Hi,

I am trying to replicate some code I previously used to undertake a dbRDA
analysis, however since updating my R software and all associated packages
to the latest version it seems the analysis does not work.

I have two dist objects: gendist and geodist.

I first reduce geodist using pcnm().

geo_pcnm<-pcnm(geodist)

I then use these scores in capscale().

geo_rda<-capscale(gendist~scores(geo_pcnm))

To forward select the variables to use in further analyses, so I want to
know which ones are significant - and herein lies my problem.

After running:

anova(geo_rda,by="axis",perm=9999)

I get the following error:

Error in eval(expr, envir, enclos) : could not find function "Condition"

I have run traceback() and this is what I get:

traceback()
14: eval(expr, envir, enclos)
13: eval(predvars, data, env)
12: model.frame.default(formula, data, na.action = na.pass, xlev = xlev)
11: model.frame(formula, data, na.action = na.pass, xlev = xlev)
10: ordiParseFormula(fla, if (is.data.frame(data) && !is.null(comm))
cbind(data,
        comm) else data, envdepth = 1, na.action = na.action, subset =
substitute(subset))
9: capscale(formula = gendist ~ CAP1 + Condition(CAP2 + CAP3 + CAP4 +
       CAP5 + CAP6 + CAP7 + CAP8 + CAP9 + CAP10 + CAP11 + CAP12 +
       CAP13 + CAP14 + CAP15 + CAP16 + CAP17 + CAP18 + CAP19 + CAP20 +
       CAP21 + CAP22 + CAP23 + CAP24 + CAP25 + CAP26 + CAP27 + CAP28 +
       CAP29 + CAP30 + CAP31 + CAP32 + CAP33 + CAP34 + CAP35 + CAP36 +
       CAP37 + CAP38 + CAP39 + CAP40 + CAP41 + CAP42 + CAP43 + CAP44 +
       CAP45 + CAP46 + CAP47 + CAP48 + CAP49 + CAP50 + CAP51 + CAP52 +
       CAP53 + CAP54 + CAP55 + CAP56 + CAP57 + CAP58 + CAP59 + CAP60 +
       CAP61 + CAP62 + CAP63 + CAP64 + CAP65), data = lc)
8: eval(expr, envir, enclos)
7: eval(call, parent.frame())
6: update.default(object, fla, data = lc)
5: update(object, fla, data = lc)
4: anova(update(object, fla, data = lc), ...)
3: anova.ccabyaxis(object, alpha = alpha, beta = beta, step = step,
       perm.max = perm.max, by = NULL, ...)
2: anova.cca(geo_rda, by = "axis", perm = 9999)
1: anova(geo_rda, by = "axis", perm = 9999)




Is this a problem with the update? This code has worked multiple times for
me in the past using older versions.

Cheers
Dan

Dan Edwards
Postdoctoral Research Associate
Department of Ecology & Evolutionary Biology
Yale University
21 Sachem St, New Haven CT 06520
E: Danielle.Edwards@yale.edu
W: https://sites.google.com/site/drdanielleedwards/


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