In brouwern/DRmencia: Data and code to replicate analyses for Latta, Brouwer, et al. 2018. PeerJ.
knitr::opts_chunk$set(echo = TRUE)
This script create the Sampe size, age ratio, and sex ratio part of tables 5 and 6
It uses a dataset where Mencia and Aceitillar data have been combined into a single long-format dataframe
Libraries
library(reshape2)
library(here)
Load data
Load annual Captures data with Mencia AND Aceitillar combined
filename <- "annual_captures.RData"
load(here::here("data",filename))
Subset just by focal species
These are the spp focused on in teh original MS; they are the most commonly caught
Names of species
focal.mig <- c("OVEN","BAWW","COYE","AMRE","CMWA",
"BTBW","PAWA","PRAW")
focal.res <- c("HILC" # formerly HLCU
,"STOF"
,"RLTH"
,"NOMO"
,"GTGT" # formerly GRWA
,"BANA"
,"BCPT"
,"YFGR"
,"BFGR"
,"GABU")
focals <- c(focal.mig,focal.res)
Subset
i.focals <- which(ann_caps$spp.code %in% focals)
ann_caps.foc <- ann_caps[i.focals,]
dim(ann_caps.foc)
dim(ann_caps)
Set spp order for tables
replicate order from tables in oridingal MS
ann_caps.foc$spp.code <- factor(ann_caps.foc$spp.code,
levels = focals)
Order sites by age
ann_caps.foc$site <- factor(ann_caps.foc$site,
levels = c("La Cueva",
"La Caoba",
"Morelia",
"El Corral",
"Aceitillar"))
Create Unique ID
Index of that yields each individual only once per year, but allows individuals to appear in subsequent years.
dataframe has been organized by date so this should select the 1st time an individual was captured
i.within.yr <- match(unique(ann_caps.foc$ID.yr),
ann_caps.foc$ID.yr)
Calcualte sample size
cast.N <- dcast(data= ann_caps.foc[i.within.yr,],
formula = spp.code + status2 ~ site,
value.var = "site",
fun.aggregate = length)
cast for sex ratio
cast.sex <- dcast(data= ann_caps.foc[i.within.yr,],
formula = spp.code + status2 ~ site + sex.M,
value.var = "site",
fun.aggregate = length)
cast for age
cast.age <- dcast(data= ann_caps.foc[i.within.yr,],
formula = spp.code + status2 ~ site + age.AHY.01,
value.var = "site",
fun.aggregate = length)
Calcualte sex ratios
la.cueva.M <- cast.sex$`La Cueva_M`/(cast.sex$`La Cueva_M`+cast.sex$`La Cueva_other`)
la.cueva.M.n <- cast.sex$`La Cueva_M`+cast.sex$`La Cueva_other`
la.caoba.M <- cast.sex$`La Caoba_M`/(cast.sex$`La Caoba_M`+cast.sex$`La Caoba_other`)
la.caoba.M.n <- cast.sex$`La Caoba_M`+cast.sex$`La Caoba_other`
morelia.M <- cast.sex$`Morelia_M`/(cast.sex$`Morelia_M`+cast.sex$`Morelia_other`)
morelia.M.n <- cast.sex$`Morelia_M`+cast.sex$`Morelia_other`
corral.M <- cast.sex$`El Corral_M`/(cast.sex$`El Corral_M`+ cast.sex$`El Corral_other`)
Corral_M.n <- cast.sex$`El Corral_M`+ cast.sex$`El Corral_other`
Aceitillar.M <- cast.sex$`Aceitillar_M`/(cast.sex$`Aceitillar_M`+cast.sex$`Aceitillar_other`)
Aceitillar_M.n <- cast.sex$`Aceitillar_M`+cast.sex$`Aceitillar_other`
Calcualte age ratios
la.cueva.AHY <- cast.age$`La Cueva_age1`/(cast.age$`La Cueva_age1`+cast.age$`La Cueva_age2`)
la.cueva.AHY.n <- cast.age$`La Cueva_age1`+cast.age$`La Cueva_age2`
