09-01-2015
SMATT1
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Subject Views Posted 2569 05-29-2012 01:12 PM 2569 05-29-2012 12:49 PM 2569 05-29-2012 11:13 AM 3052 05-28-2012 04:43 PM 8800 03-31-2012 02:05 PM 3300 03-20-2012 11:38 AM 3300 03-20-2012 10:11 AM 3300 03-20-2012 09:46 AM 3393 03-19-2012 07:02 PM 4210 03-15-2012 04:39 PM -
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- Got a Like for PROC GLIMMIX NEGBIN RCBD- question regarding presentation of results. 05-29-2014 12:15 PM
- Posted Re: PROC GLIMMIX NEGBIN RCBD- question regarding presentation of results on Statistical Procedures. 05-29-2012 01:12 PM
- Posted Re: PROC GLIMMIX NEGBIN RCBD- question regarding presentation of results on Statistical Procedures. 05-29-2012 12:49 PM
- Posted Re: PROC GLIMMIX NEGBIN RCBD- question regarding presentation of results on Statistical Procedures. 05-29-2012 11:13 AM
- Posted PROC GLIMMIX NEGBIN RCBD- question regarding presentation of results on Statistical Procedures. 05-28-2012 04:43 PM
- Posted GLIMMIX negative binomial distribution question on Statistical Procedures. 03-31-2012 02:05 PM
- Posted PROC GLIMMIX POISSON RCBD question regarding parameters and best fit statistics on Statistical Procedures. 03-20-2012 11:38 AM
- Posted PROC GLIMMIX POISSON RCBD question regarding parameters and best fit statistics on Statistical Procedures. 03-20-2012 10:11 AM
- Posted PROC GLIMMIX POISSON RCBD question regarding parameters and best fit statistics on Statistical Procedures. 03-20-2012 09:46 AM
- Posted PROC GLIMMIX POISSON RCBD question regarding parameters and best fit statistics on Statistical Procedures. 03-19-2012 07:02 PM
- Posted PROC GLIMMIX POISSON RCBD question regarding parameters and best fit statistics on Statistical Procedures. 03-15-2012 04:39 PM
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Subject Likes Posted 1 05-28-2012 04:43 PM
05-29-2012
01:12 PM
This is all very interesting. Although I have taken two semesters of graduate level statistics the emphasis seems to have been placed entirely on assumptions of normality and wrestling your data via transformations to fit that distribution. My professor never enthusiastically supported transformations for achieving normality but couldn't necessarily equip us with the tools to launch us into this non-parametric world. This is all very new and I really appreciate the feedback... Thanks, Serena
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05-29-2012
12:49 PM
Yes! I understand... Thank you, Serena
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05-29-2012
11:13 AM
Thank you for these helpful comments Steve, When calculating means and SE's of the original data, I am not transforming and then back transforming. Though these values are provided by the ILINK statement I hesitated using them b/c they were quite different from the means and SE's calculated from my raw data. To make sure I understand: You think it is better to present the means and SE's generated by the analysis rather than parameters calculated from raw data and even transformed, then back-transformed data. Intuitively this is hard to grasp b/c rather than saying I sampled an overall average of 2 insects per m^2 on each blank wall and 25 on each green wall, I am saying I sampled an average of -1.45 and 1.92. I think I understand though, because the non- normal distribution of my data means that calcs of mean and SE are not truly showing the mean and SE of my data. But I still don't see why the back transformed parameters would make any sense to present either. These seem doubly distant, they are neither parameters generated by the analysis nor parameters of the original data... Thank you again for this advice! Serena
