trouble with procD.pgls function
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Omar Mejía
Jun 30, 2025, 9:54:19 AMJun 30
to geomorph R package
Hi , I have trouble with procD.pgls function:
This is my code
landmarks=readland.tps("test.tps",specID="ID")
Procrustes=gpagen(landmarks)
phy=read.tree("Oscar.tre")
habitat=read.csv("habitat.csv", row.names=1)
species=read.csv("species.csv", row.names=1)
name.check(Procrustes,phy)
> name.check(Procrustes,phy)
[1] "OK"
gdf2 <- geomorph.data.frame(Procrustes, species = species,
habitat =habitat,phy=phy)
attributes(gdf2)
$names
[1] "species.x" "habitat.x" "coords" "Csize"
[5] "phy"
$class
[1] "geomorph.data.frame"
fit1 <- procD.lm(coords ~ species.x,
data = gdf2, iter = 999, turbo = TRUE,
RRPP = FALSE, print.progress = FALSE) # randomize raw values
summary(fit1)
Analysis of Variance, using Residual Randomization
Permutation procedure: Randomization of raw values (residuals of mean)
Number of permutations: 1000
Estimation method: Ordinary Least Squares
Sums of Squares and Cross-products: Type I
Effect sizes (Z) based on F distributions
Df SS MS Rsq F Z
species.x 20 0.046158 0.0023079 1 NaN 0
Total 20 0.046158
Pr(>F)
species.x < 2.2e-16 ***
Total
---
Signif. codes:
0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
####Here appears the trouble###
sp.pgls <- procD.pgls(coords ~ Csize, phy = phy, data = gdf2)
Sums of Squares calculations: 1000 permutations.
|==========================================| 100%
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'as.matrix': una dimensión es cero
Procrustes=gpagen(landmarks)
phy=read.tree("Oscar.tre")
habitat=read.csv("habitat.csv", row.names=1)
species=read.csv("species.csv", row.names=1)
name.check(Procrustes,phy)
> name.check(Procrustes,phy)
[1] "OK"
gdf2 <- geomorph.data.frame(Procrustes, species = species,
habitat =habitat,phy=phy)
attributes(gdf2)
$names
[1] "species.x" "habitat.x" "coords" "Csize"
[5] "phy"
$class
[1] "geomorph.data.frame"
fit1 <- procD.lm(coords ~ species.x,
data = gdf2, iter = 999, turbo = TRUE,
RRPP = FALSE, print.progress = FALSE) # randomize raw values
summary(fit1)
Analysis of Variance, using Residual Randomization
Permutation procedure: Randomization of raw values (residuals of mean)
Number of permutations: 1000
Estimation method: Ordinary Least Squares
Sums of Squares and Cross-products: Type I
Effect sizes (Z) based on F distributions
Df SS MS Rsq F Z
species.x 20 0.046158 0.0023079 1 NaN 0
Total 20 0.046158
Pr(>F)
species.x < 2.2e-16 ***
Total
---
Signif. codes:
0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
####Here appears the trouble###
sp.pgls <- procD.pgls(coords ~ Csize, phy = phy, data = gdf2)
Sums of Squares calculations: 1000 permutations.
|==========================================| 100%
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'as.matrix': una dimensión es cero
I read in another message that the trouble arise with RRPP library, I am using version 2.1.2 updated directly from github
If I create the dataframe taking out the species and habitat classifiers its the same case
I have no problem running the plethspecies example
KIndly appreciate any help
Best regards
![Adams, Dean [EEOB]'s profile photo](http://lh3.googleusercontent.com/a-/ALV-UjUomU2zWXKEvkeqS7V1RLiTf4TsQsGkMNYfyjBB3M5ggNYAFA=s40-c)
Adams, Dean [EEOB]
Jun 30, 2025, 3:18:59 PMJun 30
to geomorph R package
Omar,
An analysis of Shape ~ Species does not make sense to perform, because there is no replication. Every species is found only once in the dataset, so the NaN is all that can be observed for certain components of the linear model.
