A slope from RMA will always be > than the corresponding OLS slope because RMA = OLS/r, where r is the correlation coefficient. And note that the RMA slope calculated this way is undefined if r = 0.
This is why you want to use measurement-error models. Cheers, Ted On Tue, Jun 9, 2020 at 1:34 PM Ted Stankowich <theodore.stankow...@csulb.edu> wrote: > Thank you Liam and Ted! > That worked. I've never named my data columns this way and when I call > names(Data), it does give me the column names "Binomial", "Skull", and > "Tusk". This method appears to pull out the vectors and use them outside of > the original dataframe, is this a particular requirement/feature of > phyl.RMA? > > Regarding RMA vs. other methods, this is a study of allometry of tusks and > antlers. In our first submission of this project we got raked over the > coals for only using OLS methods so we're doing both OLS and RMA this time > around, but are struggling to interpret the slope discrepancies between the > two methods (RMA always returns larger slopes). There is measurement error > in our independent factor (Skull) since some of those data come from PCA > estimates based on landmark measures in skulls that were broken/partial > (full skull length wasn't possible). We'll definitely look at the paper Ted > posted though. There appears to be some strong divergent methodological > opinions among the allometry community though, so it's hard to know the > best way to proceed! > > Thanks! > -Ted > > > > -----Original Message----- > From: Liam J. Revell [mailto:liam.rev...@umb.edu] > Sent: Tuesday, June 9, 2020 1:07 PM > To: Ted Stankowich <theodore.stankow...@csulb.edu>; > r-sig-phylo@r-project.org > Subject: Re: [R-sig-phylo] phyl.RMA error > > CAUTION: This email was sent from an external source. Use caution when > replying, opening links or attachments. > > > Hi Ted. > > It's a good bet that your input vectors, log(Skull) and log(Tusk), don't > have names. > > In your case, if your data frame is called Data, you might first compute: > > ln.Skull<-setNames(log(Data$Skull),Data$Binomial) > ln.Tusk<-setNames(log(Data$Tusk),Data$Binomial) > > and then run: > > Model<-phyl.RMA(ln.Skull,ln.Tusk,tree,h0=1.0) > Model > plot(Model) ## this is kind of cool. > > Note, that as pointed out in the documentation of the function: "some > statistician think there is never a condition in which a reduced-major-axis > regression should be used" (I believe this has even been discussed on this > list); and "The statistical hypothesis testing is based on Clarke (1980; > reviewed in McArdle 1988), which differs from some other implementations of > non-phylogenetic major axis regression in R." > > All the best, Liam > > Liam J. Revell > Associate Professor, University of Massachusetts Boston Profesor > Asistente, Universidad Católica de la Ssma Concepción > web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org > > Academic Director UMass Boston Chile Abroad: > https://www.umb.edu/academics/caps/international/biology_chile > > On 6/8/2020 4:18 PM, Ted Stankowich wrote: > > [EXTERNAL SENDER] > > > > Hello, > > > > We're trying to run phylogenetically corrected reduced major axes > regression analyses and have encountered an error we can't debug. We're > using the function phyl.RMA in the package 'phytools'. Here is the code we > are using and the error it returns. > > > > > > > >> Model <- phyl.RMA(log(Skull), log(Tusk), tree, h0=1.0) > > > > Error in if (sign(beta1) != sign(h0)) { : > > > > missing value where TRUE/FALSE needed > > > > We can't seem to figure out which argument is missing, and we've tried > including all of the T/F based arguments we think are possible. Our species > dataset and nexus file are printed below. Any advice would be greatly > appreciated. > > > > We have the following dataset: > > Binomial Skull Tusk > > <chr> <dbl> <dbl> > > 1 Tragulus_javanicus 93.7 14.6 > > 2 Tragulus_kanchil 99.7 13.9 > > 3 Tragulus_napu 98.1 11.1 > > 4 Tragulus_nigricans 99.8 13.2 > > 5 Moschiola_meminna 101. 