data-raw/equations_Dubi2012.R
In SCAR/solong: Allometric Equations for Southern Ocean Taxa
refs$Dubi2012 <- bibentry(bibtype = "Article",key = "Dubi2012",
author = c(person(c("C","D"),"Dubischar"),person(c("E","A"),"Pakhomov"),person(c("L"),"von Harbou"),person(c("B","P","V"),"Hunt"),person(c("U","V"),"Bathmann")),
year = 2012,title = "Salps in the Lazarev Sea, Southern Ocean: II. Biochemical composition and potential prey value",
journal = "Marine Biology",
volume = 159,pages = "15-24",doi = "10.1007/s00227-011-1785-5")
if (FALSE) {
## refit some equations because the published ones appear to be incorrect
library(dplyr)
library(readxl)
x <- read_xls("../../data/dubischar/Data Dubischar et al 2012.xls")
names(x) <- sub("_$", "", gsub("\\.+", "_", make.names(tolower(names(x)))))
## autumn WW~OAL equations
## Ihlea
myx <- x %>% dplyr::filter(season == "Fall 2004" & salp_species == "I. racovitzai" & oal_mm < 42)
fit <- lm(log(ww_ind_1_mg) ~ log(oal_mm), data = myx)
a <- coefficients(fit)[1] ## -3.911235
b <- coefficients(fit)[2] ## 2.785379
df_residual <- fit$df.residual ## 9
s2_residual <- sum(fit$residuals^2) ## 0.3130059
V <- vcov(fit) ## matrix(c(2.9891509, -0.8306561, -0.8306561, 0.2310757), nrow = 2, byrow = TRUE)
r2 <- summary(fit)$r.squared ## 0.789
N <- nrow(myx) ## 11
## Salpa
myx <- x %>% dplyr::filter(season == "Fall 2004" & salp_species == "S. thompsoni")
fit <- lm(log(ww_ind_1_mg) ~ log(oal_mm), data = myx)
a <- coefficients(fit)[1] ## -0.8037035
b <- coefficients(fit)[2] ## 2.152319
r2 <- summary(fit)$r.squared ## 0.885
N <- nrow(myx) ## 30
## CW~OAL summer
## for the two summer equations, the printed curves in the paper do not match the equations given
## Ihlea
myx <- x %>% dplyr::filter(season == "Summer 2006" & salp_species == "I. racovitzai")
fit <- lm(log(c_mg_ind_1) ~ log(oal_mm), data = myx)
a <- coefficients(fit)[1] ## -6.341833
b <- coefficients(fit)[2] ## 2.239424
r2 <- summary(fit)$r.squared ## 0.883
N <- nrow(myx) ## 62
## Salpa
myx <- x %>% dplyr::filter(season == "Summer 2006" & salp_species == "S. thompsoni")
fit <- lm(log(c_mg_ind_1) ~ log(oal_mm), data = myx)
a <- coefficients(fit)[1] ## -5.254129
b <- coefficients(fit)[2] ## 1.855174
r2 <- summary(fit)$r.squared ## 0.947
N <- nrow(myx) ## 73
## CW~OAL winter
## Ihlea
myx <- x %>% dplyr::filter(season == "Winter 2006" & salp_species == "I. racovitzai")
fit <- lm(log(c_mg_ind_1) ~ log(oal_mm), data = myx)
a <- coefficients(fit)[1] ## -8.395922
b <- coefficients(fit)[2] ## 2.719844
r2 <- summary(fit)$r.squared ## 0.981
N <- nrow(myx) ## 59
## Salpa
myx <- x %>% dplyr::filter(season == "Winter 2006" & salp_species == "S. thompsoni")
fit <- lm(log(c_mg_ind_1) ~ log(oal_mm), data = myx)
a <- coefficients(fit)[1] ## -4.380123
b <- coefficients(fit)[2] ## 1.578182
r2 <- summary(fit)$r.squared ## 0.693
N <- nrow(myx) ## 17
## lipid weight vs OAL
myx <- tibble(OAL = c(60, 40, 30, 35, 55, 31, 54, 55, 40, 30, 24, 32, 9, 8, 56, 65, 9, 33, 33, 52, 50, 44, 47, 18, 27, 18, 27, 26, 25, 20, 20, 24, 26, 25, 50, 60, 65, 57, 28, 39, 34),
LW = c(2.178, 1.170, 0.413, 1.555, 2.795, 0.628, 1.492, 1.898, 1.573, 0.995, 0.679, 0.734, 0.318, 0.167, 2.841, 4.462, 0.065, 1.073, 0.585, 1.825, 3.925, 2.750, 3.100, 0.275, 1.325, 0.280, 0.850, 0.950, 0.750, 0.575, 0.380, 0.950, 0.750, 1.150, 4.080, 3.513, 4.811, 2.413, 0.972, 2.005, 0.749))
fit <- lm(log(LW) ~ log(OAL), data = myx)
a <- coefficients(fit)[1] ## -5.606497
b <- coefficients(fit)[2] ## 1.63873
r2 <- summary(fit)$r.squared ## 0.824
N <- nrow(myx) ## 41
}
alleq_Dubi2012 <- function(id) {
switch(id,
## WW~OAL summer
## Ihlea racovitzai 266542
"266542_WW~OAL_summer_Dubi2012" = list(taxon_name = "Ihlea racovitzai",
taxon_aphia_id = 266542,
equation = function(OAL) tibble(allometric_value = 0.008 * (OAL ^ 3.092)),
inputs = tibble(property = "oral-atrial length",units = "mm", sample_minimum = 15, sample_maximum = 60),
return_property = "wet weight",
return_units = "mg",
reliability = tribble(~type,~value,
"R^2",0.809),
notes = "From specimens caught during a summer cruise, Dec-2005 to Jan-2006",
reference = refs$Dubi2012),
## Salpa thompsoni 266545
"266545_WW~OAL_summer_Dubi2012" = list(taxon_name = "Salpa thompsoni",
taxon_aphia_id = 266545,
equation = function(OAL) tibble(allometric_value = 0.136*(OAL ^ 2.376)),
inputs = tibble(property = "oral-atrial length",units = "mm", sample_minimum = 8, sample_maximum = 115),
return_property = "wet weight",
return_units = "mg",
reliability = tribble(~type,~value,
"R^2",0.988),
notes = "From specimens caught during a summer cruise, Dec-2005 to Jan-2006",
reference = refs$Dubi2012),
