Spatio-Temporal Analysis Project Modelling and Analysis of Spatially Correlated Data: STAT8303

BAHIR DAR UNIVERSITY
COLLEGE OF SCIENCE
DEPARTMENT OF STATISTICS
PhD Programme in Statistics
Spatio-Temporal Analysis project
Modelling and Analysis of Spatially Correlated Data: STAT8303
Submitted by: Changkuoth Jock Chol

Id.№: BDU1500785
Submitted to: Dr. Aweke Abebaw Mitku, PhD

Associate Professor of Statistics
Department of Statistics
College of Science
Bahir Dar University
July 02, 2003 G.C

Bahir Dar, Ethiopia
Use the EDHS 2000, 2005, 2011 and 2016 datasets for the project
a) Perform data management. Sample 2000 data set from the four EDHS datasets the
number of child deaths under age of Five (under-five child mortality) and Use this
data for the project (b-d).
Under-Five Child Mortality

Background of the Data
The EDHS Program produces many different types of datasets. These types vary by individual
survey, but are based upon the types of data collected and the file formats used for dataset
distribution. In order to facilitate the analysis of data, EDHS has developed the concept of recode
files. Use the questionnaires to determine whether the information you want to analyze was
collected in your survey of interest, and who you want to analyze (your unit of analysis). If for
example I want to analyze data about under-five child mortality, I can find that the relevant
questions were asked in the children questionnaire, and my unit of analysis is children. It is
important to mention again that matching files is only necessary when variables required for the
analysis are not present in the distributed file but are present in any other file. When merging
data files it’s important to know the type of relationship that exists between the files to be
merged as well as the type of output file desired (unit of analysis).
Methodology of DHS Mortality Rates Estimation
There are two principal categories of estimation methods for calculating infant and child
mortality rates: direct and indirect. Direct methods of calculation use data on the date of birth of
children, their survival status, and the dates of death or ages at death of deceased children.
Indirect methods use information on survival status of children to specific cohorts of mothers,
typically age cohorts or time since first birth cohorts.
The direct methods require data that are usually obtained only in specifically designed surveys
with birth histories or from vital statistics systems (which are generally deficient in less-
developed countries). The indirect methods can utilize data that are commonly collected in
By: Changkuoth Jock Chol Id.№: BDU1500785 Course Code: STAT8303 Page 1
censuses and many general surveys: the number of children ever born and the number living to
women and the age or time since first birth for the women.
Estimates of indirect methods can suffer if women do not know their ages or the age of their
first child, as is common in many less-developed countries. The bias that results can be even
greater if age is estimated on the basis of characteristics linked directly or indirectly to mortality
levels; for example, number of children ever born. Censuses and surveys not specifically
designed to gather data for mortality estimation have also been shown to be very prone to suffer
from omission of reports of dead children. On the other hand, there have also been some cases
where both stillbirths and live births have been included in the answer to the question on children
ever born, thus leading to overestimates of mortality rates. Violations of the assumptions of the
indirect methods also commonly occur.
Another problem with indirect methods is the location of the estimate in time. Indirect methods
estimate the probability of dying on the basis of experience that can extend over many years,
resulting in an average over that period. Depending on changes in fertility and trends in
mortality, the methods used to place the mortality estimate in time can be more or less in error.
Because of the number of assumptions that may or may not hold, but that need to be made to use
the indirect methods and the limited amount of information that they provide, EDHS has chosen
to use direct estimation methods.
There are three variants of direct estimation methods for estimating under-5 mortality rates and
other rates:
 A vital statistics approach
 A true cohort life table approach
 A synthetic cohort life table approach
In DHS surveys, under-5 mortality rates are calculated using a synthetic cohort life table
approach, in which mortality probabilities for small age segments are combined into the more
common age segments. The under-5 mortality indicators are calculated based on a reference
period of five years or ten years preceding the survey and can be defined as:
The under-5 mortality rate is the probability (expressed as a rate per 1,000 live births) of a
child exposed in a specific period dying before reaching the age of five years.
Coverage:
 Population base: Live births to respondents (BR file)

