error with modavg() and colext models

[Scott Pearson]

I am seeing a new error with R ver. 4.5.1 when using modavg() to compute model averaged parameter estimates from a set of colext() models.  Here is example code from the modavg help page that now throws the error: 

---------

library(AICcmodavg) # ver. 2.3-4
require(unmarked) # ver. 1.5.1

data(frogs)
umf <- formatMult(masspcru)
obsCovs(umf) <- scale(obsCovs(umf))
siteCovs(umf) <- rnorm(numSites(umf))
yearlySiteCovs(umf) <- data.frame(year = factor(rep(1:7,
                                    numSites(umf))))

fm <- colext(psiformula = ~ 1, gammaformula = ~ 1, epsilonformula = ~ 1,
             pformula = ~ JulianDate + I(JulianDate^2), data = umf,
             control = list(trace=1, maxit=1e4))

fm.yearly <- colext(psiformula = ~ 1, gammaformula = ~ year,
                    epsilonformula = ~ year,
                    pformula = ~ JulianDate + I(JulianDate^2),
                    data = umf)

Cand.mods <- list(fm, fm.yearly)
Modnames <- c("psi1(.)gam(.)eps(.)p(Date + Date2)",
              "psi1(.)gam(Year)eps(Year)p(Date + Date2)")

modavg(cand.set = Cand.mods, modnames = Modnames, parm = "(Intercept)",
       parm.type = "psi")
# Error in FUN(X[[i]], ...) :
#   no slot of name "psiformula" for this object of class "unmarkedFitColExt"

modavg(cand.set = Cand.mods, modnames = Modnames,
       parm = "I(JulianDate^2)", parm.type = "detect")
# Error in FUN(X[[i]], ...) :
#   no slot of name "detformula" for this object of class "unmarkedFitColExt"

---------
Thanks for any advice,

Scott P.

[Ken Kellner]

Hi Scott,

This is due to an internal change in unmarked in version 1.5.1 that results in an incompability with AICcmodavg. One short-term solution is to revert to the previous version of unmarked (1.5.0). Alternatively, I've attached a patch file. If you load unmarked and AICcmodavg, then run

source("patch.R")

The modavg function should work again. I'll work on a permanent fix.

Ken

On Fri, Oct 10, 2025 at 07:42:52AM -0700, 'Scott Pearson' via unmarked wrote:
> I am seeing a new error with R ver. 4.5.1 when using *modavg()* to compute
> model averaged parameter estimates from a set of *colext()* models. Here
> is example code from the *modavg* help page that now throws the error:

> ---------
> library(AICcmodavg) # ver. 2.3-4
> require(unmarked) # ver. 1.5.1
>
> data(frogs)
> umf <- formatMult(masspcru)
> obsCovs(umf) <- scale(obsCovs(umf))
> siteCovs(umf) <- rnorm(numSites(umf))
> yearlySiteCovs(umf) <- data.frame(year = factor(rep(1:7,
> numSites(umf))))
>
> fm <- colext(psiformula = ~ 1, gammaformula = ~ 1, epsilonformula = ~ 1,
> pformula = ~ JulianDate + I(JulianDate^2), data = umf,
> control = list(trace=1, maxit=1e4))
>
> fm.yearly <- colext(psiformula = ~ 1, gammaformula = ~ year,
> epsilonformula = ~ year,
> pformula = ~ JulianDate + I(JulianDate^2),
> data = umf)
>
> Cand.mods <- list(fm, fm.yearly)
> Modnames <- c("psi1(.)gam(.)eps(.)p(Date + Date2)",
> "psi1(.)gam(Year)eps(Year)p(Date + Date2)")
>
> modavg(cand.set = Cand.mods, modnames = Modnames, parm = "(Intercept)",
> parm.type = "psi")
>

> *# Error in FUN(X[[i]], ...) : # no slot of name "psiformula" for this
> object of class "unmarkedFitColExt"*

>
> modavg(cand.set = Cand.mods, modnames = Modnames,
> parm = "I(JulianDate^2)", parm.type = "detect")
>

> *# Error in FUN(X[[i]], ...) : # no slot of name "detformula" for this
> object of class "unmarkedFitColExt"*

> ---------
> Thanks for any advice,
> Scott P.
>

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[Ken Kellner]

Forgot to attach the file.

On Fri, Oct 10, 2025 at 07:42:52AM -0700, 'Scott Pearson' via unmarked wrote:

> I am seeing a new error with R ver. 4.5.1 when using *modavg()* to compute
> model averaged parameter estimates from a set of *colext()* models. Here
> is example code from the *modavg* help page that now throws the error:

> ---------
> library(AICcmodavg) # ver. 2.3-4
> require(unmarked) # ver. 1.5.1
>
> data(frogs)
> umf <- formatMult(masspcru)
> obsCovs(umf) <- scale(obsCovs(umf))
> siteCovs(umf) <- rnorm(numSites(umf))
> yearlySiteCovs(umf) <- data.frame(year = factor(rep(1:7,
> numSites(umf))))
>
> fm <- colext(psiformula = ~ 1, gammaformula = ~ 1, epsilonformula = ~ 1,
> pformula = ~ JulianDate + I(JulianDate^2), data = umf,
> control = list(trace=1, maxit=1e4))
>
> fm.yearly <- colext(psiformula = ~ 1, gammaformula = ~ year,
> epsilonformula = ~ year,
> pformula = ~ JulianDate + I(JulianDate^2),
> data = umf)
>
> Cand.mods <- list(fm, fm.yearly)
> Modnames <- c("psi1(.)gam(.)eps(.)p(Date + Date2)",
> "psi1(.)gam(Year)eps(Year)p(Date + Date2)")
>
> modavg(cand.set = Cand.mods, modnames = Modnames, parm = "(Intercept)",
> parm.type = "psi")
>

> *# Error in FUN(X[[i]], ...) : # no slot of name "psiformula" for this
> object of class "unmarkedFitColExt"*

>
> modavg(cand.set = Cand.mods, modnames = Modnames,
> parm = "I(JulianDate^2)", parm.type = "detect")
>

> *# Error in FUN(X[[i]], ...) : # no slot of name "detformula" for this
> object of class "unmarkedFitColExt"*

> ---------
> Thanks for any advice,
> Scott P.
>

[Scott Pearson]

Thank you, Ken.  The patch worked.  --Scott

[Marc J. Mazerolle]

Hi Scott,

Thanks for pointing this out. I'll make the changes in AICcmodavg. 

Best,

Marc
--
____________________________________
Marc J. Mazerolle
Professeur titulaire et directeur du bac. en environnements naturels et
aménagés
Département des sciences du bois et de la forêt
2405 rue de la Terrasse
Université Laval
Québec, Québec G1V 0A6, Canada
Tel: (418) 656-2131 ext. 407120
Email: marc.ma...@sbf.ulaval.ca


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De: 'Scott Pearson' via unmarked <unma...@googlegroups.com>
Répondre à: unma...@googlegroups.com
À: unmarked <unma...@googlegroups.com>
Objet: [unmarked] error with modavg() and colext models
Date: 2025-10-10 10:42:52