As to the second issue (the error), please read previous posts on this google group. There was a bug that was fixed in RRPP and should likely resolve your issue also. Please re-install geomorph and RRPP from their Github repositories (not CRAN).
Dean
--Dr. Dean C. AdamsDistinguished ProfessorDepartment of Ecology, Evolution, and Organismal BiologyIowa State Universityphone: 515-294-3834
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Sent: Monday, June 30, 2025 8:54 AM
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Subject: [geomorph-r-package] trouble with procD.pgls function
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Subject: [geomorph-r-package] trouble with procD.pgls function
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Omar Mejía
Jul 1, 2025, 9:46:31 AMJul 1
to geomorph-...@googlegroups.com
Dear Dean,
Kindly appreciate your message, I follow your suggestion, uninstall both libraries, geomorph and RRPP, and then install directly from github using devtools and the problem persists. I spent several hours trying to solve the problem without success :(
This is what I am doing:
landmarks=readland.tps("test.tps",specID="None")
Procrustes=gpagen(landmarks)
phy=read.tree("Oscar.tre")
gdf2 <- geomorph.data.frame(Procrustes,phy=phy)
attributes(gdf2)
Procrustes=gpagen(landmarks)
phy=read.tree("Oscar.tre")
gdf2 <- geomorph.data.frame(Procrustes,phy=phy)
attributes(gdf2)
sp.pgls <- procD.pgls(coords ~ Csize, phy = phy, data = gdf2)
Preliminary Model Fit...
Error: Data names and covariance matrix names do not match.
#### I check the names in both, my tps and phylogeny and apparently match###
name.check(Procrustes,phy)
[1] "OK"
##but i found errors with this function###
match(rownames(Procrustes),phy$tip.labels)
integer(0)
obj<-name.check(phy,landmarks)
obj
$tree_not_data
[1] "Chuco_intermedium" "Chuco_microphthalmus"
[3] "Cincelichthys_pearsei" "Kihnichthys_ufermanni"
[5] "Maskaheros_argenteus" "Maskaheros_regani"
[7] "Oscura_heterospila" "Paraneetroplus_bulleri"
[9] "Paraneetroplus_nebuliferus" "Rheoheros_lentiginosus"
[11] "Theraps_irregularis" "Trichromis_salvini"
[13] "Vieja_bifasciata" "Vieja_breidohri"
[15] "Vieja_fenestrata" "Vieja_guttulata"
[17] "Vieja_hartwegi" "Vieja_maculicauda"
[19] "Vieja_melanurus" "Vieja_zonata"
[21] "Wajpamheros_nourissati"
$data_not_tree
NULL
###### I see that my coords have not name###
dim(Procrustes$coords)
[1] 44 2 21
dimnames(Procrustes$coords)
[[3]]
[1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15"
[16] "16" "17" "18" "19" "20" "21"
