Mahen, I think the issue is because you might not have all levels of Location matched with all Levels of Stages. It appears you have 5 stages and 2 locations. For the model that worked, you will notice 5 rows in your ANOVA table. In the one that didn’t, it was attempting to create a table with 9 rows, which would include the 4 interactions created by your new model. (Sorry I did not catch this before.) The error implies that the the number of SS items and df items do not match, which suggests to me that two of the interactions do not work, based on your sample.
You might consider the following, model.matrix( ~ Csize * ind$Stages * ind$Location) This will be a large matrix. Check the matrix for columns of all 0s. If you find that, it suggests that you are missing some factor interactions. If this is not the issue, then maybe you could send me your data and R script and I’ll try to figure out if there is a different problem. Best, Mike > On May 18, 2018, at 2:56 AM, mahendiran mylswamy <mahenr...@gmail.com> wrote: > > My sample size is 147 not either 9 or 7 in any case. I agree that the > computer displays these numbers! don't know why? > > Nevertheless, in this analysis the number of specimens (dependent shape > variable) is 147, obviously, with the equal number of observations for each > independent variables (here, we used two factors ind$Stages and ind$Location > ). > > It is interesting to note that I am getting good results using single factor > Manova; dependent shape variable over, either ind$stages or ind$location, at > a given time, though with/without interactions as well. Even, it works fine > with more factors if I model without any effect of interaction, and the > results are given below > > > Paint<-procD.lm(coords ~ Csize + ind$Stages + ind$Location, data = > > Paintgeo147, iter = 9999, RRPP = FALSE, print.progress = FALSE, int.first = > > FALSE) > > Paint3factor > > Call: > procD.lm(f1 = coords ~ Csize + ind$Stages + ind$Location, iter = 9999, > RRPP = FALSE, int.first = FALSE, data = Paintgeo147, print.progress = > FALSE) > > > > Type I (Sequential) Sums of Squares and Cross-products > Randomization of Raw Values used > 10000 Permutations > > Df SS MS Rsq F Z Pr(>F) > Csize 1 0.04688 0.046880 0.064257 13.4431 7.9867 1e-04 *** > ind$Stages 4 0.17575 0.043938 0.240899 12.5994 8.3726 1e-04 *** > ind$Location 1 0.01871 0.018713 0.025650 5.3662 3.2145 0.0042 ** > Residuals 140 0.48822 0.003487 > Total 146 0.72956 > --- > Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 > > > The main issue, here, is that somehow I don’t know how to use the proper > command to quantify effects of interaction, say for example ind$Stages: > ind$Location, Csize: ind$Stages, Csize: ind$Locations... etc. ???? > > Thanks for spending your time and effort! > > Looking forward > > Truly > > Mahen > > > > On Fri, May 18, 2018 at 12:05 AM, Mike Collyer <mlcoll...@gmail.com > <mailto:mlcoll...@gmail.com>> wrote: > OK, this error is indicating you have variables of different size - one with > 9 and one with 7. This does not appear to be because of the int.first issue, > but rather that you introduced a new variable with a different number of > observations. Also, I’m not sure what kind of result you expect with such a > complex model and so few observations. It might not work, anyway, because > the number of independent variables exceeds the number of observations. Just > a warning. > > Mike > > >> On May 17, 2018, at 2:19 PM, mahendiran mylswamy <mahenr...@gmail.com >> <mailto:mahenr...@gmail.com>> wrote: >> >> Hi Mike >> >> Thanks indeed for the quick response. >> error messages are given below >> >> > PSfact<-procD.lm(coords ~ Csize * ind$Stages * ind$Location, data = rough, >> > iter = 99, RRPP = FALSE, int.first = TRUE, print.progress = FALSE) >> Error in data.frame(df, SS, MS, Rsq = R2, F = Fs) : >> arguments imply differing number of rows: 9, 7 >> In addition: Warning message: >> In SS/df : longer object length is not a multiple of shorter object length >> >> >> >> >> >> >> On Thu, May 17, 2018 at 6:22 PM, Mike Collyer <mlcoll...