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min20Gee.Rmd
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min20Gee.Rmd
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---
title: "min20GEE"
author: "Walker M"
date: "2023-09-11"
output: html_document
---
```{r results="hide"}
library(ape)
library(nlme)
library(rms)
library(phytools)
library(geiger)
library(caper)
library(tidyverse)
library(cowplot)
library(ggrepel)
library(ggsci)
library(patchwork)
library(gee)
#read data
Data <- read.csv("min20-2022.05.16.csv")
Age <- read.csv("cleanPath.min20.062822.csv")
#sometimes this returns error stating "argument "by" is missing". Restarting R via session dropdown will fix this
max_longevity.months_per_species <- Age %>%
group_by(Species) %>%
summarize(max_longevity.months = max(age_months))
Data <- merge(Data, max_longevity.months_per_species, by = "Species", all.x = TRUE)
```
#adult weight neo
```{r}
cutData <- Data[,c(1,5,9,10,11,12,38,42),drop=FALSE]
cutData[cutData$adult_weight == -1, ] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
adultWeight<-log10(cutData$adult_weight.g.)
NeoplasiaOccurences<-cutData$NeoplasiaWithDenominators
NonOccurences<-(cutData$RecordsWithDenominators-cutData$NeoplasiaWithDenominators)
compar<-compar.gee(cbind(NeoplasiaOccurences, NonOccurences) ~adultWeight, phy = pruned.tree, family = "binomial")
compar
coef(compar)[2]
```
#adult weight mal
```{r}
cutData <- Data[,c(1,5,9,10,11,16,38,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies <- cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
MalignancyOccurences<-cutData$Malignant
NonOccurences<-(cutData$RecordsWithDenominators-cutData$Malignant)
compar<-compar.gee(cbind(MalignancyOccurences, NonOccurences) ~adultWeight, phy = pruned.tree, family = "binomial")
compar
```
max age neo
```{r}
cutData <- Data[,c(1,5,9,10,11,12,40,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
max_longevity.months.<-log10(cutData$max_longevity.months.)
NeoplasiaOccurences<-cutData$NeoplasiaWithDenominators
NonOccurences<-(cutData$RecordsWithDenominators-cutData$NeoplasiaWithDenominators)
compar<-compar.gee(cbind(NeoplasiaOccurences, NonOccurences) ~max_longevity.months., phy = pruned.tree, family = "binomial")
compar
```
max age mal
```{r}
cutData <- Data[,c(1,5,9,10,11,16,40,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
MalignancyOccurences<-cutData$Malignant
NonOccurences<-(cutData$RecordsWithDenominators-cutData$Malignant)
compar<-compar.gee(cbind(MalignancyOccurences, NonOccurences) ~max_longevity.months., phy = pruned.tree, family = "binomial")
compar
```
Gest neo
```{r}
cutData <- Data[,c(1,5,9,10,11,12,30,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
Gestation<-log10(cutData$Gestation.months.)
NeoplasiaOccurences<-cutData$NeoplasiaWithDenominators
NonOccurences<-(cutData$RecordsWithDenominators-cutData$NeoplasiaWithDenominators)
compar<-compar.gee(cbind(NeoplasiaOccurences, NonOccurences) ~Gestation, phy = pruned.tree, family = "binomial")
compar
```
Gest mal
```{r}
cutData <- Data[,c(1,5,9,10,11,16,30,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
MalignancyOccurences<-cutData$Malignant
NonOccurences<-(cutData$RecordsWithDenominators-cutData$Malignant)
compar<-compar.gee(cbind(MalignancyOccurences, NonOccurences) ~Gestation, phy = pruned.tree, family = "binomial")
compar
```
Long+Gest+Mass Neo
```{r}
cutData <- Data[,c(1,5,9,10,11,12,30,40,38,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
Gestation<-log10(cutData$Gestation.months.)
Longevity<-log10(cutData$max_longevity.months.)