## WW~OAL autumn
## Ihlea racovitzai 266542
## refitted eq
"266542_WW~OAL_autumn_Dubi2012" = list(taxon_name = "Ihlea racovitzai",
taxon_aphia_id = 266542,
equation = function(OAL) tibble(allometric_value = exp(-3.911235) * (OAL ^ 2.785379)),
inputs = tibble(property = "oral-atrial length",units = "mm", sample_minimum = 26, sample_maximum = 40),
return_property = "wet weight",
return_units = "mg",
reliability = tribble(~type,~value,
"N", 11,
"R^2",0.816),
notes = "From specimens caught during a summer cruise, Dec-2005 to Jan-2006. Equation refitted from original data, because published equation appears to be incorrect",
reference = refs$Dubi2012),
## Salpa thompsoni 266545
## refitted eq
"266545_WW~OAL_autumn_Dubi2012" = list(taxon_name = "Salpa thompsoni",
taxon_aphia_id = 266545,
equation = function(OAL) tibble(allometric_value = exp(-0.8037035) * (OAL ^ 2.152319)),
inputs=tibble(property = "oral-atrial length", units = "mm", sample_minimum = 9, sample_maximum = 40),
return_property = "wet weight",
return_units = "mg",
reliability=tribble(~type, ~value,
"N", 30,
"R^2", 0.885),
notes = "From specimens caught during an autumn cruise, Apr-May 2004. Equation refitted from original data, because published equation appears to be incorrect",
reference = refs$Dubi2012),
## WW~OAL winter
## Ihlea racovitzai 266542
"266542_WW~OAL_winter_Dubi2012" = list(taxon_name = "Ihlea racovitzai",
taxon_aphia_id = 266542,
equation = function(OAL) tibble(allometric_value = 0.057 * (OAL ^ 2.462)),
inputs = tibble(property = "oral-atrial length", units = "mm", sample_minimum = 14, sample_maximum = 71),
return_property = "wet weight",
return_units = "mg",
reliability = tribble(~type, ~value,
"R^2", 0.875),
notes = "From specimens caught during a winter cruise, Jul-Aug 2006",
reference = refs$Dubi2012),
## Salpa thompsoni 266545
"266545_WW~OAL_winter_Dubi2012" = list(taxon_name = "Salpa thompsoni",
taxon_aphia_id = 266545,
equation = function(OAL) tibble(allometric_value = 0.011 * (OAL ^ 3.049)),
inputs = tibble(property = "oral-atrial length", units = "mm", sample_minimum = 12, sample_maximum = 43),
return_property = "wet weight",
return_units = "mg",
reliability = tribble(~type, ~value,
"R^2", 0.98),
notes = "From specimens caught during a winter cruise, Jul-Aug 2006",
reference = refs$Dubi2012),
## ---
## DW~OAL summer
## Ihlea racovitzai 266542
"266542_DW~OAL_summer_Dubi2012"=list(taxon_name="Ihlea racovitzai",
taxon_aphia_id=266542,
equation=function(...)tibble(allometric_value=0.002*(...^2.731)),
inputs=tibble(property="oral-atrial length",units="mm", sample_minimum = 15, sample_maximum = 60),
return_property="dry weight",
return_units="mg",
reliability=tribble(~type,~value,
"R^2",0.76),
notes="From specimens caught during a summer cruise, Dec-2005 to Jan-2006",
reference=refs$Dubi2012),
## Salpa thompsoni 266545
"266545_DW~OAL_summer_Dubi2012"=list(taxon_name="Salpa thompsoni",
taxon_aphia_id=266545,
equation=function(...)tibble(allometric_value=0.005*(...^2.44)),
inputs=tibble(property="oral-atrial length",units="mm", sample_minimum = 8, sample_maximum = 115),
return_property="dry weight",
return_units="mg",
reliability=tribble(~type,~value,
"R^2",0.998),
notes="From specimens caught during a summer cruise, Dec-2005 to Jan-2006",
reference=refs$Dubi2012),
## DW~OAL autumn
## Ihlea racovitzai 266542
"266542_DW~OAL_autumn_Dubi2012"=list(taxon_name="Ihlea racovitzai",
taxon_aphia_id=266542,
equation=function(...)tibble(allometric_value=1.4e-05*(...^4.043)),
inputs=tibble(property="oral-atrial length",units="mm", sample_minimum = 26, sample_maximum = 40),
return_property="dry weight",
return_units="mg",
reliability=tribble(~type,~value,
"R^2",0.774),
notes="From specimens caught during an autumn cruise, Apr-May 2004",
reference=refs$Dubi2012),
## Salpa thompsoni 266545
"266545_DW~OAL_autumn_Dubi2012"=list(taxon_name="Salpa thompsoni",
taxon_aphia_id=266545,
equation=function(...)tibble(allometric_value=0.047*(...^1.96)),
inputs=tibble(property="oral-atrial length",units="mm", sample_minimum = 9, sample_maximum = 40),
return_property="dry weight",
return_units="mg",
reliability=tribble(~type,~value,
"R^2",0.946),
notes="From specimens caught during an autumn cruise, Apr-May 2004",
reference=refs$Dubi2012),
## DW~OAL winter
## Ihlea racovitzai 266542
"266542_DW~OAL_winter_Dubi2012"=list(taxon_name="Ihlea racovitzai",
taxon_aphia_id=266542,
equation=function(...)tibble(allometric_value=0.0037*(...^2.426)),
inputs=tibble(property="oral-atrial length",units="mm", sample_minimum = 14, sample_maximum = 71),
return_property="dry weight",
return_units="mg",
reliability=tribble(~type,~value,
"R^2",0.906),
notes="From specimens caught during a winter cruise, Jul-Aug 2006",
