Home » Topics » Child Health » Rotav Vaccine and nutrition
| Rotav Vaccine and nutrition [message #27423] |
Thu, 10 August 2023 22:01  |
backclac
Messages: 25
Registered: August 2023
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Member |
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I am new here. I am not sure of which DHS file to use(I guess the PR is appropriate) for these variables and the corresponding recode:
Categorical covariates:
1. Sex (male or female)
2. BCG vaccination (yes or no)
3. Exclusively Breastfed (yes or no)
4. Pneumococcal vaccination (none, incomplete, complete)
5. Rotavirus vaccination
6. Diarrhea
7. Any insurance coverage (yes or no)
8. Education level of the mother (none or primary, high school, college or university)
9. Source of drinking water (piped, well or surface, bottled, other)
10. Type of toilet facility (flush toilet, latrine, without installation)
11. Wealth index (very low, low, medium, high, very high)
12. Treating water for drinking (yes or no)
Quantitative covariates:
1. Altitude (m above sea level)
2. Child age (months)
3. Birth weight (grams)
4. Number of residents in the household
5. Children's Height, Weight, Z-score
Please are these codes from pr file right for the variables above?
Variables: Description
V106: The highest level of education the household member attended.
HV205: Type of toilet facility in the household. Individual codes are country-specific, but the major categories are standard.
HV230B: Presence of water at hand washing place
HV235: Location of source for water
HV238A: Location of toilet facility
HV270: Wealth Index Variables
HA67:: Woman's highest year of education (see HV107)
HC1A: Child's age in days, calculated as HV807A HC32A.
HC2: Weight in kilograms (1 dec.)
HC3: Height in centimeters (1 dec.)
HC5: Height/Age Standard deviations
HC8: Weight/Age Standard deviations
HC11: Weight/Height Standard deviations
HC70: Height for age standard deviation (according to WHO)
HC71: Weight for age standard deviation (according to WHO)
HC72: Weight for height standard deviations (according to WHO)
HC70: Height for age standard deviation (according to WHO)
V418: Number of entries in the immunization history
H2: Whether a date of vaccination was recorded on the health card for BCG
H2D: BCG vaccination date - day.
H9A: Measles 2 vaccination. As for H2, H2D, H2M, H2Y
H56: Pneumococcal 3
H59: Rotavirus 3
M34: The first digit gives the units in which the respondent gave her answer.
M38: Whether the child drank anything from a bottle with a nipple during the previous day and night.
M39: The number of times the children received anything to eat, aside from breast milk, including both meals and snacks. Children who are exclusively breastfed are coded 0.BASE: Youngest children under 24 (36) months living with their mother.
Please I couldn't find these
??: Sex (male or female)
??: Diarrhea
??: Altitude (above sea level)
Thank you
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| Re: Rotav Vaccine and nutrition [message #27441 is a reply to message #27423] |
Tue, 15 August 2023 06:03  |
backclac
Messages: 25
Registered: August 2023
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Member |
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Hello,
Please help merge the pr file from Sub-Saharan African Countries(38 countries)
I get error message whenever I do this:
...r
> sa4<-merge(gh,ug,by=c("hv001","hv002"),all.x=TRUE, all.y=TRUE)
> sa5<-merge(sa4,sz,by=c("hv001","hv002"),all.x=TRUE, all.y=TRUE)
> sa6<-merge(sa5,td,by=c("hv001","hv002"),all.x=TRUE, all.y=TRUE)
Error: cannot allocate vector of size 16.4 Mb
...r
kindly help me
Thank you
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| Re: Rotav Vaccine and nutrition [message #27538 is a reply to message #27505] |
Thu, 31 August 2023 08:07 |
backclac
Messages: 25
Registered: August 2023
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Member |
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Thank you
I can't access the API indicator today (31st August 2023, 20:01 China time). There is an error message when using the code I have been using to access the indicators for countries.