### I follow suggestions and assign names ####
newnames=c("Paraneetroplus_nebuliferus","Chuco_intermedium","Chuco_microphtalmus","Cincelichthys_pearsei","Kihnichthys_uefermanni","Maskaheros_argenteus","Maskaheros_regani","Oscura_heterospila","Paraneetroplus_bulleri","Rheoheros_lentiginosus","Theraps_irregularis","Thrichromis_salvini","Vieja_bifasciata","Vieja_breidhori","Vieja_fenestrata","Vieja_gutttulata","Vieja_hartwegii","Vieja_maculicauda","Vieja_melanurus","Vieja_zonata","Wajpamheros_nourisatti")
dimnames(Procrustes$coords)[[3]]=newnames
dimnames(Procrustes$coords)
### Now my coords have a name ###
[[3]]
[1] "Paraneetroplus_nebuliferus" "Chuco_intermedium"
[3] "Chuco_microphtalmus" "Cincelichthys_pearsei"
[5] "Kihnichthys_uefermanni" "Maskaheros_argenteus"
[7] "Maskaheros_regani" "Oscura_heterospila"
[9] "Paraneetroplus_bulleri" "Rheoheros_lentiginosus"
[11] "Theraps_irregularis" "Thrichromis_salvini"
[13] "Vieja_bifasciata" "Vieja_breidhori"
[15] "Vieja_fenestrata" "Vieja_gutttulata"
[17] "Vieja_hartwegii" "Vieja_maculicauda"
[19] "Vieja_melanurus" "Vieja_zonata"
[21] "Wajpamheros_nourisatti"
## names apparently are ok ###
name.check(Procrustes,phy)
[1] "OK"
### but not ###
match(rownames(Procrustes),phy$tip.labels)
integer(0)
obj<-name.check(phy,landmarks)
obj
$tree_not_data
[1] "Chuco_intermedium" "Chuco_microphthalmus"
[3] "Cincelichthys_pearsei" "Kihnichthys_ufermanni"
[5] "Maskaheros_argenteus" "Maskaheros_regani"
[7] "Oscura_heterospila" "Paraneetroplus_bulleri"
[9] "Paraneetroplus_nebuliferus" "Rheoheros_lentiginosus"
[11] "Theraps_irregularis" "Trichromis_salvini"
[13] "Vieja_bifasciata" "Vieja_breidohri"
[15] "Vieja_fenestrata" "Vieja_guttulata"
[17] "Vieja_hartwegi" "Vieja_maculicauda"
[19] "Vieja_melanurus" "Vieja_zonata"
[21] "Wajpamheros_nourissati"
$data_not_tree
NULL
#### I compare the order of the names in both, Procrustes$coords and tiplabels,
I assume that R needs that the names must be in the same position to match###
dimnames(Procrustes$coords)
[[3]]
[1] "Paraneetroplus_nebuliferus" "Chuco_intermedium"
[3] "Chuco_microphtalmus" "Cincelichthys_pearsei"
[5] "Kihnichthys_uefermanni" "Maskaheros_argenteus"
[7] "Maskaheros_regani" "Oscura_heterospila"
[9] "Paraneetroplus_bulleri" "Rheoheros_lentiginosus"
[11] "Theraps_irregularis" "Thrichromis_salvini"
[13] "Vieja_bifasciata" "Vieja_breidhori"
[15] "Vieja_fenestrata" "Vieja_gutttulata"
[17] "Vieja_hartwegii" "Vieja_maculicauda"
[19] "Vieja_melanurus" "Vieja_zonata"
[21] "Wajpamheros_nourisatti"
phy$tip.label
[1] "Chuco_microphthalmus" "Chuco_intermedium"
[3] "Cincelichthys_pearsei" "Kihnichthys_ufermanni"
[5] "Theraps_irregularis" "Wajpamheros_nourissati"
[7] "Rheoheros_lentiginosus" "Oscura_heterospila"
[9] "Maskaheros_argenteus" "Maskaheros_regani"
[11] "Paraneetroplus_bulleri" "Paraneetroplus_nebuliferus"
[13] "Vieja_bifasciata" "Vieja_breidohri"
[15] "Vieja_hartwegi" "Vieja_fenestrata"
