vignettes/gh2.R

In AustralianAntarcticDivision/ZooScatR: ZooScatR - Acoustic Scattering of zooplankton using DWBA

## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)
library(knitr)

## ---- echo=FALSE--------------------------------------------------------------
taxa <- c("Euphausiids and Decapod Shrimp",
          "Larval Crustacean",
          "Amphipods",
          "Ostracods",
          "Chaetognaths and Polychaetes",
          "Gymnosome Pteropods (Clione)",
          "Salps",
          "Copepods",
          "Medusae",
          "Eggs",
          "Calanus finmarchicus",
          "Calanus hyperboreus",
          "Acartia clausi",
          "Calanus marshallae",
          "Meganyctiphanes norvegica",
          "Thysanoessa",
          "Calanus",
          "General",
          "Euphausia superba",
          "Euphausia crystallorophias",
          "Neocalanus cristatus",
          "Neocalanus plumchrus",
          "Ammodytes personatus (juvenile)",
          "Ammodytes personatus (adult)",
          "Salpa thompsoni")

La <- c("10.5",
        "2.55 [@lawson_acoustically-inferred_2004]",
        "3.00 [@lawson_acoustically-inferred_2004]",
        2.55,
        17.15,
        1.83,
        4.0,
        2.55,
        NA,
        NA,
        NA,
        NA,
        NA,
        NA,
        NA,
        NA,
        NA,
        NA,
        NA,
        NA,NA,NA,NA,NA,10)

Orientation <- c("N(20,20) [@benfield_estimating_2000], average ~0 [@lawson_improved_2006]",
                 "N(0.30) [@lawson_acoustically-inferred_2004]",
                 "N(0,30) [@lawson_acoustically-inferred_2004]",
                 "N(0,30)",
                 "N(0,30)",
                 "N(0,30)",
                 "N(0,30)",
                 "N(90,30)",
                 NA,
                 NA,
                 NA,
                 NA,
                 NA,
                 NA,
                 NA,
                 NA,
                 NA,
                 NA,
                 NA,
                 NA,
                 NA,
                 NA,
                 NA,
                 NA,"Uniform [0, π]")


g <- c("$$\\frac{5.485*L}{10^4}+1.002; L>25$$ $$1.016; L<25$$ [@lawson_acoustically-inferred_2004]",
       "1.058 [@lawson_acoustically-inferred_2004]",
       "1.058 [@lawson_acoustically-inferred_2004]",
       "1.03 [pers. comm. Dezhang Chu in @lavery_determining_2007]",
       "1.03 [pers. comm. Dezhang Chu in @lavery_determining_2007]",
       "1.03 [pers. comm. Dezhang Chu in @lavery_determining_2007]",
       "1.004 [@stanton_acoustic_1994]",
       "1.02 [pers. comm. Dezhang Chu in @lavery_determining_2007]",
       "1.02 [inferred from @monger_sound_1998 as reported in @lavery_determining_2007]",
       "0.979 [@chu_material_2003]",
       "1.025 - 1.029  g/cm^3^ depending on season [@kogeler_density-and_1987]",
       "1.022 - 1.036  g/cm^3^ depending on season [@kogeler_density-and_1987]",
       "1.04 g/cm^3^ [@greenlaw_acoustical_1979]",
       "1.04 g/cm^3^ [@greenlaw_acoustical_1979]",
       "1.057 g/cm^3^ [@kils_swimming_1981]",
       "1.052 - 1.074 g/cm^3^ depending on season and species [@kogeler_density-and_1987]",
       "1.022 - 1.036 g/cm^3^ depending on season and species [@kogeler_density-and_1987]",
       "0.9402 - 1.051 [@chu_measurements_2005]",
       "1.0241 [@chu_measurements_2005], 1.0357 [@foote_speed_1990]",
       "1.009 & 1.000 depth dependent [@chu_measurements_2005]",
       "0.997 - 1.009 [@matsukura_measurements_2009]",
       "0.995 - 1.009 [@matsukura_measurements_2009]",
       "1.021 [@yasuma_density_2009]",
       "1.032 [@yasuma_density_2009]",
       "1 - 1.0039 [@wiebe_acoustic_2009]"
       )



h <- c("$$\\frac{5.94*2L}{10^ 4}; L>25$$ $$1.019; L<25$$  [@lawson_acoustically-inferred_2004]",
       "1.058 [@lawson_acoustically-inferred_2004]",
       "1.058 [@lawson_acoustically-inferred_2004]",
       "1.03 [pers. comm. Dezhang Chu in @lavery_determining_2007]",
       "1.03 [pers. comm. Dezhang Chu in @lavery_determining_2007]",
       "1.03 [pers. comm. Dezhang Chu in @lavery_determining_2007]",
       "1.004 [@stanton_acoustic_1994]",
       "1.058 [@chu_inference_2000]",
       "1.02 [inferred from @monger_sound_1998 as reported in @lavery_determining_2007]",
       "1.017 [@stanton_simple_1989]",
       "1.027 (mixture C. finmarchicus and C. hyperboreus) [@kogeler_density-and_1987]",
       "1.027 (mixture C. finmarchicus and C. hyperboreus) [@kogeler_density-and_1987]",
       "NA",
       "1.007 [@kogeler_density-and_1987]",
       "1.030 [@kogeler_density-and_1987]",
       "1.026 [@kogeler_density-and_1987]",
       "1.027 [@kogeler_density-and_1987];  0.949 & 1.013 - Depth dependent [@chu_measurements_2005]",
       "0.949 - 1.096 [@chu_measurements_2005]",
       "1.031 [@chu_measurements_2005], 1.0279 [@foote_speed_1990]",
       "1.025 & 1.029 depth dependent [@chu_measurements_2005]",
       "1.013 - 1.025 [@matsukura_measurements_2009]",
       "1.006 - 1.021 [@matsukura_measurements_2009]",
       "1.02 [@yasuma_density_2009]",
       "1.02 [@yasuma_density_2009]",
       "1.006 - 1.0201 [@wiebe_acoustic_2009]")


model <- c("DWBA uniformly-bent cylinder","DWBA uniformly-bent cylinder","DWBA uniformly-bent cylinder","DWBA uniformly-bent cylinder","DWBA uniformly-bent cylinder","DWBA uniformly-bent cylinder","DWBA uniformly-bent cylinder","DWBA prolate spheroid", "DWBA two prolate spheroid surfaces", "High-pass fluid sphere","NA","NA","NA","NA","NA","NA","NA",NA,NA,NA,"DWBA Deformed Cylinder","DWBA Deformed Cylinder",NA,NA,"DWBA")

gh <- as.data.frame(cbind(taxa,La,Orientation,g,h,model))
names(gh)<- c("Taxon",
              "Length-to-girth ratio $\\frac{L}{a}$",
              "Orientation",
              "Density Contrast g", 
              "Sound Speed Contrast h",
              "Scattering model")
kable(gh)
#datatable(gh)