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05-28-2012
04:43 PM
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Hello all, With the help of SAS for Mixed Models, I am still slowly learning to interpret results generated by PROC GLIMMIX for a simple RCBD. I am trying to figure out how to correctly present my results. I am not sure whether I should be presenting transformed or original parameters. Because my data consists of counts my rationale for using PROC GLIMMIX was that it would allow me to specify a non-normal distribution and interpret, discuss and present parameters for untransformed data but now I am not so sure. Background: RCBD, 1 treatment, 2 levels (vegetated walls and un-vegetated walls). 10 green walls, 10 blank walls (equivalent to 20 observational units). Vacuum sampled insects from within 10 quadrats (subsamples) on each green wall and 3 on each blank wall. Testing if green walls have significantly higher number of insects than blank walls during three separate months of sampling. I am using the p-value presented in the Type III Test of Fixed Effects to determine whether the difference between the means of insects present in the two treatments was significant. It was, with p<0.0001 Traditionally, to present my results I would create a bar graph showing the means of the treatments, their standard errors, and letters indicating significant differences between the two means. I am not sure if this is appropriate anymore. What I think I should be presenting is the significant difference between the means of log transformed predicted values generated by a model based on my original data. Should I then be showing these means instead? If so, I assume I would use the values under the Estimates column generated by the LSMEANS statement. But do these values have “real world” meaning? I realize that I could use ILINK statement to back transform but these values are still quite different from means calculated from my original data. In a nutshell I am wondering if it is appropriate to present the means and standard errors of my original data although the significant differences detected are based on these transformed expected parameters… I hope this question makes sense. Thank you for any thoughts or suggestions. Sincerely, Serena Code below is for sampling in August: data abundancevisit3withsub; input blk trt$ subsample y; lines; 1 g 1 1 1 g 2 4 1 g 3 5 1 g 4 4 1 g 5 0 1 g 6 14 1 g 7 3 1 g 8 7 1 g 9 2 1 g 10 4 1 b 11 0 1 b 12 0 1 b 13 0 2 g 1 9 2 g 2 8 2 g 3 4 2 g 4 5 2 g 5 3 2 g 6 9 2 g 7 5 2 g 8 6 2 g 9 2 2 g 10 1 2 b 11 1 2 b 12 0 2 b 13 0 3 g 1 2 3 g 2 0 3 g 3 1 3 g 4 0 3 g 5 0 3 g 6 1 3 g 7 0 3 g 8 0 3 g 9 0 3 g 10 2 3 b 11 0 3 b 12 0 3 b 13 0 4 g 1 5 4 g 2 0 4 g 3 2 4 g 4 2 4 g 5 0 4 g 6 4 4 g 7 4 4 g 8 3 4 g 9 5 4 g 10 14 4 b 11 1 4 b 12 . 4 b 13 0 5 g 1 62 5 g 2 16 5 g 3 28 5 g 4 30 5 g 5 63 5 g 6 57 5 g 7 61 5 g 8 45 5 g 9 36 5 g 10 24 5 b 11 0 5 b 12 1 5 b 13 2 6 g 1 4 6 g 2 18 6 g 3 7 6 g 4 8 6 g 5 10 6 g 6 18 6 g 7 15 6 g 8 18 6 g 9 4 6 g 10 10 6 b 11 0 6 b 12 0 6 b 13 0 7 g 1 19 7 g 2 43 7 g 3 24 7 g 4 34 7 g 5 11 7 g 6 20 7 g 7 38 7 g 8 85 7 g 9 47 7 g 10 85 7 b 11 1 7 b 12 0 7 b 13 0 8 g 1 3 8 g 2 3 8 g 3 3 8 g 4 4 8 g 5 5 8 g 6 6 8 g 7 11 8 g 8 7 8 g 9 5 8 g 10 2 8 b 11 1 8 b 12 0 8 b 13 0 9 g 1 1 9 g 2 0 9 g 3 1 9 g 4 2 9 g 5 15 9 g 6 3 9 g 7 3 9 g 8 3 9 g 9 4 9 g 10 4 9 b 11 1 9 b 12 1 9 b 13 1 10 g 1 9 10 g 2 2 10 g 3 6 10 g 4 6 10 g 5 5 10 g 6 13 10 g 7 18 10 g 8 8 10 g 9 5 10 g 10 16 10 b 11 0 10 b 12 0 10 b 13 0; proc print data=abundancevisit3withsub; run; proc glimmix data=abundancevisit3withsub method=quad; class trt blk subsample; model y = trt / solution dist=negbin link=log; random int trt / sub=blk; lsmeans trt/ilink; ods select LSMeans Estimates; run;
