data-raw/allometry.R
In SCAR/solong: Allometric Equations for Southern Ocean Taxa
## NOTES for new equation entry
## Prior to June 2021 we entered equations using the valid name and aphia ID. If the equation was published under an unaccepted name, that would also be entered by manually adding a row here. As of June 2021 we have alleq_tbl(..., check_name = TRUE) will automatically add a duplicate equation with the valid name, so we can just enter the equation under the invalid name in data-raw
library(dplyr)
library(assertthat)
requireNamespace("dietdataentry")
#worms_cache_directory <- "~/.cache/R/R.cache/"
#worms_cache_dir(worms_cache_directory)
refs <- list(
JaMc1996=bibentry(bibtype="Article",key="JaMc1996",
author=c(person(c("G","D"),"Jackson"),person(c("J","F"),"McKinnon")),
year=1996,
title="Beak length analysis of arrow squid Nototodarus sloanii (Cephalopoda: Ommastrephidae) in southern New Zealand waters",
journal="Polar Biology",volume=16,pages="227-230",
doi="10.1007/BF02329211"),
GaBu1988=bibentry(bibtype="Article",key="GaBu1988",
author=c(person(c("N","J"),"Gales"),person(c("H","R"),"Burton")),
year=1988,
title="Use of emetics and anaesthesia for dietary assessment of Weddell seals",
journal="Australian Wildlife Research",volume=15,pages="423-433"),
EaDe1997=bibentry(bibtype="Article",key="EaDe1997",
author=c(person(c("J","T"),"Eastman"),person(c("A","L"),"Devries")),
year=1997,
title="Biology and phenotypic plasticity of the Antarctic nototheniid fish Trematomus newnesi in McMurdo Sound",
journal="Antarctic Science",volume=9,pages="27-35",
doi="10.1017/S0954102097000047")
)
## fish
source("data-raw/equations_Arti2003.R")
source("data-raw/equations_fish_other.R")
source("data-raw/equations_krill.R")
source("data-raw/equations_Lake2003.R")
source("data-raw/equations_Smal1993.R")
source("data-raw/equations_WiMc1990.R")
source("data-raw/equations_Bush2005.R")
source("data-raw/equations_XaCh2016.R")
source("data-raw/equations_East2019.R")
source("data-raw/equations_LaMe2020.R")
source("data-raw/equations_EsFl2020.R")
source("data-raw/equations_crustaceans.R")
source("data-raw/equations_Schw2019.R")
## energetics
source("data-raw/equations_VanD2006.R")
source("data-raw/equations_FrHa1994.R")
source("data-raw/equations_Vane2005.R")
source("data-raw/equations_Dubi2012.R")
source("data-raw/equations_AhSh1998.R")
source("data-raw/equations_UrMe1998.R")
alleq_other <- function(id) {
switch(id,
## Bayesian length-weight: a=0.00575 (0.00309 - 0.01073), b=3.18 (3.01 - 3.35), in cm Total Length, based on LWR estimates for this species & (Sub)family-body (Ref. 93245).
## Froese, R., J. Thorson and R.B. Reyes Jr., 2013. A Bayesian approach for estimating length-weight relationships in fishes. J. Appl. Ichthyol. (2013):1-7.
## also http://oceanrep.geomar.de/21875/
## W=a*(TL^b)
## Brown and Klages 1987
## OD = otolith diameter. OD , SL, TL all mm. M in g
##The general relationship relating standard length to total length in myctophid fish was:
##SL = 0.17+0.80 TL (r2 = 0.97, S.D. = 0.018)
##Protomyctophum tenisoni and P. normani
##OD = 0.3 +0.027 SL (r2 = 0.85, n = 46)
##M = 1.282e-05 TL^2.868(r2 = 0.90, n = 28)
##Krefftichthys anderssoni
##OD = 0.416+0.022 SL (r2 = 0.88, n = 27)
##M = 5.36e-06 TL^3.080 (r2 = 0.90, n = 16)
##Electrona carlsbergi and E. subaspera
##OD = 0.254 + 0.042 SL (r2 = 0.9 1, n = 90)
##M = 7.43e-06 SL^3.159 ( r2 = 0.90, n = 60)
##Notothenia magellanica (Hecht & Cooper, 1986)
##TL = 30.96 OD^1.801 (r2 = 0.75, n = 82)
##M = 2.19e-05 TL^3.00 (r2 = 0.99, n = 133)
##Species: Leptonychotes weddellii
##Gender: male
##Equation: WEIGHT_KG=3.66*STANDARD_LENGTH_CM-489.3 (N=15)
##Source: Gales, N.J. and Burton, H.R. (1988) Use of emetics and anaesthesia for dietary assessment of Weddell seals. Australian Wildlife Research 15:423--433
"195932_WW_GaBu1988"=list(taxon_name="Leptonychotes weddellii",
taxon_aphia_id=195932,
equation=function(...)tibble(allometric_value= 3.66*...-489.3),
inputs=tibble(property="standard length",units="cm",sample_minimum=170,sample_maximum=236),
return_property="wet weight",
return_units="kg",
reliability=tribble(~type,~value,
"N",15),
notes="Applies to male animals",
reference=refs$GaBu1988),
## Nototodarus sloanii
"342378_ML_JaMc1996"=list(taxon_name="Nototodarus sloanii",
taxon_aphia_id=342378,
equation=function(...)tibble(allometric_value=168.83*log(...)+25.52),
inputs=tibble(property="lower rostral length",units="mm",sample_minimum=2,sample_maximum=7.2),
return_property="mantle length",
return_units="mm",
reliability=tribble(~type,~value,
"N",170,
"R^2",0.90),
reference=refs$JaMc1996),
"342378_ML_JaMc1996"=list(taxon_name="Nototodarus sloanii",
taxon_aphia_id=342378,
equation=function(...)tibble(allometric_value=236.10*...-512.99),
inputs=tibble(property="lower rostral length",units="mm",sample_minimum=2,sample_maximum=7.2),
return_property="wet weight",
return_units="g",
reliability=tribble(~type,~value,
"N",170,
"R^2",0.90),
reference=refs$JaMc1996),
## Trematomus newnesi from EaDe1997
"234628_WW~SL_EaDe1997"=list(taxon_name="Trematomus newnesi",
taxon_aphia_id=234628,
equation=function(...)tibble(allometric_value=3.17e-06*(...^3.34)),
inputs=tibble(property="standard length",units="mm",sample_minimum=93,sample_maximum=239),
return_property="wet weight",
return_units="g",
reliability=tribble(~type,~value,
"N",67,
"R^2",0.95),
reference=refs$EaDe1997),
stop("unrecognized equation ID: ",id))
}
## wrapper function around alleq. Can override the taxon, if e.g. applying an equation developed for one species to another species
## can override reference. Notes get added to any notes in the original equation
alleq_tbl <- function(id, with_id = NULL, taxon_name = NULL, taxon_aphia_id = NULL, notes = NULL, reference = NULL, thiseq = NULL, check_name) {
if (missing(check_name)) check_name <- is.null(with_id)
was_as_eq <- FALSE
if (is.null(thiseq)) {
try(thiseq <- alleq_other(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_Arti2003(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_fish_other(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_krill(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_crustaceans_other(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_Lake2003(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_Smal1993(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_WiMc1990(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_Bush2005(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_XaCh2016(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_VanD2006(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_FrHa1994(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_Vane2005(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_Dubi2012(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_AhSh1998(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_UrMe1998(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_LaMe2020(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_EsFl2020(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_Schw2019(id), silent = TRUE)
if (is.null(thiseq)) stop("equation id not recognized or has an error: ", id)
} else {
was_as_eq <- TRUE
id <- thiseq$id
}
if (!is.null(thiseq$check_name) && isTRUE(thiseq$check_name) != isTRUE(check_name)) {
message("equation ", id, " specifies check_name = ", isTRUE(thiseq$check_name), ", using this")
check_name <- isTRUE(thiseq$check_name)
}
## use the equation defaults for some things, if not already specified
if (is.null(with_id)) with_id <- id
if (is.null(taxon_name)) taxon_name <- thiseq$taxon_name
if (is.null(taxon_aphia_id)) taxon_aphia_id <- thiseq$taxon_aphia_id
if (is.null(reference)) reference <- thiseq$reference
if (is.null(notes)) {
notes <- ""
}
if (is.null(thiseq$notes) || !nzchar(thiseq$notes)) {
## no notes in coded equation, use notes supplied here as arg
} else {
if (nzchar(notes)) {
## use both sets of notes
notes <- paste0(notes,". ",thiseq$notes)
} else {
notes <- thiseq$notes ## use notes from thiseq
}
}
if (is.null(thiseq$reliability)) thiseq$reliability <- tibble(type=character(),value=numeric())
## old direct code
## tribble(~equation_id,~taxon_name,~taxon_aphia_id,~equation,~inputs,~return_property,~return_units,~reliability,~notes,~reference,
## id,taxon_name,taxon_aphia_id,thiseq$equation,thiseq$inputs,thiseq$return_property,thiseq$return_units,thiseq$reliability,notes,reference)
e2 <- sol_make_equation(equation_id = with_id,
taxon_name = taxon_name,
taxon_aphia_id = taxon_aphia_id,
equation = thiseq$equation,
inputs = thiseq$inputs,
return_property = thiseq$return_property,
return_units = thiseq$return_units,
reliability = thiseq$reliability,
notes = notes,
reference = reference,
check_packaged_ids = FALSE)
class(e2) <- setdiff(class(e2), "sol_equation")
## finally check the taxonomy
if (isTRUE(check_name)) {
ar <- dietdataentry::search_worms(scientific = e2$taxon_name)
if (nrow(ar) > 0 && !is.na(ar$AphiaID) && (is.na(e2$taxon_aphia_id) || (e2$taxon_aphia_id != ar$AphiaID))) {
## the existing name resolves to a different taxon_id than listed in the data-raw code
##cat(str(ar))
##cat(str(e2))
message(e2$taxon_name, " (aphia_id ", e2$taxon_aphia_id, " resolves to ", ar$scientificname, " (aphia_id ", ar$AphiaID, "), adding note and duplicate record")
e2$notes <- sub("^[[:space:]]+", "", paste0(e2$notes, " Accepted taxon name is ", ar$scientificname))
## create duplicate record
if (was_as_eq) {
duprec <- alleq_tbl(thiseq = thiseq, with_id = sub(paste0("^", e2$taxon_aphia_id), ar$AphiaID, id), taxon_name = ar$scientificname, taxon_aphia_id = ar$AphiaID)
} else {
duprec <- alleq_tbl(id = id, with_id = sub(paste0("^", e2$taxon_aphia_id), ar$AphiaID, id), taxon_name = ar$scientificname, taxon_aphia_id = ar$AphiaID, notes = notes)
}
e2 <- bind_rows(e2, duprec)
}
}
e2
}
build_allometry_df <- function() {
## equations from Xavier and Cherel
## Ancistrocheirus lesueurii
x <- bind_rows(alleq_tbl("138747_ML_Clar1986"), alleq_tbl("138747_WW_Clar1986"))
## Architeuthis dux
x <- bind_rows(x,alleq_tbl("342218_ML_Clar1986"),alleq_tbl("342218_WW_Clar1986"),alleq_tbl("342218_ML_Roel2000"))
## Bathyteuthis abyssicola
x <- bind_rows(x,alleq_tbl("138848_ML_Clar1986"),alleq_tbl("138848_WW_Clar1986"))
## Batoteuthis skolops (no specific equations)
x <- bind_rows(x,alleq_tbl("137777_ML_Clar1986",
with_id="325293_MLa_Clar1986",
taxon_name="Batoteuthis skolops",
taxon_aphia_id=325293,
notes="Based on Chiroteuthis spp. formula from Clarke (1986). There are no specific equations for Batoteuthis skolops"),
alleq_tbl("137777_WW_Clar1986",
with_id="325293_WWa_Clar1986",
taxon_name="Batoteuthis skolops",
taxon_aphia_id=325293,
notes="Based on Chiroteuthis spp. formula from Clarke (1986). There are no specific equations for Batoteuthis skolops"),
alleq_tbl("138168_ML_Clar1986",
with_id="325293_MLb_Clar1986",
taxon_name="Batoteuthis skolops",
taxon_aphia_id=325293,
notes="Based on Mastigoteuthis spp. formula from Clarke (1986). There are no specific equations for Batoteuthis skolops"),
alleq_tbl("138168_WW_Clar1986",
with_id="325293_WWb_Clar1986",
taxon_name="Batoteuthis skolops",
taxon_aphia_id=325293,
notes="Based on Mastigoteuthis spp. formula from Clarke (1986). There are no specific equations for Batoteuthis skolops"))
## family Brachioteuthidae
x <- bind_rows(x,alleq_tbl("11758_ML_Clar1986"),alleq_tbl("11758_WW_Clar1986"))
## note that this will require some additional coding in the user function, so that e.g. an input taxon_name of "Brachioteuthis picta" will find its way to this equation even though it does not directly match the taxon_name or taxon_aphia_id specified here
## Chiroteuthis veranyi (no specific equations)
x <- bind_rows(x,alleq_tbl("137777_ML_Clar1986",
with_id="139125_ML_Clar1986",
taxon_name="Chiroteuthis veranii",
taxon_aphia_id=139125,
notes="Based on Chiroteuthis spp. formula from Clarke (1986). There are no specific equations for Chiroteuthis veranii"),
alleq_tbl("137777_WW_Clar1986",
with_id="139125_WW_Clar1986",
taxon_name="Chiroteuthis veranii",
taxon_aphia_id=139125,
notes="Based on Chiroteuthis spp. formula from Clarke (1986). There are no specific equations for Chiroteuthis veranii"))
## Chiroteuthis sp.
x <- bind_rows(x,alleq_tbl("137777_ML_Clar1986"),alleq_tbl("137777_WW_Clar1986"))
## Galiteuthis glacialis
x <- bind_rows(x,alleq_tbl("325297_ML_LuWi1994"),alleq_tbl("325297_WW_LuWi1994"))
## Galiteuthis stC sp. (Imber) (no specific equations)
## Galiteuthis sp. 3 (Imber) (no specific equations)
## Taonius sp. B (Voss) (no specific equations)
## Taonius sp. (Clarke) (no specific equations)
## Taonius sp
## Note that this is given as Taonius pavo in Rodhouse et al. 1990, but Taonius sp. in X&C
x <- bind_rows(x,alleq_tbl("137853_ML_Rodh1990"),alleq_tbl("137853_WW_Rodh1990"))
