Appendix-6b-Model-diagnostics-and-outliers.RmdFor your independent project you need to carry out relevant model diagnostics. If your major analysis only requires t-tests, you should re-fit at least one of your t-tests a linear model using lm() and check for normality and homogeneity of variance using relevant techniques.
The following script is just a place holder. For full information on model diangostics see the the (diagnostics tutorial](https://brouwern.github.io/mammalsmilk/articles/g-linear_reg_diagnostics.html) in the mammalsmilk package.
In this the mammalsmilkRA repository I have split up the analysis into several subscripts:
These can be combined if you want.
library(dplyr) # for exploratory analyses
library(ggpubr) # plotting using ggplto2
library(cowplot)
library(lme4)
library(arm)
library(stringr)
library(bbmle)
library(plotrix) ##std.error function for SE
library(psych)
library(here)file. <- "Appendix-2-Analysis-Data_mammalsmilkRA.csv"
path. <- here("/inst/extdata/",file.)
milk <- read.csv(path., skip = 3)
genus_spp_subspp_mat <- milk$spp %>% str_split_fixed(" ", n = 3)
milk$genus <- genus_spp_subspp_mat[,1]head(milk)
#> ord fam spp mass.fem gest.mo
#> 1 Artiodactyla Bovidae Bos frontalis 800000 9.02
#> 2 Artiodactyla Bovidae Capra ibex 53000 5.60
#> 3 Artiodactyla Bovidae Connocheates taurinus taurinus 170500 8.32
#> 4 Artiodactyla Bovidae Connocheates gnou 200000 8.50
#> 5 Artiodactyla Bovidae Damaliscus pygargus phillipsi 61000 8.00
#> 6 Artiodactyla Bovidae Gazella dorcas 20600 4.74
#> lac.mo mass.litter repro.output dev.birth diet arid biome N
#> 1 4.5 26949 0.03 3 herbivore no terrestrial 4+
#> 2 7.5 3489 0.07 3 herbivore no terrestrial 24
#> 3 8.0 17717 0.10 3 herbivore yes terrestrial 5
#> 4 7.5 11110 0.06 3 herbivore yes terrestrial 3
#> 5 4.0 6500 0.11 3 herbivore yes terrestrial 4
#> 6 2.8 1771 0.09 3 herbivore yes terrestrial 16
#> fat gest.month lacat.mo prot sugar energy genus
#> 1 7.0 9.02 4.5 6.3 5.2 1.21 Bos
#> 2 12.4 5.60 7.5 5.7 NA NA Capra
#> 3 7.5 8.32 8.0 4.1 5.3 1.13 Connocheates
#> 4 5.5 8.50 7.5 4.3 4.1 0.91 Connocheates
#> 5 8.6 8.00 4.0 5.6 4.9 1.31 Damaliscus
#> 6 8.8 4.74 2.8 8.8 NA NA Gazella
tail(milk)
#> ord fam spp mass.fem gest.mo
#> 125 Rodentia Muridae Pseudomys australis 65 1.02
#> 126 Rodentia Muridae Rattus norvegicus 253 0.71
#> 127 Rodentia Octodontidae Octodon degus 235 2.96
#> 128 Rodentia Scuiridae Tamias amoenus 53 0.98
#> 129 Rodentia Scuiridae Urocitellus columbianus 406 0.84
#> 130 Soricomorpha11 Soricidae Crocidura russula 14 0.97
#> lac.mo mass.litter repro.output dev.birth diet arid biome
#> 125 0.9 13 0.20 0 herbivore yes terrestrial
#> 126 0.8 51 0.20 0 omnivore no terrestrial
#> 127 1.2 74 0.31 3 herbivore yes terrestrial
#> 128 1.5 14 0.26 0 omnivore no terrestrial
#> 129 1.0 32 0.08 0 herbivore no terrestrial
#> 130 0.8 4 0.29 0 carnivore no terrestrial
#> N fat gest.month lacat.mo prot sugar energy genus
#> 125 7-Jun 12.1 1.02 0.9 6.4 3.6 1.62 Pseudomys
#> 126 18-Mar 8.8 0.71 0.8 8.1 3.8 1.43 Rattus
#> 127 7 20.1 2.96 1.2 4.4 2.7 2.20 Octodon
#> 128 11 21.7 0.98 1.5 8.1 4.3 2.62 Tamias
#> 129 26 9.2 0.84 1.0 10.7 3.4 1.60 Urocitellus
#> 130 3 30.0 0.97 0.8 9.4 3.0 3.40 Crocidura
summary(milk)
#> ord fam spp
#> Artiodactyla :23 Bovidae :13 Acomys cahirinus : 1
#> Carnivora :23 Cercopithecidae: 8 Alces alces : 1
#> Primates :22 Cervidae : 7 Aloutta palliata : 1
#> Rodentia :17 Muridae : 7 Aloutta seniculus : 1
#> Chiroptera :10 Otariidae : 7 Arctocephalus australis: 1
#> Diprotodontia:10 Phocidae : 7 Arctocephalus gazella : 1
#> (Other) :25 (Other) :81 (Other) :124
#> mass.fem gest.mo lac.mo mass.litter
#> Min. : 8 Min. : 0.400 Min. : 0.300 Min. : 0.3
#> 1st Qu.: 857 1st Qu.: 1.405 1st Qu.: 1.625 1st Qu.: 42.0
#> Median : 5716 Median : 5.000 Median : 4.500 Median : 423.5
#> Mean : 2229475 Mean : 5.624 Mean : 6.092 Mean : 52563.8
#> 3rd Qu.: 107500 3rd Qu.: 8.365 3rd Qu.: 8.225 3rd Qu.: 7038.2
#> Max. :170000000 Max. :21.460 Max. :42.000 Max. :2272500.0
#>
#> repro.output dev.birth diet arid
#> Min. :0.00003 Min. :0.000 carnivore:32 no :91
#> 1st Qu.:0.04000 1st Qu.:1.000 herbivore:61 yes:39
#> Median :0.08000 Median :2.000 omnivore :37
#> Mean :0.10374 Mean :1.831
#> 3rd Qu.:0.13750 3rd Qu.:3.000
#> Max. :0.50000 Max. :4.000
#>
#> biome N fat gest.month
#> aquatic : 22 4 :13 Min. : 0.20 Min. : 0.400
#> terrestrial:108 3 :11 1st Qu.: 4.65 1st Qu.: 1.405
#> 6 :10 Median : 8.55 Median : 5.000
#> 7 : 9 Mean :13.99 Mean : 5.624
#> 5 : 8 3rd Qu.:16.82 3rd Qu.: 8.365
#> 24 : 5 Max. :61.10 Max. :21.460
#> (Other):74
#> lacat.mo prot sugar energy
#> Min. : 0.300 Min. : 1.100 Min. : 0.02 Min. :0.360
#> 1st Qu.: 1.625 1st Qu.: 4.125 1st Qu.: 3.00 1st Qu.:0.965
#> Median : 4.500 Median : 6.750 Median : 4.70 Median :1.365
#> Mean : 6.092 Mean : 6.673 Mean : 4.94 Mean :1.680
#> 3rd Qu.: 8.225 3rd Qu.: 9.200 3rd Qu.: 6.60 3rd Qu.:2.045
#> Max. :42.000 Max. :15.800 Max. :14.00 Max. :5.890
#> NA's :16 NA's :16
#> genus
#> Length:130
#> Class :character
#> Mode :character
#>
#>
#>
#>