Mass<-log10(cutData$adult_weight.g.)
NeoplasiaOccurences<-cutData$NeoplasiaWithDenominators
NonOccurences<-(cutData$RecordsWithDenominators-cutData$NeoplasiaWithDenominators)
compar<-compar.gee(cbind(NeoplasiaOccurences, NonOccurences) ~Gestation+Longevity+Mass, phy = pruned.tree, family = "binomial")
compar
```
Long+Gest+Mass Mal
```{r}
cutData <- Data[,c(1,5,9,10,11,16,30,40,38,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
Gestation<-log10(cutData$Gestation.months.)
Longevity<-log10(cutData$max_longevity.months.)
Mass<-log10(cutData$adult_weight.g.)
MalignancyOccurences<-cutData$Malignant
NonOccurences<-(cutData$RecordsWithDenominators-cutData$Malignant)
compar<-compar.gee(cbind(MalignancyOccurences, NonOccurences) ~Gestation+Longevity+Mass, phy = pruned.tree, family = "binomial")
compar
```
Gest+Mass Neo
```{r}
cutData <- Data[,c(1,5,9,10,11,12,30,38,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
Gestation<-log10(cutData$Gestation.months.)
Mass<-log10(cutData$adult_weight.g.)
NeoplasiaOccurences<-cutData$NeoplasiaWithDenominators
NonOccurences<-(cutData$RecordsWithDenominators-cutData$NeoplasiaWithDenominators)
compar<-compar.gee(cbind(NeoplasiaOccurences, NonOccurences) ~Gestation+Mass, phy = pruned.tree, family = "binomial")
compar
```
Gest+Mass Mal
```{r}
cutData <- Data[,c(1,5,9,10,11,16,30,38,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
Gestation<-log10(cutData$Gestation.months.)
Mass<-log10(cutData$adult_weight.g.)
MalignancyOccurences<-cutData$Malignant
NonOccurences<-(cutData$RecordsWithDenominators-cutData$Malignant)
compar<-compar.gee(cbind(MalignancyOccurences, NonOccurences) ~Gestation+Mass, phy = pruned.tree, family = "binomial")
compar
```
Filter for Mammals
```{r}
#read data
Data <- read.csv("min20-2022.05.16.csv")
Data<- filter(Data, Clade == "Mammalia")
Age <- read.csv("cleanPath.min20.062822.csv")
max_longevity.months._per_species <- Age %>%
group_by(Species) %>%
summarize(max_longevity.months. = max(age_months))
Data <- merge(Data, max_longevity.months._per_species, by = "Species", all.x = TRUE)
```
#adult weight neo mammals
```{r}
cutData <- Data[,c(1,5,9,10,11,12,38,42),drop=FALSE]
cutData[cutData$adult_weight == -1, ] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
adultWeight<-log10(cutData$adult_weight.g.)
NeoplasiaOccurences<-cutData$NeoplasiaWithDenominators
NonOccurences<-(cutData$RecordsWithDenominators-cutData$NeoplasiaWithDenominators)
compar<-compar.gee(cbind(NeoplasiaOccurences, NonOccurences) ~adultWeight, phy = pruned.tree, family = "binomial")
compar
```
#adult weight mal mammals
```{r}
cutData <- Data[,c(1,5,9,10,11,16,38,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies <- cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
MalignancyOccurences<-cutData$Malignant
NonOccurences<-(cutData$RecordsWithDenominators-cutData$Malignant)
compar<-compar.gee(cbind(MalignancyOccurences, NonOccurences) ~adultWeight, phy = pruned.tree, family = "binomial")
compar
```
max age neo mammals
```{r}
cutData <- Data[,c(1,5,9,10,11,12,40,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
max_longevity.months.<-log10(cutData$max_longevity.months.)