## Teuthowenia pellucida
## Note that the Rodhouse et al 1990 paper does NOT have equations for T.p.
## this info taken from X&C
x <- bind_rows(x,alleq_tbl("341823_ML_Rodh1990"),alleq_tbl("341823_WW_Rodh1990"))
## Mesonychoteuthis hamiltoni
x <- bind_rows(x,alleq_tbl("325299_ML_Rodh1990"))
## Cranchiidae
x <- bind_rows(x,alleq_tbl("11774_WW_Clar1962"))
## Cycloteuthis akimushkini
x <- bind_rows(x,alleq_tbl("341824_ML_Clar1986"),alleq_tbl("341824_WW_Clar1986"))
## Gonatus
x <- bind_rows(x,alleq_tbl("138036_ML_Clar1986"),alleq_tbl("138036_WW_Clar1986"))
## Gonatus (small specimens)
x <- bind_rows(x,alleq_tbl("138036small_ML_Clar1986"),alleq_tbl("138036small_WW_Clar1986"))
## Gonatus antarcticus (no specific equations)
x <- bind_rows(x,alleq_tbl("138036_ML_Clar1986",
with_id="325300_ML_Clar1986",
taxon_name="Gonatus antarcticus",
taxon_aphia_id=325300,
notes="Based on Gonatus spp. formula from Clarke (1986). There are no specific equations for Gonatus antarcticus"),
alleq_tbl("138036_WW_Clar1986",
with_id="325300_WW_Clar1986",
taxon_name="Gonatus antarcticus",
taxon_aphia_id=325300,
notes="Based on Gonatus spp. formula from Clarke (1986). There are no specific equations for Gonatus antarcticus"))
## (small specimens)
x <- bind_rows(x,alleq_tbl("138036small_ML_Clar1986",
with_id="325300small_ML_Clar1986",
taxon_name="Gonatus antarcticus",
taxon_aphia_id=325300,
notes="Based on Gonatus spp. formula from Clarke (1986). There are no specific equations for Gonatus antarcticus"),
alleq_tbl("138036small_WW_Clar1986",
with_id="325300small_WW_Clar1986",
taxon_name="Gonatus antarcticus",
taxon_aphia_id=325300,
notes="Based on Gonatus spp. formula from Clarke (1986). There are no specific equations for Gonatus antarcticus"))
## Histioteuthis A, which has a deep notch in back of hood and a well-developed ridge
## running to free corner of lateral wall:
## Histioteuthis arcturi (no specific equations)
## Histioteuthis bonnellii corpuscula (valid name Histioteuthis bonnellii)
x <- bind_rows(x,alleq_tbl("140111_ML_Clar1986"),alleq_tbl("140111_ML_LuIc2002"), alleq_tbl("140111_WW_LuIc2002"))
## Histioteuthis macrohista
x <- bind_rows(x,alleq_tbl("341870_ML_LuIc2002"),alleq_tbl("341870_WW_LuIc2002"))
## Histioteuthis miranda
x <- bind_rows(x,alleq_tbl("341871_ML_Clar1986"),alleq_tbl("341871_WW_Clar1986"))
x <- bind_rows(x,alleq_tbl("341871_ML_LuIc2002"),alleq_tbl("341871_WW_LuIc2002"))
## Histioteuthis B has a shallow notch in back of hood and a weakly-developed ridge under
## the hood (evident in Histioteuthis atlantica juveniles) that becomes a slight fold running to free corner
## of lateral wall:
## Histioteuthis atlantica
x <- bind_rows(x,alleq_tbl("341864_ML_LuIc2002"),alleq_tbl("341864_WW_LuIc2002"))
## Histioteuthis eltaninae
x <- bind_rows(x,alleq_tbl("341867_ML_LuIc2002"),alleq_tbl("341867_WW_LuIc2002"))
## Lepidoteuthis grimaldii
x <- bind_rows(x,alleq_tbl("140193_ML_BASUnpub"),alleq_tbl("140193_WW_BASUnpub"),alleq_tbl("140193_ML_LuIc2002"))
## Loligo gahi (accepted name Doryteuthis (Amerigo) gahi)
x <- bind_rows(x,alleq_tbl("341880_ML_HatfUnpub"),alleq_tbl("341880_WW_HatfUnpub"))
## also manually add one for Doryteuthis gahi
x <- bind_rows(x,alleq_tbl("341880_ML_HatfUnpub",
with_id="574538_ML_HatfUnpub",
taxon_name="Doryteuthis gahi",
taxon_aphia_id=574538,
notes="Accepted taxon name is Doryteuthis (Amerigo) gahi"),
alleq_tbl("341880_WW_HatfUnpub",
with_id="574538_WW_HatfUnpub",
taxon_name="Doryteuthis gahi",
taxon_aphia_id=574538,
notes="Accepted taxon name is Doryteuthis (Amerigo) gahi"))
## Lycoteuthis lorigera
x <- bind_rows(x,alleq_tbl("342361_ML_LuIc2002"),alleq_tbl("342361_WW_LuIc2002"))
## Mastigoteuthis psychrophila
x <- bind_rows(x,alleq_tbl("341904_ML_BASUnpub"),alleq_tbl("341904_WW_BASUnpub"))
## ?Mastigoteuthis A (Clarke) (no specific equations)
## Alluroteuthis antarcticus
x <- bind_rows(x,alleq_tbl("325302_ML_Piat2001"),alleq_tbl("325302_WW_Piat2001"))
## Nototeuthis dimegacotyle (no specific equations)
## Taningia danae
x <- bind_rows(x,alleq_tbl("140609_ML_Clark1986"),alleq_tbl("140609_WW_Clark1986"))
## Octopoteuthis sp.
x <- bind_rows(x,alleq_tbl("138271_ML_Clark1986"),alleq_tbl("138271_WW_Clark1986"))
## Martialia hyadesi
x <- bind_rows(x,alleq_tbl("325305_ML_RoYe1990"),alleq_tbl("325305_WW_RoYe1990"))
## Illex argentinus
x <- bind_rows(x,alleq_tbl("342064_ML_SaHa2000"),alleq_tbl("342064_WW_SaHa2000"))
## Todarodes sp. (no specific equations)
x <- bind_rows(x,alleq_tbl("138281_ML_Clar1986"),alleq_tbl("138281_WW_Clar1986"))
## Kondakovia longimana
x <- bind_rows(x,alleq_tbl("325308_ML_BrKl1987"),alleq_tbl("325308_WW_BrKl1987"))
## Moroteuthis ingens
x <- bind_rows(x,alleq_tbl("410381M_ML_Jack1995"),alleq_tbl("410381F_ML_Jack1995"),
alleq_tbl("410381M_WW_Jack1995"),alleq_tbl("410381F_WW_Jack1995"))
## Moroteuthis knipovitchi (valid name is Filippovia knipovitchi)
x <- bind_rows(x,alleq_tbl("325310_ML_CherUnpub"),alleq_tbl("325310_WW_CherUnpub"))
## Moroteuthis robsoni (valid name Onykia robsoni)
x <- bind_rows(x,alleq_tbl("342256_ML_LuIc2002"),alleq_tbl("342256_WW_LuIc2002"))
## Moroteuthis sp . B (Imber) (no specific equations)
## Onychoteuthis banksii
x <- bind_rows(x,alleq_tbl("140649_ML_LuIc2002"),alleq_tbl("140649_WW_LuIc2002"))
## Pholidoteuthis massyae
x <- bind_rows(x,alleq_tbl("410388_ML_Clar1986"),alleq_tbl("410388_WW_Clar1986"))
## Psychroteuthis glacialis
x <- bind_rows(x,alleq_tbl("325312_ML_Grog2000"),alleq_tbl("325312_WW_Grog2000"))
## FAMILY SEPIOLIDAE
## cf. Stoloteuthis leucoptera (no allometric equations available)
## Oegopsida sp. A (Cherel) (no allometric equations available)
## Haliphron atlanticus
x <- bind_rows(x,alleq_tbl("341781_WW_BASUnpub"))
## Cirrata sp. A (Cherel) (no allometric equations available)
## Pareledone turqueti
x <- bind_rows(x,alleq_tbl("239393_ML_CollUnpub"),alleq_tbl("239393_WW_CollUnpub"))
## Adelieledone polymorpha
x <- bind_rows(x,alleq_tbl("325319_ML_CollUnpub"),alleq_tbl("325319_WW_CollUnpub"))
## Benthoctopus thielei (valid name is Muusoctopus thielei)
x <- bind_rows(x,alleq_tbl("341931_ML_CherUnpub"),alleq_tbl("341931_WW_CherUnpub"))
## Graneledone gonzalezi
x <- bind_rows(x,alleq_tbl("342224_ML_CherUnpub"),alleq_tbl("342224_WW_CherUnpub"))