reference=refs$Dubi2012),
## Salpa thompsoni 266545
"266545_DW~OAL_winter_Dubi2012"=list(taxon_name="Salpa thompsoni",
taxon_aphia_id=266545,
equation=function(...)tibble(allometric_value=0.0034*(...^2.535)),
inputs=tibble(property="oral-atrial length",units="mm", sample_minimum = 12, sample_maximum = 43),
return_property="dry weight",
return_units="mg",
reliability=tribble(~type,~value,
"R^2",0.95),
notes="From specimens caught during a winter cruise, Jul-Aug 2006",
reference=refs$Dubi2012),
## ---
## CW~OAL summer
## the two summer equations are excluded here, the printed curves in the paper do not match the equations given
## Ihlea racovitzai 266542
"266542_CW~OAL_summer_Dubi2012" = list(taxon_name = "Ihlea racovitzai",
taxon_aphia_id = 266542,
equation = function(OAL) tibble(allometric_value = exp(-6.341833) * (OAL ^ 2.239424)),
inputs = tibble(property = "oral-atrial length", units = "mm", sample_minimum = 15, sample_maximum = 60),
return_property = "carbon weight",
return_units = "mg",
reliability = tribble(~type, ~value,
"N", 62,
"R^2", 0.883),
notes="From specimens caught during a summer cruise, Dec-2005 to Jan-2006. Equation refitted from original data, because published equation appears to be incorrect",
reference=refs$Dubi2012),
## Salpa thompsoni 266545
"266545_CW~OAL_summer_Dubi2012"=list(taxon_name="Salpa thompsoni",
taxon_aphia_id=266545,
equation=function(OAL) tibble(allometric_value = exp(-5.254129) * (OAL ^ 1.855174)),
inputs=tibble(property="oral-atrial length",units="mm", sample_minimum = 8, sample_maximum = 115),
return_property="carbon weight",
return_units="mg",
reliability=tribble(~type,~value,
"N", 73,
"R^2",0.947),
notes="From specimens caught during a summer cruise, Dec-2005 to Jan-2006. Equation refitted from original data, because published equation appears to be incorrect",
reference=refs$Dubi2012),
## CW~OAL autumn
## Salpa thompsoni 266545
"266545_CW~OAL_autumn_Dubi2012"=list(taxon_name="Salpa thompsoni",
taxon_aphia_id=266545,
equation=function(...)tibble(allometric_value=0.016*(...^1.641)),
inputs=tibble(property="oral-atrial length",units="mm", sample_minimum = 9, sample_maximum = 40),
return_property="carbon weight",
return_units="mg",
reliability=tribble(~type,~value,
"R^2",0.851),
notes="From specimens caught during an autumn cruise, Apr-May 2004",
reference=refs$Dubi2012),
## CW~OAL winter
## Ihlea racovitzai 266542
## error in the printed equation in Figure 4: curve is exponential but equation is linear
"266542_CW~OAL_winter_Dubi2012"=list(taxon_name="Ihlea racovitzai",
taxon_aphia_id=266542,
equation=function(OAL) tibble(allometric_value = exp(-8.395922) * (OAL ^ 2.719844)),
inputs=tibble(property="oral-atrial length",units="mm", sample_minimum = 14, sample_maximum = 71),
return_property="carbon weight",
return_units="mg",
reliability=tribble(~type,~value,
"N", 59,
"R^2",0.981),
notes="From specimens caught during a winter cruise, Jul-Aug 2006. Equation refitted from original data, because published equation appears to be incorrect",
reference=refs$Dubi2012),
## Salpa thompsoni 266545
## the equation here does not match the printed curve
"266545_CW~OAL_winter_Dubi2012"=list(taxon_name="Salpa thompsoni",
taxon_aphia_id=266545,
equation=function(OAL) tibble(allometric_value = exp(-4.380123) * (OAL ^ 1.578182)),
inputs=tibble(property="oral-atrial length",units="mm", sample_minimum = 12, sample_maximum = 43),
return_property="carbon weight",
return_units="mg",
reliability=tribble(~type,~value,
"N", 17,
"R^2",0.693),
notes="From specimens caught during a winter cruise, Jul-Aug 2006. Equation refitted from original data, because published equation appears to be incorrect",
reference=refs$Dubi2012),
## all specimens, all seasons: lipid weight~OAL
## printed curve does not match equation given
"137217_LpW~OAL_Dubi2012"=list(taxon_name="Salpidae",
taxon_aphia_id=137217,
equation=function(OAL) tibble(allometric_value = exp(-5.606497) * (OAL ^ 1.63873)),
inputs = tibble(property = "oral-atrial length", units = "mm", sample_minimum = 8, sample_maximum = 65),
return_property="lipid weight",
return_units="mg",
reliability=tribble(~type,~value,
"N",41,
"R^2",0.824),
notes="Based on specimens of Salpa thompsoni and Ihlea racovitzai. Equation refitted from original data, because published equation appears to be incorrect",
reference=refs$Dubi2012),
## convert wet weight to energetic content
## Lipids correspond to 9.3 kcal/g = 9.3*4.2 kJ/g, proteins to 4.1 kcal/g = 4.2*4.2 kJ/g and carbohydrates to 4.1 kcal/g = 4.1*4.2 kJ/g
## summer
"266542_EC~WW_summer_Dubi2012"=list(taxon_name="Ihlea racovitzai",
taxon_aphia_id=266542,
equation=function(...) {
dw <- 0.065*...
