LobsterHSI

The goal of LobsterHSI is to calculate Suitability Index (SI) values and plot Habitat Suitability Index (HSI) maps.

Installation

You can install the development version of LobsterHSI from GitHub with:

# install.packages("pak")
pak::pak("XiangyanYang/LobsterHSI")

Example

This is a basic example which shows you how to use code:

devtools::load_all()
#> ℹ Loading LobsterHSI
library(LobsterHSI)
## basic example code
data("Lobster_SI_9020")
data("LobsterHSI_mapData")
SIData=SIcurve(surveydata = Lobster_SI_9020, 
            envVariable = c("Latitude","Longitude","Depth", "SST"), 
            int_n = 20, 
            Seasons =c("Spring","Fall"))

plots=plot_SI_curves(surveydata = Lobster_SI_9020,
                     envVariable = c("Latitude","Longitude","Depth", "SST"),
                     int_n = 20, 
                     Seasons =c("Spring","Fall"),
                     filename = "SI_curves.jpg")
# for project users, define months 1-6 as spring, define months 7-12 as fall
# data("LobsterHSI_monthData")
# LobsterHSI_mapData <- LobsterHSI_monthData %>%
#   dplyr::mutate(Season = case_when(
#     Month %in% c(1:6) ~ "Spring",
#     Month %in% c(7:12)   ~ "Fall",
#     TRUE               ~ NA_character_))%>%
#   dplyr::select(-Month)


HSI <- get_HSI(surveydata = Lobster_SI_9020, 
               MapData = LobsterHSI_mapData,
               envVariable = c("Latitude","Longitude","Depth", "SST"), 
               int_n = 20, 
               Seasons =c("Spring","Fall"),
               weights=c(0.25,0.25,0.25,0.25))



HSImap=HSImap(surveydata = Lobster_SI_9020, 
        MapData = LobsterHSI_mapData,
        envVariable = c("Latitude","Longitude","Depth", "SST"), 
        Seasons =c("Spring","Fall"),
        int_n = 20, 
        weights=c(0.25,0.25,0.25,0.25), 
        filename="HSIplot.jpg")
#> [using ordinary kriging]
#> [using ordinary kriging]

example plots:

#> png 
#>   2
#> [using ordinary kriging]
#> [using ordinary kriging]
#> png 
#>   2