## Opisthoteuthis sp.
## ML=-26.0047+12.4858CL; logM=0.5893+0.2413CL (n= 13 for ML, n=9 for M) (Smale
## et al. 1993) where CL = Crest length (in mm)
## see equations for Smale et al. 1993
## Stauroteuthis gilchristi (no allometric equations available)
## ---
## Smale et al. 1993
## Octopus vulgaris
x <- bind_rows(x,alleq_tbl("140605_ML_Smal1993"),
alleq_tbl("140605_HL_Smal1993"),
alleq_tbl("140605_WW_Smal1993"))
## Enteroctopus magnificus
x <- bind_rows(x,alleq_tbl("225568_ML_Smal1993"),
alleq_tbl("225568_HL_Smal1993"),
alleq_tbl("225568_WW_Smal1993"))
## Velodona togata
x <- bind_rows(x,alleq_tbl("342415_ML_Smal1993"),
alleq_tbl("342415_HL_Smal1993"))
## Bathypolypus valdiviae
x <- bind_rows(x,alleq_tbl("341910_ML_Smal1993"),
alleq_tbl("341910_HL_Smal1993"),
alleq_tbl("341910_WW_Smal1993"))
## Opisthoteuthis
x <- bind_rows(x,alleq_tbl("138294_ML_Smal1993"),
alleq_tbl("138294_HL_Smal1993"),
alleq_tbl("138294_WW_Smal1993"))
## Tremoctopus violaceus
x <- bind_rows(x,alleq_tbl("141694_ML_Smal1993"),
alleq_tbl("141694_HL_Smal1993"),
alleq_tbl("141694_WW_Smal1993"))
## Argonauta
x <- bind_rows(x,alleq_tbl("137676_ML_Smal1993"),
alleq_tbl("137676_HL_Smal1993"),
alleq_tbl("137676_WW_Smal1993"))
## ---
## Schwarz et al 2019
x <- bind_rows(x,alleq_tbl("325319_WW~DML_Schw2019"),
alleq_tbl("325319M_WW~DML_Schw2019"),
alleq_tbl("325319F_WW~DML_Schw2019"),
alleq_tbl("325324_WW~DML_Schw2019"),
alleq_tbl("325324M_WW~DML_Schw2019"),
alleq_tbl("325324F_WW~DML_Schw2019"),
alleq_tbl("527162_WW~DML_Schw2019"),
alleq_tbl("527162M_WW~DML_Schw2019"),
alleq_tbl("527162F_WW~DML_Schw2019"),
alleq_tbl("325325_WW~DML_Schw2019"),
alleq_tbl("325325M_WW~DML_Schw2019"),
alleq_tbl("325325F_WW~DML_Schw2019"),
alleq_tbl("239392_WW~DML_Schw2019"),
alleq_tbl("239392M_WW~DML_Schw2019"),
alleq_tbl("239392F_WW~DML_Schw2019"),
alleq_tbl("325336_WW~DML_Schw2019"),
alleq_tbl("325336M_WW~DML_Schw2019"),
alleq_tbl("325336F_WW~DML_Schw2019"),
alleq_tbl("239393_WW~DML_Schw2019"),
alleq_tbl("239393M_WW~DML_Schw2019"),
alleq_tbl("239393F_WW~DML_Schw2019"))
## ---
## Williams & McEldowney 1990 otoliths
## Bathylagus antarcticus
x <- bind_rows(x,alleq_tbl("234631_SL~OL_WiMc1990"),
alleq_tbl("234631_SL~OW_WiMc1990"),
alleq_tbl("234631_WW~SL_WiMc1990"))
## Krefftichthys anderssoni
x <- bind_rows(x,alleq_tbl("234641_SL~OL_WiMc1990"),
alleq_tbl("234641_SL~OW_WiMc1990"),
alleq_tbl("234641_WW~SL_WiMc1990"))
## Pleuragramma antarctica
x <- bind_rows(x,alleq_tbl("234721_SL~OL_WiMc1990"),
alleq_tbl("234721_SL~OW_WiMc1990"),
alleq_tbl("234721_WW~SL_WiMc1990"))
## Protomyctophum bolini
x <- bind_rows(x,alleq_tbl("234714_SL~OL_WiMc1990"),
alleq_tbl("234714_SL~OW_WiMc1990"),
alleq_tbl("234714_WW~SL_WiMc1990"))
## Electrona antarctica
x <- bind_rows(x,alleq_tbl("217697_SL~OL_WiMc1990"),
alleq_tbl("217697_SL~OW_WiMc1990"),
alleq_tbl("217697_WW~SL_WiMc1990"))
## Electrona carlsbergi
x <- bind_rows(x,alleq_tbl("234638_SL~OL_WiMc1990"),
alleq_tbl("234638_SL~OW_WiMc1990"),
alleq_tbl("234638_WW~SL_WiMc1990"))
## Electrona subaspera
x <- bind_rows(x,alleq_tbl("234791_SL~OL_WiMc1990"),
alleq_tbl("234791_SL~OW_WiMc1990"),
alleq_tbl("234791_WW~SL_WiMc1990"))
## Gymnoscopelus braueri
x <- bind_rows(x,alleq_tbl("234642_SL~OL_WiMc1990"),
alleq_tbl("234642_SL~OW_WiMc1990"),
alleq_tbl("234642_WW~SL_WiMc1990"))
## Gymnoscopelus nicholsi
x <- bind_rows(x,alleq_tbl("234821_SL~OL_WiMc1990"),
alleq_tbl("234821_SL~OW_WiMc1990"),
alleq_tbl("234821_WW~SL_WiMc1990"))
## Gymnoscopelus fraseri
x <- bind_rows(x,alleq_tbl("234657_SL~OL_WiMc1990"),
alleq_tbl("234657_SL~OW_WiMc1990"),
alleq_tbl("234657_WW~SL_WiMc1990"))
## Muraenolepis marmoratus, valid name Muraenolepis marmorata
x <- bind_rows(x,alleq_tbl("234705_SL~OL_WiMc1990"),
alleq_tbl("234705_SL~OW_WiMc1990"),
alleq_tbl("234705_WW~SL_WiMc1990"))
## Macrourus holotrachys
x <- bind_rows(x,alleq_tbl("234831_TL~OL_WiMc1990"),
alleq_tbl("234831_TL~OW_WiMc1990"),
alleq_tbl("234831_WW~TL_WiMc1990"))
## Zanclorhynchus spinifer
x <- bind_rows(x,alleq_tbl("234683_SL~OL_WiMc1990"),
alleq_tbl("234683_SL~OW_WiMc1990"),
alleq_tbl("234683_WW~SL_WiMc1990"))
## Dolloidraco longedorsalis
x <- bind_rows(x,alleq_tbl("234696_SL~OL_WiMc1990"),
alleq_tbl("234696_SL~OW_WiMc1990"),
alleq_tbl("234696_WW~SL_WiMc1990"))
## Pogonophryne phyllopogon, valid name is Pogonophryne scotti
x <- bind_rows(x,alleq_tbl("313416_SL~OL_WiMc1990"),
alleq_tbl("313416_SL~OW_WiMc1990"),
alleq_tbl("313416_WW~SL_WiMc1990"))
## Dissostichus eleginoides
x <- bind_rows(x,alleq_tbl("234700_SL~OL_WiMc1990"),
alleq_tbl("234700_SL~OW_WiMc1990"),
alleq_tbl("234700_WW~SL_WiMc1990"))
## Dissostichus mawsoni
x <- bind_rows(x,alleq_tbl("234836_SL~OL_WiMc1990"),
alleq_tbl("234836_SL~OW_WiMc1990"),
alleq_tbl("234836_WW~SL_WiMc1990"))
## Notothenia coriiceps
x <- bind_rows(x,alleq_tbl("234679_SL~OL_WiMc1990"),
alleq_tbl("234679_SL~OW_WiMc1990"),
alleq_tbl("234679_WW~SL_WiMc1990"))
## Notothenia neglecta
x <- bind_rows(x,alleq_tbl("234740_SL~OL_WiMc1990"),
alleq_tbl("234740_SL~OW_WiMc1990"),
alleq_tbl("234740_WW~SL_WiMc1990"))
## Notothenia rossii
x <- bind_rows(x,alleq_tbl("234840_SL~OL_WiMc1990"),
alleq_tbl("234840_SL~OW_WiMc1990"),
alleq_tbl("234840_WW~SL_WiMc1990"))
## Notothenia kempi (now considered to be synonymous with L. squamifrons according to WoRMS, but enter both here
## N. kempi uses an "unaccepted" aphia_id here
x <- bind_rows(x,alleq_tbl("313363_SL~OL_WiMc1990"),
alleq_tbl("313363_SL~OW_WiMc1990"),
alleq_tbl("313363_WW~SL_WiMc1990"))
## Lepidonotothen squamifrons
x <- bind_rows(x,alleq_tbl("234788_SL~OL_WiMc1990"),
alleq_tbl("234788_SL~OW_WiMc1990"),
alleq_tbl("234788_WW~SL_WiMc1990"))
## Notothenia acuta
x <- bind_rows(x,alleq_tbl("234624_SL~OL_WiMc1990"),
alleq_tbl("234624_SL~OW_WiMc1990"),
alleq_tbl("234624_WW~SL_WiMc1990"))
## Nototheniops mizops
x <- bind_rows(x,alleq_tbl("313401_SL~OL_WiMc1990"),
alleq_tbl("313401_SL~OW_WiMc1990"),
alleq_tbl("313401_WW~SL_WiMc1990"))
## Pagothenia bernacchii
x <- bind_rows(x,alleq_tbl("313391_SL~OL_WiMc1990"),
alleq_tbl("313391_SL~OW_WiMc1990"),
alleq_tbl("313391_WW~SL_WiMc1990"))
## Pagothenia borchgrevinki
x <- bind_rows(x,alleq_tbl("234801_SL~OL_WiMc1990"),
alleq_tbl("234801_SL~OW_WiMc1990"),
alleq_tbl("234801_WW~SL_WiMc1990"))
## Trematomus hansoni
x <- bind_rows(x,alleq_tbl("313392_SL~OL_WiMc1990"),
alleq_tbl("313392_SL~OW_WiMc1990"),
alleq_tbl("313392_WW~SL_WiMc1990"))
## Trematomus pennellii
x <- bind_rows(x,alleq_tbl("313409_SL~OL_WiMc1990"),
alleq_tbl("313409_SL~OW_WiMc1990"),
alleq_tbl("313409_WW~SL_WiMc1990"))
## Trematomus eulepidotus
x <- bind_rows(x,alleq_tbl("234754_SL~OL_WiMc1990"),
alleq_tbl("234754_SL~OW_WiMc1990"),
alleq_tbl("234754_WW~SL_WiMc1990"))
## Trematomus lepidorhinus
x <- bind_rows(x,alleq_tbl("234770_SL~OL_WiMc1990"),
alleq_tbl("234770_SL~OW_WiMc1990"),
alleq_tbl("234770_WW~SL_WiMc1990"))
## Trematomus loennbergii
x <- bind_rows(x,alleq_tbl("234828_SL~OL_WiMc1990"),
alleq_tbl("234828_SL~OW_WiMc1990"),
alleq_tbl("234828_WW~SL_WiMc1990"))
## Trematomus newnesi
x <- bind_rows(x,alleq_tbl("234628_SL~OL_WiMc1990"),
alleq_tbl("234628_SL~OW_WiMc1990"),
alleq_tbl("234628_WW~SL_WiMc1990"))
## Trematomus nicolai
x <- bind_rows(x,alleq_tbl("234644_SL~OL_WiMc1990"),
alleq_tbl("234644_SL~OW_WiMc1990"),
alleq_tbl("234644_WW~SL_WiMc1990"))
## Trematomus scotti
x <- bind_rows(x,alleq_tbl("234665_SL~OL_WiMc1990"),
alleq_tbl("234665_SL~OW_WiMc1990"),
alleq_tbl("234665_WW~SL_WiMc1990"))
## Akarotaxis nudiceps
x <- bind_rows(x,alleq_tbl("234600_SL~OL_WiMc1990"),
alleq_tbl("234600_SL~OW_WiMc1990"),
alleq_tbl("234600_WW~SL_WiMc1990"))
## Bathydraco marri
x <- bind_rows(x,alleq_tbl("234816_SL~OL_WiMc1990"),
alleq_tbl("234816_SL~OW_WiMc1990"),
alleq_tbl("234816_WW~SL_WiMc1990"))
## Cygnodraco mawsoni
x <- bind_rows(x,alleq_tbl("234834_SL~OL_WiMc1990"),
alleq_tbl("234834_SL~OW_WiMc1990"),
alleq_tbl("234834_WW~SL_WiMc1990"))
## Gymnodraco acuticeps
x <- bind_rows(x,alleq_tbl("234800_SL~OL_WiMc1990"),
alleq_tbl("234800_SL~OW_WiMc1990"),
alleq_tbl("234800_WW~SL_WiMc1990"))
## Prionodraco evansii
x <- bind_rows(x,alleq_tbl("234777_SL~OL_WiMc1990"),
alleq_tbl("234777_SL~OW_WiMc1990"),
alleq_tbl("234777_WW~SL_WiMc1990"))
## Racovitzia glacialis
x <- bind_rows(x,alleq_tbl("234799_SL~OL_WiMc1990"),
alleq_tbl("234799_SL~OW_WiMc1990"),
alleq_tbl("234799_WW~SL_WiMc1990"))
## Chaenodraco wilsoni
x <- bind_rows(x,alleq_tbl("234609_SL~OL_WiMc1990"),
alleq_tbl("234609_SL~OW_WiMc1990"),
alleq_tbl("234609_WW~SL_WiMc1990"))
## Champsocephalus gunnari
x <- bind_rows(x,alleq_tbl("234797_SL~OL_WiMc1990"),
alleq_tbl("234797_SL~OW_WiMc1990"),
alleq_tbl("234797_WW~SL_WiMc1990"))
## Channichthys rhinoceratus
x <- bind_rows(x,alleq_tbl("234619_SL~OL_WiMc1990"),
alleq_tbl("234619_SL~OW_WiMc1990"),
alleq_tbl("234619_WW~SL_WiMc1990"))
## Chionodraco hamatus
x <- bind_rows(x,alleq_tbl("234795_SL~OL_WiMc1990"),
alleq_tbl("234795_SL~OW_WiMc1990"),
alleq_tbl("234795_WW~SL_WiMc1990"))
## Chionodraco myersi
x <- bind_rows(x,alleq_tbl("234646_SL~OL_WiMc1990"),
alleq_tbl("234646_SL~OW_WiMc1990"),
alleq_tbl("234646_WW~SL_WiMc1990"))
## Cryodraco antarcticus
x <- bind_rows(x,alleq_tbl("234720_SL~OL_WiMc1990"),
alleq_tbl("234720_SL~OW_WiMc1990"),
alleq_tbl("234720_WW~SL_WiMc1990"))
## Paradiplospinus gracilis
x <- bind_rows(x,alleq_tbl("219693_SL~OL_WiMc1990"),
alleq_tbl("219693_SL~OW_WiMc1990"))##,
## alleq_tbl("219693_WW~SL_WiMc1990"))
warning("Paradiplospinus gracilis WW equation looks wrong, needs checking")
