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.Rhistory
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hola
asd
asd
11+1
12
13
82*3.35
68*3.35
320*5
60*3.35
640*0.18
30+30+30+50+30+118
60*3.35
120+90+60+80
85*3.35
285+160
90*3.35
90*3.5
350+1500+500
79+59+90+120
citation()
require(INLA)
install.packages("INLA", repos="https://inla.r-inla-download.org/R/stable")
require(INLA)
dlvcomp2 <- function(N, alpha, rd = c(1, 1)) {
N1.t1 <- N[1] + rd[1] * N[1] * (1 - alpha[1, 1] * N[1] - alpha[1, 2] * N[2])
N2.t1 <- N[2] + rd[2] * N[2] * (1 - alpha[2, 1] * N[1] - alpha[2, 2] * N[2])
c(N1.t1, N2.t1)
}
alphs <- matrix(c(0.01, 0.005, 0.008, 0.01), ncol = 2, byrow = TRUE)
t <- 20
alphs
N <- matrix(NA, nrow = t + 1, ncol = 2)
N[1, ] <- c(10, 10)
for (i in 1:t) N[i + 1, ] <- dlvcomp2(N[i, ], alphs)
matplot(0:t, N, type = "l", col = 1, ylim = c(0, 110))
abline(h = 1/alphs[1, 1], lty = 3)
text(0, 1/alphs[1, 1], "K", adj = c(0, 0))
legend("right", c(expression("Sp.1 " * (alpha[21] == 0.008)),
expression("Sp.2 " * (alpha[12] == 0.005))), lty = 1:2,
bty = "n")
alphs
alphs <- matrix(c(0.1, 0.005, 0.008, 0.01), ncol = 2, byrow = TRUE)
N <- matrix(NA, nrow = t + 1, ncol = 2)
N[1, ] <- c(10, 10)
for (i in 1:t) N[i + 1, ] <- dlvcomp2(N[i, ], alphs)
N
lines(0:t, N[,1], col = "red")
lines(0:t, N[,2], col = "red", lty = 2)
library(deSolve)
install.packages("deSolve")
library(deSolve)
parms <- c(r1 = 1, r2 = 0.1, a11 = 0.2, a21 = 0.1, a22 = 0.02,
a12 = 0.01)
initialN <- c(2, 1)
out <- ode(y = initialN, times = 1:100, func = lvcomp2, parms = parms)
lvcomp2 <- function(t, n, parms) {
with(as.list(parms), {
dn1dt <- r1 * n[1] * (1 - a11 * n[1] - a12 * n[2])
dn2dt <- r2 * n[2] * (1 - a22 * n[2] - a21 * n[1])
list(c(dn1dt, dn2dt))
})
}
library(deSolve)
parms <- c(r1 = 1, r2 = 0.1, a11 = 0.2, a21 = 0.1, a22 = 0.02,
a12 = 0.01)
initialN <- c(2, 1)
out <- ode(y = initialN, times = 1:100, func = lvcomp2, parms = parms)
matplot(out[, 1], out[, -1], type = "l")
out[, -1]
out
out[, 1]
out[, -1]
matplot(x = out[, 1], y = out[, -1], type = "l")
a <- matrix(c(0.01, 0.005, 0.005, 0.01), ncol = 2, byrow = TRUE)
N2iso <- expression(1/a[2, 2] - (a[2, 1]/a[2, 2]) * N1)
N1 <- 0:200
plot(N1, eval(N2iso), type = "l", ylim = c(0, 200), xlim = c(0,
200), ylab = expression("N"[2]))
arrows(x0 = 90, y0 = 150, x1 = 90, y1 = 80, length = 0.1)
arrows(x0 = 75, y0 = 0, x1 = 75, y1 = 50, length = 0.1)
N1Star <- expression((a22 - a12)/(a22 * a11 - a12 * a21))
N2Star <- expression((a11 - a21)/(a22 * a11 - a12 * a21))
a11 <- a22 <- 0.01
a12 <- 0.001; a21 <- 0.001
N1 <- eval(N1Star); N2 <- eval(N2Star)
N1
dN1dt <- expression(r1 * N1 - r1 * a11 * N1^2 - r1 * a12 *
+ N1 * N2)
