Research report 1_Computing: COMH7189A/7198A/7294A/7308A
Vusumuzi Mabasa 
Thandeka Mchunu
Nontobeko Mnisi
Phindile Stowe
Prosperity Hadebe
Shantel Mphogo
options(scipen = 999)
library(Statamarkdown)Warning: package 'Statamarkdown' was built under R version 4.4.2Stata found at C:/Program Files/Stata18/StataSE-64.exeThe 'stata' engine is ready to use.stataexe <- "C:/Program Files/Stata18/StataSE-64.exe"
knitr::opts_chunk$set(engine.path = list(stata=stataexe))cd "C:\Users\VUSI\Downloads\Group 7 Biostats Assignment"C:\Users\VUSI\Downloads\Group 7 Biostats AssignmentpwdC:\Users\VUSI\Downloads\Group 7 Biostats Assignment
sysuse demo, clear
codebook(HonsMSc20257_DATA_NOHDRS_2025-02-14_1523.csv)
-------------------------------------------------------------------------------
record_id Record ID
-------------------------------------------------------------------------------
Type: Numeric (byte)
Range: [1,31] Units: 1
Unique values: 24 Missing .: 0/24
Mean: 15.2083
Std. dev.: 9.25005
Percentiles: 10% 25% 50% 75% 90%
3 7.5 15 23 27
-------------------------------------------------------------------------------
redcap_event_name Event Name
-------------------------------------------------------------------------------
Type: String (str24)
Unique values: 1 Missing "": 0/24
Tabulation: Freq. Value
24 "demographic_inform_arm_1"
-------------------------------------------------------------------------------
redcap_survey_identifier Survey Identifier
-------------------------------------------------------------------------------
Type: Numeric (byte)
Range: [.,.] Units: .
Unique values: 0 Missing .: 24/24
Tabulation: Freq. Value
24 .
-------------------------------------------------------------------------------
demographic_informat_v_0 Survey Timestamp
-------------------------------------------------------------------------------
Type: String (str19)
Unique values: 23 Missing "": 0/24
Examples: "2025-02-08 21:02:10"
"2025-02-09 20:40:32"
"2025-02-10 16:56:02"
"2025-02-11 14:32:22"
Warning: Variable has embedded blanks.
-------------------------------------------------------------------------------
dob Date of birth
-------------------------------------------------------------------------------
Type: Numeric daily date (float)
Range: [10894,23875] Units: 1
Or equivalently: [29oct1989,14may2025] Units: days
Unique values: 24 Missing .: 0/24
Mean: 15287 = 08nov2001(+ 1 hour)
Std. dev.: 3164.95
Percentiles: 10% 25% 50% 75% 90%
12072 13174.5 15629 15883.5 18295
19jan1993 26jan1996 16oct2002 27jun2003 02feb2010
-------------------------------------------------------------------------------
consent_date Consent date.
-------------------------------------------------------------------------------
Type: Numeric daily date (float)
Range: [20005,23785] Units: 1
Or equivalently: [09oct2014,13feb2025] Units: days
Unique values: 8 Missing .: 0/24
Tabulation: Freq. Value
1 20005 09oct2014
1 21663 24apr2019
1 23779 07feb2025
5 23780 08feb2025
4 23781 09feb2025
2 23782 10feb2025
5 23783 11feb2025
5 23785 13feb2025
-------------------------------------------------------------------------------
age Age
-------------------------------------------------------------------------------
Type: Numeric (byte)
Range: [0,35] Units: 1
Unique values: 14 Missing .: 0/24
Mean: 23
Std. dev.: 7.72348
Percentiles: 10% 25% 50% 75% 90%
15 21 22 28.5 32
-------------------------------------------------------------------------------
edu_level What is your highest level of education?
-------------------------------------------------------------------------------
Type: Numeric (byte)
Label: edu_level_
Range: [1,3] Units: 1
Unique values: 3 Missing .: 0/24
Tabulation: Freq. Numeric Label
1 1 Primary school
5 2 High school
18 3 Tertiary education
-------------------------------------------------------------------------------
employ_status What is your current employment status?