## ---
## Artigues 2003 equations
x <- bind_rows(x,alleq_tbl("234660_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234660M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234660F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234836_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234704_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234704M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234704F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234788_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234788M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234788F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234610_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234610M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234610F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234608_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234608M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234608F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("712788_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("712788M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("712788F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234754_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234754M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234754F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234772_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234770_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234770M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234770F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234828_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234644_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234644M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234644F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234709_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234709M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234709F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234665_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234665M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234665F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234615_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234615M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234615F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234592_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234592M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234592F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234817_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234817M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234817F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234621_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234621M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234621F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234696_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234696M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234696F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234790_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234826_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234730_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234730M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234730F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234611_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234837_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234816_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234816M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234816F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234834_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234834M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234834F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234808_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234808M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234808F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234800_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234800M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234800F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234777_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234777M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234777F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234799_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234799M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234799F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234720_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234720M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234720F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234725_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234725M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234725F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234609_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234797_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234797M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234797F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234650_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234650M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234650F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234795_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234795M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234795F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234646_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234646M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234646F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234678_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234678M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234678F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234614_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234685_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234796_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234695_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("217697_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234729_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234821_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234831_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234831M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234831F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234606_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("126486_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234675_WW~TL_Arti2003"))
## from Bush2005
x <- bind_rows(x, alleq_tbl("234610_WW~SL_Bush2005"),
alleq_tbl("234610_DW~SL_Bush2005"),
alleq_tbl("234595_WW~SL_Bush2005"),
alleq_tbl("234595_DW~SL_Bush2005"))
## misc fish
x <- bind_rows(x, alleq_tbl("234628_WW~TL_Dec_LaMe2000"),
alleq_tbl("234628_WW~TL_Feb_LaMe2000"))
x <- bind_rows(x, alleq_tbl("234700_WW~TL_Troc2020"), ## Dissostichus eleginoides
alleq_tbl("234626_WW~TL_Llom2020"), ## Harpagifer bispinus
alleq_tbl("234626_TL~age_Llom2020"))
## Pinkerton et al. 2013
x <- bind_rows(x, alleq_tbl("712470F_WW~TL_Pink2013"),
alleq_tbl("712470F_WW~PAL_Pink2013"),
alleq_tbl("712470M_WW~TL_Pink2013"),
alleq_tbl("712470M_WW~PAL_Pink2013"),
alleq_tbl("234606_WW~TL_Pink2013"),
alleq_tbl("234606_WW~PAL_Pink2013"),
alleq_tbl("234606_PAL~TL_Pink2013"),
alleq_tbl("234606_TL~PAL_Pink2013"),
alleq_tbl("712470F_PAL~TL_Pink2013"),
alleq_tbl("712470F_TL~PAL_Pink2013"),
alleq_tbl("712470M_PAL~TL_Pink2013"),
alleq_tbl("712470M_TL~PAL_Pink2013"),
alleq_tbl("234606M_TL~age_Pink2013"),
alleq_tbl("234606F_TL~age_Pink2013"),
alleq_tbl("712470M_TL~age_Pink2013"),
alleq_tbl("712470F_TL~age_Pink2013"))
## from LaMe2018
x <- bind_rows(x, alleq_tbl("234660F_WW~SL_LaMe2018"))
x <- bind_rows(x, alleq_tbl("234660M_WW~SL_LaMe2018"))
x <- bind_rows(x, alleq_tbl("234660_SL~OL_LaMe2018"))
## La Mesa et al 2020
x <- bind_rows(x, alleq_tbl("234720M_WW~TL_LaMe2020"),
alleq_tbl("234720F_WW~TL_LaMe2020"),
alleq_tbl("234720M_TL~age_LaMe2020"),
alleq_tbl("234720F_TL~age_LaMe2020"))
## Escobar-Flores et al 2020
x <- bind_rows(x, alleq_tbl("234631_WW~SL_EsFl2020"),
alleq_tbl("127286_WW~SL_EsFl2020"),
alleq_tbl("125819_WW~SL_EsFl2020"),
alleq_tbl("126194_WW~SL_EsFl2020"),
alleq_tbl("217719_WW~SL_EsFl2020"),
alleq_tbl("125832_WW~SL_EsFl2020"),
alleq_tbl("712788_WW~SL_EsFl2020"),
alleq_tbl("400296_WW~SL_EsFl2020"),
alleq_tbl("234695_WW~SL_EsFl2020"),
alleq_tbl("221503_WW~SL_EsFl2020"),
alleq_tbl("274968_WW~SL_EsFl2020"),
alleq_tbl("313344_WW~SL_EsFl2020"),
alleq_tbl("125825_WW~SL_EsFl2020"),
alleq_tbl("217704_WW~SL_EsFl2020"),
alleq_tbl("234641_WW~SL_EsFl2020"),
alleq_tbl("205276_WW~SL_EsFl2020"),
alleq_tbl("206941_WW~SL_EsFl2020"),
alleq_tbl("125821_WW~SL_EsFl2020"),
alleq_tbl("234638_WW~SL_EsFl2020"),
alleq_tbl("217697_WW~SL_EsFl2020"))
## ---
## Krill
x <- bind_rows(x,alleq_tbl("236217J_TL_Goeb2007"),
alleq_tbl("236217F_TL_Goeb2007"),
alleq_tbl("236217M_TL_Goeb2007"))
x <- bind_rows(x,alleq_tbl("236217_WW_Morr1988"))
x <- bind_rows(x,alleq_tbl("236217_WW_Hewi2004"))
## Mayz2003
x <- bind_rows(x, alleq_tbl("236219A_WW~TL_Mayz2003"),
alleq_tbl("236219J_WW~TL_Mayz2003"),
alleq_tbl("221054M_WW~TL_Mayz2003"),
alleq_tbl("221054F_WW~TL_Mayz2003"),
alleq_tbl("221054_LpW~WW_Mayz2003"),
alleq_tbl("236219F_LpW~WW_Mayz2003"),
alleq_tbl("236219M_LpW~WW_Mayz2003"),
alleq_tbl("236219J_LpW~WW_Mayz2003"))
## Farb1994
x <- bind_rows(x, alleq_tbl("236219_WW~TL_Farb1994"),
alleq_tbl("236219SA_WW~TL_Farb1994"),
alleq_tbl("236219A_WW~TL_Farb1994"),
alleq_tbl("236219M_WW~TL_Farb1994"),
alleq_tbl("236219F_WW~TL_Farb1994"),
alleq_tbl("236219SA_WW~CL_Farb1994"),
alleq_tbl("236219A_WW~CL_Farb1994"),
alleq_tbl("236219M_WW~CL_Farb1994"),
alleq_tbl("236219F_WW~CL_Farb1994"),
alleq_tbl("236217_WW~TL_Farb1994"),
alleq_tbl("236217SA_WW~TL_Farb1994"),
alleq_tbl("236217MI_WW~TL_Farb1994"),
alleq_tbl("236217MII_WW~TL_Farb1994"),
alleq_tbl("236217F_WW~TL_Farb1994"),
alleq_tbl("236217SF_WW~TL_Farb1994"),
alleq_tbl("236217SA_WW~CL_Farb1994"),
alleq_tbl("236217MI_WW~CL_Farb1994"),
alleq_tbl("236217MII_WW~CL_Farb1994"),
alleq_tbl("236217F_WW~CL_Farb1994"),
alleq_tbl("236217SF_WW~CL_Farb1994"))
## Melv2018
x <- bind_rows(x, alleq_tbl("236217F_TL~CL_Melv2018"),
alleq_tbl("236217M_TL~CL_Melv2018"))
x <- bind_rows(x, alleq_tbl("236216_TL~CL_PuJo1988"),
alleq_tbl("236217_TL~CL_PuJo1988"),
alleq_tbl("236219_ED~CL_FaMa2010"),
alleq_tbl("236219_ED~TL_FaMa2010"),
alleq_tbl("236219_ED~WW_FaMa2010"),
alleq_tbl("236219_CL~TL_FaMa2010"),
alleq_tbl("236219_WW~TL_FaMa2010"),
alleq_tbl("236219_WW~CL_FaMa2010"),
alleq_tbl("236219_LpWW~WW_FaMa2010"))
x <- bind_rows(x, alleq_tbl("236217SAJ_TL~CL_Farb1990"),
alleq_tbl("236217M1_TL~CL_Farb1990"),
alleq_tbl("236217M2_TL~CL_Farb1990"),
alleq_tbl("236217F_TL~CL_Farb1990"),
alleq_tbl("236219J_TL~CL_Farb1990"),
alleq_tbl("236219M_TL~CL_Farb1990"),
alleq_tbl("236219F_TL~CL_Farb1990"),
alleq_tbl("236219A_TL~CL_Farb1990"),
alleq_tbl("236219_TL~CL_Farb1990"))
## crustaceans
x <- bind_rows(x, alleq_tbl("369204_TL~CL_ArGo1991"),
alleq_tbl("369214_TL~CL_ArGo1991"),
alleq_tbl("515320_WW~TL_Rido1994"),
alleq_tbl("515320_WW~ED_Kuun1999"),
alleq_tbl("515320_DW~ED_Kuun1999"),
alleq_tbl("515320_AFDW~ED_Kuun1999"),