 Time period: Five-year or ten-year periods of time preceding the survey (v008-1 to
v008-60 or v008-120 months), excluding the month of interview
Live birth: The complete expulsion or extraction from its mother of a product of conception,
irrespective of the duration of the pregnancy, which, after such separation, breathes or shows any
other evidence of life, such as beating of heart, pulsation of the umbilical cord, or definite
movement of voluntary muscles, whether or not the umbilical cord has been cut or the placenta is
attached.
Numerators: In general, it’s the number of deaths to live-born children during specified age
range and specified time period. For Under-5 mortality: Deaths at ages 0 to 4 years, including
deaths reported at ages 0 to 59 months and 0 to 99 days.
Denominator: Number of surviving children at beginning of specified age range during the
specified time period.
Calculation
Component probabilities:
Component death probabilities are first tabulated. Then the component death probabilities are
combined into the mortality rates. The component death probabilities are calculated for age
segments 0, 1-2, 3-5, 6-11, 12-23, 24-35, 36-47, and 48-59 months of completed age.
Each component death probability is defined by a time period and an age interval. Within these
two parameters, three birth cohorts of children are included, as indicated in the figure below:
Figure 1: Cohorts exposed to mortality at ages a1 to a2 during the period t1 to t 2 .
One cohort of children (cohort B) is completely included and two (cohorts A and C) are partially
included in the time period. If the lower and upper limits of the age interval are given by a1 and
a2 , respectively, and the lower and upper limits of the time period are given by t1 and t 2 ,
respectively, then the three cohorts are defined as children born between dates:
 t1 - a2 , and t1 - a1 (cohort A),

 t1 - a1 and t 2 - a2 , (cohort B), and
 t 2 - a2 , and t 2 - a1 (cohort C)
Cohorts A and C are only partially exposed to mortality between ages a1 and a2 , during time
period t1 to t 2 . Therefore, account needs to be taken of the partial exposure. Because of the small
age intervals of the component probabilities, the assumption is made that the exposure to
mortality and deaths of birth cohorts A and C are well represented by taking one-half of the total
exposure and one-half of the deaths (with the exception noted below).
Time periods:
The time period used is typically five years or ten years preceding the month of interview (v008-
1 to v008-60, or v008-1 to v008-120), excluding the month of interview as this would only
contribute a partial month. Time periods are expressed in the form [t1 , t 2 ), i.e. from t1 up to but
not including t2 as follows:
 0-4 years preceding the survey t1 = v008-60 t 2 = v008

 5-9 years preceding the survey t1 = v008-120 t 2 = v008-60
 10-14 years preceding the survey t1 = v008-120 t 2 = v008-180
Age groups:
Age groups are expressed in the form [a1 , a2 ), i.e. from a1 up to but not including a2 .
Table 1: The bounds of the age segments for the component death probabilities
Age segment i 𝐚𝟏 𝐚𝟐
0 1 0 1
1-2 2 1 2
3-5 3 3 6
6-11 4 6 12
12-23 5 12 24
24-35 6 24 36
36-47 7 36 48
48-59 8 48 60
Taking the partial and full exposure into account, the component death probabilities can be
calculated as follows:
2 ( 1 3)
( )
2 ( 1 13 )
where 1 denotes the number of deaths for children in age segment i (between ages a1 and a2 )
during a time period between t1 and t 2 , and 1 denotes the number of survivors at the lower
bound a1 of the age segment i, during the same time period for cohort A. Similar definitions
apply in case of 2, 3 , 2, and 3 for cohorts B and C. The Eq(1) above is valid to calculate
component death probabilities for any time period, except when the time period ends with the
date of the survey. In this case, the component death probabilities should be calculated as
follows:
1 2 3
( )
2 ( 1 13 )
where an assumption is made that all the deaths reported in the survey for cohort C for a time
period that ends with the date of the survey represent one-half of the deaths that will have
occurred to the cohort between ages a1 and a2 .
Once the component probabilities are calculated for each age segment, the under-five child
mortality rates (U5MR) can be calculated as:
( ∏ ( )) ( )
*1 2 3 4 5 6 7 8+
Survey Variables needed to Calculate Under-Five Childhood Mortality Rates

In the majority of DHS surveys, a full birth history is collected from interviewed women about
each live-born child to whom the woman has ever given birth. The birth history section includes
variables for the date of birth (month and year) of each live birth, sex of each child, survival
status of each child, age of each surviving child, and age at death of each deceased child. All
dates are coded in month and year in separate variables, which are then recoded into a Century
Month Code (CMC) format that corresponds to the number of months since January 1900,
calculated as follows,
𝐶 𝐶 (𝑌 9 ) (4)
where Y denotes the year of the event and M denotes the month of the event.
In addition to the variables needed to calculate the rates, other variables are needed to account
for the sampling design and for estimating the standard error, such as the women’s survey
weight, sampling cluster, and sampling strata. All information and variables needed to calculate
under-five child mortality rates are listed in table 2 below.
Table 2: Survey variables needed to calculate under-five child mortality rates
Variable Code Variable Description