la.caoba.AHY <- cast.age$`La Caoba_age1`/(cast.age$`La Caoba_age1`+cast.age$`La Caoba_age2`)
la.caoba.AHY.n <- cast.age$`La Caoba_age1`+cast.age$`La Caoba_age2`
morelia.AHY <- cast.age$`Morelia_age1`/(cast.age$`Morelia_age1`+cast.age$`Morelia_age2`)
morelia.AHY.n <- cast.age$`Morelia_age1`+cast.age$`Morelia_age2`
corral.AHY <- cast.age$`El Corral_age1`/(cast.age$`El Corral_age1`+cast.age$`El Corral_age2`)
corral.AHY.n <- cast.age$`El Corral_age1`+cast.age$`El Corral_age2`
Aceitillar.AHY <- cast.age$`Aceitillar_age1`/(cast.age$`Aceitillar_age1`+cast.age$`Aceitillar_age2`)
Aceitillar.AHY.n <- cast.age$`Aceitillar_age1`+cast.age$`Aceitillar_age2`
Build table
dig <- 2
tables5.6 <- data.frame(cast.N[,c("spp.code","status2")],
La.Cueva.N = cast.N$`La Cueva`,
La.Cueva.M = round(la.cueva.M,2),
la.cueva.M.n = la.cueva.M.n,
La.Cueva.AHY = round(la.cueva.AHY,2),
la.cueva.AHY.n = la.cueva.AHY.n,
La.Caoba.N = cast.N$`La Caoba`,
La.Caoba.M = round(la.caoba.M,2),
la.caoba.M.n = la.caoba.M.n,
La.Caoba.AHY = round(la.caoba.AHY,2),
la.caoba.AHY.n = la.caoba.AHY.n,
Morelia.N = cast.N$Morelia,
Morelia.M = round(morelia.M,2),
morelia.M.n = morelia.M.n,
Morelia.AHY = round(morelia.AHY,2),
morelia.AHY.n = morelia.AHY.n,
El.Corral.N = cast.N$`El Corral`,
El.Corral.M = round(corral.M,2),
Corral_M.n = Corral_M.n,
El.Corral.AHY = round(corral.AHY,2),
corral.AHY.n = corral.AHY.n,
Aceitillar.N = cast.N$`Aceitillar`,
Aceitillar.M = round(Aceitillar.M,2),
Aceitillar_M.n = Aceitillar_M.n,
Aceitillar.AHY = round(Aceitillar.AHY,2),
Aceitillar.AHY.n = Aceitillar.AHY.n)
Paste together
make.column <- function(df,col.name,sample.size){
x <- paste(df[,col.name]," (",df[,sample.size],")", sep = "")
x[grep("N",x)] <- ""
return(x)
}
La.Cueva.M <- make.column(tables5.6,
"La.Cueva.M","la.cueva.M.n")
La.Caoba.M <- make.column(tables5.6,
"La.Caoba.M","la.caoba.M.n")
Morelia.M <- make.column(tables5.6,
"Morelia.M","morelia.M.n")
El.Corral.M <- make.column(tables5.6,
"El.Corral.M","Corral_M.n")
Aceitillar.M <- make.column(tables5.6,
"Aceitillar.M","Aceitillar_M.n")
La.Cueva.AHY <- make.column(tables5.6,
"La.Cueva.AHY","la.cueva.AHY.n")
La.Caoba.AHY <- make.column(tables5.6,
"La.Caoba.AHY","la.caoba.AHY.n")
Morelia.AHY <- make.column(tables5.6,
"Morelia.AHY","morelia.AHY.n")
El.Corral.AHY <- make.column(tables5.6,
"El.Corral.AHY","corral.AHY.n")
Aceitillar.AHY <- make.column(tables5.6,
"Aceitillar.AHY","Aceitillar.AHY.n")
data.frame(El.Corral.AHY,
tables5.6$El.Corral.AHY,
tables5.6$Corral_M.n)
tables5.6.final <- data.frame(tables5.6[,c("spp.code","status2")],
La.Cueva.N = tables5.6$La.Cueva.N,
La.Cueva.AHY,
La.Cueva.M,
La.Caoba.N = tables5.6$La.Caoba.N,
La.Caoba.AHY,
La.Caoba.M,
Morelia.N = tables5.6$Morelia.N,
Morelia.AHY,
Morelia.M,
El.Corral.N = tables5.6$El.Corral.N,
El.Corral.AHY,
El.Corral.M,
Aceitillar.N = tables5.6$Aceitillar.N,
Aceitillar.AHY,
Aceitillar.M)
Save table
write.csv(tables5.6.final,
file = "./tables/temp_tables_5_6_age_etc.csv",
row.names = F)