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03-31-2012
02:05 PM
Hello all, This posting is a follow-up question to a previous posting regarding using PROC GLIMMIX for a simple RCBD. Study Background: I vacuum sampled insects off of 10 wallscovered in vines and 10 adjacent blank walls during three separate months last summer. At each site 10 subsamples were taken. Study mimics an RBCD. Single treatment factor has 2 levels-green and not green. Each site is treated as a block containing both a blank and a green wall and each site contains 10 0.75 m^2 subsamples. Insect abundance data from the walls follow a non normal distribution and lack equality of variance. Thus the PROC GLIMMIX. Based on helpful suggestions from IVM and PGSTATS I included subsamples in my model and did not normalize my data by subsample size. This resulted in data which contained many zeros for blank walls and many higher numbers for green walls. Although I originally was using a Poisson distribution, by including my raw data and my subsamples my Pierson Chi Square/DF became very high (example 9.1). I tried using a negative binomial distribution and obtained a much better fit statistic (1.15). I basically wanted to make sure my code is correct and wanted to see if people had any comments on the use of negative binomial distribution for this kind of data. An example for one month’s sampling is below data abundancevisit1withsub; input blk trt$ subsample y; lines; 1 g 1 4 1 g 2 2 1 g 3 1 1 g 4 7 1 g 5 2 1 g 6 3 1 g 7 . 1 g 8 7 1 g 9 5 1 g 10 10 1 b 11 0 1 b 12 0 1 b 13 0 2 g 1 6 2 g 2 3 2 g 3 7 2 g 4 5 2 g 5 17 2 g 6 14 2 g 7 7 2 g 8 4 2 g 9 4 2 g 10 . 2 b 11 0 2 b 12 0 2 b 13 0 3 g 1 0 3 g 2 2 3 g 3 0 3 g 4 3 3 g 5 2 3 g 6 3 3 g 7 0 3 g 8 0 3 g 9 0 3 g 10 0 3 b 11 0 3 b 12 0 3 b 13 0 4 g 1 1 4 g 2 6 4 g 3 7 4 g 4 9 4 g 5 6 4 g 6 3 4 g 7 5 4 g 8 1 4 g 9 6 4 g 10 11 4 b 11 0 4 b 11 1 4 b 11 0 5 g 1 110 5 g 2 157 5 g 3 106 5 g 4 58 5 g 5 183 5 g 6 64 5 g 7 5 5 g 8 46 5 g 9 25 5 g 10 23 5 b 11 0 5 b 12 2 5 b 13 4 6 g 1 12 6 g 2 12 6 g 3 5 6 g 4 4 6 g 5 3 6 g 6 29 6 g 7 3 6 g 8 18 6 g 9 3 6 g 10 52 6 b 11 0 6 b 12 2 6 b 13 0 7 g 1 . 7 g 2 25 7 g 3 . 7 g 4 39 7 g 5 26 7 g 6 28 7 g 7 47 7 g 8 58 7 g 9 20 7 g 10 . 7 b 11 1 7 b 12 1 7 b 13 1 8 g 1 58 8 g 2 2 8 g 3 1 8 g 4 2 8 g 5 3 8 g 6 3 8 g 7 4 8 g 8 3 8 g 9 2 8 g 10 1 8 b 11 0 8 b 12 0 8 b 13 0 9 g 1 6 9 g 2 10 9 g 3 16 9 g 4 20 9 g 5 14 9 g 6 15 9 g 7 22 9 g 8 10 9 g 9 13 9 g 10 14 9 b 11 0 9 b 12 0 9 b 13 0 10 g 1 11 10 g 2 4 10 g 3 8 10 g 4 14 10 g 5 17 10 g 6 27 10 g 7 36 10 g 8 34 10 g 9 32 10 g 10 34 10 b 11 0 10 b 12 2 10 b 13 2; proc print data=abundancevisit1withsub; run; proc glimmix data=abundancevisit1withsub method=quad; class trt blk subsample; model y = trt / dist=negbinomial link=log; random int trt / sub=blk; lsmeans trt / cl ilink; run;
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03-20-2012
11:38 AM
Last questions on this topic-I promise! If I include subsamples does it matter that I have unequal replication of subsamples for the two different treatments? Blank walls did not require as many quadrats as vegetated thus there were 3 on the blank and 10 on the vegetated...(although I still had equal replication of experiemntal units). I am not sure if this would require modifications to the code at all. And, IVM mentioned that Pearson Chi/DF less than 1 shows adequate fit of poisson- is there a lower limit of some sort? I wasn't sure if lack of fit was shown by departures from 1 or actually being greater than 1. Data from my second sampling visit yeilds a value of 0.17-not sure if this is too low. Serena
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03-20-2012
10:11 AM
Thanks again
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03-20-2012
09:46 AM