b3 Date of birth of child (CMC)
b5 Child is alive (1 = Yes, 0 = No)
b7 Age at death in months (imputed)
v008 Date of interview (CMC)
v005 Woman’s individual sample weight
v0021 Primary sampling unit
Handling of Missing Values
Five variables are used in the calculation of infant and child mortality: date of interview, date of
birth of the child, survival of the child, age at death of the child, and the women’s sampling
weight. The date of interview is not allowed to be missing on the questionnaire. Survival status
for children is also not allowed to be missing. If missing or unknown, the date of birth and age at
death are imputed before the creation of the standard recode.
Notes and Considerations
Typically, mortality rates are calculated for five-year periods preceding the date of the survey for
national estimates. To provide stability in estimates for smaller subgroups, the ten-year period
before the survey is used. To calculate the component death probabilities for the ten-year period,
the numerators for the 2 five-year periods are summed, as are the denominators, before dividing
the numerators by the denominators.
Changes over Time

In prior rounds of the EDHS Program, five-year periods were used only for national estimates,
and ten-year periods were used for all disaggregation of the mortality rates. In EDHS-7, as
sample sizes have increased over the years, five-year periods are also used for mortality rates
disaggregated by sex and by urban/rural residence.
Table 3: The total number of participants and the year of the survey
Year of survey Child is alive Total

