The model output coefficients list only two out of the three discrete values. What am I doing wrong?
> mammaldata<-read.table("C:/Users/Cheryl/Google Drive/Uni/Life706 - Project/Data//Data 2.txt",sep = "\t",header = TRUE)
> View(mammaldata)
> str(mammaldata)
'data.frame': 54 obs. of 11 variables:
$ Order : Factor w/ 11 levels "Artiodactyla",..: 1 11 11 1 1 11 11 11 6 11 ...
$ Family : Factor w/ 31 levels "Antilocapridae",..: 1 20 20 2 3 4 7 20 29 28 ...
$ Species : Factor w/ 54 levels "Antilocapra_americana",..: 1 2 3 4 5 6 7 8 9 10 ...
$ P50 : num 28.3 33.5 38.4 28.7 25.9 29 26.8 33.2 36.9 22 ...
$ BMR : num 5.62 36.4 23.28 3.18 1.99 ...
$ Adult_Body_Mass_g : num 47450 21.9 120 618642.4 492714.5 ...
$ Gestation_Period_days: num 248 23.7 21.2 280.5 386.5 ...
$ Litter_Size : num 1.93 5.16 4.76 1 0.98 3.45 2.5 4.31 4.04 4.43 ...
$ Litters_per_Year : num 1 3.75 3.5 1 1 5 2.5 3.5 3.5 1 ...
$ Max._Longevity_years : num 15.5 6.3 2.5 20 28.4 12 10 4.9 4 11 ...
$ Placenta_Type : Factor w/ 3 levels "Endotheliochorial",..: 2 3 3 2 2 3 3 3 3 3 ...
> names(mammaldata)
[1] "Order" "Family" "Species"
[4] "P50" "BMR" "Adult_Body_Mass_g"
[7] "Gestation_Period_days" "Litter_Size" "Litters_per_Year"
[10] "Max._Longevity_years" "Placenta_Type"
> mammaltree<-read.nexus("C:/Users/Cheryl/Google Drive/Uni/Life706 - Project/Data/1 tree.nex")
> mammaldata$dropped$unmatched.rows
NULL
> mammals$dropped$unmatched.rows
character(0)
> mammaltree
Phylogenetic tree with 4510 tips and 2108 internal nodes.
Tip labels:
Tachyglossus_aculeatus, Zaglossus_bruijni, Ornithorhynchus_anatinus, Anomalurus_beecrofti, Anomalurus_derbianus, Anomalurus_pelii, ...
Node labels:
'1', '2_Monotremata', '3_Tachyglossidae', '4', '5_Eutheria', '6', ...
Rooted; includes branch lengths.
> mod2<-pgls(log(P50)~ log(Gestation_Period_days)+Placenta_Type,data = mammals, lambda = "ML")
> summary(mod2)
Call:
pgls(formula = log(P50) ~ log(Gestation_Period_days) + Placenta_Type,
data = mammals, lambda = "ML")
Residuals:
Min 1Q Median 3Q Max
-0.03301 -0.01658 -0.00183 0.01022 0.03765
Branch length transformations:
kappa [Fix] : 1.000
lambda [ ML] : 0.746
lower bound : 0.000, p = 0.001461
upper bound : 1.000, p = 0.00073547
95.0% CI : (0.295, 0.944)
delta [Fix] : 1.000
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 4.425391 0.239126 18.5065 < 2.2e-16 ***
log(Gestation_Period_days) -0.171626 0.042427 -4.0452 0.000181 ***
Placenta_TypeEpitheliochorial -0.148696 0.116891 -1.2721 0.209228
Placenta_TypeHemochorial -0.291269 0.105203 -2.7686 0.007875 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 0.01904 on 50 degrees of freedom
Multiple R-squared: 0.2788, Adjusted R-squared: 0.2356
F-statistic: 6.444 on 3 and 50 DF, p-value: 0.0008945
I've included as much of the code as I thought may be informative. Any help would be greatly appreciated.