NeoplasiaOccurences<-cutData$NeoplasiaWithDenominators
NonOccurences<-(cutData$RecordsWithDenominators-cutData$NeoplasiaWithDenominators)
compar<-compar.gee(cbind(NeoplasiaOccurences, NonOccurences) ~max_longevity.months., phy = pruned.tree, family = "binomial")
compar
```
max age mal mammals
```{r}
cutData <- Data[,c(1,5,9,10,11,16,40,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
MalignancyOccurences<-cutData$Malignant
NonOccurences<-(cutData$RecordsWithDenominators-cutData$Malignant)
compar<-compar.gee(cbind(MalignancyOccurences, NonOccurences) ~max_longevity.months., phy = pruned.tree, family = "binomial")
compar
```
Gest neo mammals
```{r}
cutData <- Data[,c(1,5,9,10,11,12,30,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
Gestation<-log10(cutData$Gestation.months.)
NeoplasiaOccurences<-cutData$NeoplasiaWithDenominators
NonOccurences<-(cutData$RecordsWithDenominators-cutData$NeoplasiaWithDenominators)
compar<-compar.gee(cbind(NeoplasiaOccurences, NonOccurences) ~Gestation, phy = pruned.tree, family = "binomial")
compar
```
Gest mal mammals
```{r}
cutData <- Data[,c(1,5,9,10,11,16,30,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
MalignancyOccurences<-cutData$Malignant
NonOccurences<-(cutData$RecordsWithDenominators-cutData$Malignant)
compar<-compar.gee(cbind(MalignancyOccurences, NonOccurences) ~Gestation, phy = pruned.tree, family = "binomial")
compar
```
Long+Gest+Mass Neo mammals
```{r}
cutData <- Data[,c(1,5,9,10,11,12,30,40,38,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
Gestation<-log10(cutData$Gestation.months.)
Longevity<-log10(cutData$max_longevity.months.)
Mass<-log10(cutData$adult_weight.g.)
NeoplasiaOccurences<-cutData$NeoplasiaWithDenominators
NonOccurences<-(cutData$RecordsWithDenominators-cutData$NeoplasiaWithDenominators)
compar<-compar.gee(cbind(NeoplasiaOccurences, NonOccurences) ~Gestation+Longevity+Mass, phy = pruned.tree, family = "binomial")
compar
```
Long+Gest+Mass Mal mammals
```{r}
cutData <- Data[,c(1,5,9,10,11,16,30,40,38,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
Gestation<-log10(cutData$Gestation.months.)
Longevity<-log10(cutData$max_longevity.months.)
Mass<-log10(cutData$adult_weight.g.)
MalignancyOccurences<-cutData$Malignant
NonOccurences<-(cutData$RecordsWithDenominators-cutData$Malignant)
compar<-compar.gee(cbind(MalignancyOccurences, NonOccurences) ~Gestation+Longevity+Mass, phy = pruned.tree, family = "binomial")
compar
```
Filter for Sauropsids
```{r}
#read data
Data <- read.csv("min20-2022.05.16.csv")
Data<- filter(Data, Clade == "Sauropsida")
Age <- read.csv("cleanPath.min20.062822.csv")
max_longevity.months._per_species <- Age %>%
group_by(Species) %>%
summarize(max_longevity.months. = max(age_months))
Data <- merge(Data, max_longevity.months._per_species, by = "Species", all.x = TRUE)
```
#adult weight neo Sauropsids
```{r}
cutData <- Data[,c(1,5,9,10,11,12,38,42),drop=FALSE]
cutData[cutData$adult_weight == -1, ] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
adultWeight<-log10(cutData$adult_weight.g.)
