Test for incidence-rate trend in Stata

[Abdullah Algarni]

Dear colleagues
I am using Stata 17.0 MB and working on a dataset of Enterococci bacteria infections in the previous ten years (2012–2021). These bacteria have more dangerous subtypes resistant to one antibiotic (vancomycin; hence called VRE).

I want to test whether there is a significant trend in the incidence rate of these subtypes over the previous ten years.

What is the appropriate statistical test I have to use to check whether the noted increase in the incidence rate is statistically significant in stata?

My dataset and variables are illustrated below. Thank you in advance

. describe vre year

Variable      Storage   Display    Value
    name         type    format    label      Variable label
------------------------------------------------------------------------------------------------------------------------------------
vre             byte    %9.1f      YesNo      Vancomycin-resistant Enterococci?
year            byte    %ty        Year       Year of culture

. tab vre year, column nokey

Vancomycin |
-resistant |
Enterococc |                                                Year of culture
        i? |      2012       2013       2014       2015       2016       2017       2018       2019       2020       2021 |     Total
-----------+--------------------------------------------------------------------------------------------------------------+----------
        No |        42        129        101        108        155        178        179        281        203        293 |     1,669 
           |     80.77      90.85      93.52      91.53      94.51      91.75      87.75      88.36      85.29      86.43 |     88.92 
-----------+--------------------------------------------------------------------------------------------------------------+----------
       Yes |        10         13          7         10          9         16         25         37         35         46 |       208 
           |     19.23       9.15       6.48       8.47       5.49       8.25      12.25      11.64      14.71      13.57 |     11.08 
-----------+--------------------------------------------------------------------------------------------------------------+----------
     Total |        52        142        108        118        164        194        204        318        238        339 |     1,877 
           |    100.00     100.00     100.00     100.00     100.00     100.00     100.00     100.00     100.00     100.00 |    100.00

[Nick Cox]

Cross-posted at https://www.reddit.com/r/stata/comme...rend_in_stata/

https://stats.stackexchange.com/ques...trend-in-stata

[Clyde Schechter]

-help nptrend- may give you a start. Or perhaps -logit vre c.Year-.

That said, just eyeballing your tabulation, while it is only based on 10 vre responses, the data from 2012 seem unlikely if there is a simple trend in play over this time period. So I would suggest also analyzing the data with year 2012 excluded and reporting the results both ways (even if they reach different conclusions).

[Rich Goldstein]

have you looked at the following FAQ: https://www.stata.com/support/faqs/s...end/index.html

added: your original post is not very clear but you might also want to think about poisson regression in addition to the techniques in the FAQ

[Abdullah Algarni]

Cross-posted at https://www.reddit.com/r/stata/comme...rend_in_stata/

https://stats.stackexchange.com/ques...trend-in-stata

Thanks Dr. Cox
I'm not sure if cross-posting violates rules of StataList, if so, I'm so sorry

[Abdullah Algarni]

-help nptrend- may give you a start. Or perhaps -logit vre c.Year-.

That said, just eyeballing your tabulation, while it is only based on 10 vre responses, the data from 2012 seem unlikely if there is a simple trend in play over this time period. So I would suggest also analyzing the data with year 2012 excluded and reporting the results both ways (even if they reach different conclusions).

Thank you,
I am totally agree regarding 2012 data (clearly outlier)
I will double check nptrend and make sure my data fit well with these tests assumptions

[Abdullah Algarni]

have you looked at the following FAQ: https://www.stata.com/support/faqs/s...end/index.html

added: your original post is not very clear but you might also want to think about poisson regression in addition to the techniques in the FAQ

Thank you,
I got two idea from reddit and Cross-Valid
reddit:
https://www.reddit.com/r/stata/comme...m_source=share

Cross-Validated
In each year there is a given number of Enterococcae nallE of which the nVRE is a part and what you call incidence rate is nVRE/nallE. This could be modelled as the probability p in a Binomial process. Use a binomial GLM with the probability p being linearity dependent on the number of the year.

[Nick Cox]

#5

https://www.statalist.org/forums/help#crossposting explains our policy about cross-posting (and is in a document that every new message prompt asks you to read). Telling us about cross-posting is requested, but it is not called a rule.

r/stata on Reddit cites "Notify others of cross-posts (x-posts) and updates" as a rule. It is there out front with their other rules (a short list).

I am active on Cross Validated but am not aware of explicit policy on cross-posting outside Stack Exchange.

Regardless of what is stated as a rule or a request, the logic and etiquette seem simple to me:

If other people are interested in your question, they should want to see an answer even if it is posted elsewhere.

If other people want to answer, they should want to know about other answers, especially if an answer as good as or better than what they have to say has already been said. I've often found I wasted my time posting something already said elsewhere.

Scanning all other possible forums really doesn't appeal to many people -- even I won't be systematic about keeping an eye on more than about three places that might include Stata questions -- and in any case it's the poster's responsibility to be informative. You are asking people to give you some of their time and to share their expertise. so some courtesy does no harm.

I have seen an opinion that posting on say Y and Z as well as X is offensive to people in any of those forums, as implying that you don't trust people to come up with a good answer or that you don't care about people wasting time and effort. I wouldn't call this behaviour offensive at all -- almost always it's just a little thoughtless -- but beware that the attitude exists.

[Nick Cox]

FWIW: the plural of Enterococcus is surely Enterococci, not Enterococcae.

[Abdullah Algarni]

#5

https://www.statalist.org/forums/help#crossposting explains our policy about cross-posting (and is in a document that every new message prompt asks you to read). Telling us about cross-posting is requested, but it is not called a rule.

r/stata on Reddit cites "Notify others of cross-posts (x-posts) and updates" as a rule. It is there out front with their other rules (a short list).

I am active on Cross Validated but am not aware of explicit policy on cross-posting outside Stack Exchange.

Regardless of what is stated as a rule or a request, the logic and etiquette seem simple to me:

If other people are interested in your question, they should want to see an answer even if it is posted elsewhere.

If other people want to answer, they should want to know about other answers, especially if an answer as good as or better than what they have to say has already been said. I've often found I wasted my time posting something already said elsewhere.

Scanning all other possible forums really doesn't appeal to many people -- even I won't be systematic about keeping an eye on more than about three places that might include Stata questions -- and in any case it's the poster's responsibility to be informative. You are asking people to give you some of their time and to share their expertise. so some courtesy does no harm.

I have seen an opinion that posting on say Y and Z as well as X is offensive to people in any of those forums, as implying that you don't trust people to come up with a good answer or that you don't care about people wasting time and effort. I wouldn't call this behaviour offensive at all -- almost always it's just a little thoughtless -- but beware that the attitude exists.

Thanks Dr. Cox I'm 100% agree with you, I would apologize of what happened. I do trust our colleagues here and in other forums.

Again, we're on same page, will not cross-posting again.
again.💐