dN2dt <- expression(r2 * N2 - r2 * a22 * N2^2 - r2 * a21 *
+ N1 * N2)
ddN1dN1 <- D(dN1dt, "N1")
ddN1dN1
ddN1dN2 <- D(dN1dt, "N2")
ddN2dN1 <- D(dN2dt, "N1")
ddN2dN2 <- D(dN2dt, "N2")
J <- expression(matrix(c(eval(ddN1dN1), eval(ddN1dN2), eval(ddN2dN1),
eval(ddN2dN2)), nrow = 2, byrow = TRUE))
J
r1 <- r2 <- 1
J1 <- eval(J)
J1
eigStable <- eigen(J1)
eigStable[["values"]]
a11 <- a22 <- 0.01
a12 <- a21 <- 0.011
N1 <- eval(N1Star); N2 <- eval(N2Star)
eigen(eval(J))$values
a11 <- a22 <- 0.01
a12 <- a21 <- 0.011
N1 <- eval(N1Star); N2 <- eval(N2Star)
eigen(eval(J))$values
a11 <- a21 <- 0.01
a22 <- a12 <- 0.015
N1 <- N2 <- 1/(a11 + a22)
eigen(eval(J))[["values"]]
N1 <- 1/(a11)
N2 <- 0
eigen(eval(J))[["values"]]
xa = c(1,2,3,4,5)
xb = c(10,11,12,13,14)
xa[1:3]*xb[1:3]
xa[1:3]*xb[1:3]/3
sum(xa[1:3]*xb[1:3])/3
sum(xa[1:3]*xb[1:3])/6
sum(xa[4:5]*xb[4:5])/9
(11.3333+13.55556)/2
sum(xa[1:5]*xb[1:5])/15
5/3 + 25/7
5.238/2
1+4+9+16
30/10
515/160
160/515
11.1+20.19+36.88
1030-160
ks.test(1,1)
ks.test(1,1, alternative = "greater")
1.716+1.96*1.065
0.27+1.96*1.065
0.389+1.96*0.092
0.389-1.96*0.092
4.644+1.96*0.158
4.644-1.96*0.158
x1 = c(1,2,3)
x2 = c(4,5,6)
x3 = c(7,8,9)
mean(x1,x2,x3)
sum(1:9)
sum(1:9)/9
mean(x1)
mean(x2)
mean(x3)
67*2
134*3.3
450.84/134
158*3.3
47*3.3
29.5+17.74+16.09+59+450.84+489+49.9+37.6+19.21+80+57+60+8+66+19.3+159
29.5+17.74+16.09+59+450.84+489+49.9+37.6+19.21+80+57+60+8+66+19.3+159+5
require(TropFishR)
output <- ELEFAN(x = synLFQ4, Linf_fix = 80,
K_range = seq(0.3,0.7,0.1),C = 0.75, ts = 0.5, MA = 11)
plot(output)
require(NbClust)
11500+3500
15000-1000
15000-1000-900
15000-1000-900-1000
exp(0.6)
exp(0.6*1)
exp(0.6*0)
exp(-0.6*0)
exp(-0.6*1)
exp(-0.2*1)
exp(0.2*1)
require(devtools)
install.packages("devtools")
devtools::install_github("ss3sim/ss3sim", build_vignettes = TRUE)
devtools::install_github("ss3sim/ss3sim", build_vignettes = TRUE)
devtools::install_github("ss3sim/ss3sim")
install.packages("ss3sim")
library(ss3sim)
library(ss3sim)
devtools::install_github("ss3sim/ss3sim", build_vignettes = TRUE)
remove.packages("tibble")
remove.packages("dplyr")
install.packages("dplyr")
devtools::install_github("ss3sim/ss3sim", build_vignettes = TRUE)
devtools::install_github("ss3sim/ss3sim")
install_github("PabloMBooster/fenix")
require(devtools)
install_github("PabloMBooster/fenix")
install_github("PabloMBooster/fenix")
devtools::install_github("ss3sim/ss3sim", build_vignettes = TRUE)
require(devtools)
devtools::install_github("ss3sim/ss3sim", build_vignettes = TRUE)
library(ss3sim)
devtools::install_github("ss3sim/ss3sim")
install.packages("httr")
library(httr)
with_config(use_proxy(...), install_github(...))