carbs <- 0.012*dw; prot <- 0.323*dw; Lp <- 0.035*dw
tibble(allometric_value=9.3*4.2*Lp+4.2*4.2*prot+4.1*4.2*carbs)},
inputs=tibble(property="wet weight",units="g"),
return_property="total energy content",
return_units="kJ",
reliability=tribble(~type,~value,
"N",12),
notes="From specimens caught during a summer cruise, Dec-2005 to Jan-2006. Lipid fraction based on measurements of 12 specimens, other components based on measurements of more specimens",
reference=refs$Dubi2012),
"266545_EC~WW_summer_Dubi2012"=list(taxon_name="Salpa thompsoni",
taxon_aphia_id=266545,
equation=function(...) {
dw <- 0.075*...
carbs <- 0.028*dw; prot <- 0.092*dw; Lp <- 0.038*dw
tibble(allometric_value=9.3*4.2*Lp+4.2*4.2*prot+4.1*4.2*carbs)},
inputs=tibble(property="wet weight",units="g"),
return_property="total energy content",
return_units="kJ",
reliability=tribble(~type,~value,
"N",4),
notes="From specimens caught during a summer cruise, Dec-2005 to Jan-2006. Lipid, protein, carbohydrate fractions based on measurements of 4 specimens, dry weight based on measurements of 21 specimens",
reference=refs$Dubi2012),
## autumn
"266542_EC~WW_autumn_Dubi2012"=list(taxon_name="Ihlea racovitzai",
taxon_aphia_id=266542,
equation=function(...) {
dw <- 0.068*...
carbs <- 0.022*dw; prot <- 0.302*dw; Lp <- 0.043*dw
tibble(allometric_value=9.3*4.2*Lp+4.2*4.2*prot+4.1*4.2*carbs)},
inputs=tibble(property="wet weight",units="g"),
return_property="total energy content",
return_units="kJ",
reliability=tribble(~type,~value,
"N",5),
notes="From specimens caught during an autumn cruise, Apr-May 2004. Lipid fraction based on measurements of 5 specimens, other components based on measurements of more specimens",
reference=refs$Dubi2012),
"266545_EC~WW_autumn_Dubi2012"=list(taxon_name="Salpa thompsoni",
taxon_aphia_id=266545,
equation=function(...) {
dw <- 0.055*...
carbs <- 0.02*dw; prot <- 0.102*dw; Lp <- 0.024*dw
tibble(allometric_value=9.3*4.2*Lp+4.2*4.2*prot+4.1*4.2*carbs)},
inputs=tibble(property="wet weight",units="g"),
return_property="total energy content",
return_units="kJ",
reliability=tribble(~type,~value,
"N",12),
notes="From specimens caught during an autumn cruise, Apr-May 2004. Lipid fraction based on measurements of 12 specimens, other components based on measurements of more specimens",
reference=refs$Dubi2012),
## winter
"266542_EC~WW_winter_Dubi2012"=list(taxon_name="Ihlea racovitzai",
taxon_aphia_id=266542,
equation=function(...) {
dw <- 0.058*...
carbs <- 0.013*dw; prot <- 0.317*dw; Lp <- 0.031*dw
tibble(allometric_value=9.3*4.2*Lp+4.2*4.2*prot+4.1*4.2*carbs)},
inputs=tibble(property="wet weight",units="g"),
return_property="total energy content",
return_units="kJ",
reliability=tribble(~type,~value,
"N",4),
notes="From specimens caught during a winter cruise, Jul-Aug 2006. Lipid fraction based on measurements of 4 specimens, other components based on measurements of more specimens",
reference=refs$Dubi2012),
"266545_EC~WW_winter_Dubi2012"=list(taxon_name="Salpa thompsoni",
taxon_aphia_id=266545,
equation=function(...) {
dw <- 0.062*...
carbs <- 0.02*dw; prot <- 0.113*dw; Lp <- 0.036*dw
tibble(allometric_value=9.3*4.2*Lp+4.2*4.2*prot+4.1*4.2*carbs)},
inputs=tibble(property="wet weight",units="g"),
return_property="total energy content",
return_units="kJ",
reliability=tribble(~type,~value,
"N",1),
notes="From specimens caught during a winter cruise, Jul-Aug 2006. Carbohydrate and protein fractions based on measurements of 1 specimen, other components based on measurements of more specimens",
reference=refs$Dubi2012),
## all seasons combined
"266542_EC~WW_Dubi2012"=list(taxon_name="Ihlea racovitzai",
taxon_aphia_id=266542,
equation=function(...) {
dw <- 0.062*...
carbs <- 0.014*dw; prot <- 0.316*dw; Lp <- 0.036*dw
tibble(allometric_value=9.3*4.2*Lp+4.2*4.2*prot+4.1*4.2*carbs)}, ##ww*0.062*4.2*(9.3*0.036+4.2*0.316+4.1*0.014) = ww*0.4477
inputs=tibble(property="wet weight",units="g"),
return_property="total energy content",
return_units="kJ",
reliability=tribble(~type,~value,
"N",21),
notes="Combined across summer, autumn, and winter samples. Lipid fraction based on measurements of 21 specimens, other components based on measurements of more specimens",
reference=refs$Dubi2012),
"266545_EC~WW_Dubi2012"=list(taxon_name="Salpa thompsoni",
taxon_aphia_id=266545,
equation=function(...) {
dw <- 0.063*...
