## ---- echo = FALSE, message = FALSE------------------------------------------- library(kableExtra) library(gnomonicM) ## ---- eval=FALSE-------------------------------------------------------------- # install.packages("gnomonicM") ## ---- eval=FALSE-------------------------------------------------------------- # # install.packages("devtools") # devtools::install_github("ejosymart/gnomonicM") ## ---- eval=FALSE-------------------------------------------------------------- # library("gnomonicM") ## ----echo=TRUE---------------------------------------------------------------- model_hf <- gnomonic(nInterval = 7, eggDuration = 2, longevity = 365, fecundity = 200000, a_init = 2) ## ----echo=TRUE---------------------------------------------------------------- model_lf <- gnomonic(nInterval = 7, eggDuration = 2, longevity = 365, fecundity = 135, a_init = 2) ## ----echo=TRUE, results = 'hide'---------------------------------------------- modelAddInfo <- gnomonic(nInterval = 7, eggDuration = 2, addInfo = c(4, NA, NA, 40, NA, NA), longevity = 365, fecundity = 200000, a_init = 2) ## ----echo = TRUE-------------------------------------------------------------- #Species with high fecundity. print(model_hf) plot(model_hf) #Species with low fecundity. print(model_lf) plot(model_lf, xlab = "My X label", ylab = "My Y label", cex = 3, bg = "blue") ## ---- echo=FALSE-------------------------------------------------------------- data_hf <- data.frame(Gnomonic_interval = 1:7, interval_duration_day = c(2.00, 2.76, 6.58, 15.67, 37.33, 88.91, 211.75), M_year = c(300.16, 217.25, 91.27, 38.30, 16.08, 6.75, 2.84), No_Surv = c(38614, 7455, 1439, 278, 54, 10, 2)) data_hf %>% kbl(caption = "Results provided by Caddy (1996) in the estimation of M based on high fecundity species (MLF = 200,000 eggs, egg stage duration = 2 days, and longevity = 365 days)", booktabs = T) %>% kable_styling(full_width = F, position = "center", latex_options = c("striped", "hold_position")) ## ---- echo=FALSE-------------------------------------------------------------- data_lf <- data.frame(Gnomonic_interval = 1:7, interval_duration_day = c(2.00, 2.76, 6.58, 15.67, 37.33, 88.91, 211.75), M_year = c(109.82, 79.48, 33.37, 14.01, 5.88, 2.47, 1.04), No_Surv = c(74, 41, 22, 12, 7, 4, 2)) data_lf %>% kbl(caption = "Results provided by Caddy (1996) in the estimation of M based on low fecundity species (MLF = 135, egg stage duration = 2 days, and longevity = 365 days)", booktabs = T) %>% kable_styling(full_width = F, position = "center", latex_options = c("striped", "hold_position")) ## ----echo=TRUE---------------------------------------------------------------- model_cm_hf <- gnomonicStochastic(nInterval = 8, eggDuration = 2.33, longevity = 2920, distr = "uniform", min_fecundity = 11805, max_fecundity = 144543, niter = 1000, a_init = 2) model_cm_lf <- gnomonicStochastic(nInterval = 8, eggDuration = 2.33, longevity = 2920, distr = "uniform", min_fecundity = 7603, max_fecundity = 53921, niter = 1000, a_init = 2) ## ----echo = TRUE, results = 'hide'-------------------------------------------- #The results are not shown here. Please run it in your console. print(model_cm_hf) print(model_cm_lf) ## ----echo = TRUE-------------------------------------------------------------- par(mar = c(6,6,6,6)) plot(model_cm_hf, main = "M for chub mackerel, MLF = [11 805 - 144 543]", dayUnits = FALSE) plot(model_cm_lf, main = "M for chub mackerel, MLF = [7 603 - 53 921]", dayUnits = FALSE) ## ----echo=TRUE---------------------------------------------------------------- modelUniformAddInfo <- gnomonicStochastic(nInterval = 7, eggDuration = 2, addInfo = c(4, NA, NA, 40, NA, NA), longevity = 365, distr = "uniform", min_fecundity = 100000, max_fecundity = 300000, niter = 1000, a_init = 2) modelNormal <- gnomonicStochastic(nInterval = 7, eggDuration = 2, longevity = 365, distr = "normal", fecundity = 200000, sd_fecundity = 50000, niter = 1000, a_init = 2) modelTriangle <- gnomonicStochastic(nInterval = 7, eggDuration = 2, longevity = 365, distr = "triangle", fecundity = 200000, min_fecundity = 100000, max_fecundity = 300000, niter = 1000, a_init = 2) ## ----echo = TRUE-------------------------------------------------------------- plot(modelUniformAddInfo, main = "Uniform distribution in MLF, with additional information") plot(modelNormal, main = "Normal distribution in MLF") plot(modelTriangle, main = "Triangular distribution in MLF") ## ----echo=TRUE---------------------------------------------------------------- Farfantopenaeus <- gnomonic(nInterval = 7, eggDuration = 1.5, longevity = 480, fecundity = 500000, a_init = 1) Vannamei <- gnomonic(nInterval = 7, eggDuration = 0.54, longevity = 365, fecundity = 265000, a_init = 3) Sardinops <- gnomonicStochastic(nInterval = 10, eggDuration = 2.5, longevity = 2555, min_fecundity = 646763, max_fecundity = 1090678, niter = 1000, a_init = 2) Epinephelus <- gnomonicStochastic(nInterval = 11, eggDuration = 2, longevity = 7300, min_fecundity = 102000, max_fecundity = 573500, niter = 1000, a_init = 2) Dosidicus <- gnomonicStochastic(nInterval = 5, eggDuration = 6, longevity = 438, min_fecundity = 813000, max_fecundity = 25887000, niter = 1000, a_init = 2) Isostichopus <- gnomonicStochastic(nInterval = 6, eggDuration = 2, longevity = 3650, min_fecundity = 13500, max_fecundity = 5062490, niter = 1000, a_init = 2) ## ----echo = TRUE-------------------------------------------------------------- par(mar=c(5.1, 4.1, 6, 2.1)) plot(Farfantopenaeus, main = "M for Farfantopenaeus duorarum", dayUnits = FALSE) plot(Vannamei, main = "M for Penaeus vannamei", col = "darkred", dayUnits = FALSE) plot(Sardinops, main = "M for Sardinops caeruleus", col = "blue") plot(Epinephelus, main = "M for Epinephelus morio", col = "darkgreen", dayUnits = FALSE) plot(Dosidicus, main = "M for Dodisicus gigas", col = "purple", dayUnits = FALSE) plot(Isostichopus, main = "M for Isostichopus badionotus", col = "skyblue", dayUnits = FALSE)