NeoplasiaOccurences<-cutData$NeoplasiaWithDenominators
NonOccurences<-(cutData$RecordsWithDenominators-cutData$NeoplasiaWithDenominators)
compar<-compar.gee(cbind(NeoplasiaOccurences, NonOccurences) ~adultWeight, phy = pruned.tree, family = "binomial")
compar
```
#adult weight mal Sauropsids
```{r}
cutData <- Data[,c(1,5,9,10,11,16,38,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies <- cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
MalignancyOccurences<-cutData$Malignant
NonOccurences<-(cutData$RecordsWithDenominators-cutData$Malignant)
compar<-compar.gee(cbind(MalignancyOccurences, NonOccurences) ~adultWeight, phy = pruned.tree, family = "binomial")
compar
```
max age neo saur
```{r}
cutData <- Data[,c(1,5,9,10,11,12,40,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
max_longevity.months.<-log10(cutData$max_longevity.months.)
NeoplasiaOccurences<-cutData$NeoplasiaWithDenominators
NonOccurences<-(cutData$RecordsWithDenominators-cutData$NeoplasiaWithDenominators)
compar<-compar.gee(cbind(NeoplasiaOccurences, NonOccurences) ~max_longevity.months., phy = pruned.tree, family = "binomial")
compar
```
max age mal saur
```{r}
cutData <- Data[,c(1,5,9,10,11,16,40,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
MalignancyOccurences<-cutData$Malignant
NonOccurences<-(cutData$RecordsWithDenominators-cutData$Malignant)
compar<-compar.gee(cbind(MalignancyOccurences, NonOccurences) ~max_longevity.months., phy = pruned.tree, family = "binomial")
compar
```
Gest neo saur
```{r}
cutData <- Data[,c(1,5,9,10,11,12,30,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
Gestation<-log10(cutData$Gestation.months.)
NeoplasiaOccurences<-cutData$NeoplasiaWithDenominators
NonOccurences<-(cutData$RecordsWithDenominators-cutData$NeoplasiaWithDenominators)
compar<-compar.gee(cbind(NeoplasiaOccurences, NonOccurences) ~Gestation, phy = pruned.tree, family = "binomial")
compar
```
Gest mal saur
```{r}
cutData <- Data[,c(1,5,9,10,11,16,30,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
MalignancyOccurences<-cutData$Malignant
NonOccurences<-(cutData$RecordsWithDenominators-cutData$Malignant)
compar<-compar.gee(cbind(MalignancyOccurences, NonOccurences) ~Gestation, phy = pruned.tree, family = "binomial")
compar
```
Long+Gest+Mass Neo suar
```{r}
cutData <- Data[,c(1,5,9,10,11,12,30,40,38,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
Gestation<-log10(cutData$Gestation.months.)
Longevity<-log10(cutData$max_longevity.months.)
Mass<-log10(cutData$adult_weight.g.)
NeoplasiaOccurences<-cutData$NeoplasiaWithDenominators
NonOccurences<-(cutData$RecordsWithDenominators-cutData$NeoplasiaWithDenominators)
compar<-compar.gee(cbind(NeoplasiaOccurences, NonOccurences) ~Gestation+Longevity+Mass, phy = pruned.tree, family = "binomial")
compar
```
Long+Gest+Mass Mal saur
```{r}
cutData <- Data[,c(1,5,9,10,11,16,30,40,38,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
Gestation<-log10(cutData$Gestation.months.)
Longevity<-log10(cutData$max_longevity.months.)
Mass<-log10(cutData$adult_weight.g.)
MalignancyOccurences<-cutData$Malignant
NonOccurences<-(cutData$RecordsWithDenominators-cutData$Malignant)
compar<-compar.gee(cbind(MalignancyOccurences, NonOccurences) ~Gestation+Longevity+Mass, phy = pruned.tree, family = "binomial")
compar
```
Filter for Amphibians
```{r}
#read data
Data <- read.csv("min20-2022.05.16.csv")
Data<- filter(Data, Clade == "Amphibia")
Age <- read.csv("cleanPath.min20.062822.csv")
max_longevity.months._per_species <- Age %>%
group_by(Species) %>%
summarize(max_longevity.months. = max(age_months))
Data <- merge(Data, max_longevity.months._per_species, by = "Species", all.x = TRUE)
```
#adult weight neo Amphibians
```{r}
cutData <- Data[,c(1,5,9,10,11,12,38,42),drop=FALSE]
cutData[cutData$adult_weight == -1, ] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
adultWeight<-log10(cutData$adult_weight.g.)