alleq_tbl("515320_WW~CL_Kuun1999"),
alleq_tbl("515320_DW~CL_Kuun1999"),
alleq_tbl("515320_AFDW~CL_Kuun1999"),
alleq_tbl("515320_WW~TL_Kuun1999"),
alleq_tbl("515320_CL~TL_Kuun1999"),
alleq_tbl("515320_ED~CL_Kuun1999"),
alleq_tbl("515320_DW~WW_Kuun1999"),
alleq_tbl("515320_AFDW~WW_Kuun1999"),
alleq_tbl("392346M_WW~CL_TaLo2006"),
alleq_tbl("392346F_WW~CL_TaLo2006"),
alleq_tbl("392346_WW~CL_TaLo2006"),
alleq_tbl("392346M_DW~CL_TaLo2006"),
alleq_tbl("392346F_DW~CL_TaLo2006"),
alleq_tbl("392346_DW~CL_TaLo2006"),
alleq_tbl("392886M_WW~CL_TaLo2006"),
alleq_tbl("392886F_WW~CL_TaLo2006"),
alleq_tbl("392886M_DW~CL_TaLo2006"),
alleq_tbl("392886F_DW~CL_TaLo2006"),
alleq_tbl("392346_TL~CL_TaLo2006"),
alleq_tbl("392346_ACW~CL_TaLo2006"),
alleq_tbl("392346_MCW~CL_TaLo2006"),
alleq_tbl("392346_RBW~CL_TaLo2006"),
alleq_tbl("392346_RL~CL_TaLo2006"),
alleq_tbl("392886_TL~CL_TaLo2006"),
alleq_tbl("392886_ACW~CL_TaLo2006"),
alleq_tbl("392886_MCW~CL_TaLo2006"),
alleq_tbl("392886_RBW~CL_TaLo2006"),
alleq_tbl("392886_RL~CL_TaLo2006"))
## ---
## Miscellaneous others
##
## Leptonychotes weddellii
x <- bind_rows(x,alleq_tbl("195932_WW_GaBu1988"))
## Chorismus antarcticus
x <- bind_rows(x,alleq_tbl("369214_WW_Lake2003"))
## also applicable to Notocrangon antarcticus
x <- bind_rows(x,alleq_tbl("369214_WW_Lake2003",
with_id="369204_WW_Lake2003",
taxon_name="Notocrangon antarcticus",
taxon_aphia_id=369204,
notes="Uses equation developed by Lake et al. for Chorismus antarcticus but noted as also applicable to Notocrangon antarcticus"))
## Tremtomus newnesi
x <- bind_rows(x,alleq_tbl("234628_WW~SL_EaDe1997"))
## energetics
## Electrona antarctica
x <- bind_rows(x,alleq_tbl("217697_EDDW~SL_VanD2006"),
alleq_tbl("217697_EDWW~SL_VanD2006"),
alleq_tbl("217697_EDDW~WW_VanD2006"),
alleq_tbl("217697_EDWW~WW_VanD2006"),
alleq_tbl("217697_EDDW~DW_VanD2006"),
alleq_tbl("217697_EDWW~DW_VanD2006"))
## Aethotaxis mitopteryx
x <- bind_rows(x,alleq_tbl("234660_LpDW~SL_FrHa1994"))
x <- bind_rows(x,alleq_tbl("234660_LpDW~WW_FrHa1994"))
x <- bind_rows(x,alleq_tbl("234660_WC~LpWW_FrHa1994"))
## Pleuragramma antarcticum 234721, proper name is Pleuragramma antarctica
x <- bind_rows(x,alleq_tbl("234721_LpDW~SL_FrHa1994"),
alleq_tbl("234721_WC~LpWW_FrHa1994"))
## Trematomus lepidorhinus
x <- bind_rows(x,alleq_tbl("234770_LpDW~SL_FrHa1994"),
alleq_tbl("234770_WC~LpWW_FrHa1994"))
## Bathydraco marri
x <- bind_rows(x,alleq_tbl("234816_WC~LpWW_FrHa1994"))
## Dolloidraco longedorsalis
x <- bind_rows(x,alleq_tbl("234696_WC~LpWW_FrHa1994"))
## from Vane2005
x <- bind_rows(x,alleq_tbl("234725_WW~TL_Vane2005"),
alleq_tbl("234725_TEC~TL_Vane2005"),
alleq_tbl("234797_WW~TL_Vane2005"),
alleq_tbl("234797_TEC~TL_Vane2005"),
alleq_tbl("234667_WW~TL_Vane2005"),
alleq_tbl("234667_TEC~TL_Vane2005"),
alleq_tbl("234678_WW~TL_Vane2005"),
alleq_tbl("234678_TEC~TL_Vane2005"),
alleq_tbl("234704_WW~TL_Vane2005"),
alleq_tbl("234704_TEC~TL_Vane2005"),
alleq_tbl("234700_WW~TL_Vane2005"),
alleq_tbl("234700_TEC~TL_Vane2005"),
alleq_tbl("313344_WW~TL_Vane2005"),
alleq_tbl("313344_TEC~TL_Vane2005"))
## from Dubi2012
x <- bind_rows(x, alleq_tbl("266542_WW~OAL_summer_Dubi2012"),
alleq_tbl("266545_WW~OAL_summer_Dubi2012"),
alleq_tbl("266542_WW~OAL_autumn_Dubi2012"),
alleq_tbl("266545_WW~OAL_autumn_Dubi2012"),
alleq_tbl("266542_WW~OAL_winter_Dubi2012"),
alleq_tbl("266545_WW~OAL_winter_Dubi2012"),
alleq_tbl("266542_DW~OAL_summer_Dubi2012"),
alleq_tbl("266545_DW~OAL_summer_Dubi2012"),
alleq_tbl("266542_DW~OAL_autumn_Dubi2012"),
alleq_tbl("266545_DW~OAL_autumn_Dubi2012"),
alleq_tbl("266542_DW~OAL_winter_Dubi2012"),
alleq_tbl("266545_DW~OAL_winter_Dubi2012"),
alleq_tbl("266542_CW~OAL_summer_Dubi2012"),
alleq_tbl("266545_CW~OAL_summer_Dubi2012"),
alleq_tbl("266545_CW~OAL_autumn_Dubi2012"),
alleq_tbl("266542_CW~OAL_winter_Dubi2012"),
alleq_tbl("266545_CW~OAL_winter_Dubi2012"),
alleq_tbl("137217_LpW~OAL_Dubi2012")
)
## from AhSh1998
x <- bind_rows(x, alleq_tbl("197217_AFDW~SHL_AhSh1998"),
alleq_tbl("197217_OCR~AFDW_AhSh1998"))
## from UrMe1998
x <- bind_rows(x, alleq_tbl("197217_SFDW~SHL_UrMe1998"),
alleq_tbl("197217_SFDW~SHL_postspawn_UrMe1998"),
alleq_tbl("197217_AFDW~SHL_UrMe1998"),
alleq_tbl("197217_AFDW~SFDW_UrMe1998"),
alleq_tbl("197217_SL~age_UrMe1998"))
## East2019
temp <- lapply(alleq_East2019(), function(z) alleq_tbl(thiseq = z)) ## all equations from this source
x <- bind_rows(x, bind_rows(temp))
x
}
allometric_equations <- build_allometry_df()
## todo: check each row that taxon_name and taxon_aphia_id match (or are expected mismatches, at least)
## todo: move these tests to testthat
## check worrms aphia_id
## unique ids
assert_that(!any(duplicated(allometric_equations$equation_id)))
## unique rows
## check that all eqs return a tibble/df with a_v col at least
chk <- vapply(seq_len(nrow(allometric_equations)),function(z) {
tmp <- allometric_equations[z,]$equation[[1]](0)
is.data.frame(tmp) && "allometric_value" %in% names(tmp)},
FUN.VALUE=TRUE)
assert_that(all(chk))
## more checks
assert_that(all(grepl("WW",allometric_equations$equation_id[allometric_equations$return_property=="wet weight"])))
assert_that(all(grepl("ML",allometric_equations$equation_id[allometric_equations$return_property=="mantle length"])))
## check that masses look ok
idx <- grepl("WiMc1990", allometric_equations$equation_id) & allometric_equations$return_property == "wet weight" & vapply(seq_len(nrow(allometric_equations)), function(z) identical(allometric_equations[z, ]$inputs[[1]]$property, "standard length"), FUN.VALUE = TRUE)
tmp <- vapply(which(idx),function(z) allometric_equations[z, ]$equation[[1]](100)$allometric_value,FUN.VALUE = 1)
assert_that(!any(abs(tmp)<1 | abs(tmp)>50))
## SL from OL
idx <- grepl("WiMc1990", allometric_equations$equation_id) & allometric_equations$return_property == "standard length" & vapply(seq_len(nrow(allometric_equations)), function(z) identical(allometric_equations[z, ]$inputs[[1]]$property, "otolith length"), FUN.VALUE = TRUE)
tmp <- vapply(which(idx),function(z)allometric_equations[z, ]$equation[[1]](4)$allometric_value,FUN.VALUE = 1)
assert_that(!any(abs(tmp)<50 | abs(tmp)>500))
## SL from OW
idx <- grepl("WiMc1990",allometric_equations$equation_id) & allometric_equations$return_property=="standard length" & vapply(seq_len(nrow(allometric_equations)),function(z) identical(allometric_equations[z,]$inputs[[1]]$property, "otolith width"), FUN.VALUE=TRUE)
tmp <- vapply(which(idx),function(z)allometric_equations[z,]$equation[[1]](4)$allometric_value,FUN.VALUE = 1)
assert_that(!any(abs(tmp)<50 | abs(tmp)>1000))
## taxonomy check
utn <- allometric_equations %>% mutate(noted_invalid = grepl("Accepted taxon name is", .data$notes)) %>% distinct(.data$taxon_name, .data$taxon_aphia_id, .data$noted_invalid) %>% dplyr::arrange(.data$taxon_name)
if (any(duplicated(utn$taxon_name))) stop("There must be at least one invalid taxon that is not noted as invalid")
chk <- utn %>% rowwise %>% mutate(taxon_aphia_id_new = { tmp <- search_worms(.data$taxon_name); if (nrow(tmp) == 1) tmp$AphiaID else NA_integer_ }) %>% ungroup %>% as.data.frame
##chk %>% dplyr::filter(.data$taxon_aphia_id != .data$taxon_aphia_id_new | is.na(.data$taxon_aphia_id_new)) %>% count(.data$taxon_name, .data$taxon_aphia_id, .data$noted_invalid, .data$taxon_aphia_id_new)
chk %>% dplyr::filter(.data$taxon_aphia_id != .data$taxon_aphia_id_new | is.na(.data$taxon_aphia_id_new)) %>% count(.data$taxon_name, .data$taxon_aphia_id, .data$noted_invalid, .data$taxon_aphia_id_new) %>% dplyr::filter(!noted_invalid)
## usethis::use_data(allometric_equations, internal = FALSE, overwrite = TRUE)
SCAR/solong documentation built on Aug. 5, 2022, 9:04 p.m.
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## NOTES for new equation entry
## Prior to June 2021 we entered equations using the valid name and aphia ID. If the equation was published under an unaccepted name, that would also be entered by manually adding a row here. As of June 2021 we have alleq_tbl(..., check_name = TRUE) will automatically add a duplicate equation with the valid name, so we can just enter the equation under the invalid name in data-raw
library(dplyr)
library(assertthat)
requireNamespace("dietdataentry")
#worms_cache_directory <- "~/.cache/R/R.cache/"
#worms_cache_dir(worms_cache_directory)
refs <- list(
JaMc1996=bibentry(bibtype="Article",key="JaMc1996",
author=c(person(c("G","D"),"Jackson"),person(c("J","F"),"McKinnon")),
year=1996,
title="Beak length analysis of arrow squid Nototodarus sloanii (Cephalopoda: Ommastrephidae) in southern New Zealand waters",
journal="Polar Biology",volume=16,pages="227-230",
doi="10.1007/BF02329211"),
GaBu1988=bibentry(bibtype="Article",key="GaBu1988",
author=c(person(c("N","J"),"Gales"),person(c("H","R"),"Burton")),
year=1988,
title="Use of emetics and anaesthesia for dietary assessment of Weddell seals",
journal="Australian Wildlife Research",volume=15,pages="423-433"),
EaDe1997=bibentry(bibtype="Article",key="EaDe1997",
author=c(person(c("J","T"),"Eastman"),person(c("A","L"),"Devries")),
year=1997,
title="Biology and phenotypic plasticity of the Antarctic nototheniid fish Trematomus newnesi in McMurdo Sound",
journal="Antarctic Science",volume=9,pages="27-35",
doi="10.1017/S0954102097000047")
)
## fish
source("data-raw/equations_Arti2003.R")
source("data-raw/equations_fish_other.R")
source("data-raw/equations_krill.R")
source("data-raw/equations_Lake2003.R")
source("data-raw/equations_Smal1993.R")
source("data-raw/equations_WiMc1990.R")
source("data-raw/equations_Bush2005.R")
source("data-raw/equations_XaCh2016.R")
source("data-raw/equations_East2019.R")
source("data-raw/equations_LaMe2020.R")
source("data-raw/equations_EsFl2020.R")
source("data-raw/equations_crustaceans.R")
source("data-raw/equations_Schw2019.R")
## energetics
source("data-raw/equations_VanD2006.R")
source("data-raw/equations_FrHa1994.R")
source("data-raw/equations_Vane2005.R")
source("data-raw/equations_Dubi2012.R")
source("data-raw/equations_AhSh1998.R")
source("data-raw/equations_UrMe1998.R")
alleq_other <- function(id) {
switch(id,
## Bayesian length-weight: a=0.00575 (0.00309 - 0.01073), b=3.18 (3.01 - 3.35), in cm Total Length, based on LWR estimates for this species & (Sub)family-body (Ref. 93245).
## Froese, R., J. Thorson and R.B. Reyes Jr., 2013. A Bayesian approach for estimating length-weight relationships in fishes. J. Appl. Ichthyol. (2013):1-7.
