topic Comparison in a logistic model at a specific level of dep variable in Statistical Procedures

Comparison in a logistic model at a specific level of dep variable

palolix — Wed, 14 May 2025 00:50:10 GMT

Dear SAS Community,

Looking at the this graph, I would like to know if the percentage of PeelColor 3 (red) is significantly different between the Variety BL516 and Hass for the Season 2021. PeelColor is the dep categorical variable (ordinal) with more than 2 levels.

If I am correct, with an lsmestimate statement I should be able to answer that, so this is the code I am using. However I would like to know how to specify the level of the dep var (PeelColor=3) for this comparison.

proc logistic data=one desc;
where Season=2021;
class Variety/param=glm;
model PeelColor= Variety/ link=clogit/*y is ordinal*/ ;
lsmeans Variety/diff;
lsmestimate Variety 'BL516 vs Hass' 0 0 0 0 0 1 0 0 0 0 -1/adjust=simulate(seed=1);
run;

I would greatly appreciate your help!

Thanks

Re: Comparison in a logistic model at a specific level of dep variable

StatDave — Wed, 14 May 2025 01:06:17 GMT

A logistic model for this is overkill. For what you want, you can just use PROC FREQ since you are only looking at data for 2021. Also, I would assume that PeelColor is a nominal response, not ordinal, unless you are really interested in the color frequency. Effectively, you just have data for a 2x2 table with Variety as the rows and PeelColor (red vs anything else) as the columns. So, create a ColorRed variable which is 1 for Red and 0 otherwise and the use PROC FREQ:

proc freq; 
where season=2021;
table variety*colorred/chisq;
run;

This tests whether the proportions of ColorRed in the two varieties are equal.

Re: Comparison in a logistic model at a specific level of dep variable

Ksharp — Wed, 14 May 2025 02:06:29 GMT

As StatDave said, no need PROC LOGISTIC.
PROC FREQ + riskdiff option OR relrisk option is more than suffice.

https://support.sas.com/kb/23/003.html
https://support.sas.com/kb/57/798.html

Re: Comparison in a logistic model at a specific level of dep variable

palolix — Wed, 14 May 2025 15:47:35 GMT

Thank you so much for your reply StatDave, that makes sense.

I will then apply these steps for every level of the dep var PeelColor I'm interested in, in order to get a 2x2 table:

data one1; set one;
if PeelColor=3 then ColorRed=1;
else ColorRed=0;
run;

proc freq data=one1;
where Season=2021 and Variety in('BL516', 'Hass');
table Variety*colorRed/chisq riskdiff;
run;

Re: Comparison in a logistic model at a specific level of dep variable

palolix — Wed, 14 May 2025 15:48:42 GMT

Thank you very much Ksharp for this useful option!

Re: Comparison in a logistic model at a specific level of dep variable

palolix — Wed, 14 May 2025 19:21:23 GMT

I have a question; Is the two-sided Pearson chi-square test in the Fisher's Exact Test Table the one that will tell me if the proportions for ColorRed (1) are significantly different between the two Varieties?

BL516

224

37.27

74.42

44.01

12.81

25.58

83.70

301

50.08

Hass

285

47.42

95.00

55.99

2.50

5.00

16.30

300

49.92

Total

509

84.69

15.31

601

100.00

Statistics for Table of Variety by Colorred

Statistic	DF	Value	Prob
Chi-Square	1	49.0915	<.0001
Likelihood Ratio Chi-Square	1	53.0439	<.0001
Continuity Adj. Chi-Square	1	47.5168	<.0001
Mantel-Haenszel Chi-Square	1	49.0098	<.0001
Phi Coefficient		-0.2858
Contingency Coefficient		0.2748
Cramer's V		-0.2858

Fisher's Exact Test
Cell (1,1) Frequency (F)	224
Left-sided Pr <= F	<.0001
Right-sided Pr >= F	1.0000

Table Probability (P)	<.0001
Two-sided Pr <= P	<.0001

Re: Comparison in a logistic model at a specific level of dep variable

SAS_Rob — Wed, 14 May 2025 19:38:21 GMT

Yes, the Pearson Chi-Square test will test the equality of the two proportions as detailed in this usage note.

22561 - Testing the equality of two or more proportions from independent samples

If you want an exact test, then you can report Fisher's exact test.

Re: Comparison in a logistic model at a specific level of dep variable

palolix — Wed, 14 May 2025 20:18:54 GMT

Thanks. So should I use the Fisher's exact test (two -sided Pr<=P) in case the cell counts are too small, but otherwise the Chi square test I get with the chisq option?

Re: Comparison in a logistic model at a specific level of dep variable

SAS_Rob — Wed, 14 May 2025 20:32:33 GMT

Yes, that is a reasonable approach.

Re: Comparison in a logistic model at a specific level of dep variable

palolix — Wed, 14 May 2025 22:23:21 GMT

Great, thanks!