```{r}
json_file<- fromJSON(" http://api.dhsprogram.com/rest/dhs/v8/data?countryIds=AO,BF, BJ,BU,CD,CF,CG,CI,CM,ET,GA,GH,GM,GN,KE,KM,LB,LS,MD,ML,MR,MW, MZ,NG,NI,NM,RW,SL,SN,ST,SZ,TD,TG,TZ,UG,ZA,ZM&indicatorId s=CN_NUTS_C_HA3")
Error in fromJSON(content, handler, default.size, depth, allowComments, :
invalid JSON input
```
Kindly advise me. Thank you
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| Re: Rotav Vaccine and nutrition [message #27541 is a reply to message #27538] |
Thu, 31 August 2023 10:57 |
admin
Messages: 50
Registered: November 2012
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Senior Member
Administrator |
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The JSON from your API request appears fine to us. Please check it again.
You can validate it here.
https://jsonlint.com/
Also the recommended format is this:
https://api.dhsprogram.com/rest/dhs/data?countryIds=AO,BF,BJ ,BU,CD,CF,CG,CI,CM,ET,GA,GH,GM,GN,KE,KM,LB,LS,MD,ML,MR,MW,MZ ,NG,NI,NM,RW,SL,SN,ST,SZ,TD,TG,TZ,UG,ZA,ZM&indicatorIds= CN_NUTS_C_HA3
We now have repositories of code written in Stata and SPSS available on Github. Please reference these code repositories as a resource for code for matching or calculating DHS indicators. The code repositories can be found at:
https://github.com/DHSProgram/DHS-Indicators-Stata
https://github.com/DHSProgram/DHS-Indicators-SPSS
[Updated on: Thu, 31 August 2023 11:00] Report message to a moderator |
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| Re: Rotav Vaccine and nutrition [message #27558 is a reply to message #27557] |
Sun, 03 September 2023 21:48 |
backclac
Messages: 25
Registered: August 2023
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Member |
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Hello Prof,
I have been able to extract the indicators needed for my project from the API using the following r syntax;
```{r}
#library
> library(devtools)
> library(usethis)
> library(rdhs)
> library(RJSONIO)
> library(tidyverse)
#example
#No education ED_EDUC_W_NED
> json_file<- fromJSON(" https://api.dhsprogram.com/rest/dhs/data?countryIds=AO,BF,BJ ,BU,CD,CF,CG,CI,CM,ET,GA,GH,GM,GN,KE,KM,LB,LS,MD,ML,MR,MW,MZ ,NG,NI,NM,RW,SL,SN,ST,SZ,TD,TG,TZ,UG,ZA,ZM&indicatorIds= ED_EDUC_W_NED")
> json_data1<- lapply(json_file$Data, function(x){unlist(x)})
> APIdata23<-as.data.frame(do.call("rbind",json_data1),stringsAsFactors = FALSE)
> xtabs(as.numeric(Value)~SurveyId,data=APIdata23)
#Selecting specific variables
xt1<-APIdata23 %>%
select(CountryName,SurveyYearLabel,Survey,Value, DenominatorWeighted)
View(xt1)
```
#I then selected and copied the viewed table to Excel
#I then calculate the number of population (N) as
N =(Value/100)*DenominatorWeighted
# I will then import the Excel file into r for complex analysis but I want to be sure if I am on track.
I have also realized that the indicator code CH_DIAT_C_ORZ has some different values for the same survey year due to a change in DenominatorWeighted.
I guess it is appropriate to use the values with the highest DenominatorWeighted
Kindly advice me
Thank you
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| Re: Rotav Vaccine and nutrition [message #27648 is a reply to message #27595] |
Wed, 13 September 2023 15:58 |
backclac
Messages: 25
Registered: August 2023
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Member |
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I have replicated your CH_VAC.R file in the GitHub ( https://github.com/DHSProgram/DHS-Indicators-R/blob/main/Cha p10_CH/CH_VAC.R), which is helpful for my research project.
However, I need your advice on the following;
1. I noticed that Angola's KR file does not have the variable "KRdata$h54" for Pneumococcal vaccines but rather h2d, h2m and h2y.
These codes are the same for the Pneumococcal vaccination 1,2,& 3.