carbs <- 0.021*dw; prot <- 0.101*dw; Lp <- 0.029*dw
tibble(allometric_value=9.3*4.2*Lp+4.2*4.2*prot+4.1*4.2*carbs)},
inputs=tibble(property="wet weight",units="g"),
return_property="total energy content",
return_units="kJ",
reliability=tribble(~type,~value,
"N",19),
notes="Combined across summer, autumn, and winter samples. Lipid fraction based on measurements of 19 specimens, other components based on measurements of more specimens",
reference=refs$Dubi2012),
stop("unrecognized equation ID: ",id))
}
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refs$Dubi2012 <- bibentry(bibtype = "Article",key = "Dubi2012",
author = c(person(c("C","D"),"Dubischar"),person(c("E","A"),"Pakhomov"),person(c("L"),"von Harbou"),person(c("B","P","V"),"Hunt"),person(c("U","V"),"Bathmann")),
year = 2012,title = "Salps in the Lazarev Sea, Southern Ocean: II. Biochemical composition and potential prey value",
journal = "Marine Biology",
volume = 159,pages = "15-24",doi = "10.1007/s00227-011-1785-5")
if (FALSE) {
## refit some equations because the published ones appear to be incorrect
library(dplyr)
library(readxl)
x <- read_xls("../../data/dubischar/Data Dubischar et al 2012.xls")
names(x) <- sub("_$", "", gsub("\\.+", "_", make.names(tolower(names(x)))))
## autumn WW~OAL equations
## Ihlea
myx <- x %>% dplyr::filter(season == "Fall 2004" & salp_species == "I. racovitzai" & oal_mm < 42)
fit <- lm(log(ww_ind_1_mg) ~ log(oal_mm), data = myx)
a <- coefficients(fit)[1] ## -3.911235
b <- coefficients(fit)[2] ## 2.785379
df_residual <- fit$df.residual ## 9
s2_residual <- sum(fit$residuals^2) ## 0.3130059
V <- vcov(fit) ## matrix(c(2.9891509, -0.8306561, -0.8306561, 0.2310757), nrow = 2, byrow = TRUE)
r2 <- summary(fit)$r.squared ## 0.789
N <- nrow(myx) ## 11
## Salpa
myx <- x %>% dplyr::filter(season == "Fall 2004" & salp_species == "S. thompsoni")
fit <- lm(log(ww_ind_1_mg) ~ log(oal_mm), data = myx)
a <- coefficients(fit)[1] ## -0.8037035
b <- coefficients(fit)[2] ## 2.152319
r2 <- summary(fit)$r.squared ## 0.885
N <- nrow(myx) ## 30
## CW~OAL summer
## for the two summer equations, the printed curves in the paper do not match the equations given
## Ihlea
myx <- x %>% dplyr::filter(season == "Summer 2006" & salp_species == "I. racovitzai")
fit <- lm(log(c_mg_ind_1) ~ log(oal_mm), data = myx)
a <- coefficients(fit)[1] ## -6.341833
b <- coefficients(fit)[2] ## 2.239424
r2 <- summary(fit)$r.squared ## 0.883
N <- nrow(myx) ## 62
## Salpa
myx <- x %>% dplyr::filter(season == "Summer 2006" & salp_species == "S. thompsoni")
fit <- lm(log(c_mg_ind_1) ~ log(oal_mm), data = myx)
a <- coefficients(fit)[1] ## -5.254129
b <- coefficients(fit)[2] ## 1.855174
r2 <- summary(fit)$r.squared ## 0.947
N <- nrow(myx) ## 73
## CW~OAL winter
## Ihlea
myx <- x %>% dplyr::filter(season == "Winter 2006" & salp_species == "I. racovitzai")
fit <- lm(log(c_mg_ind_1) ~ log(oal_mm), data = myx)
a <- coefficients(fit)[1] ## -8.395922
b <- coefficients(fit)[2] ## 2.719844
r2 <- summary(fit)$r.squared ## 0.981
N <- nrow(myx) ## 59
## Salpa
myx <- x %>% dplyr::filter(season == "Winter 2006" & salp_species == "S. thompsoni")
fit <- lm(log(c_mg_ind_1) ~ log(oal_mm), data = myx)
a <- coefficients(fit)[1] ## -4.380123
b <- coefficients(fit)[2] ## 1.578182
r2 <- summary(fit)$r.squared ## 0.693
N <- nrow(myx) ## 17
## lipid weight vs OAL
myx <- tibble(OAL = c(60, 40, 30, 35, 55, 31, 54, 55, 40, 30, 24, 32, 9, 8, 56, 65, 9, 33, 33, 52, 50, 44, 47, 18, 27, 18, 27, 26, 25, 20, 20, 24, 26, 25, 50, 60, 65, 57, 28, 39, 34),
LW = c(2.178, 1.170, 0.413, 1.555, 2.795, 0.628, 1.492, 1.898, 1.573, 0.995, 0.679, 0.734, 0.318, 0.167, 2.841, 4.462, 0.065, 1.073, 0.585, 1.825, 3.925, 2.750, 3.100, 0.275, 1.325, 0.280, 0.850, 0.950, 0.750, 0.575, 0.380, 0.950, 0.750, 1.150, 4.080, 3.513, 4.811, 2.413, 0.972, 2.005, 0.749))
fit <- lm(log(LW) ~ log(OAL), data = myx)
a <- coefficients(fit)[1] ## -5.606497
b <- coefficients(fit)[2] ## 1.63873
r2 <- summary(fit)$r.squared ## 0.824
N <- nrow(myx) ## 41
}
alleq_Dubi2012 <- function(id) {
switch(id,
## WW~OAL summer
## Ihlea racovitzai 266542
"266542_WW~OAL_summer_Dubi2012" = list(taxon_name = "Ihlea racovitzai",
taxon_aphia_id = 266542,
equation = function(OAL) tibble(allometric_value = 0.008 * (OAL ^ 3.092)),
inputs = tibble(property = "oral-atrial length",units = "mm", sample_minimum = 15, sample_maximum = 60),
return_property = "wet weight",
return_units = "mg",
reliability = tribble(~type,~value,
"R^2",0.809),
notes = "From specimens caught during a summer cruise, Dec-2005 to Jan-2006",
reference = refs$Dubi2012),
## Salpa thompsoni 266545
"266545_WW~OAL_summer_Dubi2012" = list(taxon_name = "Salpa thompsoni",
taxon_aphia_id = 266545,
equation = function(OAL) tibble(allometric_value = 0.136*(OAL ^ 2.376)),
inputs = tibble(property = "oral-atrial length",units = "mm", sample_minimum = 8, sample_maximum = 115),