[17] "Vieja_guttulata" "Vieja_zonata"
[19] "Vieja_maculicauda" "Vieja_melanurus"
[21] "Trichromis_salvini"
### I cannot change my phylogeny topology, so, I change the order of
the species in my tps file and set names according to phy tip labels ##
newnames2=c("Chuco_microphtalmus","Chuco_intermedium","Cincelichthys_pearsei","Kihnichthys_uefermanni","Theraps_irregularis", "Wajpamheros_nourisatti", "Rheoheros_lentiginosus", "Oscura_heterospila","Maskaheros_argenteus","Maskaheros_regani","Paraneetroplus_bulleri","Paraneetroplus_nebuliferus","Vieja_bifasciata","Vieja_breidhori","Vieja_hartwegii","Vieja_fenestrata","Vieja_gutttulata","Vieja_zonata","Vieja_maculicauda","Vieja_melanurus","Thrichromis_salvini")
dimnames(Procrustes$coords)[[3]]=newnames2
dimnames(Procrustes$coords)
[[3]]
[1] "Chuco_microphtalmus" "Chuco_intermedium"
[3] "Cincelichthys_pearsei" "Kihnichthys_uefermanni"
[5] "Theraps_irregularis" "Wajpamheros_nourisatti"
[7] "Rheoheros_lentiginosus" "Oscura_heterospila"
[9] "Maskaheros_argenteus" "Maskaheros_regani"
[11] "Paraneetroplus_bulleri" "Paraneetroplus_nebuliferus"
[13] "Vieja_bifasciata" "Vieja_breidhori"
[15] "Vieja_hartwegii" "Vieja_fenestrata"
[17] "Vieja_gutttulata" "Vieja_zonata"
[19] "Vieja_maculicauda" "Vieja_melanurus"
[21] "Thrichromis_salvini"
phy$tip.label
[1] "Chuco_microphthalmus" "Chuco_intermedium"
[3] "Cincelichthys_pearsei" "Kihnichthys_ufermanni"
[5] "Theraps_irregularis" "Wajpamheros_nourissati"
[7] "Rheoheros_lentiginosus" "Oscura_heterospila"
[9] "Maskaheros_argenteus" "Maskaheros_regani"
[11] "Paraneetroplus_bulleri" "Paraneetroplus_nebuliferus"
[13] "Vieja_bifasciata" "Vieja_breidohri"
[15] "Vieja_hartwegi" "Vieja_fenestrata"
[17] "Vieja_guttulata" "Vieja_zonata"
[19] "Vieja_maculicauda" "Vieja_melanurus"
[21] "Trichromis_salvini"
##Now the names are identical and in the same position, but the trouble persists##
name.check(Procrustes,phy)
[1] "OK
match(rownames(Procrustes),phy$tip.labels)
integer(0)
obj<-name.check(phy,landmarks)
obj
$tree_not_data
[1] "Chuco_intermedium" "Chuco_microphthalmus"
[3] "Cincelichthys_pearsei" "Kihnichthys_ufermanni"
[5] "Maskaheros_argenteus" "Maskaheros_regani"
[7] "Oscura_heterospila" "Paraneetroplus_bulleri"
[9] "Paraneetroplus_nebuliferus" "Rheoheros_lentiginosus"
[11] "Theraps_irregularis" "Trichromis_salvini"
[13] "Vieja_bifasciata" "Vieja_breidohri"
[15] "Vieja_fenestrata" "Vieja_guttulata"
[17] "Vieja_hartwegi" "Vieja_maculicauda"
[19] "Vieja_melanurus" "Vieja_zonata"
[21] "Wajpamheros_nourissati"
$data_not_tree
NULL
##### I update geomorph and RRPP directly from Github and also update Matrix library##
I am using R 4.5.1, geomorph 4.0.10, RRPP 2.1.2 and Matrix 1.7-3
Error: Data names and covariance matrix names do not match.
