted the distribution of raw length measurements by age and sex against different percentiles of the World Health Organization child growth standard distribution. The majority of observations fell within 3 standard deviations of the mean of the standard for males and females. There were certain cohorts, such as COHORTs Guatemala, that had a larger proportion of observations outside of 3 standard deviations from the mean. There was a higher variability of length measurements in the PROBIT, ZVITAMBO, and Keneba cohorts.
To check for outliers in length measurements, we plotted the distribution of raw length measurements by age and sex against different percentiles of the World Health Organization child growth standard distribution. The majority of observations fell within 3 standard deviations of the mean of the standard for males and females. There were certain cohorts, such as the Keneba cohort, that had a larger proportion of observations outside of 3 standard deviations from the mean. There was a higher variability of length measurements in the PROBIT, ZVITAMBO, and Keneba cohorts.



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2 changes: 1 addition & 1 deletion docs/03-secular-trends.md
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\raggedright

This study included cohorts that measured child growth from 1969 to 2014. To assess potential secular trends, we plotted the mean length-for-age Z-score (LAZ) over time. The plot below shows the individual observations from included studies over this range of years. Curves were fit to the data using generalized additive models, with the solid line fit through the median LAZ by birth year, and the dashed lines mark the 1st and 3rd quartiles. There does not appear to be a secular trend in LAZ.
This study included cohorts that measured child growth from 1987 to 2017. To assess potential secular trends, we plotted the mean length-for-age Z-score (LAZ) over time. The plot below shows the individual observations from included studies over this range of years. Curves were fit to the data using generalized additive models, with the solid line fit through the median LAZ by birth year, and the dashed lines mark the 1st and 3rd quartiles. There does not appear to be a secular trend in LAZ.



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30 changes: 15 additions & 15 deletions docs/06-cohort-specific.md
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Expand Up @@ -18,63 +18,63 @@ Here, we present cohort-specific estimates of length-for-age Z-score by age, age
## Mean length-for-age Z-score by age

### Africa
<img src="figures//stunting/fig-laz-2-quant-cohort-africa-allage-primary.png" width="4200" />
<img src="figures//stunting/fig-laz-2-quant-cohort-africa-allage-primary.png" width="1500" />

### Latin America
<img src="figures//stunting/fig-laz-2-quant-cohort-latamer-allage-primary.png" width="4200" />
<img src="figures//stunting/fig-laz-2-quant-cohort-latamer-allage-primary.png" width="1500" />

### South Asia
<img src="figures//stunting/fig-laz-2-quant-cohort-asia-allage-primary.png" width="4200" />
<img src="figures//stunting/fig-laz-2-quant-cohort-asia-allage-primary.png" width="1500" />


<!-- ##################################################################################### -->
## Age-specific prevalence

### Africa
<img src="figures//stunting/fig-stunt-2-prev-cohort-africa-allage-primary.png" width="3000" />
<img src="figures//stunting/fig-stunt-2-prev-cohort-africa-allage-primary.png" width="1500" />

### Latin America
<img src="figures//stunting/fig-stunt-2-prev-cohort-latamer-allage-primary.png" width="3000" />
<img src="figures//stunting/fig-stunt-2-prev-cohort-latamer-allage-primary.png" width="1500" />

### South Asia
<img src="figures//stunting/fig-stunt-2-prev-cohort-asia-allage-primary.png" width="4500" />
<img src="figures//stunting/fig-stunt-2-prev-cohort-asia-allage-primary.png" width="2250" />


<!-- ##################################################################################### -->
## Age-specific incidence

### Africa
<img src="figures//stunting/fig-stunt-2-inc-cohort-africa-allage-primary.png" width="3000" />
<img src="figures//stunting/fig-stunt-2-inc-cohort-africa-allage-primary.png" width="1500" />

### Latin America
<img src="figures//stunting/fig-stunt-2-inc-cohort-latamer-allage-primary.png" width="3000" />
<img src="figures//stunting/fig-stunt-2-inc-cohort-latamer-allage-primary.png" width="1500" />

### South Asia
<img src="figures//stunting/fig-stunt-2-inc-cohort-asia-allage-primary.png" width="4500" />
<img src="figures//stunting/fig-stunt-2-inc-cohort-asia-allage-primary.png" width="2250" />


<!-- ##################################################################################### -->
## Length velocity by age and sex

### Africa
<img src="figures//stunting/fig-length-2-length_vel-cohort-africa-allage-primary.png" width="5400" />
<img src="figures//stunting/fig-length-2-length_vel-cohort-africa-allage-primary.png" width="2700" />

### Latin America
<img src="figures//stunting/fig-length-2-length_vel-cohort-latamer-allage-primary.png" width="5400" />
<img src="figures//stunting/fig-length-2-length_vel-cohort-latamer-allage-primary.png" width="2700" />

### South Asia
<img src="figures//stunting/fig-length-2-length_vel-cohort-asia-allage-primary.png" width="5400" />
<img src="figures//stunting/fig-length-2-length_vel-cohort-asia-allage-primary.png" width="2700" />


<!-- ##################################################################################### -->
## LAZ velocity by age and sex

### Africa
<img src="figures//stunting/fig-laz-2-laz_vel-cohort-africa-allage-primary.png" width="5400" />
<img src="figures//stunting/fig-laz-2-laz_vel-cohort-africa-allage-primary.png" width="2700" />