## also http://oceanrep.geomar.de/21875/
## W=a*(TL^b)
## Brown and Klages 1987
## OD = otolith diameter. OD , SL, TL all mm. M in g
##The general relationship relating standard length to total length in myctophid fish was:
##SL = 0.17+0.80 TL (r2 = 0.97, S.D. = 0.018)
##Protomyctophum tenisoni and P. normani
##OD = 0.3 +0.027 SL (r2 = 0.85, n = 46)
##M = 1.282e-05 TL^2.868(r2 = 0.90, n = 28)
##Krefftichthys anderssoni
##OD = 0.416+0.022 SL (r2 = 0.88, n = 27)
##M = 5.36e-06 TL^3.080 (r2 = 0.90, n = 16)
##Electrona carlsbergi and E. subaspera
##OD = 0.254 + 0.042 SL (r2 = 0.9 1, n = 90)
##M = 7.43e-06 SL^3.159 ( r2 = 0.90, n = 60)
##Notothenia magellanica (Hecht & Cooper, 1986)
##TL = 30.96 OD^1.801 (r2 = 0.75, n = 82)
##M = 2.19e-05 TL^3.00 (r2 = 0.99, n = 133)
##Species: Leptonychotes weddellii
##Gender: male
##Equation: WEIGHT_KG=3.66*STANDARD_LENGTH_CM-489.3 (N=15)
##Source: Gales, N.J. and Burton, H.R. (1988) Use of emetics and anaesthesia for dietary assessment of Weddell seals. Australian Wildlife Research 15:423--433
"195932_WW_GaBu1988"=list(taxon_name="Leptonychotes weddellii",
taxon_aphia_id=195932,
equation=function(...)tibble(allometric_value= 3.66*...-489.3),
inputs=tibble(property="standard length",units="cm",sample_minimum=170,sample_maximum=236),
return_property="wet weight",
return_units="kg",
reliability=tribble(~type,~value,
"N",15),
notes="Applies to male animals",
reference=refs$GaBu1988),
## Nototodarus sloanii
"342378_ML_JaMc1996"=list(taxon_name="Nototodarus sloanii",
taxon_aphia_id=342378,
equation=function(...)tibble(allometric_value=168.83*log(...)+25.52),
inputs=tibble(property="lower rostral length",units="mm",sample_minimum=2,sample_maximum=7.2),
return_property="mantle length",
return_units="mm",
reliability=tribble(~type,~value,
"N",170,
"R^2",0.90),
reference=refs$JaMc1996),
"342378_ML_JaMc1996"=list(taxon_name="Nototodarus sloanii",
taxon_aphia_id=342378,
equation=function(...)tibble(allometric_value=236.10*...-512.99),
inputs=tibble(property="lower rostral length",units="mm",sample_minimum=2,sample_maximum=7.2),
return_property="wet weight",
return_units="g",
reliability=tribble(~type,~value,
"N",170,
"R^2",0.90),
reference=refs$JaMc1996),
## Trematomus newnesi from EaDe1997
"234628_WW~SL_EaDe1997"=list(taxon_name="Trematomus newnesi",
taxon_aphia_id=234628,
equation=function(...)tibble(allometric_value=3.17e-06*(...^3.34)),
inputs=tibble(property="standard length",units="mm",sample_minimum=93,sample_maximum=239),
return_property="wet weight",
return_units="g",
reliability=tribble(~type,~value,
"N",67,
"R^2",0.95),
reference=refs$EaDe1997),
stop("unrecognized equation ID: ",id))
}
## wrapper function around alleq. Can override the taxon, if e.g. applying an equation developed for one species to another species
## can override reference. Notes get added to any notes in the original equation
alleq_tbl <- function(id, with_id = NULL, taxon_name = NULL, taxon_aphia_id = NULL, notes = NULL, reference = NULL, thiseq = NULL, check_name) {
if (missing(check_name)) check_name <- is.null(with_id)
was_as_eq <- FALSE
if (is.null(thiseq)) {
try(thiseq <- alleq_other(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_Arti2003(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_fish_other(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_krill(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_crustaceans_other(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_Lake2003(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_Smal1993(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_WiMc1990(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_Bush2005(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_XaCh2016(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_VanD2006(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_FrHa1994(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_Vane2005(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_Dubi2012(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_AhSh1998(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_UrMe1998(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_LaMe2020(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_EsFl2020(id), silent = TRUE)
if (is.null(thiseq)) try(thiseq <- alleq_Schw2019(id), silent = TRUE)
if (is.null(thiseq)) stop("equation id not recognized or has an error: ", id)
} else {
was_as_eq <- TRUE
id <- thiseq$id
}
if (!is.null(thiseq$check_name) && isTRUE(thiseq$check_name) != isTRUE(check_name)) {
message("equation ", id, " specifies check_name = ", isTRUE(thiseq$check_name), ", using this")
check_name <- isTRUE(thiseq$check_name)
}
## use the equation defaults for some things, if not already specified
if (is.null(with_id)) with_id <- id
if (is.null(taxon_name)) taxon_name <- thiseq$taxon_name
if (is.null(taxon_aphia_id)) taxon_aphia_id <- thiseq$taxon_aphia_id
if (is.null(reference)) reference <- thiseq$reference
if (is.null(notes)) {
notes <- ""
}
if (is.null(thiseq$notes) || !nzchar(thiseq$notes)) {
## no notes in coded equation, use notes supplied here as arg
} else {
if (nzchar(notes)) {
## use both sets of notes
notes <- paste0(notes,". ",thiseq$notes)
} else {
notes <- thiseq$notes ## use notes from thiseq
}
}
if (is.null(thiseq$reliability)) thiseq$reliability <- tibble(type=character(),value=numeric())
## old direct code
## tribble(~equation_id,~taxon_name,~taxon_aphia_id,~equation,~inputs,~return_property,~return_units,~reliability,~notes,~reference,
## id,taxon_name,taxon_aphia_id,thiseq$equation,thiseq$inputs,thiseq$return_property,thiseq$return_units,thiseq$reliability,notes,reference)
e2 <- sol_make_equation(equation_id = with_id,
taxon_name = taxon_name,
taxon_aphia_id = taxon_aphia_id,
equation = thiseq$equation,
inputs = thiseq$inputs,
return_property = thiseq$return_property,
return_units = thiseq$return_units,
reliability = thiseq$reliability,
notes = notes,
reference = reference,
check_packaged_ids = FALSE)
class(e2) <- setdiff(class(e2), "sol_equation")
## finally check the taxonomy
if (isTRUE(check_name)) {
ar <- dietdataentry::search_worms(scientific = e2$taxon_name)
if (nrow(ar) > 0 && !is.na(ar$AphiaID) && (is.na(e2$taxon_aphia_id) || (e2$taxon_aphia_id != ar$AphiaID))) {
## the existing name resolves to a different taxon_id than listed in the data-raw code
##cat(str(ar))
##cat(str(e2))
message(e2$taxon_name, " (aphia_id ", e2$taxon_aphia_id, " resolves to ", ar$scientificname, " (aphia_id ", ar$AphiaID, "), adding note and duplicate record")
e2$notes <- sub("^[[:space:]]+", "", paste0(e2$notes, " Accepted taxon name is ", ar$scientificname))
## create duplicate record
if (was_as_eq) {
duprec <- alleq_tbl(thiseq = thiseq, with_id = sub(paste0("^", e2$taxon_aphia_id), ar$AphiaID, id), taxon_name = ar$scientificname, taxon_aphia_id = ar$AphiaID)
} else {
duprec <- alleq_tbl(id = id, with_id = sub(paste0("^", e2$taxon_aphia_id), ar$AphiaID, id), taxon_name = ar$scientificname, taxon_aphia_id = ar$AphiaID, notes = notes)
}
e2 <- bind_rows(e2, duprec)
}
}
e2
}
build_allometry_df <- function() {
## equations from Xavier and Cherel
## Ancistrocheirus lesueurii
x <- bind_rows(alleq_tbl("138747_ML_Clar1986"), alleq_tbl("138747_WW_Clar1986"))
## Architeuthis dux
x <- bind_rows(x,alleq_tbl("342218_ML_Clar1986"),alleq_tbl("342218_WW_Clar1986"),alleq_tbl("342218_ML_Roel2000"))
## Bathyteuthis abyssicola
x <- bind_rows(x,alleq_tbl("138848_ML_Clar1986"),alleq_tbl("138848_WW_Clar1986"))
## Batoteuthis skolops (no specific equations)
x <- bind_rows(x,alleq_tbl("137777_ML_Clar1986",
with_id="325293_MLa_Clar1986",
taxon_name="Batoteuthis skolops",
taxon_aphia_id=325293,
notes="Based on Chiroteuthis spp. formula from Clarke (1986). There are no specific equations for Batoteuthis skolops"),
alleq_tbl("137777_WW_Clar1986",
with_id="325293_WWa_Clar1986",
taxon_name="Batoteuthis skolops",
taxon_aphia_id=325293,
notes="Based on Chiroteuthis spp. formula from Clarke (1986). There are no specific equations for Batoteuthis skolops"),
alleq_tbl("138168_ML_Clar1986",
with_id="325293_MLb_Clar1986",
taxon_name="Batoteuthis skolops",
taxon_aphia_id=325293,
notes="Based on Mastigoteuthis spp. formula from Clarke (1986). There are no specific equations for Batoteuthis skolops"),
alleq_tbl("138168_WW_Clar1986",
with_id="325293_WWb_Clar1986",
taxon_name="Batoteuthis skolops",
taxon_aphia_id=325293,
notes="Based on Mastigoteuthis spp. formula from Clarke (1986). There are no specific equations for Batoteuthis skolops"))
## family Brachioteuthidae
x <- bind_rows(x,alleq_tbl("11758_ML_Clar1986"),alleq_tbl("11758_WW_Clar1986"))
## note that this will require some additional coding in the user function, so that e.g. an input taxon_name of "Brachioteuthis picta" will find its way to this equation even though it does not directly match the taxon_name or taxon_aphia_id specified here
## Chiroteuthis veranyi (no specific equations)
x <- bind_rows(x,alleq_tbl("137777_ML_Clar1986",
with_id="139125_ML_Clar1986",
taxon_name="Chiroteuthis veranii",
taxon_aphia_id=139125,
notes="Based on Chiroteuthis spp. formula from Clarke (1986). There are no specific equations for Chiroteuthis veranii"),
alleq_tbl("137777_WW_Clar1986",
with_id="139125_WW_Clar1986",
taxon_name="Chiroteuthis veranii",
taxon_aphia_id=139125,
notes="Based on Chiroteuthis spp. formula from Clarke (1986). There are no specific equations for Chiroteuthis veranii"))
## Chiroteuthis sp.
x <- bind_rows(x,alleq_tbl("137777_ML_Clar1986"),alleq_tbl("137777_WW_Clar1986"))
## Galiteuthis glacialis
x <- bind_rows(x,alleq_tbl("325297_ML_LuWi1994"),alleq_tbl("325297_WW_LuWi1994"))
## Galiteuthis stC sp. (Imber) (no specific equations)
## Galiteuthis sp. 3 (Imber) (no specific equations)
## Taonius sp. B (Voss) (no specific equations)
## Taonius sp. (Clarke) (no specific equations)
## Taonius sp
## Note that this is given as Taonius pavo in Rodhouse et al. 1990, but Taonius sp. in X&C
x <- bind_rows(x,alleq_tbl("137853_ML_Rodh1990"),alleq_tbl("137853_WW_Rodh1990"))
## Teuthowenia pellucida
## Note that the Rodhouse et al 1990 paper does NOT have equations for T.p.
## this info taken from X&C
x <- bind_rows(x,alleq_tbl("341823_ML_Rodh1990"),alleq_tbl("341823_WW_Rodh1990"))
## Mesonychoteuthis hamiltoni
x <- bind_rows(x,alleq_tbl("325299_ML_Rodh1990"))
## Cranchiidae
x <- bind_rows(x,alleq_tbl("11774_WW_Clar1962"))
## Cycloteuthis akimushkini
x <- bind_rows(x,alleq_tbl("341824_ML_Clar1986"),alleq_tbl("341824_WW_Clar1986"))
## Gonatus
x <- bind_rows(x,alleq_tbl("138036_ML_Clar1986"),alleq_tbl("138036_WW_Clar1986"))
## Gonatus (small specimens)
x <- bind_rows(x,alleq_tbl("138036small_ML_Clar1986"),alleq_tbl("138036small_WW_Clar1986"))
## Gonatus antarcticus (no specific equations)
x <- bind_rows(x,alleq_tbl("138036_ML_Clar1986",
with_id="325300_ML_Clar1986",
taxon_name="Gonatus antarcticus",
taxon_aphia_id=325300,
notes="Based on Gonatus spp. formula from Clarke (1986). There are no specific equations for Gonatus antarcticus"),
alleq_tbl("138036_WW_Clar1986",
with_id="325300_WW_Clar1986",
taxon_name="Gonatus antarcticus",
taxon_aphia_id=325300,
notes="Based on Gonatus spp. formula from Clarke (1986). There are no specific equations for Gonatus antarcticus"))
## (small specimens)
x <- bind_rows(x,alleq_tbl("138036small_ML_Clar1986",
with_id="325300small_ML_Clar1986",
taxon_name="Gonatus antarcticus",
taxon_aphia_id=325300,
notes="Based on Gonatus spp. formula from Clarke (1986). There are no specific equations for Gonatus antarcticus"),
alleq_tbl("138036small_WW_Clar1986",
with_id="325300small_WW_Clar1986",
taxon_name="Gonatus antarcticus",
taxon_aphia_id=325300,
notes="Based on Gonatus spp. formula from Clarke (1986). There are no specific equations for Gonatus antarcticus"))
## Histioteuthis A, which has a deep notch in back of hood and a well-developed ridge
## running to free corner of lateral wall:
## Histioteuthis arcturi (no specific equations)
## Histioteuthis bonnellii corpuscula (valid name Histioteuthis bonnellii)
x <- bind_rows(x,alleq_tbl("140111_ML_Clar1986"),alleq_tbl("140111_ML_LuIc2002"), alleq_tbl("140111_WW_LuIc2002"))
## Histioteuthis macrohista
x <- bind_rows(x,alleq_tbl("341870_ML_LuIc2002"),alleq_tbl("341870_WW_LuIc2002"))
## Histioteuthis miranda
x <- bind_rows(x,alleq_tbl("341871_ML_Clar1986"),alleq_tbl("341871_WW_Clar1986"))
x <- bind_rows(x,alleq_tbl("341871_ML_LuIc2002"),alleq_tbl("341871_WW_LuIc2002"))
## Histioteuthis B has a shallow notch in back of hood and a weakly-developed ridge under
## the hood (evident in Histioteuthis atlantica juveniles) that becomes a slight fold running to free corner
## of lateral wall:
## Histioteuthis atlantica
x <- bind_rows(x,alleq_tbl("341864_ML_LuIc2002"),alleq_tbl("341864_WW_LuIc2002"))
## Histioteuthis eltaninae
x <- bind_rows(x,alleq_tbl("341867_ML_LuIc2002"),alleq_tbl("341867_WW_LuIc2002"))
## Lepidoteuthis grimaldii
x <- bind_rows(x,alleq_tbl("140193_ML_BASUnpub"),alleq_tbl("140193_WW_BASUnpub"),alleq_tbl("140193_ML_LuIc2002"))
## Loligo gahi (accepted name Doryteuthis (Amerigo) gahi)
x <- bind_rows(x,alleq_tbl("341880_ML_HatfUnpub"),alleq_tbl("341880_WW_HatfUnpub"))
## also manually add one for Doryteuthis gahi
x <- bind_rows(x,alleq_tbl("341880_ML_HatfUnpub",
with_id="574538_ML_HatfUnpub",
taxon_name="Doryteuthis gahi",
taxon_aphia_id=574538,
notes="Accepted taxon name is Doryteuthis (Amerigo) gahi"),
alleq_tbl("341880_WW_HatfUnpub",
with_id="574538_WW_HatfUnpub",
taxon_name="Doryteuthis gahi",
taxon_aphia_id=574538,
notes="Accepted taxon name is Doryteuthis (Amerigo) gahi"))
## Lycoteuthis lorigera
x <- bind_rows(x,alleq_tbl("342361_ML_LuIc2002"),alleq_tbl("342361_WW_LuIc2002"))
## Mastigoteuthis psychrophila
x <- bind_rows(x,alleq_tbl("341904_ML_BASUnpub"),alleq_tbl("341904_WW_BASUnpub"))
## ?Mastigoteuthis A (Clarke) (no specific equations)
## Alluroteuthis antarcticus
x <- bind_rows(x,alleq_tbl("325302_ML_Piat2001"),alleq_tbl("325302_WW_Piat2001"))
## Nototeuthis dimegacotyle (no specific equations)
## Taningia danae
x <- bind_rows(x,alleq_tbl("140609_ML_Clark1986"),alleq_tbl("140609_WW_Clark1986"))