No (%) Yes (%)
2000 1508 (12.3%) 10752 (87.7%) 12260
2005 1054 (9.44%) 10109 (90.56%) 11163
2011 830 (6.99%) 11042 (93.01%) 11872
2016 605 (5.49%) 10417 (94.51%) 11022
Total 3997 (8.63%) 42320 (91.37%) 46318
For this project, a total of 46318 children were extracted from four surveys and included in the
analysis with 3997 children are not alive and 42320 children alive.
Table 4: The total number of participants and the year of the survey after the missing cluster
deleted
Year of survey Participants
2000 11984
2005 9737
2011 9311
2016 10466
Total 41498
In the table 4 above, the total of the participants in this project analysis below in the questions
b,c, and d are 41498 children. Due to missing data in the datasets I was deleted the geographic
point in the analysis of this project.
Table 5: The total number of cluster, total missing EDHS cluster, missing cluster number and
total of EDHS cluster available per the year of the survey
Year Total of Total of Missing EDHS Cluster number Total of
of EDHS missing EDHS
Survey Cluster EDHS Cluster
Cluster available
2000 540 5 327,329,330,520,526 535
2005 540 12 120,132,154,217,223,257,412,417,437,477,506,532 528
2011 650 79 11,13,15,19,31,32,45,52,57,70,72,98,102,109,111,127, 521
129,134,144,146,153,155,163,165,168,175,178,190,201,
208,211,216,220,221,237,251,256,258,263,298,304,335,
338,348,361,362,379,384,387,393,399,410,424,444,452,
459,479,486,489,496,500,507,508,522,524,527,531,537,
539,540,565,566,569,571,574,584,608,626,644
2016 645 23 2,9,16,42,48,67,72,96,131,222,250,301,323, 622
328,356,367,379,525,530,540,561,625,641
b) Explore the regional spatial patterns and temporal patterns of child mortality (Use
ArcGIS to plot maps across EDHS survey years 2000, 2005, 2011 and 20016).
Interpret the spatial variations and temporal trends
Table 6: National and regional under-five child mortality rate per 1000 live births in Ethiopia
(2000, 2005, 2011, and 2016)
Region Year of survey
2000 2005 2011 2016
Tigray 169 (144–194) 106 (90–122) 85 (71–100) 59 (47–70)
Afar 229 (193–266) 123 (88–158) 127 (105–149) 125 ( 101–149)
Amhara 183 (168–199) 154 (137–172) 108 (89–127) 85 (70–101)
Oromia 194 (174–214) 122 (109–136) 112 (98–127) 79 (66–91)
Somalia 184 (140–229) 93 (74–113) 122 (108–137) 94 (80–108)
Benishangul-Gumuz 198 (163–232) 157 (125–190) 169 (143–196) 98 (77–118)
SNNPR 192 (171–212) 142 (125–160) 116 (100–132) 88 (69–108)
Gambela 233 (203–263) 156 (97–214) 123 (92–154) 88 (69–107)
Harari 191 (158–224) 103 (70–136) 94 (74–115) 72 (52–93)
Addis Ababa 114 (C86–141) 72 (39–104) 53 (34–72) 39 (24–53)
Dire Dawa 176 (136–215) 136 (98–175) 97 (78–116) 93 (62–123)
Total (Ten years preceding the survey) 188 (178–198) 132 (124–140) 110 (102–118) 82 (74–89)
Total (Five years preceding the survey) 166 (155–177) 123 (113–134) 88 (79–97) 67 (58–76)
Notes: Probability of dying before the fifth birthday in the five or ten years preceding the survey,
per 1,000 live births. Estimates are given for ten year periods for all characteristics, but for five
year periods only for the national total, by residence, and by sex.
In the table 6 above and figure 3 below, the results show that the national under-five child
mortality rate in Ethiopia declined from 166 per 1000 live births in 2000 to 67 per 1000 live
births in 2016. The spatial variation in under-five child mortality was observed at the regional
level with the highest rates reported in Gambella (233 per 1000 live births), Afar (229 per 1000
live births), Benishagul-Gumuz (198 per 1000 live births), Oromia (194 per 1000 live births),
Southern, Nations, the Nationalities and Peoples region (192 per 1000 live births) and Harari
(191 per 1000 live births) in 2000 EDHS. For 2005 EDHS, the high mortality rate was observed
in Benishagul-Gumuz (157 per 1000 live births), Gambella (156 per 1000 live births), Amhara
(154 per 1000 live births), Southern, Nations, the Nationalities and Peoples region (142 per 1000
live births) and Dire Dawa (136 per 1000 live births). Similarly, in 2011 EDHS high mortality
rate was observed in Benishagul-Gumuz (169 per 1000 live births), Gambella (123 per 1000 live
births), Somalia (122 per 1000 live births), Southern, Nations, the Nationalities and Peoples
region (116 per 1000 live births) and Oramia (112 per 1000 live births) regions. Finally, in 2016
EDHS the spatial variation in under-five child mortality was observed at the regional level with
the highest rates reported in Afar (125 per 1000 live births), Benishagul-Gumuz (98 per 1000 live
births), Somalia (94 per 1000 live births), Dire Dawa (93 per 1000 live births), Gambella (88 per
1000 live births), Southern, Nations, the Nationalities and Peoples region (88 per 1000 live
births) and Amhara (85 per 1000 live births). In all four surveys, the lowest under-five mortality
was observed in Addis Ababa. The results also show that the regional under-five child mortality
rate declined from 2000-2016 in many regions in Ethiopia except three regions Afar, Somalia
and Benishagul-Gumuz.
Figure 2: Under-five mortality rate Probability of dying before the fifth birthday in the five years
preceding the survey, per 1,000 live births in Ethiopia.
In the figure 2 above shows the temporal trends of the under-five mortality rate in Ethiopia from
2000 to 2016. The mortality rate declined from 166 per 1000 live births in 2000 to 67 per 1000
live births in 2019. While the decline in under-five mortality was faster in the first two surveys, it
remains stagnant in the last two surveys.
2000 Under Five Child Mortality 2005 Under Five Child Mortality
Figure 3: Geographical locations of data points and under-five child mortality in Ethiopia
Figure 4: Spatial autocorrelation of under-five child mortality in Ethiopia
The figure 4 above is the spatial autocorrelation (Moran I) for under-five child mortality in
Ethiopia in 2000, 2005, 2011 and 2016. Since the results of Moran I statistics is bigger than 0 for
2000, 2005, 2011 and 2016, the spatial pattern is “clustered”.
Figure 5: Anselin’s Local Moran’s I for under-five child mortality in Ethiopia
The figure above is Anselin’s Local Moran’s I for under-five child mortality in Ethiopia within
different time. From the result in the maps above, it is apparent that there is a statistically
significant geographic pattern to the clustering of under-five child mortality in Ethiopia across
the regions. However, it is not possible to understand if these are clusters of high or low values.
Figure 6: Hotspot analysis of under-five child mortality in Ethiopia
The figure above show the Hotspot clusters of under-five child mortality in Ethiopia across
regions. In summary, the Anselin Local Moran’s I statistic identified hotspot clusters and cold
spot clusters of under-five child mortality in Ethiopia across regions within different years.
From results the North West, South West, North East and South East parts identified as a hotspot
areas for under-five child mortality in Ethiopia. And Central, North Central and South Central
parts are identified the cold spot clusters areas (see also figure 17).
c) Fit a Spatio-temporal model to predict child mortality in Ethiopia. Write the results of
the analysis (USE R)
Table 7: Regression coefficient mean and 95% credible intervals (CrI) of a Bayesian spatial
model with binomial response for the under-five mortality in Ethiopia between 2000 and 2016
Parameter Under-five mortality Regression coefficients of Mean (95% CrI)
Estimates 2000 2005 2011 2016
(Intercept) 143.21(138.80-147.62) 99.76(96.86-102.67) 85.98 (82.88-89.09) 68.87 (66.60 -71.13)
sigma2 2723.68(2417.72-3067.73) 1175.11(1042.65-1324.14) 1493.912 (1333.83-1672.90) 859.66 (770.77- 958.63)
Table 8: Model Choice Statistics