return_property = "wet weight",
return_units = "mg",
reliability = tribble(~type,~value,
"R^2",0.988),
notes = "From specimens caught during a summer cruise, Dec-2005 to Jan-2006",
reference = refs$Dubi2012),
## WW~OAL autumn
## Ihlea racovitzai 266542
## refitted eq
"266542_WW~OAL_autumn_Dubi2012" = list(taxon_name = "Ihlea racovitzai",
taxon_aphia_id = 266542,
equation = function(OAL) tibble(allometric_value = exp(-3.911235) * (OAL ^ 2.785379)),
inputs = tibble(property = "oral-atrial length",units = "mm", sample_minimum = 26, sample_maximum = 40),
return_property = "wet weight",
return_units = "mg",
reliability = tribble(~type,~value,
"N", 11,
"R^2",0.816),
notes = "From specimens caught during a summer cruise, Dec-2005 to Jan-2006. Equation refitted from original data, because published equation appears to be incorrect",
reference = refs$Dubi2012),
## Salpa thompsoni 266545
## refitted eq
"266545_WW~OAL_autumn_Dubi2012" = list(taxon_name = "Salpa thompsoni",
taxon_aphia_id = 266545,
equation = function(OAL) tibble(allometric_value = exp(-0.8037035) * (OAL ^ 2.152319)),
inputs=tibble(property = "oral-atrial length", units = "mm", sample_minimum = 9, sample_maximum = 40),
return_property = "wet weight",
return_units = "mg",
reliability=tribble(~type, ~value,
"N", 30,
"R^2", 0.885),
notes = "From specimens caught during an autumn cruise, Apr-May 2004. Equation refitted from original data, because published equation appears to be incorrect",
reference = refs$Dubi2012),
## WW~OAL winter
## Ihlea racovitzai 266542
"266542_WW~OAL_winter_Dubi2012" = list(taxon_name = "Ihlea racovitzai",
taxon_aphia_id = 266542,
equation = function(OAL) tibble(allometric_value = 0.057 * (OAL ^ 2.462)),
inputs = tibble(property = "oral-atrial length", units = "mm", sample_minimum = 14, sample_maximum = 71),
return_property = "wet weight",
return_units = "mg",
reliability = tribble(~type, ~value,
"R^2", 0.875),
notes = "From specimens caught during a winter cruise, Jul-Aug 2006",
reference = refs$Dubi2012),
## Salpa thompsoni 266545
"266545_WW~OAL_winter_Dubi2012" = list(taxon_name = "Salpa thompsoni",
taxon_aphia_id = 266545,
equation = function(OAL) tibble(allometric_value = 0.011 * (OAL ^ 3.049)),
inputs = tibble(property = "oral-atrial length", units = "mm", sample_minimum = 12, sample_maximum = 43),
return_property = "wet weight",
return_units = "mg",
reliability = tribble(~type, ~value,
"R^2", 0.98),
notes = "From specimens caught during a winter cruise, Jul-Aug 2006",
reference = refs$Dubi2012),
## ---
## DW~OAL summer
## Ihlea racovitzai 266542
"266542_DW~OAL_summer_Dubi2012"=list(taxon_name="Ihlea racovitzai",
taxon_aphia_id=266542,
equation=function(...)tibble(allometric_value=0.002*(...^2.731)),
inputs=tibble(property="oral-atrial length",units="mm", sample_minimum = 15, sample_maximum = 60),
return_property="dry weight",
return_units="mg",
reliability=tribble(~type,~value,
"R^2",0.76),
notes="From specimens caught during a summer cruise, Dec-2005 to Jan-2006",
reference=refs$Dubi2012),
## Salpa thompsoni 266545
"266545_DW~OAL_summer_Dubi2012"=list(taxon_name="Salpa thompsoni",
taxon_aphia_id=266545,
equation=function(...)tibble(allometric_value=0.005*(...^2.44)),
inputs=tibble(property="oral-atrial length",units="mm", sample_minimum = 8, sample_maximum = 115),
return_property="dry weight",
return_units="mg",
reliability=tribble(~type,~value,
"R^2",0.998),
notes="From specimens caught during a summer cruise, Dec-2005 to Jan-2006",
reference=refs$Dubi2012),
## DW~OAL autumn
## Ihlea racovitzai 266542
"266542_DW~OAL_autumn_Dubi2012"=list(taxon_name="Ihlea racovitzai",
taxon_aphia_id=266542,
equation=function(...)tibble(allometric_value=1.4e-05*(...^4.043)),
inputs=tibble(property="oral-atrial length",units="mm", sample_minimum = 26, sample_maximum = 40),
return_property="dry weight",
return_units="mg",
reliability=tribble(~type,~value,
"R^2",0.774),
notes="From specimens caught during an autumn cruise, Apr-May 2004",
reference=refs$Dubi2012),
## Salpa thompsoni 266545
"266545_DW~OAL_autumn_Dubi2012"=list(taxon_name="Salpa thompsoni",
taxon_aphia_id=266545,
equation=function(...)tibble(allometric_value=0.047*(...^1.96)),
inputs=tibble(property="oral-atrial length",units="mm", sample_minimum = 9, sample_maximum = 40),
return_property="dry weight",
return_units="mg",
reliability=tribble(~type,~value,
"R^2",0.946),
notes="From specimens caught during an autumn cruise, Apr-May 2004",
reference=refs$Dubi2012),
## DW~OAL winter
## Ihlea racovitzai 266542
"266542_DW~OAL_winter_Dubi2012"=list(taxon_name="Ihlea racovitzai",
taxon_aphia_id=266542,
equation=function(...)tibble(allometric_value=0.0037*(...^2.426)),
inputs=tibble(property="oral-atrial length",units="mm", sample_minimum = 14, sample_maximum = 71),