## Octopoteuthis sp.
x <- bind_rows(x,alleq_tbl("138271_ML_Clark1986"),alleq_tbl("138271_WW_Clark1986"))
## Martialia hyadesi
x <- bind_rows(x,alleq_tbl("325305_ML_RoYe1990"),alleq_tbl("325305_WW_RoYe1990"))
## Illex argentinus
x <- bind_rows(x,alleq_tbl("342064_ML_SaHa2000"),alleq_tbl("342064_WW_SaHa2000"))
## Todarodes sp. (no specific equations)
x <- bind_rows(x,alleq_tbl("138281_ML_Clar1986"),alleq_tbl("138281_WW_Clar1986"))
## Kondakovia longimana
x <- bind_rows(x,alleq_tbl("325308_ML_BrKl1987"),alleq_tbl("325308_WW_BrKl1987"))
## Moroteuthis ingens
x <- bind_rows(x,alleq_tbl("410381M_ML_Jack1995"),alleq_tbl("410381F_ML_Jack1995"),
alleq_tbl("410381M_WW_Jack1995"),alleq_tbl("410381F_WW_Jack1995"))
## Moroteuthis knipovitchi (valid name is Filippovia knipovitchi)
x <- bind_rows(x,alleq_tbl("325310_ML_CherUnpub"),alleq_tbl("325310_WW_CherUnpub"))
## Moroteuthis robsoni (valid name Onykia robsoni)
x <- bind_rows(x,alleq_tbl("342256_ML_LuIc2002"),alleq_tbl("342256_WW_LuIc2002"))
## Moroteuthis sp . B (Imber) (no specific equations)
## Onychoteuthis banksii
x <- bind_rows(x,alleq_tbl("140649_ML_LuIc2002"),alleq_tbl("140649_WW_LuIc2002"))
## Pholidoteuthis massyae
x <- bind_rows(x,alleq_tbl("410388_ML_Clar1986"),alleq_tbl("410388_WW_Clar1986"))
## Psychroteuthis glacialis
x <- bind_rows(x,alleq_tbl("325312_ML_Grog2000"),alleq_tbl("325312_WW_Grog2000"))
## FAMILY SEPIOLIDAE
## cf. Stoloteuthis leucoptera (no allometric equations available)
## Oegopsida sp. A (Cherel) (no allometric equations available)
## Haliphron atlanticus
x <- bind_rows(x,alleq_tbl("341781_WW_BASUnpub"))
## Cirrata sp. A (Cherel) (no allometric equations available)
## Pareledone turqueti
x <- bind_rows(x,alleq_tbl("239393_ML_CollUnpub"),alleq_tbl("239393_WW_CollUnpub"))
## Adelieledone polymorpha
x <- bind_rows(x,alleq_tbl("325319_ML_CollUnpub"),alleq_tbl("325319_WW_CollUnpub"))
## Benthoctopus thielei (valid name is Muusoctopus thielei)
x <- bind_rows(x,alleq_tbl("341931_ML_CherUnpub"),alleq_tbl("341931_WW_CherUnpub"))
## Graneledone gonzalezi
x <- bind_rows(x,alleq_tbl("342224_ML_CherUnpub"),alleq_tbl("342224_WW_CherUnpub"))
## Opisthoteuthis sp.
## ML=-26.0047+12.4858CL; logM=0.5893+0.2413CL (n= 13 for ML, n=9 for M) (Smale
## et al. 1993) where CL = Crest length (in mm)
## see equations for Smale et al. 1993
## Stauroteuthis gilchristi (no allometric equations available)
## ---
## Smale et al. 1993
## Octopus vulgaris
x <- bind_rows(x,alleq_tbl("140605_ML_Smal1993"),
alleq_tbl("140605_HL_Smal1993"),
alleq_tbl("140605_WW_Smal1993"))
## Enteroctopus magnificus
x <- bind_rows(x,alleq_tbl("225568_ML_Smal1993"),
alleq_tbl("225568_HL_Smal1993"),
alleq_tbl("225568_WW_Smal1993"))
## Velodona togata
x <- bind_rows(x,alleq_tbl("342415_ML_Smal1993"),
alleq_tbl("342415_HL_Smal1993"))
## Bathypolypus valdiviae
x <- bind_rows(x,alleq_tbl("341910_ML_Smal1993"),
alleq_tbl("341910_HL_Smal1993"),
alleq_tbl("341910_WW_Smal1993"))
## Opisthoteuthis
x <- bind_rows(x,alleq_tbl("138294_ML_Smal1993"),
alleq_tbl("138294_HL_Smal1993"),
alleq_tbl("138294_WW_Smal1993"))
## Tremoctopus violaceus
x <- bind_rows(x,alleq_tbl("141694_ML_Smal1993"),
alleq_tbl("141694_HL_Smal1993"),
alleq_tbl("141694_WW_Smal1993"))
## Argonauta
x <- bind_rows(x,alleq_tbl("137676_ML_Smal1993"),
alleq_tbl("137676_HL_Smal1993"),
alleq_tbl("137676_WW_Smal1993"))
## ---
## Schwarz et al 2019
x <- bind_rows(x,alleq_tbl("325319_WW~DML_Schw2019"),
alleq_tbl("325319M_WW~DML_Schw2019"),
alleq_tbl("325319F_WW~DML_Schw2019"),
alleq_tbl("325324_WW~DML_Schw2019"),
alleq_tbl("325324M_WW~DML_Schw2019"),
alleq_tbl("325324F_WW~DML_Schw2019"),
alleq_tbl("527162_WW~DML_Schw2019"),
alleq_tbl("527162M_WW~DML_Schw2019"),
alleq_tbl("527162F_WW~DML_Schw2019"),
alleq_tbl("325325_WW~DML_Schw2019"),
alleq_tbl("325325M_WW~DML_Schw2019"),
alleq_tbl("325325F_WW~DML_Schw2019"),
alleq_tbl("239392_WW~DML_Schw2019"),
alleq_tbl("239392M_WW~DML_Schw2019"),
alleq_tbl("239392F_WW~DML_Schw2019"),
alleq_tbl("325336_WW~DML_Schw2019"),
alleq_tbl("325336M_WW~DML_Schw2019"),
alleq_tbl("325336F_WW~DML_Schw2019"),
alleq_tbl("239393_WW~DML_Schw2019"),
alleq_tbl("239393M_WW~DML_Schw2019"),
alleq_tbl("239393F_WW~DML_Schw2019"))
## ---
## Williams & McEldowney 1990 otoliths
## Bathylagus antarcticus
x <- bind_rows(x,alleq_tbl("234631_SL~OL_WiMc1990"),
alleq_tbl("234631_SL~OW_WiMc1990"),
alleq_tbl("234631_WW~SL_WiMc1990"))
## Krefftichthys anderssoni
x <- bind_rows(x,alleq_tbl("234641_SL~OL_WiMc1990"),
alleq_tbl("234641_SL~OW_WiMc1990"),
alleq_tbl("234641_WW~SL_WiMc1990"))
## Pleuragramma antarctica
x <- bind_rows(x,alleq_tbl("234721_SL~OL_WiMc1990"),
alleq_tbl("234721_SL~OW_WiMc1990"),
alleq_tbl("234721_WW~SL_WiMc1990"))
## Protomyctophum bolini
x <- bind_rows(x,alleq_tbl("234714_SL~OL_WiMc1990"),
alleq_tbl("234714_SL~OW_WiMc1990"),
alleq_tbl("234714_WW~SL_WiMc1990"))
## Electrona antarctica
x <- bind_rows(x,alleq_tbl("217697_SL~OL_WiMc1990"),
alleq_tbl("217697_SL~OW_WiMc1990"),
alleq_tbl("217697_WW~SL_WiMc1990"))
## Electrona carlsbergi
x <- bind_rows(x,alleq_tbl("234638_SL~OL_WiMc1990"),
alleq_tbl("234638_SL~OW_WiMc1990"),
alleq_tbl("234638_WW~SL_WiMc1990"))
## Electrona subaspera
x <- bind_rows(x,alleq_tbl("234791_SL~OL_WiMc1990"),
alleq_tbl("234791_SL~OW_WiMc1990"),
alleq_tbl("234791_WW~SL_WiMc1990"))
## Gymnoscopelus braueri
x <- bind_rows(x,alleq_tbl("234642_SL~OL_WiMc1990"),
alleq_tbl("234642_SL~OW_WiMc1990"),
alleq_tbl("234642_WW~SL_WiMc1990"))
## Gymnoscopelus nicholsi
x <- bind_rows(x,alleq_tbl("234821_SL~OL_WiMc1990"),
alleq_tbl("234821_SL~OW_WiMc1990"),
alleq_tbl("234821_WW~SL_WiMc1990"))
## Gymnoscopelus fraseri
x <- bind_rows(x,alleq_tbl("234657_SL~OL_WiMc1990"),
alleq_tbl("234657_SL~OW_WiMc1990"),
alleq_tbl("234657_WW~SL_WiMc1990"))
## Muraenolepis marmoratus, valid name Muraenolepis marmorata
x <- bind_rows(x,alleq_tbl("234705_SL~OL_WiMc1990"),
alleq_tbl("234705_SL~OW_WiMc1990"),
alleq_tbl("234705_WW~SL_WiMc1990"))
## Macrourus holotrachys
x <- bind_rows(x,alleq_tbl("234831_TL~OL_WiMc1990"),
alleq_tbl("234831_TL~OW_WiMc1990"),
alleq_tbl("234831_WW~TL_WiMc1990"))
## Zanclorhynchus spinifer
x <- bind_rows(x,alleq_tbl("234683_SL~OL_WiMc1990"),
alleq_tbl("234683_SL~OW_WiMc1990"),
alleq_tbl("234683_WW~SL_WiMc1990"))
## Dolloidraco longedorsalis
x <- bind_rows(x,alleq_tbl("234696_SL~OL_WiMc1990"),
alleq_tbl("234696_SL~OW_WiMc1990"),
alleq_tbl("234696_WW~SL_WiMc1990"))
## Pogonophryne phyllopogon, valid name is Pogonophryne scotti
x <- bind_rows(x,alleq_tbl("313416_SL~OL_WiMc1990"),
alleq_tbl("313416_SL~OW_WiMc1990"),
alleq_tbl("313416_WW~SL_WiMc1990"))
## Dissostichus eleginoides
x <- bind_rows(x,alleq_tbl("234700_SL~OL_WiMc1990"),
alleq_tbl("234700_SL~OW_WiMc1990"),
alleq_tbl("234700_WW~SL_WiMc1990"))
## Dissostichus mawsoni
x <- bind_rows(x,alleq_tbl("234836_SL~OL_WiMc1990"),
alleq_tbl("234836_SL~OW_WiMc1990"),
alleq_tbl("234836_WW~SL_WiMc1990"))
## Notothenia coriiceps
x <- bind_rows(x,alleq_tbl("234679_SL~OL_WiMc1990"),
alleq_tbl("234679_SL~OW_WiMc1990"),
alleq_tbl("234679_WW~SL_WiMc1990"))
## Notothenia neglecta
x <- bind_rows(x,alleq_tbl("234740_SL~OL_WiMc1990"),
alleq_tbl("234740_SL~OW_WiMc1990"),
alleq_tbl("234740_WW~SL_WiMc1990"))
## Notothenia rossii
x <- bind_rows(x,alleq_tbl("234840_SL~OL_WiMc1990"),
alleq_tbl("234840_SL~OW_WiMc1990"),
alleq_tbl("234840_WW~SL_WiMc1990"))
## Notothenia kempi (now considered to be synonymous with L. squamifrons according to WoRMS, but enter both here
## N. kempi uses an "unaccepted" aphia_id here
x <- bind_rows(x,alleq_tbl("313363_SL~OL_WiMc1990"),
alleq_tbl("313363_SL~OW_WiMc1990"),
alleq_tbl("313363_WW~SL_WiMc1990"))
## Lepidonotothen squamifrons
x <- bind_rows(x,alleq_tbl("234788_SL~OL_WiMc1990"),
alleq_tbl("234788_SL~OW_WiMc1990"),
alleq_tbl("234788_WW~SL_WiMc1990"))
## Notothenia acuta
x <- bind_rows(x,alleq_tbl("234624_SL~OL_WiMc1990"),
alleq_tbl("234624_SL~OW_WiMc1990"),
alleq_tbl("234624_WW~SL_WiMc1990"))
## Nototheniops mizops
x <- bind_rows(x,alleq_tbl("313401_SL~OL_WiMc1990"),
alleq_tbl("313401_SL~OW_WiMc1990"),
alleq_tbl("313401_WW~SL_WiMc1990"))
## Pagothenia bernacchii
x <- bind_rows(x,alleq_tbl("313391_SL~OL_WiMc1990"),
alleq_tbl("313391_SL~OW_WiMc1990"),
alleq_tbl("313391_WW~SL_WiMc1990"))
## Pagothenia borchgrevinki
x <- bind_rows(x,alleq_tbl("234801_SL~OL_WiMc1990"),
alleq_tbl("234801_SL~OW_WiMc1990"),
alleq_tbl("234801_WW~SL_WiMc1990"))
## Trematomus hansoni
x <- bind_rows(x,alleq_tbl("313392_SL~OL_WiMc1990"),
alleq_tbl("313392_SL~OW_WiMc1990"),
alleq_tbl("313392_WW~SL_WiMc1990"))
## Trematomus pennellii
x <- bind_rows(x,alleq_tbl("313409_SL~OL_WiMc1990"),
alleq_tbl("313409_SL~OW_WiMc1990"),
alleq_tbl("313409_WW~SL_WiMc1990"))
## Trematomus eulepidotus
x <- bind_rows(x,alleq_tbl("234754_SL~OL_WiMc1990"),
alleq_tbl("234754_SL~OW_WiMc1990"),
alleq_tbl("234754_WW~SL_WiMc1990"))
## Trematomus lepidorhinus
x <- bind_rows(x,alleq_tbl("234770_SL~OL_WiMc1990"),
alleq_tbl("234770_SL~OW_WiMc1990"),
alleq_tbl("234770_WW~SL_WiMc1990"))
## Trematomus loennbergii
x <- bind_rows(x,alleq_tbl("234828_SL~OL_WiMc1990"),
alleq_tbl("234828_SL~OW_WiMc1990"),
alleq_tbl("234828_WW~SL_WiMc1990"))
## Trematomus newnesi
x <- bind_rows(x,alleq_tbl("234628_SL~OL_WiMc1990"),
alleq_tbl("234628_SL~OW_WiMc1990"),
alleq_tbl("234628_WW~SL_WiMc1990"))
## Trematomus nicolai
x <- bind_rows(x,alleq_tbl("234644_SL~OL_WiMc1990"),
alleq_tbl("234644_SL~OW_WiMc1990"),
alleq_tbl("234644_WW~SL_WiMc1990"))
## Trematomus scotti
x <- bind_rows(x,alleq_tbl("234665_SL~OL_WiMc1990"),
alleq_tbl("234665_SL~OW_WiMc1990"),
alleq_tbl("234665_WW~SL_WiMc1990"))
## Akarotaxis nudiceps
x <- bind_rows(x,alleq_tbl("234600_SL~OL_WiMc1990"),
alleq_tbl("234600_SL~OW_WiMc1990"),
alleq_tbl("234600_WW~SL_WiMc1990"))
## Bathydraco marri
x <- bind_rows(x,alleq_tbl("234816_SL~OL_WiMc1990"),
alleq_tbl("234816_SL~OW_WiMc1990"),
alleq_tbl("234816_WW~SL_WiMc1990"))
## Cygnodraco mawsoni
x <- bind_rows(x,alleq_tbl("234834_SL~OL_WiMc1990"),
alleq_tbl("234834_SL~OW_WiMc1990"),
alleq_tbl("234834_WW~SL_WiMc1990"))
## Gymnodraco acuticeps
x <- bind_rows(x,alleq_tbl("234800_SL~OL_WiMc1990"),
alleq_tbl("234800_SL~OW_WiMc1990"),
alleq_tbl("234800_WW~SL_WiMc1990"))
## Prionodraco evansii
x <- bind_rows(x,alleq_tbl("234777_SL~OL_WiMc1990"),
alleq_tbl("234777_SL~OW_WiMc1990"),
alleq_tbl("234777_WW~SL_WiMc1990"))
## Racovitzia glacialis
x <- bind_rows(x,alleq_tbl("234799_SL~OL_WiMc1990"),
alleq_tbl("234799_SL~OW_WiMc1990"),
alleq_tbl("234799_WW~SL_WiMc1990"))
## Chaenodraco wilsoni
x <- bind_rows(x,alleq_tbl("234609_SL~OL_WiMc1990"),