-------------------------------------------------------------------------------
Type: Numeric (byte)
Label: employ_status_
Range: [1,5] Units: 1
Unique values: 5 Missing .: 0/24
Tabulation: Freq. Numeric Label
5 1 Full-time
3 2 Part-time
7 3 Unemployed
3 4 Self-employed
6 5 Student
-------------------------------------------------------------------------------
monthly_income What is your current household income (monthly, in ZAR)?
-------------------------------------------------------------------------------
Type: Numeric (byte)
Label: monthly_income_
Range: [1,5] Units: 1
Unique values: 5 Missing .: 0/24
Tabulation: Freq. Numeric Label
10 1 Less than R3,500
1 2 R3, 500-R7,000
4 3 R7, 001-R15,000
4 4 R15, 001-R30,000
5 5 More than R30,000
-------------------------------------------------------------------------------
preg_complications Did you experience any pregnancy
complications? (e.g., gestational
diabetes, pre
-------------------------------------------------------------------------------
Type: Numeric (byte)
Label: preg_complications_
Range: [0,1] Units: 1
Unique values: 2 Missing .: 2/24
Tabulation: Freq. Numeric Label
21 0 No
1 1 Yes
2 .
-------------------------------------------------------------------------------
yes_specify If yes, please specify.
-------------------------------------------------------------------------------
Type: String (str16)
Unique values: 1 Missing "": 23/24
Tabulation: Freq. Value
23 ""
1 "Placenta Previa "
Warning: Variable has embedded and trailing blanks.
-------------------------------------------------------------------------------
demographic_informat_v_1 Complete?
-------------------------------------------------------------------------------
Type: Numeric (byte)
Label: demographic_informat_v_1_
Range: [2,2] Units: 1
Unique values: 1 Missing .: 0/24
Tabulation: Freq. Numeric Label
24 2 Complete. use "demo.dta"
(HonsMSc20257_DATA_NOHDRS_2025-02-14_1523.csv)
. merge 1:1 record_id using "baseline.dta"
Result Number of obs
-----------------------------------------
Not matched 3
from master 3 (_merge==1)
from using 0 (_merge==2)
Matched 21 (_merge==3)
-----------------------------------------
. drop if _merge==1
(3 observations deleted)
.
.
.
. save "Merged.dta", replace
file Merged.dta saved
.
.
.
. use Follow_up
describe(HonsMSc20257_DATA_NOHDRS_2025-02-14_1528.csv)
Contains data from Follow_up.dta
Observations: 25 HonsMSc20257_DATA_NOHDRS_2025-0
2-14_1528.csv
Variables: 18 14 Feb 2025 17:19
-------------------------------------------------------------------------------
Variable Storage Display Value
name type format label Variable label
-------------------------------------------------------------------------------
record_id byte %8.0g Record ID
redcap_event_~e str22 %22s Event Name
redcap_survey~r byte %8.0g Survey Identifier
followup_time~p str19 %19s Survey Timestamp
baby_current_~t float %9.0g What is your babys current weight
(kg)?
baby_current_~h float %9.0g What is your babys current length
(cm)?
baby_bmi2 float %9.0g Babys BMI
recent_growth~s byte %8.0g recent_growth_issues_
Has your baby been diagnosed with
growth-related issues?
yes_issues byte %8.0g If yes, please specify.
healthcare_vi~s byte %17.0g healthcare_visits_
How many times has your baby
visited a healthcare facility
for a check-up since
feed_3month byte %39.0g feed_3month_
How is your baby currently fed?
feed_perday_3~h byte %9.0g feed_perday_3month_
If breastfeeding, how many times
per day does your baby feed?
bottles_perda~h byte %11.0g bottles_perday_3month_
If formula feeding, how many
bottles per day does your baby
consume?
complementary~h byte %8.0g complementary_food_3month_
Have you introduced any
complementary foods (e.g.,
porridge, purees)?
latest_illnes~h byte %47.0g latest_illness_3month_
Has your baby experienced any of
the following since the last
survey? (Check all
hospitalizati~h byte %8.0g hospitalization_3month_
Has your baby been hospitalized
since the last survey?
maternal_meals byte %8.0g maternal_meals_
How many meals do you eat per
day?
followup_comp~e byte %10.0g followup_complete_
Complete?