#### I check the names in both, my tps and phylogeny and apparently match###
name.check(Procrustes,phy)
[1] "OK"
##but i found errors with this function###
match(rownames(Procrustes),phy$tip.labels)
integer(0)
obj<-name.check(phy,landmarks)
obj
$tree_not_data
[1] "Chuco_intermedium" "Chuco_microphthalmus"
[3] "Cincelichthys_pearsei" "Kihnichthys_ufermanni"
[5] "Maskaheros_argenteus" "Maskaheros_regani"
[7] "Oscura_heterospila" "Paraneetroplus_bulleri"
[9] "Paraneetroplus_nebuliferus" "Rheoheros_lentiginosus"
[11] "Theraps_irregularis" "Trichromis_salvini"
[13] "Vieja_bifasciata" "Vieja_breidohri"
[15] "Vieja_fenestrata" "Vieja_guttulata"
[17] "Vieja_hartwegi" "Vieja_maculicauda"
[19] "Vieja_melanurus" "Vieja_zonata"
[21] "Wajpamheros_nourissati"
$data_not_tree
NULL
###### I see that my coords have not name###
dim(Procrustes$coords)
[1] 44 2 21
dimnames(Procrustes$coords)
[[3]]
[1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15"
[16] "16" "17" "18" "19" "20" "21"
### I follow suggestions and assign names ####
newnames=c("Paraneetroplus_nebuliferus","Chuco_intermedium","Chuco_microphtalmus","Cincelichthys_pearsei","Kihnichthys_uefermanni","Maskaheros_argenteus","Maskaheros_regani","Oscura_heterospila","Paraneetroplus_bulleri","Rheoheros_lentiginosus","Theraps_irregularis","Thrichromis_salvini","Vieja_bifasciata","Vieja_breidhori","Vieja_fenestrata","Vieja_gutttulata","Vieja_hartwegii","Vieja_maculicauda","Vieja_melanurus","Vieja_zonata","Wajpamheros_nourisatti")
dimnames(Procrustes$coords)[[3]]=newnames
dimnames(Procrustes$coords)
### Now my coords have a name ###
[[3]]
[1] "Paraneetroplus_nebuliferus" "Chuco_intermedium"
[3] "Chuco_microphtalmus" "Cincelichthys_pearsei"
[5] "Kihnichthys_uefermanni" "Maskaheros_argenteus"
[7] "Maskaheros_regani" "Oscura_heterospila"
[9] "Paraneetroplus_bulleri" "Rheoheros_lentiginosus"
[11] "Theraps_irregularis" "Thrichromis_salvini"
[13] "Vieja_bifasciata" "Vieja_breidhori"
[15] "Vieja_fenestrata" "Vieja_gutttulata"
[17] "Vieja_hartwegii" "Vieja_maculicauda"
[19] "Vieja_melanurus" "Vieja_zonata"
[21] "Wajpamheros_nourisatti"
## names apparently are ok ###
name.check(Procrustes,phy)
[1] "OK"
### but not ###
match(rownames(Procrustes),phy$tip.labels)
integer(0)
obj<-name.check(phy,landmarks)
obj
$tree_not_data
[1] "Chuco_intermedium" "Chuco_microphthalmus"
[3] "Cincelichthys_pearsei" "Kihnichthys_ufermanni"
[5] "Maskaheros_argenteus" "Maskaheros_regani"
[7] "Oscura_heterospila" "Paraneetroplus_bulleri"
[9] "Paraneetroplus_nebuliferus" "Rheoheros_lentiginosus"
[11] "Theraps_irregularis" "Trichromis_salvini"
[13] "Vieja_bifasciata" "Vieja_breidohri"
[15] "Vieja_fenestrata" "Vieja_guttulata"
[17] "Vieja_hartwegi" "Vieja_maculicauda"
[19] "Vieja_melanurus" "Vieja_zonata"
[21] "Wajpamheros_nourissati"
$data_not_tree
NULL
#### I compare the order of the names in both, Procrustes$coords and tiplabels,
I assume that R needs that the names must be in the same position to match###
dimnames(Procrustes$coords)
[[3]]
[1] "Paraneetroplus_nebuliferus" "Chuco_intermedium"
[3] "Chuco_microphtalmus" "Cincelichthys_pearsei"
[5] "Kihnichthys_uefermanni" "Maskaheros_argenteus"
[7] "Maskaheros_regani" "Oscura_heterospila"
[9] "Paraneetroplus_bulleri" "Rheoheros_lentiginosus"
[11] "Theraps_irregularis" "Thrichromis_salvini"
[13] "Vieja_bifasciata" "Vieja_breidhori"
[15] "Vieja_fenestrata" "Vieja_gutttulata"
[17] "Vieja_hartwegii" "Vieja_maculicauda"
[19] "Vieja_melanurus" "Vieja_zonata"