@gmail.com >> <mailto:mlcoll...@gmail.com>> wrote: >> Mahen, >> >> Can you be specific with the error statement? It might not me related to >> the int.first use but more so how you set up your formula. If ind$Stages >> and ind$Location are in the data frame, you are asking R to create a model >> matrix from dat in an environment within another environment. This might >> cause some problems. >> >> Please let us know what the error says, and we can see if it is obvious. >> >> Cheers! >> Mike >> >>> On May 17, 2018, at 8:22 AM, mahendiran mylswamy <mahenr...@gmail.com >>> <mailto:mahenr...@gmail.com>> wrote: >>> >>> Dear All. >>> >>> I did a single and multi-factor Manova, through Geomorph package in R, >>> using the following commands given below, it is working fine! >>> >>> Paint1factor <-procD.lm (coords ~ Csize*indep1$Stages, data = Paintgeo147, >>> iter = 9999, RRPP = FALSE, print.progress = FALSE) >>> >>> Paint3factor<-procD.lm(coords ~ Csize + ind$Stages + ind$Location, data = >>> Paintgeo3fac, iter = 99, RRPP = FALSE, print.progress = FALSE, int.first = >>> FALSE) >>> >>> HOWEVER, when I did the multifactor Manova to check the interaction >>> effects, using the command, though i inserted int.first = false, somehow >>> it’s not working often shows error >>> >>> Paint3factor<-procD.lm(coords ~ Csize * ind$Stages * ind$Location, data = >>> Paintgeo3fac, iter = 99, RRPP = FALSE, print.progress = FALSE, int.first = >>> FALSE) >>> >>> >>> >>> apart from changing, + to *, inserting int.first, any other stuff to be >>> added? >>> >>> Please help me :( >>> >>> Thanks in Advance! >>> >>> Truly >>> >>> Mahen >>> >>> >>> >>> -- >>> *************************************** >>> M Mahendiran, Ph D >>> Scientist - Division of Wetland Ecology >>> Salim Ali Centre for Ornithology and Natural History (SACON) >>> Anaikatti (PO), Coimbatore - 641108, TamilNadu, India >>> Tel: 0422-2203100 (Ext. 122), 2203122 (Direct), Mob: 09787320901 >>> Fax: 0422-2657088 >>> http://www.sacon.in/staff/dr-m-mahendiran/ >>> <http://www.sacon.in/staff/dr-m-mahendiran/> >>> >>> P Please consider the environment before printing this email >>> >>> -- >>> MORPHMET may be accessed via its webpage at http://www.morphometrics.org >>> <http://www.morphometrics.org/> >>> --- >>> You received this message because you are subscribed to the Google Groups >>> "MORPHMET" group. >>> To unsubscribe from this group and stop receiving emails from it, send an >>> email to morphmet+unsubscr...@morphometrics.org >>> <mailto:morphmet+unsubscr...@morphometrics.org>. >> >> >> >> >> -- >> *************************************** >> M Mahendiran, Ph D >> Scientist - Division of Wetland Ecology >> Salim Ali Centre for Ornithology and Natural History (SACON) >> Anaikatti (PO), Coimbatore - 641108, TamilNadu, India >> Tel: 0422-2203100 (Ext. 122), 2203122 (Direct), Mob: 09787320901 >> Fax: 0422-2657088 >> http://www.sacon.in/staff/dr-m-mahendiran/ >> <http://www.sacon.in/staff/dr-m-mahendiran/> >> >> P Please consider the environment before printing this email > > > > > -- > *************************************** > M Mahendiran, Ph D > Scientist - Division of Wetland Ecology > Salim Ali Centre for Ornithology and Natural History (SACON) > Anaikatti (PO), Coimbatore - 641108, TamilNadu, India > Tel: 0422-2203100 (Ext. 122), 2203122 (Direct), Mob: 09787320901 > Fax: 0422-2657088 > http://www.sacon.in/staff/dr-m-mahendiran/ > <http://www.sacon.in/staff/dr-m-mahendiran/> > > P Please consider the environment before printing this email -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. 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