### Latin America
<img src="figures//stunting/fig-laz-2-laz_vel-cohort-latamer-allage-primary.png" width="5400" />
<img src="figures//stunting/fig-laz-2-laz_vel-cohort-latamer-allage-primary.png" width="2700" />

### South Asia
<img src="figures//stunting/fig-laz-2-laz_vel-cohort-asia-allage-primary.png" width="5400" />
<img src="figures//stunting/fig-laz-2-laz_vel-cohort-asia-allage-primary.png" width="2700" />

12 changes: 6 additions & 6 deletions docs/07-excluding-PROBIT.md
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## Mean length-for-age Z-score by age

### Including PROBIT
<img src="figures//stunting/fig-laz-2-mean-overall_region--allage-primary.png" width="3000" />
<img src="figures//stunting/fig-laz-2-mean-overall_region--allage-primary.png" width="1500" />

### Excluding PROBIT
<img src="figures//stunting/fig-laz-2-mean-overall_region--allage-primary_no_probit.png" width="3000" />
<img src="figures//stunting/fig-laz-2-mean-overall_region--allage-primary_no_probit.png" width="1500" />


<!-- ##################################################################################### -->
## Age-specific prevalence

### Including PROBIT
<img src="figures//stunting/fig-stunt-2-prev-overall_region--allage-primary.png" width="4200" />
<img src="figures//stunting/fig-stunt-2-prev-overall_region--allage-primary.png" width="2100" />

### Excluding PROBIT
<img src="figures//stunting/fig-stunt-2-prev-overall_region--allage-primary_no_probit.png" width="4200" />
<img src="figures//stunting/fig-stunt-2-prev-overall_region--allage-primary_no_probit.png" width="2100" />

<!-- ##################################################################################### -->
## Age-specific incidence

### Including PROBIT
<img src="figures//stunting/fig-stunt-2-inc-overall_region--allage-primary.png" width="4800" />
<img src="figures//stunting/fig-stunt-2-inc-overall_region--allage-primary.png" width="2400" />

### Excluding PROBIT
<img src="figures//stunting/fig-stunt-2-inc-overall_region--allage-primary.png" width="4800" />
<img src="figures//stunting/fig-stunt-2-inc-overall_region--allage-primary.png" width="2400" />



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2 changes: 1 addition & 1 deletion docs/08-monthly-cohorts.md
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Expand Up @@ -57,5 +57,5 @@ In this sensitivity analysis, the mean length-for-age Z-score was higher in Lati

### Cohorts that measured monthly from birth to 24 months

<img src="figures//stunting/fig-stunt-2-vel-overall--allage-month24.png" width="1500" />
<img src="figures//stunting/fig-stunt-2-vel-overall--allage-month24.png" width="1800" />

16 changes: 8 additions & 8 deletions docs/09-fixed-effects.md
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Expand Up @@ -8,41 +8,41 @@ The primary analyses presented in this manuscript pooled across individual studi
## Age-specific prevalence

### Random effects
<img src="figures//stunting/fig-stunt-2-prev-overall_region--allage-primary.png" width="4200" />
<img src="figures//stunting/fig-stunt-2-prev-overall_region--allage-primary.png" width="2100" />

### Fixed effects
<img src="figures//stunting/fig-stunt-2-prev-overall_region--allage-fe.png" width="4200" />
<img src="figures//stunting/fig-stunt-2-prev-overall_region--allage-fe.png" width="2100" />


<!-- ##################################################################################### -->
## Age-specific incidence

### Random effects
<img src="figures//stunting/fig-stunt-2-inc-overall_region--allage-primary.png" width="4800" />
<img src="figures//stunting/fig-stunt-2-inc-overall_region--allage-primary.png" width="2400" />

### Fixed effects
<img src="figures//stunting/fig-stunt-2-inc-overall_region--allage-fe.png" width="4800" />
<img src="figures//stunting/fig-stunt-2-inc-overall_region--allage-fe.png" width="2400" />


<!-- ##################################################################################### -->
## Changes in stunting status by age

### Random effects
<img src="figures//stunting/fig-stunt-2-flow-overall--allage-re.png" width="3000" />
<img src="figures//stunting/fig-stunt-2-flow-overall--allage-re.png" width="1500" />

### Fixed effects
<img src="figures//stunting/fig-stunt-2-flow-overall--allage-fe.png" width="3000" />
<img src="figures//stunting/fig-stunt-2-flow-overall--allage-fe.png" width="1500" />



<!-- ##################################################################################### -->
## Linear growth velocity

### Random effects
<img src="figures//stunting/fig-stunt-2-vel-overall--allage-primary.png" width="3600" />
<img src="figures//stunting/fig-stunt-2-vel-overall--allage-primary.png" width="1800" />

### Fixed effects
<img src="figures//stunting/fig-stunt-2-vel-overall--allage-primary.png" width="3600" />
<img src="figures//stunting/fig-stunt-2-vel-overall--allage-fe.png" width="1800" />


[^1]: Hedges, L. V. & Vevea, J. L. Fixed- and random-effects models in meta-analysis. Psychol. Methods 3, 486–504 (1998).
2 changes: 1 addition & 1 deletion docs/DHS.html
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<meta name="author" content="Jade Benjamin-Chung et al." />


<meta name="date" content="2021-07-13" />
<meta name="date" content="2021-07-19" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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