-------------------------------------------------------------------------------
Sorted by: use Follow_up, clear
duplicates drop record_id, force
save Follow_upD.dta, replace(HonsMSc20257_DATA_NOHDRS_2025-02-14_1528.csv)
Duplicates in terms of record_id
(12 observations deleted)
file Follow_upD.dta saved
use Merged.dta, clear
merge 1:1 record_id using "Follow_upD", nogenerate
save "Merged1.dta", replace(HonsMSc20257_DATA_NOHDRS_2025-02-14_1523.csv)
Result Number of obs
-----------------------------------------
Not matched 8
from master 8
from using 0
Matched 13
-----------------------------------------
file Merged1.dta saved
use "Merged1", clear
misstable summarize(HonsMSc20257_DATA_NOHDRS_2025-02-14_1523.csv)
Obs<.
+------------------------------
| | Unique
Variable | Obs=. Obs>. Obs<. | values Min Max
-------------+--------------------------------+------------------------------
redcap_sur~r | 21 0 | 0 . .
preg_compl~s | 2 19 | 2 0 1
weigh_faci~y | 1 20 | 1 1 1
last_weight | 4 17 | 17 2.9 66.6
last_length | 5 16 | 13 10 96
baby_bmi | 4 17 | 17 9.608708 290
yes_select~s | 20 1 | 1 1 1
maternal_d~t | 1 20 | 4 1 4
clean_water | 1 20 | 2 0 1
mental_hea~s | 1 20 | 2 0 1
baby_curre~t | 8 13 | 12 3.5 70
baby_curre~h | 8 13 | 11 25.99 98
baby_bmi2 | 8 13 | 13 6.6482 458.7848
recent_gro~s | 8 13 | 1 0 0
yes_issues | 21 0 | 0 . .
healthcare~s | 8 13 | 4 1 4
feed_3month | 8 13 | 3 2 4
feed_perda~h | 20 1 | 1 2 2
bottles_pe~h | 20 1 | 1 2 2
complement~h | 8 13 | 2 0 1
latest_ill~h | 8 13 | 4 3 6
hospitaliz~h | 8 13 | 2 0 1
maternal_m~s | 8 13 | 2 2 3
followup_c~e | 8 13 | 1 2 2
-----------------------------------------------------------------------------
use "Merged1", clear
expand 2 if _n <= 10
#replace record_id = record_id + " " if mod(_n, 5) == 0
replace redcap_event_name = "wrong_event" if mod(_n, 7) == 0
save merged_data_with_errors.dta, replace(HonsMSc20257_DATA_NOHDRS_2025-02-14_1523.csv)
(10 observations created)
Unknown #command
(4 real changes made)
file merged_data_with_errors.dta saveduse merged_data_with_errors, clear
duplicates drop record_id redcap_event_name, force
replace redcap_event_name = "baseline_arm_1" if redcap_event_name == "wrong_event"
replace redcap_event_name = trim(redcap_event_name)
save merged_data_clean.dta, replace(HonsMSc20257_DATA_NOHDRS_2025-02-14_1523.csv)
Duplicates in terms of record_id redcap_event_name
(10 observations deleted)
(3 real changes made)
(0 real changes made)
file merged_data_clean.dta saveduse merged_data_clean, clear
gen dob_str = string(dob, "%td")
gen dob_date = date(dob_str, "DMY")
format dob_date %td(HonsMSc20257_DATA_NOHDRS_2025-02-14_1523.csv)use merged_data_clean, clear
describe(HonsMSc20257_DATA_NOHDRS_2025-02-14_1523.csv)
Contains data from merged_data_clean.dta
Observations: 21 HonsMSc20257_DATA_NOHDRS_2025-0
2-14_1523.csv
Variables: 45 8 Mar 2025 09:51
-------------------------------------------------------------------------------
Variable Storage Display Value
name type format label Variable label
-------------------------------------------------------------------------------
record_id byte %8.0g Record ID
redcap_event_~e str24 %24s Event Name
redcap_survey~r byte %8.0g Survey Identifier
demographic_i~0 str19 %19s Survey Timestamp
dob float %dM_d,_CY Date of birth
consent_date float %dM_d,_CY Consent date.
age byte %8.0g Age
edu_level byte %18.0g edu_level_
What is your highest level of
education?
employ_status byte %13.0g employ_status_
What is your current employment
status?
monthly_income byte %17.0g monthly_income_
What is your current household
income (monthly, in ZAR)?