But if my experimental unit is a wall, then the 10 quadrat samples taken on the wall are just subsamples of the EU and must be averaged...right? Otherwise aren't I introducing some sort of false replication? Thanks again, S
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03-19-2012
07:02 PM
Thank you for these helpful comments!! IVM: In summary Iwant to make sure I understand. “Modeling the log(ExpectedCount) as a linearfunction of the treatment factor” means that based on my data, glimmix generatesexpected values on a log scale. It thenuses these to determine if the treatment significantly explains differences in expectedOR actual counts OR both? I guess I did not realize that GLIMMIXgenerates expected data. PG STATS: data containsdecimals because data was normalized by sample size. Ten 0.75m^2 quadrats were sampled at eachwall (10 subsamples). I divided theaverage abundance of insects per quadrat by 0.75m^2 to obtain average per m^2. From my understanding it seems like the 0.75m^2 value falls within that up to count=5y limit you discussed? I am a little hesitant to include the offsetmainly b/c I am not totally clear on what that is doing. If I use the non-normalized data why includearea at all? I am guessing the offsetsomehow normalizes for sample area within the model. Area is log’d b/c expected counts arepresented in log scale. Or something! Thank you all, so informativeand helpful!
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03-15-2012
04:39 PM
Hello all, I am an environmental science graduate student attempting to use PROC GLIMMIX per the suggestion of my statistics professor. I have a few general questions about using this model due to my pretty underdeveloped stats understanding. Study Background: I vacuum sampled insects off of 10 walls covered in vines and 10 adjacent blank walls during three separate months last summer. Study mimics an RBCD. Single treatment factor has 2 levels-green and not green. Each site is treated as a block containing both a blank and a green wall. Insect abundance data from the walls follow a non normal distribution and lack equality of variance. I could solve this with a simple log transformation but was hoping to avoid losing the ability to discuss my original values. Thus the PROC GLIMMIX. An example of my code is shown below involving data from one month of sampling (repeated measures were not used in this study). dataabundancevisit3; inputblk trt$ y; lines; 1g 5.867 1b 0 2g 6.933 2b 0.444 3g 0.8 3b 0 4g 5.2 4b 0.667 5g 56.267 5b 1.333 6g 14.933 6b 0 7g 54.133 7b 0.444 8g 5.026 8b 0 9g 4.8 9b 1.333 10g 11.733 10b 0 ; optionsnocenter; procprint data=abundancevisit3; run; procglimmix data=abundancevisit3; classtrt blk; modely=trt/dist=poisson link=log; randomblk; lsmeanstrt/cl ilink; run; Questions From output it looks as though my data, or at least my parameters, are being transformed. Does this limit my ability to talk about my original dataset? Or is my data left untransformed and only the parameters transformed? Can I use backtransformed means when discussing results though it is not the same as my original data means? I guess I just want a simplistic idea of what SAS is doing to my data vs parameters. What is being transformed exactly? My other question involves assessment of the POISSON model fit. I have seen some codes using the pearson chi square/DF to determine whether their poisson distribution is over dispersed but my output only contains gen chai square/DF. I gather I could change this by inserting a MODEL= statement but have no real idea of what I would put there…any tips on what I need to examine to make sure this model is an OK fit for the analysis? Thank you so much in advance for any tips!!! Serena
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