"The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data."
John Tukey Cheers, Bert On Tue, Jan 31, 2023 at 7:44 AM Carolyn J Miller via R-help < r-help@r-project.org> wrote: > Hi Boris, > > It's hair cortisol so it shouldn't have an effect. My study species are > ungulates, which retain their coat through the winter into the spring > shedding out around April/May so in theory these two sampling periods > should provide the same results as hair cort provides an average of > accumulated cort levels released into the hair over that growth period > until they shed out. Of course the individuals that had hair collected in > March instead of December have had longer to incorporate more cort levels > into the hair collected in comparison to their conspecifics captured in > December. > > I had a repeated measures approach to this previously but due to missing > data from uneven captures the model gets angry since there's only 2 levels > of replication and many are not repeated at all. We're considering dividing > up the dataset by season to eliminate the need for repeated measures. I've > had it suggested that we should use the single measure of cort (which is > what most individuals have) in both rows (March and December) based on this > logic, and then just run the models as separate seasons. > > I ran the t-test between the march and december cort samples and they are > not representing the same information. > > The joys of data analysis! > > Thanks for your feedback, > > Carolyn J. Miller > M.S. Student, Ecology > SUNY-ESF, Environmental Biology > > > ________________________________ > From: Boris Steipe <boris.ste...@utoronto.ca> > Sent: Tuesday, January 31, 2023 10:16 AM > To: Carolyn J Miller <cjmil...@syr.edu> > Cc: r-help@r-project.org <r-help@r-project.org> > Subject: Re: [R] question > > Perhaps, rather than looking to compress your observations into a single > number, you could simply visualize what you observed: use a boxplot to show > the March and December observations, and overlay the three animals that > were recaptured as individual points, connected with a line. > > Feel free to ask again if you are not sure how to do that. > > Cheers, > Boris > > > PS. Lets hope that the capture did not stress them to the degree that > their cortisol is elevated at recapture :-) > > > > > > On 2023-01-31, at 09:52, Carolyn J Miller via R-help < > r-help@r-project.org> wrote: > > > > Thank you! > > > > Carolyn J. Miller > > M.S. Student, Ecology > > SUNY-ESF, Environmental Biology > > > > > > ________________________________ > > From: Ebert,Timothy Aaron <teb...@ufl.edu> > > Sent: Tuesday, January 31, 2023 9:50 AM > > To: Carolyn J Miller <cjmil...@syr.edu>; PIKAL Petr < > petr.pi...@precheza.cz>; r-help@r-project.org <r-help@r-project.org> > > Subject: RE: question > > > > > > As indicated here: > https://www.geeksforgeeks.org/compute-the-correlation-coefficient-value-between-two-vectors-in-r-programming-cor-function/ > > > > The cor() function needs two vectors. The only way that works is if you > are looking at the correlation between �Month� and �Cort.� > > > > If you interested in the correlation between Cort measured in month 3 > versus month 12 then you are not getting the right answer. > > > > > > > > Animal ID is not relevant in this analysis (as presented). > > > > The animals that have been measured twice would be a repeated measures > analysis (by default) unless there is some reason to suspect that the six > month lag is too long for an outcome in month 3 to influence the outcome in > month 12. The remaining animals are an experimental design for avoiding a > repeated measures analysis. This would be something like a t-test to > determine if the animals in Month 3 are different than Month 12. > > > > > > > > Tim > > > > > > > > From: Carolyn J Miller <cjmil...@syr.edu> > > Sent: Tuesday, January 31, 2023 9:30 AM > > To: PIKAL Petr <petr.pi...@precheza.cz>; r-help@r-project.org; > Ebert,Timothy Aaron <teb...@ufl.edu> > > Subject: Re: question > > > > > > > > [External Email] > > > > Hi Timothy, > > > > > > > > Here's some example data that might help to demonstrate how the data > currently looks. > > > > > > > > AnimalID > > > > Month > > > > Cort > > > > 1 > > > > 12 > > > > 0.00591 > > > > 1 > > > > 3 > > > > 0.00583 > > > > 2 > > > > 3 > > > > 0.005722 > > > > 3 > > > > 3 > > > > 0.005838 > > > > 4 > > > > 3 > > > > 0.005873 > > > > 4 > > > > 12 > > > > 0.0059 > > > > 5 > > > > 3 > > > > 0.005724 > > > > 6 > > > > 12 > > > > 0.005924 > > > > 7 > > > > 12 > > > > 0.005758 > > > > 8 > > > > 12 > > > > 0.005901 > > > > 9 > > > > 12 > > > > 0.005894 > > > > 10 > > > > 3 > > > > 0.005731 > > > > 11 > > > > 3 > > > > 