[21] "Wajpamheros_nourisatti"
phy$tip.label
[1] "Chuco_microphthalmus" "Chuco_intermedium"
[3] "Cincelichthys_pearsei" "Kihnichthys_ufermanni"
[5] "Theraps_irregularis" "Wajpamheros_nourissati"
[7] "Rheoheros_lentiginosus" "Oscura_heterospila"
[9] "Maskaheros_argenteus" "Maskaheros_regani"
[11] "Paraneetroplus_bulleri" "Paraneetroplus_nebuliferus"
[13] "Vieja_bifasciata" "Vieja_breidohri"
[15] "Vieja_hartwegi" "Vieja_fenestrata"
[17] "Vieja_guttulata" "Vieja_zonata"
[19] "Vieja_maculicauda" "Vieja_melanurus"
[21] "Trichromis_salvini"
### I cannot change my phylogeny topology, so, I change the order of
the species in my tps file and set names according to phy tip labels ##
newnames2=c("Chuco_microphtalmus","Chuco_intermedium","Cincelichthys_pearsei","Kihnichthys_uefermanni","Theraps_irregularis", "Wajpamheros_nourisatti", "Rheoheros_lentiginosus", "Oscura_heterospila","Maskaheros_argenteus","Maskaheros_regani","Paraneetroplus_bulleri","Paraneetroplus_nebuliferus","Vieja_bifasciata","Vieja_breidhori","Vieja_hartwegii","Vieja_fenestrata","Vieja_gutttulata","Vieja_zonata","Vieja_maculicauda","Vieja_melanurus","Thrichromis_salvini")
dimnames(Procrustes$coords)[[3]]=newnames2
dimnames(Procrustes$coords)
[[3]]
[1] "Chuco_microphtalmus" "Chuco_intermedium"
[3] "Cincelichthys_pearsei" "Kihnichthys_uefermanni"
[5] "Theraps_irregularis" "Wajpamheros_nourisatti"
[7] "Rheoheros_lentiginosus" "Oscura_heterospila"
[9] "Maskaheros_argenteus" "Maskaheros_regani"
[11] "Paraneetroplus_bulleri" "Paraneetroplus_nebuliferus"
[13] "Vieja_bifasciata" "Vieja_breidhori"
[15] "Vieja_hartwegii" "Vieja_fenestrata"
[17] "Vieja_gutttulata" "Vieja_zonata"
[19] "Vieja_maculicauda" "Vieja_melanurus"
[21] "Thrichromis_salvini"
phy$tip.label
[1] "Chuco_microphthalmus" "Chuco_intermedium"
[3] "Cincelichthys_pearsei" "Kihnichthys_ufermanni"
[5] "Theraps_irregularis" "Wajpamheros_nourissati"
[7] "Rheoheros_lentiginosus" "Oscura_heterospila"
[9] "Maskaheros_argenteus" "Maskaheros_regani"
[11] "Paraneetroplus_bulleri" "Paraneetroplus_nebuliferus"
[13] "Vieja_bifasciata" "Vieja_breidohri"
[15] "Vieja_hartwegi" "Vieja_fenestrata"
[17] "Vieja_guttulata" "Vieja_zonata"
[19] "Vieja_maculicauda" "Vieja_melanurus"
[21] "Trichromis_salvini"
##Now the names are identical and in the same position, but the trouble persists##
name.check(Procrustes,phy)
[1] "OK
match(rownames(Procrustes),phy$tip.labels)
integer(0)
obj<-name.check(phy,landmarks)
obj
$tree_not_data
[1] "Chuco_intermedium" "Chuco_microphthalmus"
[3] "Cincelichthys_pearsei" "Kihnichthys_ufermanni"
[5] "Maskaheros_argenteus" "Maskaheros_regani"
[7] "Oscura_heterospila" "Paraneetroplus_bulleri"
[9] "Paraneetroplus_nebuliferus" "Rheoheros_lentiginosus"
[11] "Theraps_irregularis" "Trichromis_salvini"
[13] "Vieja_bifasciata" "Vieja_breidohri"
[15] "Vieja_fenestrata" "Vieja_guttulata"
[17] "Vieja_hartwegi" "Vieja_maculicauda"
[19] "Vieja_melanurus" "Vieja_zonata"
[21] "Wajpamheros_nourissati"
$data_not_tree
NULL
##### I update geomorph and RRPP directly from Github and also update Matrix library##
I am using R 4.5.1, geomorph 4.0.10, RRPP 2.1.2 and Matrix 1.7-3
Kindly appreciate any help
Best regards
--
Omar Mejía G
Laboratorio de Variación Biológica y Evolución
Departamento de Zoología
Escuela Nacional de Ciencias Biológicas-IPN
Adams, Dean [EEOB]
Jul 1, 2025, 5:43:03 PMJul 1
to geomorph-...@googlegroups.com
Oscar,
There are two problems with your code and what you are trying to do.