return_property="dry weight",
return_units="mg",
reliability=tribble(~type,~value,
"R^2",0.906),
notes="From specimens caught during a winter cruise, Jul-Aug 2006",
reference=refs$Dubi2012),
## Salpa thompsoni 266545
"266545_DW~OAL_winter_Dubi2012"=list(taxon_name="Salpa thompsoni",
taxon_aphia_id=266545,
equation=function(...)tibble(allometric_value=0.0034*(...^2.535)),
inputs=tibble(property="oral-atrial length",units="mm", sample_minimum = 12, sample_maximum = 43),
return_property="dry weight",
return_units="mg",
reliability=tribble(~type,~value,
"R^2",0.95),
notes="From specimens caught during a winter cruise, Jul-Aug 2006",
reference=refs$Dubi2012),
## ---
## CW~OAL summer
## the two summer equations are excluded here, the printed curves in the paper do not match the equations given
## Ihlea racovitzai 266542
"266542_CW~OAL_summer_Dubi2012" = list(taxon_name = "Ihlea racovitzai",
taxon_aphia_id = 266542,
equation = function(OAL) tibble(allometric_value = exp(-6.341833) * (OAL ^ 2.239424)),
inputs = tibble(property = "oral-atrial length", units = "mm", sample_minimum = 15, sample_maximum = 60),
return_property = "carbon weight",
return_units = "mg",
reliability = tribble(~type, ~value,
"N", 62,
"R^2", 0.883),
notes="From specimens caught during a summer cruise, Dec-2005 to Jan-2006. Equation refitted from original data, because published equation appears to be incorrect",
reference=refs$Dubi2012),
## Salpa thompsoni 266545
"266545_CW~OAL_summer_Dubi2012"=list(taxon_name="Salpa thompsoni",
taxon_aphia_id=266545,
equation=function(OAL) tibble(allometric_value = exp(-5.254129) * (OAL ^ 1.855174)),
inputs=tibble(property="oral-atrial length",units="mm", sample_minimum = 8, sample_maximum = 115),
return_property="carbon weight",
return_units="mg",
reliability=tribble(~type,~value,
"N", 73,
"R^2",0.947),
notes="From specimens caught during a summer cruise, Dec-2005 to Jan-2006. Equation refitted from original data, because published equation appears to be incorrect",
reference=refs$Dubi2012),
## CW~OAL autumn
## Salpa thompsoni 266545
"266545_CW~OAL_autumn_Dubi2012"=list(taxon_name="Salpa thompsoni",
taxon_aphia_id=266545,
equation=function(...)tibble(allometric_value=0.016*(...^1.641)),
inputs=tibble(property="oral-atrial length",units="mm", sample_minimum = 9, sample_maximum = 40),
return_property="carbon weight",
return_units="mg",
reliability=tribble(~type,~value,
"R^2",0.851),
notes="From specimens caught during an autumn cruise, Apr-May 2004",
reference=refs$Dubi2012),
## CW~OAL winter
## Ihlea racovitzai 266542
## error in the printed equation in Figure 4: curve is exponential but equation is linear
"266542_CW~OAL_winter_Dubi2012"=list(taxon_name="Ihlea racovitzai",
taxon_aphia_id=266542,
equation=function(OAL) tibble(allometric_value = exp(-8.395922) * (OAL ^ 2.719844)),
inputs=tibble(property="oral-atrial length",units="mm", sample_minimum = 14, sample_maximum = 71),
return_property="carbon weight",
return_units="mg",
reliability=tribble(~type,~value,
"N", 59,
"R^2",0.981),
notes="From specimens caught during a winter cruise, Jul-Aug 2006. Equation refitted from original data, because published equation appears to be incorrect",
reference=refs$Dubi2012),
## Salpa thompsoni 266545
## the equation here does not match the printed curve
"266545_CW~OAL_winter_Dubi2012"=list(taxon_name="Salpa thompsoni",
taxon_aphia_id=266545,
equation=function(OAL) tibble(allometric_value = exp(-4.380123) * (OAL ^ 1.578182)),
inputs=tibble(property="oral-atrial length",units="mm", sample_minimum = 12, sample_maximum = 43),
return_property="carbon weight",
return_units="mg",
reliability=tribble(~type,~value,
"N", 17,
"R^2",0.693),
notes="From specimens caught during a winter cruise, Jul-Aug 2006. Equation refitted from original data, because published equation appears to be incorrect",
reference=refs$Dubi2012),
## all specimens, all seasons: lipid weight~OAL
## printed curve does not match equation given
"137217_LpW~OAL_Dubi2012"=list(taxon_name="Salpidae",
taxon_aphia_id=137217,
equation=function(OAL) tibble(allometric_value = exp(-5.606497) * (OAL ^ 1.63873)),
inputs = tibble(property = "oral-atrial length", units = "mm", sample_minimum = 8, sample_maximum = 65),
return_property="lipid weight",
return_units="mg",
reliability=tribble(~type,~value,
"N",41,
"R^2",0.824),
notes="Based on specimens of Salpa thompsoni and Ihlea racovitzai. Equation refitted from original data, because published equation appears to be incorrect",
reference=refs$Dubi2012),
## convert wet weight to energetic content
## Lipids correspond to 9.3 kcal/g = 9.3*4.2 kJ/g, proteins to 4.1 kcal/g = 4.2*4.2 kJ/g and carbohydrates to 4.1 kcal/g = 4.1*4.2 kJ/g
## summer
"266542_EC~WW_summer_Dubi2012"=list(taxon_name="Ihlea racovitzai",
taxon_aphia_id=266542,
equation=function(...) {
dw <- 0.065*...