Apparently I used h2 for PCV1, h2y for both PVC2 & PVC3
Please is this right?
2. Does the "#Total" variable, created in the Excel sheet represent the coverage for each vaccine or do I have to calculate it?
Please how do I calculate it, if I am supposed to?
3. Is it appropriate to use the "KRhw" variables to calculate the stunt and wast indicators for each SSA country?
Please let me know how to proceed
4. I also have to calculate the following indicators; "Exclusive Breastfeeding", "wealth index" and educational level.
Please are there variables in the KR file that will help me calculate those indicators or do I have to use a different file?
5. I will do logistic regression, multivariate regression, Propensity and Forest. Is it appropriate to use the "#Total" variable in the Excel table to calculate these variables?
Please permit me, because I am trying to understand DHS data and R programming language.
Thank you
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| Re: Rotav Vaccine and nutrition [message #27664 is a reply to message #27648] |
Fri, 15 September 2023 17:36 |
Janet-DHS
Messages: 893
Registered: April 2022
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Senior Member |
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Following is a response from DHS staff member, Tom Pullum:
You have asked a number of very specific questions and I probably can't answer all of them, especially since I do not use R. However, I have problems understanding your basic approach. Why are you using Excel? I can understand exporting summary results into Excel because of its advantages for formatting and graphics, but Excel is not good for analysis. The methods you describe in step 5 are not available in Excel (so far as I know, anyway). For example, I just don't understand your questions about "#Total" in steps 2 and 5.
Stunting, underweight, and wasting are calculated using hc70-hc72 in the PR file or hw70-hw72 in the KR file. You will find the steps in previous forum posts and in the Guide to DHS Statistics. The estimates from the PR file refer to all children in the sample households and the estimates from the KR file refer to the children who are also in the birth histories of the women in the survey of women.
Exclusive breastfeeding is also a constructed variable, using code related to infant and young child feeding (IYCF) that is available on github. The wealth quintiles are coded in all the files--hv270 in the PR file and v190 in the IR and KR files.
Your goal of assembling lots of indicators for all SSA surveys is very ambitious. I suggest that you either (a) use the indicators as they exist in STATcompiler or the API, or (b) dramatically reduce the number of surveys or indicators that you want to include. When I suggested going to the KR files, I didn't realize that you planned to use so many indicators.
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| Re: Rotav Vaccine and nutrition [message #27865 is a reply to message #27862] |
Sat, 14 October 2023 06:25 |
backclac
Messages: 25
Registered: August 2023
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Member |
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Thank you for the response.
I thought my project should focus only on children under 5 years old who had diarrhoea but I understand you. It should be a Kind of "case" and "control" group.
By standardization or uniformity; I meant using the same target group that had diarrhoea for calculating my indicators. After determining those who had diarrhoea and those who did not.
However, I will use both populations in the calculation as advised.
I am just wondering about the effect of this indicator variable "ch_diar==1" in my syntax below, adopted from CH_DIA.R. on github.
My understanding is to generate only children who answered yes to "Diarrhea in the 2 weeks before the survey" and were exclusively breastfed or breastfeeding. This will be the same for estimating other indicators.
Please how do I submit the cross-tabulation generated from my R syntax for verification? I believe it will help me explain my confusion better.
Example
# //Diarrhea symptoms
```{r}
cgkr <- cgkr %>%
mutate(ch_diar =
case_when(
(h11==1 | h11==2) & b5==1 ~ 1,
b5==1 ~ 0 )) %>%
set_value_labels(ch_diar = c("Yes" = 1, "No"=0)) %>%
set_variable_labels(ch_diar = "Diarrhea in the 2 weeks before the survey")
```
#//# //Diarrhea treatment
```{r}
cgkr <- cgkr %>%
mutate(ch_diar_care =
case_when(
ch_diar==1 &
(h12a == 1 | h12b == 1 | h12c == 1 | h12d == 1 | h12e == 1 | h12f == 1 |
h12g == 1 | h12h == 1 | h12i == 1 | h12j == 1 | h12k == 1 | h12l == 1 |
h12m == 1 | h12n == 1 | h12o == 1 | h12p == 1 | h12q == 1 | h12r == 1 |
h12s == 1 | h12u == 1 | h12v == 1 | h12w == 1 | h12x == 1 ) ~ 1 ,
ch_diar==1 ~ 0)) %>%
set_value_labels(ch_diar_care = c("Yes" = 1, "No"=0)) %>%
set_variable_labels(ch_diar_care = "Advice or treatment sought for diarrhea")