with_config(use_proxy(...), install_github(...))
set_config(use_proxy(url = "******_", port = "_*"))
require(devtools)
install_github("ss3sim/ss3sim", build_vignettes = TRUE)
traceback()
options(download.file.method = "wininet")
library(devtools)
install_github("ss3sim/ss3sim", build_vignettes = TRUE)
options(download.file.method = "wininet")
require(devtools)
install_github("ss3sim/ss3sim", build_vignettes = TRUE)
install.packages("ss3sim")
library(ss3sim)
?ss3sim
library(ss3sim)
library(ss3sim)
vignette("ss3-sim-vignette")
vignette("ss3sim-vignette")
vignette("ss3sim-vignette")
?ss3sim
library(ss3sim)
install_github("ss3sim/ss3sim", build_vignettes = TRUE)
library(ss3sim)
vignette("introduction", "ss3sim")
help(package = "ss3sim")
exp(-0.57)
exp(0.65)
exp(-0.07)
exp(-0.5)
exp(0.67)
exp(-0.67)
exp(0.685)
exp(-0.59)
seq(2, 20, 0.5)
c(0,0,0,1,2,3,2,1,0,0,1,2,3,4,5,4,3,2,1,0,0,0,0)
length(c(0,0,0,1,2,3,2,1,0,0,1,2,3,4,5,4,3,2,1,0,0,0,0))
length(seq(2, 20, 0.5))
c(0,0,0,0,0,0,0,0,1,2,3,2,1,0,0,1,2,3,4,5,4,3,2,1,0,0,0,0)
c(0,0,0,0,0,0,0,0,1,2,3,2,1,0,0,1,2,3,4,5,4,3,2,1,0,0,0,0,0,0,0,0)
length(c(0,0,0,0,0,0,0,0,1,2,3,2,1,0,0,1,2,3,4,5,4,3,2,1,0,0,0,0,0,0,0,0))
c(0,0,0,0,0,0,0,0,1,2,3,2,1,0,0,1,2,3,4,5,6,5,4,3,2,1,0,0,0,0,0,0,0,0)
length(c(0,0,0,0,0,0,0,0,1,2,3,2,1,0,0,1,2,3,4,5,6,5,4,3,2,1,0,0,0,0,0,0,0,0))
plot(x = seq(2, 20, 0.5),
y = c(0,0,0,0,0,0,0,0,1,2,3,2,1,0,0,1,2,3,4,5,6,5,4,3,2,1,0,0,0,0,0,0,0,0,0,0,0))
require(tidyverse)
require(dplyr)
require(broom)
library(stringr)
387*60+1300
1600+40*14+200+300+300
50*365
40*365
40*30
38000*0.77
complex(1)
complex(real = 0, imaginary = 1)
exp(complex(real = 0, imaginary = 1))
exp(complex(real = 0, imaginary = 1))^pi
require(TropFishR)
?TropFishR
library(r4ss)
tmp2 = SS_output(dir = "models/mod_B")
setwd("~/GitHub/StockAssessmentAnchovyPeruChile")
tmp2 = SS_output(dir = "models/mod_B")
tmp2$estimated_non_rec_devparameters
SSplotPars(dir = "models/mod_B")
tmp2$estimated_non_rec_devparameters
tmp2$estimated_non_rec_devparameters[,c("Label", "Value", "Phase", "Init", "Parm_StDev")]
tmp2$estimated_non_rec_devparameters[,c("Label", "Value", "Phase", "Init", "Parm_StDev")]
library(knitr)
xa = tmp2$estimated_non_rec_devparameters[,c("Label", "Value", "Phase", "Init", "Parm_StDev")]
library(knitr)
kable(head(iris), format = "latex")
tmp2$Growth_Parameters
SSplotComps(replist = tmp2)
SSplotComps(replist = tmp2, datonly = T)
SSplotComps(replist = tmp2, datonly = T, bub = T)
SSplotComps(replist = tmp2, datonly = T, bub = T)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 1)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 2)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 3)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 4)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 5)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 6)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 7)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 8)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 7)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 8)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 9)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 10)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 11)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 12)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 13)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 14)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 15)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 16)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 17)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 18)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 19)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 20)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 21)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 22)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 23)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 25)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24, labels = "")