First, you did not correctly point readland.tps to your species names, so the function did not find them. For your file, you need 'specID="ID"' not 'none'.
Second, your Csize values are all exactly = 1.0. Thus, the regression will not run (as it should not).
Below is a fix to the code, and some 'fake' CSize data showing that data with variation will actually run.
Dean
####
library(geomorph)
library(ape)
landmarks=readland.tps("test.tps",specID="ID")
Procrustes=gpagen(landmarks)
phy=read.tree("Oscar.tre")
plot(phy)
gdf2 <- geomorph.data.frame(Procrustes,phy=phy)
attributes(gdf2)
sp.pgls <- procD.pgls(coords ~ Csize, phy = phy, data = gdf2)
gdf2$CsizeFake <- rnorm(n = length(gdf2$Csize))
sp.pgls2 <- procD.pgls(coords ~ CsizeFake, phy = phy, data = gdf2)
anova(sp.pgls2)
--Dr. Dean C. AdamsDistinguished ProfessorDepartment of Ecology, Evolution, and Organismal BiologyIowa State Universityphone: 515-294-3834
From: geomorph-...@googlegroups.com <geomorph-...@googlegroups.com> on behalf of Omar Mejía <posgradobio...@gmail.com>
Sent: Tuesday, July 1, 2025 8:46 AM
To: geomorph-...@googlegroups.com <geomorph-...@googlegroups.com>
Subject: Re: [geomorph-r-package] trouble with procD.pgls function
To: geomorph-...@googlegroups.com <geomorph-...@googlegroups.com>
Subject: Re: [geomorph-r-package] trouble with procD.pgls function
To view this discussion, visit
https://groups.google.com/d/msgid/geomorph-r-package/CAOEgSgku4PS8XKRhEnhYszwDED8CmEN8o_S-7%2BhEdeeXyXK4pw%40mail.gmail.com.
Adams, Dean [EEOB]
Jul 1, 2025, 5:43:17 PMJul 1
to geomorph-...@googlegroups.com
Sorry, Omar (not Oscar)....
Dean
--Dr. Dean C. AdamsDistinguished ProfessorDepartment of Ecology, Evolution, and Organismal BiologyIowa State Universityphone: 515-294-3834
From: geomorph-...@googlegroups.com <geomorph-...@googlegroups.com> on behalf of Omar Mejía <posgradobio...@gmail.com>
Sent: Tuesday, July 1, 2025 8:46 AM
To: geomorph-...@googlegroups.com <geomorph-...@googlegroups.com>
To: geomorph-...@googlegroups.com <geomorph-...@googlegroups.com>
Subject: Re: [geomorph-r-package] trouble with procD.pgls function
To view this discussion, visit
https://groups.google.com/d/msgid/geomorph-r-package/CAOEgSgku4PS8XKRhEnhYszwDED8CmEN8o_S-7%2BhEdeeXyXK4pw%40mail.gmail.com.
Omar Mejía
Jul 1, 2025, 6:39:07 PMJul 1
to geomorph-...@googlegroups.com
Dear Dean,
Kindly appreciate your full explanation, at least now I can explain the editor why we prefer the E-PGLS instead the suggested test
Best regards
Omar Mejía G
Laboratorio de Variación Biológica y Evolución
Departamento de Zoología
Escuela Nacional de Ciencias Biológicas-IPN
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