```
## ch_diar==1 & nt_ebf: "Diarrhea in the 2 weeks before the survey" and were/are exclusively breastfed/ breastfeeding???
```{r}
cgkr <- cgkr %>%
mutate(nt_ebf =
case_when(ch_diar==1 &
age<6 & nt_bf_status==1 ~ 1 ,
age<6 & nt_bf_status!=1 ~ 0,ch_diar==1 ~ 0)) %>%
set_value_labels(nt_ebf = c("Yes" = 1, "No"=0 )) %>%
set_variable_labels(nt_ebf = "Exclusively breastfed - last-born under 6 months")
```
I am grateful for your guidance.
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| Re: Rotav Vaccine and nutrition [message #27885 is a reply to message #27441] |
Tue, 17 October 2023 08:50 |
psychebeyondpsychologist
Messages: 1
Registered: October 2023
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Member |
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| Re: Rotav Vaccine and nutrition [message #27889 is a reply to message #27865] |
Tue, 17 October 2023 12:30 |
Janet-DHS
Messages: 893
Registered: April 2022
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Senior Member |
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Following is a response from DHS staff member, Tom Pullum:
Sorry--I don't use R. Basically I recommend that you think in terms of variables rather than sub-populations. Children can be classified according to a nutrition variable (for example, with categories for exclusive breastfeeding, partial breastfeeding, not being breastfed at all) and diarrhea in the past two weeks (yes / no). You can cross-tabulate these two variables, or you can do a logit regression of the diarrhea variable on the nutrition variable, to see whether there is an association. You need to include controls for age, etc., which is much easier with a multivariate method such as regression than with tabulation. You should be able to find many examples of this type of analysis if you search the literature on child health and nutrition.
If you restrict your analysis to children who have diarrhea, then you can only describe that group, and can't get at how they differ from children who do not have diarrhea.
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| Re: Rotav Vaccine and nutrition [message #28418 is a reply to message #28386] |
Tue, 02 January 2024 12:07 |
Janet-DHS
Messages: 893
Registered: April 2022
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Senior Member |
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Following is a response from DHS staff member, Tom Pullum:
DHS estimates apply only to the date of data collection. We do not make projections, which require at least two surveys, and I would not even recommend interpolating between surveys. If someone else has used DHS data this way, you will have to contact them to find how they did it.
In 2022 I prepared a working paper on the topic of projecting with DHS surveys (https://www.dhsprogram.com/pubs/pdf/WP182/WP182.pdf). The goal was to be able to find whether results in a new DHS survey are consistent with what would have been expected from earlier surveys. However, my basic finding was that projections are too sensitive to the amount of historical data being used, and the inclusion of covariates and nonlinear terms, and must be treated very cautiously. That's why this was issued as a working paper rather than a methodological report.
[Updated on: Tue, 02 January 2024 12:09] Report message to a moderator |
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| Re: Rotav Vaccine and nutrition [message #28590 is a reply to message #27423] |
Fri, 02 February 2024 05:57 |
rohanzx67
Messages: 1
Registered: February 2024
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Member |
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I think its hard to know since rotavirus vaccine is given around the same time as symptoms start for some babies. In my case, I think it irritated an already irritable digestive system. My baby didn't eat well for a week after each dose. But the same was true of accidental dairy or soy exposure. What helped us was a much more aggressive reflux treatment, going dairy and soy free, and using periactin to increase appetite. We see a feeding team that includes a GI, dietician, an Speech Pathologist.9apps apk
[Updated on: Tue, 06 February 2024 06:22] Report message to a moderator |
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