NeoplasiaOccurences<-cutData$NeoplasiaWithDenominators
NonOccurences<-(cutData$RecordsWithDenominators-cutData$NeoplasiaWithDenominators)
compar<-compar.gee(cbind(NeoplasiaOccurences, NonOccurences) ~adultWeight, phy = pruned.tree, family = "binomial")
compar
```
#adult weight mal Amphibians
```{r}
cutData <- Data[,c(1,5,9,10,11,16,38,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies <- cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
MalignancyOccurences<-cutData$Malignant
NonOccurences<-(cutData$RecordsWithDenominators-cutData$Malignant)
compar<-compar.gee(cbind(MalignancyOccurences, NonOccurences) ~adultWeight, phy = pruned.tree, family = "binomial")
compar
```
max age neo amph
```{r eval=FALSE, include=FALSE}
library(phytools)
cutData <- Data[,c(1,5,9,10,11,12,40,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
pruned.tree$edge.length[which(pruned.tree$edge.length <=0)] <- 1e-10
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
max_longevity.months.<-log10(cutData$max_longevity.months.)
MalignancyOccurences<-cutData$NeoplasiaWithDenominators
NonOccurences<-(cutData$RecordsWithDenominators-cutData$NeoplasiaWithDenominators)
#recompute branch lengths
tree2<-compute.brlen(phy=pruned.tree,method="Grafen",power=0.5)
compar<-compar.gee(cbind(MalignancyOccurences, NonOccurences) ~max_longevity.months., phy = tree2, family = "binomial")
compar
```
max age mal amph
```{r eval=FALSE, include=FALSE}
cutData <- Data[,c(1,5,9,10,11,16,40,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
MalignancyOccurences<-cutData$Malignant
NonOccurences<-(cutData$RecordsWithDenominators-cutData$Malignant)
#recompute branch lengths
tree2<-compute.brlen(phy=pruned.tree,method="Grafen",power=0.5)
compar<-compar.gee(cbind(MalignancyOccurences, NonOccurences) ~max_longevity.months., phy = tree2, family = "binomial")
compar
```
Gest neo amph
```{r}
cutData <- Data[,c(1,5,9,10,11,12,30,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(
tree$tip.label, includedSpecies))
pruned.tree <- keep.tip(pruned.tree,pruned.tree$tip.label)
cutData$Keep <- cutData$Species %in% pruned.tree$tip.label
cutData <- cutData[!(cutData$Keep==FALSE),]
rownames(cutData)<-cutData$Species
SE<-setNames(cutData$SE_simple,cutData$Species)[rownames(cutData)]
Gestation<-log10(cutData$Gestation.months.)
NeoplasiaOccurences<-cutData$NeoplasiaWithDenominators
NonOccurences<-(cutData$RecordsWithDenominators-cutData$NeoplasiaWithDenominators)
#recompute branch lengths
tree2<-compute.brlen(phy=pruned.tree,method="Grafen",power=0.5)
compar<-compar.gee(cbind(NeoplasiaOccurences, NonOccurences) ~Gestation, phy = tree2, family = "binomial")
compar
```
Gest mal amph
```{r}
cutData <- Data[,c(1,5,9,10,11,16,30,42),drop=FALSE]
cutData[cutData < 0] <-NA
cutData <- na.omit(cutData)
tree <- read.tree("min20Fixed516.nwk")
cutData$Species <- gsub(" ", "_", cutData$Species)
cutData$common_name<-gsub("_", "", cutData$common_name)
includedSpecies<-cutData$Species
pruned.tree<-drop.tip(
tree, setdiff(