carbs <- 0.012*dw; prot <- 0.323*dw; Lp <- 0.035*dw
tibble(allometric_value=9.3*4.2*Lp+4.2*4.2*prot+4.1*4.2*carbs)},
inputs=tibble(property="wet weight",units="g"),
return_property="total energy content",
return_units="kJ",
reliability=tribble(~type,~value,
"N",12),
notes="From specimens caught during a summer cruise, Dec-2005 to Jan-2006. Lipid fraction based on measurements of 12 specimens, other components based on measurements of more specimens",
reference=refs$Dubi2012),
"266545_EC~WW_summer_Dubi2012"=list(taxon_name="Salpa thompsoni",
taxon_aphia_id=266545,
equation=function(...) {
dw <- 0.075*...
carbs <- 0.028*dw; prot <- 0.092*dw; Lp <- 0.038*dw
tibble(allometric_value=9.3*4.2*Lp+4.2*4.2*prot+4.1*4.2*carbs)},
inputs=tibble(property="wet weight",units="g"),
return_property="total energy content",
return_units="kJ",
reliability=tribble(~type,~value,
"N",4),
notes="From specimens caught during a summer cruise, Dec-2005 to Jan-2006. Lipid, protein, carbohydrate fractions based on measurements of 4 specimens, dry weight based on measurements of 21 specimens",
reference=refs$Dubi2012),
## autumn
"266542_EC~WW_autumn_Dubi2012"=list(taxon_name="Ihlea racovitzai",
taxon_aphia_id=266542,
equation=function(...) {
dw <- 0.068*...
carbs <- 0.022*dw; prot <- 0.302*dw; Lp <- 0.043*dw
tibble(allometric_value=9.3*4.2*Lp+4.2*4.2*prot+4.1*4.2*carbs)},
inputs=tibble(property="wet weight",units="g"),
return_property="total energy content",
return_units="kJ",
reliability=tribble(~type,~value,
"N",5),
notes="From specimens caught during an autumn cruise, Apr-May 2004. Lipid fraction based on measurements of 5 specimens, other components based on measurements of more specimens",
reference=refs$Dubi2012),
"266545_EC~WW_autumn_Dubi2012"=list(taxon_name="Salpa thompsoni",
taxon_aphia_id=266545,
equation=function(...) {
dw <- 0.055*...
carbs <- 0.02*dw; prot <- 0.102*dw; Lp <- 0.024*dw
tibble(allometric_value=9.3*4.2*Lp+4.2*4.2*prot+4.1*4.2*carbs)},
inputs=tibble(property="wet weight",units="g"),
return_property="total energy content",
return_units="kJ",
reliability=tribble(~type,~value,
"N",12),
notes="From specimens caught during an autumn cruise, Apr-May 2004. Lipid fraction based on measurements of 12 specimens, other components based on measurements of more specimens",
reference=refs$Dubi2012),
## winter
"266542_EC~WW_winter_Dubi2012"=list(taxon_name="Ihlea racovitzai",
taxon_aphia_id=266542,
equation=function(...) {
dw <- 0.058*...
carbs <- 0.013*dw; prot <- 0.317*dw; Lp <- 0.031*dw
tibble(allometric_value=9.3*4.2*Lp+4.2*4.2*prot+4.1*4.2*carbs)},
inputs=tibble(property="wet weight",units="g"),
return_property="total energy content",
return_units="kJ",
reliability=tribble(~type,~value,
"N",4),
notes="From specimens caught during a winter cruise, Jul-Aug 2006. Lipid fraction based on measurements of 4 specimens, other components based on measurements of more specimens",
reference=refs$Dubi2012),
"266545_EC~WW_winter_Dubi2012"=list(taxon_name="Salpa thompsoni",
taxon_aphia_id=266545,
equation=function(...) {
dw <- 0.062*...
carbs <- 0.02*dw; prot <- 0.113*dw; Lp <- 0.036*dw
tibble(allometric_value=9.3*4.2*Lp+4.2*4.2*prot+4.1*4.2*carbs)},
inputs=tibble(property="wet weight",units="g"),
return_property="total energy content",
return_units="kJ",
reliability=tribble(~type,~value,
"N",1),
notes="From specimens caught during a winter cruise, Jul-Aug 2006. Carbohydrate and protein fractions based on measurements of 1 specimen, other components based on measurements of more specimens",
reference=refs$Dubi2012),
## all seasons combined
"266542_EC~WW_Dubi2012"=list(taxon_name="Ihlea racovitzai",
taxon_aphia_id=266542,
equation=function(...) {
dw <- 0.062*...
carbs <- 0.014*dw; prot <- 0.316*dw; Lp <- 0.036*dw
tibble(allometric_value=9.3*4.2*Lp+4.2*4.2*prot+4.1*4.2*carbs)}, ##ww*0.062*4.2*(9.3*0.036+4.2*0.316+4.1*0.014) = ww*0.4477
inputs=tibble(property="wet weight",units="g"),
return_property="total energy content",
return_units="kJ",
reliability=tribble(~type,~value,
"N",21),
notes="Combined across summer, autumn, and winter samples. Lipid fraction based on measurements of 21 specimens, other components based on measurements of more specimens",
reference=refs$Dubi2012),
"266545_EC~WW_Dubi2012"=list(taxon_name="Salpa thompsoni",
taxon_aphia_id=266545,
equation=function(...) {
dw <- 0.063*...
carbs <- 0.021*dw; prot <- 0.101*dw; Lp <- 0.029*dw
tibble(allometric_value=9.3*4.2*Lp+4.2*4.2*prot+4.1*4.2*carbs)},
inputs=tibble(property="wet weight",units="g"),
return_property="total energy content",
return_units="kJ",
reliability=tribble(~type,~value,
"N",19),
notes="Combined across summer, autumn, and winter samples. Lipid fraction based on measurements of 19 specimens, other components based on measurements of more specimens",
reference=refs$Dubi2012),
stop("unrecognized equation ID: ",id))
}
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