0.005951 > > > > > > > > So Animal ID represents individual, 3 or 12 for month represents either > a March capture event or a December capture event and then the > corresponding cort value (which I used a random number generator to create > these values above). Petr, I was afraid of that response, that by using > cor() I'm fundamentally just testing the correlation for the 3 individuals > that have both March and December samples. > > > > > > > > If you guys have other thoughts I'd appreciate any suggestions. > > > > > > > > Thanks for your help and clarifying that for me. > > > > > > > > Carolyn J. Miller > > > > M.S. Student, Ecology > > > > SUNY-ESF, Environmental Biology > > > > > > > > > > > > > > > > > > > > ________________________________ > > > > From: PIKAL Petr > > Sent: Tuesday, January 31, 2023 2:36 AM > > To: Carolyn J Miller; r-help@r-project.org<mailto:r-help@r-project.org> > > Subject: RE: question > > > > > > > > Hallo Carolyn > > > > From what you describe you cannot calculate correlations. > > > > You stated that you have two sets of data, one for December and one for > > March and that rows in one set is not related to the rows in another set > and > > even persons tested in both months do not have their values on the same > row. > > In that case cor is not appropriate. You should first adjust your data so > > that results of those 3 persons are on the same row but even after that > only > > those 3 values could be evaluated by "cor". > > > > From what you wrote I think that t.test or similar beast is the way you > > should take. > > > > But without same data sample I may be wrong. > > > > Cheers > > Petr > > > >> -----Original Message----- > >> From: R-help <r-help-boun...@r-project.org<mailto: > r-help-boun...@r-project.org>> On Behalf Of Carolyn J Miller > > via > >> R-help > >> Sent: Monday, January 30, 2023 7:16 PM > >> To: r-help@r-project.org<mailto:r-help@r-project.org> > >> Subject: [R] question > >> > >> Hi guys, > >> > >> I am using the cor() function to see if there are correlations between > > March > >> cortisol levels and December cortisol levels and I'm trying to figure > out > > if the > >> function is doing what I want it to do. > >> > >> Each sample has it's own separate row in the CSV file that I'm working > out > > of. > >> March Cort and December Cort are different columns and they come from > >> separate samples, therefore their values would not be on the same row. > > There > >> are only 3 individuals that have both December cort values and March > > cortisol > >> values but they still have different sample ID values (from different > > seasons) so > >> they are also not on the same row. > >> > >> I ran the function twice: once as cor(cortphcor, use = "complete.obs") > > first > >> > >> and then cor(cortphcor, use = "pairwise.complete.obs", method = > > "pearson"). > >> > >> I received the same output both times. I guess what I'm asking is, is > the > > output > >> simply the correlation just for those 3 samples or is the second > pairwise. > >> complete.obs version giving me the correlation for all of the cort > samples > > for > >> March against all of the samples for December despite not being on the > > same > >> row? I'm trying to figure out how many sample values are contributing to > > the > >> correlation results I'm getting. > >> > >> Thanks, > >> > >> Carolyn > >> > >> > >> [[alternative HTML version deleted]] > >> > >> ______________________________________________ > >> R-help@r-project.org<mailto:R-help@r-project.org> mailing list -- To > UNSUBSCRIBE and more, see > >> https://stat.ethz.ch/mailman/listinfo/r-help< > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-help&data=05%7C01%7Ctebert%40ufl.edu%7C6ec695ba9b8e4c83e09708db0397a6cb%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C638107722117850198%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=fGQmH7ad%2BtaJdZU4jenuac%2B46daPUmruBJp4ThoO7GM%3D&reserved=0 > > > >> PLEASE do read the posting guide > > http://www.R-project.org/posting-guide.html< > https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.r-project.org%2Fposting-guide.html&data=05%7C01%7Ctebert%40ufl.edu%7C6ec695ba9b8e4c83e09708db0397a6cb%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C638107722117850198%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=jBNNlhkoXABBzpl%2FpuW4QmIWfSHGQKUnQaoy1nmpVaQ%3D&reserved=0 > > > >> and provide commented, minimal, self-contained, reproducible code. > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > > -- > Boris Steipe MD, PhD > > Professor em. > Department of Biochemistry > Temerty Faculty of Medicine > University of Toronto > > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.