14.6 > > 6 Moschus_berezovskii 134. 55.0 > > 7 Moschus_moschiferus 152. 52.9 > > 8 Muntiacus_muntjak 193. 26.4 > > 9 Muntiacus_reevesi 159. 23.4 > > 10 Muntiacus_truongsonensis 184. 27.7 > > 11 Muntiacus_vaginalis 203. 28.6 > > 12 Hydropotes_inermis 162. 48.5 > > 13 Hyemoschus_aquaticus 122. 20.1 > > 14 Elaphodus_cephalophus 186. 17.3 > > > > And the following nexus tree: > > > > #NEXUS > > [R-package APE, Mon Jun 08 12:20:01 2020] > > > > BEGIN TAXA; > > DIMENSIONS NTAX = 12; > > TAXLABELS > > Tragulus_napu > > Tragulus_kanchil > > Tragulus_javanicus > > Hyemoschus_aquaticus > > Moschiola_meminna > > Muntiacus_reevesi > > Muntiacus_muntjak > > Muntiacus_truongsonensis > > Elaphodus_cephalophus > > Hydropotes_inermis > > Moschus_moschiferus > > Moschus_berezovskii > > ; > > END; > > BEGIN TREES; > > TRANSLATE > > 1 Tragulus_napu, > > 2 Tragulus_kanchil, > > 3 Tragulus_javanicus, > > 4 Hyemoschus_aquaticus, > > 5 Moschiola_meminna, > > 6 Muntiacus_reevesi, > > 7 Muntiacus_muntjak, > > 8 Muntiacus_truongsonensis, > > 9 Elaphodus_cephalophus, > > 10 Hydropotes_inermis, > > 11 Moschus_moschiferus, > > 12 Moschus_berezovskii > > ; > > TREE * UNTITLED = [&R] > > ((((1:5.540957781,(2:2.978817423,3:2.978817423):2.562139698):10.789111 > > 52,4:16.33006601):6.360692368,5:22.69076035):5.725388419,(((((6:1.6111 > > 49584,7:1.611149848):1.556474893,8:3.167624477):4.130280196,9:7.297904 > > 013):1.497063399,10:8.794967413):7.19682079,(11:2.539095678,12:2.53909 > > 6008):13.45269085):12.42436025); > > > > > > > > Dr. Ted Stankowich > > Associate Professor > > Department of Biological Sciences > > California State University Long Beach Long Beach, CA 90840 > > theodore.stankow...@csulb.edu<mailto:theodore.stankow...@csulb.edu> > > 562-985-4826 > > https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.c > > sulb.edu%2Fmammal-lab%2F&data=02%7C01%7Cliam.revell%40umb.edu%7C5a > > 74928c910446b96b1508d80caf5765%7Cb97188711ee94425953c1ace1373eb38%7C0% > > 7C0%7C637273294515730787&sdata=7FUGnuFJCdRHmPiVrWPPAu%2BLEyK6O%2B4 > > VyAKHz1n63qw%3D&reserved=0 > > @CSULBMammalLab > > > > > > > > Dr. Ted Stankowich > > Associate Professor > > Department of Biological Sciences > > California State University Long Beach Long Beach, CA 90840 > > theodore.stankow...@csulb.edu<mailto:theodore.stankow...@csulb.edu> > > 562-985-4826 > > https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.c > > sulb.edu%2Fmammal-lab%2F&data=02%7C01%7Cliam.revell%40umb.edu%7C5a > > 74928c910446b96b1508d80caf5765%7Cb97188711ee94425953c1ace1373eb38%7C0% > > 7C0%7C637273294515730787&sdata=7FUGnuFJCdRHmPiVrWPPAu%2BLEyK6O%2B4 > > VyAKHz1n63qw%3D&reserved=0 > > @CSULBMammalLab > > > > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > R-sig-phylo mailing list - R-sig-phylo@r-project.org > > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat > > .ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=02%7C01%7Cliam.re > > vell%40umb.edu%7C5a74928c910446b96b1508d80caf5765%7Cb97188711ee9442595 > > 3c1ace1373eb38%7C0%7C0%7C637273294515730787&sdata=fM8ulKB00NYkD5dg > > 7kKLLn60gKSn7ax30UOS8MoF4qo%3D&reserved=0 > > Searchable archive at > > https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.m > > ail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=02%7C01%7Cli > > am.revell%40umb.edu%7C5a74928c910446b96b1508d80caf5765%7Cb97188711ee94 > > 425953c1ace1373eb38%7C0%7C0%7C637273294515730787&sdata=TZmy1ZYPYlI > > l%2FbF4SWD0n7Ivy%2BP8UhB2engQzXg2CVY%3D&reserved=0 > > > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