Model Choice Statistics Year of Survey
2000 2005 20011 2016
Pdic 2.147 2.146 2.148 2.149
Pdicalt 5.635 5.635 5.649 5.659
Dicorig 5799.910 5307.187 6054.583 6176.163
Dicalt 5806.888 5314.163 6061.585 6183.183
pwaic1 1.866 2.075 2.097 2.085
pwaic2 2.053 2.277 2.304 2.297
waic1 5799.629 5307.115 6054.532 6176.098
waic2 5800.004 5307.518 6054.944 6176.523
Gof 1632144.125 691678.814 995732.851 629627.736
Penalty 1552209.596 661716.377 923858.068 576514.575
pmcc 3184353.721 1353395.191 1919590.920 1206142.311
Figure 7: Plot of residuals against fitted value for under-five child mortality in Ethiopia
Figure 8: Plot of residuals against fitted observation value for under-five child mortality in
Ethiopia
Cross-validation EDHS 2000
Fold 1 Fold 2
Fold 3 Fold 4
Figure 9: Plot of cross validation for under-five child mortality in Ethiopia EDHS 2000
Table 9: Cross validation for under-five child mortality in Ethiopia EDHS 2000
Fold 1 Fold 2 Fold 3 Fold 4
Root Mean Squared Error (RMSE) 39.014 31.727 37.197 34.395
Mean Absolute Error (MAE) 22.545 19.790 24.179 20.321
Continuous Ranked Probability Score (CRPS) 13.985 15.749 15.127 14.993
cvg 87.313 90.370 88.148 88.148
Cross-validation for EDHS 2005
Fold 1 Fold 2
Fold 3 Fold 4
cvg 88.722 89.474 85.185 92.537
Fold 1 Fold 2
Fold 3 Fold 4
cvg 88.591 88.591 91.275 88.333
Fold 1 Fold 2
Fold 3 Fold 4
cvg 86.875 85.093 87.654 90.741
Model validation for 2000
Model 1 Model 2
Figure 13: plot for model validation for EDHS 2000 Data
Table 13: Model validation for EDHS 2000 Data
Model 1 Model 2
Root Mean Squared Error (RMSE) 23.36 20.79
Mean Absolute Error (MAE) 18.12 19.00
Continuous Ranked Probability Score (CRPS) 31.25 19.07
CVg 100.00 100.00

Model 1 Model 2

Model 1 Model 2
CVg 100.00 50.00
Model 1 Model 2

Model 1 Model 2
CVg 100.00 100.00

Model 1 Model 2
Figure 16: plot for model volition for EDHS 2016 Data

Model 1 Model 2
CVg 100.00 50.00
d) Map child mortality predictions across regions of Ethiopia and write the results. (USE
R)
Figure 17: The predicted geospatial map for under-five child mortality across the regions of
Ethiopia

Spatio-Temporal Analysis Project Modelling and Analysis of Spatially Correlated Data: STAT8303

Uploaded by

Document Information

Original Description:

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Spatio-Temporal Analysis Project Modelling and Analysis of Spatially Correlated Data: STAT8303

Uploaded by

Copyright:

Available Formats

BAHIR DAR UNIVERSITY

Submitted by: Changkuoth Jock Chol

Submitted to: Dr. Aweke Abebaw Mitku, PhD

July 02, 2003 G.C

data for the project (b-d).

Under-Five Child Mortality

Methodology of DHS Mortality Rates Estimation

 A vital statistics approach

 A true cohort life table approach

 A synthetic cohort life table approach

 Population base: Live births to respondents (BR file)

 t1 - a2 , and t1 - a1 (cohort A),

 0-4 years preceding the survey t1 = v008-60 t 2 = v008

Survey Variables needed to Calculate Under-Five Childhood Mortality Rates

Table 2: Survey variables needed to calculate under-five child mortality rates

Variable Code Variable Description

Notes and Considerations

Changes over Time

Year of survey Child is alive Total

Figure 4: Spatial autocorrelation of under-five child mortality in Ethiopia

Figure 5: Anselin’s Local Moran’s I for under-five child mortality in Ethiopia

Figure 6: Hotspot analysis of under-five child mortality in Ethiopia

the analysis (USE R)

Table 8: Model Choice Statistics

Model validation for 2005

Table 14: Model validation for EDHS 2005 Data

Table 15: Model validation for EDHS 2011 Data

Model validation for 2016

Table 16: Model validation for EDHS 2016 Data

You might also like