preg_complica~s byte %8.0g preg_complications_
Did you experience any pregnancy
complications? (e.g.,
gestational diabetes, pre
yes_specify str16 %16s If yes, please specify.
demographic_i~1 byte %10.0g demographic_informat_v_1_
Complete?
baseline_info~p str19 %19s Survey Timestamp
feed_baseline byte %18.0g feed_baseline_
How is your baby currently fed?
feed_per_day byte %9.0g feed_per_day_
How often does your baby feed per
day?
solid_foods byte %8.0g solid_foods_
Have you introduced any solid
foods to your baby?
nutrition_cou~l byte %8.0g nutrition_counsel_
Do you have access to nutritional
counseling?
weigh_facility byte %8.0g weigh_facility_
Has your baby been weighed at a
healthcare facility since
birth?
last_weight float %9.0g What was your babys last recorded
weight?
last_length float %9.0g What was your babys last recorded
length (in cm)?
baby_bmi float %9.0g Babys BMI.
condition_aff~h byte %8.0g condition_affecting_growth_
Does your baby have any diagnosed
medical conditions affecting
growth?
yes_select_op~s byte %21.0g yes_select_options_
If yes, please select the
following options.
other_specify str9 %9s If other, please specify.
maternal_diet byte %121.0g maternal_diet_
What is your daily diet like?
clean_water byte %8.0g clean_water_
Do you have access to clean
drinking water?
mental_health~s byte %8.0g mental_health_concerns_
Have you experienced any mental
health concerns since giving
birth?
baseline_info~e byte %10.0g baseline_information_complete_
Complete?
_merge byte %23.0g _merge Matching result from merge
followup_time~p str19 %19s Survey Timestamp
baby_current_~t float %9.0g What is your babys current weight
(kg)?
baby_current_~h float %9.0g What is your babys current length
(cm)?
baby_bmi2 float %9.0g Babys BMI
recent_growth~s byte %8.0g recent_growth_issues_
Has your baby been diagnosed with
growth-related issues?
yes_issues byte %8.0g If yes, please specify.
healthcare_vi~s byte %17.0g healthcare_visits_
How many times has your baby
visited a healthcare facility
for a check-up since
feed_3month byte %39.0g feed_3month_
How is your baby currently fed?
feed_perday_3~h byte %9.0g feed_perday_3month_
If breastfeeding, how many times
per day does your baby feed?
bottles_perda~h byte %11.0g bottles_perday_3month_
If formula feeding, how many
bottles per day does your baby
consume?
complementary~h byte %8.0g complementary_food_3month_
Have you introduced any
complementary foods (e.g.,
porridge, purees)?
latest_illnes~h byte %47.0g latest_illness_3month_
Has your baby experienced any of
the following since the last
survey? (Check all
hospitalizati~h byte %8.0g hospitalization_3month_
Has your baby been hospitalized
since the last survey?
maternal_meals byte %8.0g maternal_meals_
How many meals do you eat per
day?
followup_comp~e byte %10.0g followup_complete_
Complete?
-------------------------------------------------------------------------------
Sorted by:
use merged_data_clean, clear
destring baby_bmi, replace
destring age, replace
dtable age preg_complications(HonsMSc20257_DATA_NOHDRS_2025-02-14_1523.csv)
baby_bmi already numeric; no replace
age already numeric; no replace
-----------------------------------------------------------------------------------------------
Summary
-----------------------------------------------------------------------------------------------
N 21
Age 22.857 (7.663)
Did you experience any pregnancy complications? (e.g., gestational diabetes, pre 0.053 (0.229)
-----------------------------------------------------------------------------------------------asdoc logistic preg_complications age Logistic regression Number of obs = 22
LR chi2(1) = 0.86
Prob > chi2 = 0.3532
Log likelihood = -3.6370114 Pseudo R2 = 0.1059
------------------------------------------------------------------------------
preg_compl~s | Odds ratio Std. err. z P>|z| [95% conf. interval]
-------------+----------------------------------------------------------------
age | 1.180138 .2443618 0.80 0.424 .7864683 1.77086
_cons | .0006154 .0037186 -1.22 0.221 4.42e-09 85.67737
------------------------------------------------------------------------------
Note: _cons estimates baseline odds.