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24, main = "")
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24, main = "as")
SSplotComps(replist = tmp2, datonly = T, bub = T,printmkt = FALSE)
SSplotComps(replist = tmp2, datonly = T, bub = T,printmkt = FALSE, printsex = FALSE)
SSplotComps(replist = tmp2, datonly = T, bub = T,printmkt = FALSE, printsex = FALSE, cex.main = 0.5)
SSplotComps(replist = tmp2, datonly = T, bub = T,printmkt = FALSE, printsex = FALSE, cex.main = 0.1)
SSplotComps(replist = tmp2, datonly = T, bub = T,printmkt = FALSE, printsex = FALSE, main = "")
SSplotComps(replist = tmp2, datonly = T, bub = T,printmkt = FALSE, printsex = FALSE, main = "")
SSplotComps(replist = tmp2, datonly = T, bub = T,printmkt = FALSE, printsex = FALSE, main = "hola")
SSplotComps(replist = tmp2, datonly = T, bub = T, main = "hola")
SSplotComps(replist = tmp2, datonly = T, bub = T, cex.main = 0)
SSplotComps(replist = tmp2, datonly = T, bub = T)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 21)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 22)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24, main = "")
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24, main = "hola")
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24, cex.main = 0)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24, cex.main = 0.1)
par()$mfg[1]
par()$mfg[1]=2
par()$mfg[1]=0
par()$mfg
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24)
title(main = "")
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24)
title(main = "")
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24, printmkt = F)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24, printmkt = F, printsex = F)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24, printmkt = F, printsex = F, print = F)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24, printmkt = F, printsex = F)
par()$mfg
par()$mfg [1] = 2
par(mar = c(4,4,1,1))
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24, printmkt = F, printsex = F)
install.packages("devtools")
require(devtools)
devtools::install_github("r4ss/r4ss")
require(r4ss)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24, printmkt = F, printsex = F)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24)
tmp2$estimated_non_rec_devparameters
tmp2 = SS_output(dir = "models/mod_B")
tmp2$estimated_non_rec_devparameters
tmp2
tmp2$estimated_non_dev_parameters
tmp2$estimated_non_dev_parameters
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24, cex.main = 0.5)
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24, cex.main = 0.2)
?SSplotCatch
?SSplotCatch
?SSplotCatch
SSplotData(replist = tmp2)
SSplotData(replist = tmp2, margins = c(4,4,1,1))
SSplotData(replist = tmp2, margins = c(4,4,1,4))
SSplotData(replist = tmp2, margins = c(4,4,1,5))
SSplotData(replist = tmp2, margins = c(4,4,1,6))
SSplotData(replist = tmp2, margins = c(4,4,1,5.5))
SSplotData(replist = tmp2, margins = c(4,1,1,5.5))
tmp2$Growth_Parameters