brouwern/DRmencia documentation built on May 6, 2019, 12:24 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
knitr::opts_chunk$set(echo = TRUE)
This script create the Sampe size, age ratio, and sex ratio part of tables 5 and 6 It uses a dataset where Mencia and Aceitillar data have been combined into a single long-format dataframe
Libraries
library(reshape2) library(here)
Load data
Load annual Captures data with Mencia AND Aceitillar combined
filename <- "annual_captures.RData" load(here::here("data",filename))
Subset just by focal species
These are the spp focused on in teh original MS; they are the most commonly caught
Names of species
focal.mig <- c("OVEN","BAWW","COYE","AMRE","CMWA", "BTBW","PAWA","PRAW") focal.res <- c("HILC" # formerly HLCU ,"STOF" ,"RLTH" ,"NOMO" ,"GTGT" # formerly GRWA ,"BANA" ,"BCPT" ,"YFGR" ,"BFGR" ,"GABU") focals <- c(focal.mig,focal.res)
Subset
i.focals <- which(ann_caps$spp.code %in% focals) ann_caps.foc <- ann_caps[i.focals,] dim(ann_caps.foc) dim(ann_caps)
Set spp order for tables
replicate order from tables in oridingal MS
ann_caps.foc$spp.code <- factor(ann_caps.foc$spp.code, levels = focals)
Order sites by age
ann_caps.foc$site <- factor(ann_caps.foc$site, levels = c("La Cueva", "La Caoba", "Morelia", "El Corral", "Aceitillar"))
Create Unique ID
Index of that yields each individual only once per year, but allows individuals to appear in subsequent years.
dataframe has been organized by date so this should select the 1st time an individual was captured
i.within.yr <- match(unique(ann_caps.foc$ID.yr), ann_caps.foc$ID.yr)
Calcualte sample size
cast.N <- dcast(data= ann_caps.foc[i.within.yr,], formula = spp.code + status2 ~ site, value.var = "site", fun.aggregate = length)
cast for sex ratio
cast.sex <- dcast(data= ann_caps.foc[i.within.yr,], formula = spp.code + status2 ~ site + sex.M, value.var = "site", fun.aggregate = length)
cast for age
cast.age <- dcast(data= ann_caps.foc[i.within.yr,], formula = spp.code + status2 ~ site + age.AHY.01, value.var = "site", fun.aggregate = length)
Calcualte sex ratios
la.cueva.M <- cast.sex$`La Cueva_M`/(cast.sex$`La Cueva_M`+cast.sex$`La Cueva_other`) la.cueva.M.n <- cast.sex$`La Cueva_M`+cast.sex$`La Cueva_other` la.caoba.M <- cast.sex$`La Caoba_M`/(cast.sex$`La Caoba_M`+cast.sex$`La Caoba_other`) la.caoba.M.n <- cast.sex$`La Caoba_M`+cast.sex$`La Caoba_other` morelia.M <- cast.sex$`Morelia_M`/(cast.sex$`Morelia_M`+cast.sex$`Morelia_other`) morelia.M.n <- cast.sex$`Morelia_M`+cast.sex$`Morelia_other` corral.M <- cast.sex$`El Corral_M`/(cast.sex$`El Corral_M`+ cast.sex$`El Corral_other`) Corral_M.n <- cast.sex$`El Corral_M`+ cast.sex$`El Corral_other` Aceitillar.M <- cast.sex$`Aceitillar_M`/(cast.sex$`Aceitillar_M`+cast.sex$`Aceitillar_other`) Aceitillar_M.n <- cast.sex$`Aceitillar_M`+cast.sex$`Aceitillar_other`
Calcualte age ratios