(file Myfile.doc not found)
Click to Open File: Myfile.doc
use merged_data_clean, clear
scatter last_length last_weight, mcolor(pink) xtitle("Weight(kg)") ytitle("Length (cm)"), ,title("length vs. Weight")
graph export "scatter.png",as(png) replace(HonsMSc20257_DATA_NOHDRS_2025-02-14_1523.csv)
file scatter.png saved as PNG formatuse merged_data_clean, clear
scatter last_length last_weight, mcolor(pink) xtitle("Weight (kg)") ytitle("Length (cm)") title("Length vs. Weight")
graph save graph1.gph, replace(HonsMSc20257_DATA_NOHDRS_2025-02-14_1523.csv)
file graph1.gph savedknitr::include_graphics("scatter.png")
use merged_data_clean, clear
graph box last_weight, over(feed_baseline) box(1, fcolor(red)) ytitle("Weight (kg)") title("Box-Plot: Weight by Feeding type") medtype(line) medline(lcolor(black))
graph export "boxplot.png", as(png) replace(HonsMSc20257_DATA_NOHDRS_2025-02-14_1523.csv)
file boxplot.png saved as PNG formatuse merged_data_clean, clear
graph box last_weight, over(feed_baseline) box(1, fcolor(red)) ytitle("Weight (kg)") title("Box-Plot: Weight by Feeding type") medtype(line) medline(lcolor(black))
graph save graph2.gph, replace(HonsMSc20257_DATA_NOHDRS_2025-02-14_1523.csv)
file graph2.gph savedknitr::include_graphics("boxplot.png")
use merged_data_clean, clear
graph bar (mean) last_weight, over(feed_baseline) bar(1, fcolor(orange)) title("Mean Weight by Feeding Type") ytitle("Mean Weight (kg)")
graph export bargraph.png, as(png) replace(HonsMSc20257_DATA_NOHDRS_2025-02-14_1523.csv)
file bargraph.png saved as PNG format
use merged_data_clean, clear
graph bar (mean) last_weight, over(feed_baseline) bar(1, fcolor(orange)) title("Mean Weight by Feeding Type") ytitle("Mean Weight (kg)")
graph save graph3.gph, replace(HonsMSc20257_DATA_NOHDRS_2025-02-14_1523.csv)
file graph3.gph savedplot3 <- knitr::include_graphics("bargraph.png")
plot3
use merged_data_clean, clear
graph pie, over(edu_level) plabel(_all percent, color(black)) ///
pie(1, color(cranberry)) pie(2, color(yellow)) pie(3, color(lime)) ///
title("Educational Level") legend(on)
graph export "piechart.png", as(png) replace(HonsMSc20257_DATA_NOHDRS_2025-02-14_1523.csv)
file piechart.png saved as PNG format
use merged_data_clean, clear
graph pie, over(edu_level) plabel(_all percent, color(black)) ///
pie(1, color(cranberry)) pie(2, color(yellow)) pie(3, color(lime)) ///
title("Educational Level") legend(on)
graph save graph4.gph, replace(HonsMSc20257_DATA_NOHDRS_2025-02-14_1523.csv)
file graph4.gph savedplot4 <- knitr::include_graphics("piechart.png")
plot4
graph combine graph1.gph graph2.gph ///
graph3.gph graph4.gph, ///
title("Combined Graphs") cols(2)
graph export Combined_GraphsG7.png, as(png) replacefile Combined_GraphsG7.png saved as PNG formatknitr::include_graphics("Combined_GraphsG7.png")
ssc install shp2dta
ssc install spmapchecking shp2dta consistency and verifying not already installed...
all files already exist and are up to date.
checking spmap consistency and verifying not already installed...
all files already exist and are up to date.