tmp2
tmp2$M_at_age
tmp2$parameters
SSplotCatch(replist = tmp2, subplots = 11, labels=c("Harvest rate/Year", #1
"Continuous F", #2
"Desembarques", #3
"Total catch", #4
"Predicted discards", #5
"Discard fraction", #6 # need to add by weight or by length
"(t)", #7
"(numbers x1000)", #8
"Observed and expected", #9
""), xlab = "")
par(mar = c(1,1,1,1))
SSplotCatch(replist = tmp2, subplots = 11, labels=c("Harvest rate/Year", #1
"Continuous F", #2
"Desembarques", #3
"Total catch", #4
"Predicted discards", #5
"Discard fraction", #6 # need to add by weight or by length
"(t)", #7
"(numbers x1000)", #8
"Observed and expected", #9
""), xlab = "")
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24, labels = c("Longitud total (cm)", "Age (yr)", "", "Observed sample size",
"Effective sample size", "Proportion", "cm", "Frequency", "Weight", "Length",
"(mt)", "(numbers x1000)", "Stdev (Age) (yr)", "Conditional AAL plot, "). andre_oma = c(1,1,1,1))
SSplotComps(replist = tmp2, datonly = T, bub = T, subplots = 24, labels = c("Longitud total (cm)", "Age (yr)", "", "Observed sample size",
"Effective sample size", "Proportion", "cm", "Frequency", "Weight", "Length",
"(mt)", "(numbers x1000)", "Stdev (Age) (yr)", "Conditional AAL plot, "). andre_oma = c(1,1,1,1))
tmp2$Data_File
tmp2$definitions
tmp2$catch_units
tmp2$startyr
pathmod = "models"
modelName = "modB_0_2"
out <- SS_output(dir = file.path(pathmod, modelName),
printstats=FALSE,verbose=FALSE)
out <- SS_output(dir = file.path(pathmod, modelName),
printstats=FALSE,verbose=FALSE)
out <- SS_output(dir = file.path(pathmod, modelName),
printstats=FALSE,verbose=FALSE)
setwd("~/GitHub/StockAssessmentAnchovyPeruChile")
out <- SS_output(dir = file.path(pathmod, modelName),
printstats=FALSE,verbose=FALSE)
out
file.path(pathmod, modelName)
modelName = "mod_B"
out <- SS_output(dir = file.path(pathmod, modelName),
printstats=FALSE,verbose=FALSE)
out
dat <- out$timeseries
out$timeseries
a1 <- which(dat$Era=="TIME")
yrs <- dat$Yr[a1]
yrs
dat
tmp2$sigma_R_info
tmp2$recruitment_dist
tmp2$recruit
modelName = "mod_C"
out <- SS_output(dir = file.path(pathmod, modelName),
printstats=FALSE,verbose=FALSE)
out$recruit
dev.me=dev.sd=vector()
dev.me<-std[which(std$name == "recdev1"),3]
dev.sd<-std[which(std$name == "recdev1"),4]
dev.sup<-dev.me+2*dev.sd
dev.inf<-dev.me-2*dev.sd
std <- read.table(file.path(pathmod, paste0(modelName, "/SS3.std")),
header=T,sep="",na="NA",fill=T) #take care other names
dev.me=dev.sd=vector()
dev.me<-std[which(std$name == "recdev1"),3]
dev.sd<-std[which(std$name == "recdev1"),4]
dev.sup<-dev.me+2*dev.sd
dev.inf<-dev.me-2*dev.sd
dev.me
dev.me
year
year <- out$startyr:out$endyr
year
out$startyr:out$endyr
length(year)
dev.me
length(dev.me)
out$recruit$dev
tmpsddev = rep(NA, length(year))
tmpsddev
std[which(std$name == "recdev1"),3]
length(std[which(std$name == "recdev1"),3])
dev.me=dev.sd=vector()
dev.me = rep(NA, length(year))
dev.sd = rep(NA, length(year))
dev.me4<-std[which(std$name == "recdev1"),3]
dev.sd4<-std[which(std$name == "recdev1"),4]
dev.me[1:length(dev.me4)] = dev.me4
dev.sd[1:length(dev.sd4)] = dev.sd4
dev.sup<-dev.me+2*dev.sd
dev.inf<-dev.me-2*dev.sd
dev.sup
dev.inf
plot(year,dev.me,col=0,xlab="",ylab="",axes = FALSE,
ylim = c(min(dev.inf), max(dev.sup)))
source("getSummaryOne_fun.R")
getSummaryOne(pathmod = "models", modelName = "mod_B")
getSummaryOne(pathmod = "models", modelName = "mod_C")
dev.me
pretty(dev.me)
source("getSummaryOne_fun.R")
getSummaryOne(pathmod = "models", modelName = "mod_C")