la.cueva.AHY <- cast.age$`La Cueva_age1`/(cast.age$`La Cueva_age1`+cast.age$`La Cueva_age2`) la.cueva.AHY.n <- cast.age$`La Cueva_age1`+cast.age$`La Cueva_age2` la.caoba.AHY <- cast.age$`La Caoba_age1`/(cast.age$`La Caoba_age1`+cast.age$`La Caoba_age2`) la.caoba.AHY.n <- cast.age$`La Caoba_age1`+cast.age$`La Caoba_age2` morelia.AHY <- cast.age$`Morelia_age1`/(cast.age$`Morelia_age1`+cast.age$`Morelia_age2`) morelia.AHY.n <- cast.age$`Morelia_age1`+cast.age$`Morelia_age2` corral.AHY <- cast.age$`El Corral_age1`/(cast.age$`El Corral_age1`+cast.age$`El Corral_age2`) corral.AHY.n <- cast.age$`El Corral_age1`+cast.age$`El Corral_age2` Aceitillar.AHY <- cast.age$`Aceitillar_age1`/(cast.age$`Aceitillar_age1`+cast.age$`Aceitillar_age2`) Aceitillar.AHY.n <- cast.age$`Aceitillar_age1`+cast.age$`Aceitillar_age2`
Build table
dig <- 2 tables5.6 <- data.frame(cast.N[,c("spp.code","status2")], La.Cueva.N = cast.N$`La Cueva`, La.Cueva.M = round(la.cueva.M,2), la.cueva.M.n = la.cueva.M.n, La.Cueva.AHY = round(la.cueva.AHY,2), la.cueva.AHY.n = la.cueva.AHY.n, La.Caoba.N = cast.N$`La Caoba`, La.Caoba.M = round(la.caoba.M,2), la.caoba.M.n = la.caoba.M.n, La.Caoba.AHY = round(la.caoba.AHY,2), la.caoba.AHY.n = la.caoba.AHY.n, Morelia.N = cast.N$Morelia, Morelia.M = round(morelia.M,2), morelia.M.n = morelia.M.n, Morelia.AHY = round(morelia.AHY,2), morelia.AHY.n = morelia.AHY.n, El.Corral.N = cast.N$`El Corral`, El.Corral.M = round(corral.M,2), Corral_M.n = Corral_M.n, El.Corral.AHY = round(corral.AHY,2), corral.AHY.n = corral.AHY.n, Aceitillar.N = cast.N$`Aceitillar`, Aceitillar.M = round(Aceitillar.M,2), Aceitillar_M.n = Aceitillar_M.n, Aceitillar.AHY = round(Aceitillar.AHY,2), Aceitillar.AHY.n = Aceitillar.AHY.n)
Paste together
make.column <- function(df,col.name,sample.size){ x <- paste(df[,col.name]," (",df[,sample.size],")", sep = "") x[grep("N",x)] <- "" return(x) }
La.Cueva.M <- make.column(tables5.6, "La.Cueva.M","la.cueva.M.n") La.Caoba.M <- make.column(tables5.6, "La.Caoba.M","la.caoba.M.n") Morelia.M <- make.column(tables5.6, "Morelia.M","morelia.M.n") El.Corral.M <- make.column(tables5.6, "El.Corral.M","Corral_M.n") Aceitillar.M <- make.column(tables5.6, "Aceitillar.M","Aceitillar_M.n")
La.Cueva.AHY <- make.column(tables5.6, "La.Cueva.AHY","la.cueva.AHY.n") La.Caoba.AHY <- make.column(tables5.6, "La.Caoba.AHY","la.caoba.AHY.n") Morelia.AHY <- make.column(tables5.6, "Morelia.AHY","morelia.AHY.n") El.Corral.AHY <- make.column(tables5.6, "El.Corral.AHY","corral.AHY.n") Aceitillar.AHY <- make.column(tables5.6, "Aceitillar.AHY","Aceitillar.AHY.n")
data.frame(El.Corral.AHY, tables5.6$El.Corral.AHY, tables5.6$Corral_M.n)
tables5.6.final <- data.frame(tables5.6[,c("spp.code","status2")], La.Cueva.N = tables5.6$La.Cueva.N, La.Cueva.AHY, La.Cueva.M, La.Caoba.N = tables5.6$La.Caoba.N, La.Caoba.AHY, La.Caoba.M, Morelia.N = tables5.6$Morelia.N, Morelia.AHY, Morelia.M, El.Corral.N = tables5.6$El.Corral.N, El.Corral.AHY, El.Corral.M, Aceitillar.N = tables5.6$Aceitillar.N, Aceitillar.AHY, Aceitillar.M)
Save table
write.csv(tables5.6.final, file = "./tables/temp_tables_5_6_age_etc.csv", row.names = F)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.