clear
shp2dta using "boundaries.shp", database(provinces) coordinates(zacoordinates) genid(id) replacetype: 5use provinces, clear
describeContains data from provinces.dta
Observations: 62
Variables: 11 8 Mar 2025 09:56
-------------------------------------------------------------------------------
Variable Storage Display Value
name type format label Variable label
-------------------------------------------------------------------------------
area_level byte %10.0g area_level
area_lev_1 str8 %9s area_lev_1
area_id str10 %10s area_id
area_name str25 %25s area_name
parent_are str9 %9s parent_are
spectrum_r byte %10.0g spectrum_r
area_sort_ byte %10.0g area_sort_
center_x double %10.0g center_x
center_y double %10.0g center_y
name str10 %10s name
id byte %12.0g
-------------------------------------------------------------------------------
Sorted by: idimport delimited "spectrum_calibration", clear
save "spectrum.dta", replace(encoding automatically selected: ISO-8859-1)
(15 vars, 1,836 obs)
file spectrum.dta saveduse Spectrum, clear
describeContains data from Spectrum.dta
Observations: 1,836
Variables: 15 8 Mar 2025 09:56
-------------------------------------------------------------------------------
Variable Storage Display Value
name type format label Variable label
-------------------------------------------------------------------------------
spectrum_reg~de byte %8.0g
spectrum_reg~me str13 %13s
sex str6 %9s
age_group str8 %9s
calendar_quar~r str8 %9s
population_sp~m float %9.0g
plhiv_spectrum float %9.0g
art_current_s~m float %9.0g
infections_sp~m float %9.0g
unaware_spect~m float %9.0g
births_hivpop~m float %9.0g
births_artpop~m float %9.0g
time_step str8 %9s
population_raw float %9.0g
population_ca~d float %9.0g
-------------------------------------------------------------------------------
Sorted by:
use Spectrum, clear
rename spectrum_reg~me area_name
save Spectrum1, replacefile Spectrum1.dta saveduse provinces, clear
duplicates drop area_name, force
save ProvD.dta, replaceDuplicates in terms of area_name
(0 observations are duplicates)
file ProvD.dta saveduse Spectrum1, clear
duplicates drop area_name, force
save SpectrumD.dta, replaceDuplicates in terms of area_name
(1,827 observations deleted)
file SpectrumD.dta saved
use provinces, clear
merge 1:1 area_name using "SpectrumD.dta"
save map1.dta, replace Result Number of obs
-----------------------------------------
Not matched 53
from master 53 (_merge==1)
from using 0 (_merge==2)
Matched 9 (_merge==3)
-----------------------------------------
file map1.dta saved
use map1, clear
describeContains data from map1.dta
Observations: 62
Variables: 26 8 Mar 2025 09:56
-------------------------------------------------------------------------------
Variable Storage Display Value
name type format label Variable label
-------------------------------------------------------------------------------
area_level byte %10.0g area_level
area_lev_1 str8 %9s area_lev_1
area_id str10 %10s area_id
area_name str25 %25s area_name
parent_are str9 %9s parent_are
spectrum_r byte %10.0g spectrum_r
area_sort_ byte %10.0g area_sort_
center_x double %10.0g center_x
center_y double %10.0g center_y
name str10 %10s name
id byte %12.0g
spectrum_regi~e byte %8.0g
sex str6 %9s
age_group str8 %9s
calendar_quar~r str8 %9s
population_sp~m float %9.0g
plhiv_spectrum float %9.0g
art_current_s~m float %9.0g
infections_sp~m float %9.0g
unaware_spect~m float %9.0g
births_hivpop~m float %9.0g
births_artpop~m float %9.0g
time_step str8 %9s
population_raw float %9.0g
population_ca~d float %9.0g
_merge byte %23.0g _merge Matching result from merge
-------------------------------------------------------------------------------
Sorted by: area_nameuse map1, clear
spmap art_current_s~m using zacoordinates, id(id) fcolor(Greens) clnumber(6)
graph export "map2.png", as(png) replacefile map2.png saved as PNG formatknitr::include_graphics("map2.png")
use map1, clear
spmap plhiv_spectrum using zacoordinates, id(id) fcolor(Blues2) clnumber(6)
graph export "map3.png", as(png) replacefile map3.png saved as PNG formatknitr::include_graphics("map3.png")
use map1, clear
spmap population_sp~m using zacoordinates, id(id) fcolor(Reds) clnumber(6)
graph export "map4.png", as(png) replacefile map4.png saved as PNG formatknitr::include_graphics("map4.png")
use map1, clear
spmap spectrum_r using zacoordinates, id(id) fcolor(Spectral) clnumber(6)
graph export "map5.png", as(png) replacefile map5.png saved as PNG formatknitr::include_graphics("map5.png")