alleq_tbl("234609_SL~OW_WiMc1990"),
alleq_tbl("234609_WW~SL_WiMc1990"))
## Champsocephalus gunnari
x <- bind_rows(x,alleq_tbl("234797_SL~OL_WiMc1990"),
alleq_tbl("234797_SL~OW_WiMc1990"),
alleq_tbl("234797_WW~SL_WiMc1990"))
## Channichthys rhinoceratus
x <- bind_rows(x,alleq_tbl("234619_SL~OL_WiMc1990"),
alleq_tbl("234619_SL~OW_WiMc1990"),
alleq_tbl("234619_WW~SL_WiMc1990"))
## Chionodraco hamatus
x <- bind_rows(x,alleq_tbl("234795_SL~OL_WiMc1990"),
alleq_tbl("234795_SL~OW_WiMc1990"),
alleq_tbl("234795_WW~SL_WiMc1990"))
## Chionodraco myersi
x <- bind_rows(x,alleq_tbl("234646_SL~OL_WiMc1990"),
alleq_tbl("234646_SL~OW_WiMc1990"),
alleq_tbl("234646_WW~SL_WiMc1990"))
## Cryodraco antarcticus
x <- bind_rows(x,alleq_tbl("234720_SL~OL_WiMc1990"),
alleq_tbl("234720_SL~OW_WiMc1990"),
alleq_tbl("234720_WW~SL_WiMc1990"))
## Paradiplospinus gracilis
x <- bind_rows(x,alleq_tbl("219693_SL~OL_WiMc1990"),
alleq_tbl("219693_SL~OW_WiMc1990"))##,
## alleq_tbl("219693_WW~SL_WiMc1990"))
warning("Paradiplospinus gracilis WW equation looks wrong, needs checking")
## ---
## Artigues 2003 equations
x <- bind_rows(x,alleq_tbl("234660_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234660M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234660F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234836_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234704_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234704M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234704F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234788_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234788M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234788F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234610_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234610M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234610F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234608_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234608M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234608F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("712788_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("712788M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("712788F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234754_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234754M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234754F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234772_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234770_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234770M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234770F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234828_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234644_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234644M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234644F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234709_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234709M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234709F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234665_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234665M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234665F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234615_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234615M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234615F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234592_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234592M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234592F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234817_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234817M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234817F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234621_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234621M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234621F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234696_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234696M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234696F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234790_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234826_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234730_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234730M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234730F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234611_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234837_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234816_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234816M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234816F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234834_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234834M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234834F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234808_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234808M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234808F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234800_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234800M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234800F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234777_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234777M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234777F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234799_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234799M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234799F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234720_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234720M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234720F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234725_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234725M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234725F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234609_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234797_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234797M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234797F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234650_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234650M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234650F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234795_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234795M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234795F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234646_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234646M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234646F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234678_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234678M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234678F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234614_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234685_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234796_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234695_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("217697_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234729_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234821_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234831_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234831M_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234831F_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234606_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("126486_WW~TL_Arti2003"))
x <- bind_rows(x,alleq_tbl("234675_WW~TL_Arti2003"))
## from Bush2005
x <- bind_rows(x, alleq_tbl("234610_WW~SL_Bush2005"),
alleq_tbl("234610_DW~SL_Bush2005"),
alleq_tbl("234595_WW~SL_Bush2005"),
alleq_tbl("234595_DW~SL_Bush2005"))
## misc fish
x <- bind_rows(x, alleq_tbl("234628_WW~TL_Dec_LaMe2000"),
alleq_tbl("234628_WW~TL_Feb_LaMe2000"))
x <- bind_rows(x, alleq_tbl("234700_WW~TL_Troc2020"), ## Dissostichus eleginoides
alleq_tbl("234626_WW~TL_Llom2020"), ## Harpagifer bispinus
alleq_tbl("234626_TL~age_Llom2020"))
## Pinkerton et al. 2013
x <- bind_rows(x, alleq_tbl("712470F_WW~TL_Pink2013"),
alleq_tbl("712470F_WW~PAL_Pink2013"),
alleq_tbl("712470M_WW~TL_Pink2013"),
alleq_tbl("712470M_WW~PAL_Pink2013"),
alleq_tbl("234606_WW~TL_Pink2013"),
alleq_tbl("234606_WW~PAL_Pink2013"),
alleq_tbl("234606_PAL~TL_Pink2013"),
alleq_tbl("234606_TL~PAL_Pink2013"),
alleq_tbl("712470F_PAL~TL_Pink2013"),
alleq_tbl("712470F_TL~PAL_Pink2013"),
alleq_tbl("712470M_PAL~TL_Pink2013"),
alleq_tbl("712470M_TL~PAL_Pink2013"),
alleq_tbl("234606M_TL~age_Pink2013"),
alleq_tbl("234606F_TL~age_Pink2013"),
alleq_tbl("712470M_TL~age_Pink2013"),
alleq_tbl("712470F_TL~age_Pink2013"))
## from LaMe2018
x <- bind_rows(x, alleq_tbl("234660F_WW~SL_LaMe2018"))
x <- bind_rows(x, alleq_tbl("234660M_WW~SL_LaMe2018"))
x <- bind_rows(x, alleq_tbl("234660_SL~OL_LaMe2018"))
## La Mesa et al 2020
x <- bind_rows(x, alleq_tbl("234720M_WW~TL_LaMe2020"),
alleq_tbl("234720F_WW~TL_LaMe2020"),
alleq_tbl("234720M_TL~age_LaMe2020"),
alleq_tbl("234720F_TL~age_LaMe2020"))
## Escobar-Flores et al 2020
x <- bind_rows(x, alleq_tbl("234631_WW~SL_EsFl2020"),
alleq_tbl("127286_WW~SL_EsFl2020"),
alleq_tbl("125819_WW~SL_EsFl2020"),
alleq_tbl("126194_WW~SL_EsFl2020"),
alleq_tbl("217719_WW~SL_EsFl2020"),
alleq_tbl("125832_WW~SL_EsFl2020"),
alleq_tbl("712788_WW~SL_EsFl2020"),
alleq_tbl("400296_WW~SL_EsFl2020"),
alleq_tbl("234695_WW~SL_EsFl2020"),
alleq_tbl("221503_WW~SL_EsFl2020"),
alleq_tbl("274968_WW~SL_EsFl2020"),
alleq_tbl("313344_WW~SL_EsFl2020"),
alleq_tbl("125825_WW~SL_EsFl2020"),
alleq_tbl("217704_WW~SL_EsFl2020"),
alleq_tbl("234641_WW~SL_EsFl2020"),
alleq_tbl("205276_WW~SL_EsFl2020"),
alleq_tbl("206941_WW~SL_EsFl2020"),
alleq_tbl("125821_WW~SL_EsFl2020"),
alleq_tbl("234638_WW~SL_EsFl2020"),
alleq_tbl("217697_WW~SL_EsFl2020"))
## ---
## Krill
x <- bind_rows(x,alleq_tbl("236217J_TL_Goeb2007"),
alleq_tbl("236217F_TL_Goeb2007"),
alleq_tbl("236217M_TL_Goeb2007"))
x <- bind_rows(x,alleq_tbl("236217_WW_Morr1988"))
x <- bind_rows(x,alleq_tbl("236217_WW_Hewi2004"))
## Mayz2003
x <- bind_rows(x, alleq_tbl("236219A_WW~TL_Mayz2003"),
alleq_tbl("236219J_WW~TL_Mayz2003"),
alleq_tbl("221054M_WW~TL_Mayz2003"),
alleq_tbl("221054F_WW~TL_Mayz2003"),
alleq_tbl("221054_LpW~WW_Mayz2003"),
alleq_tbl("236219F_LpW~WW_Mayz2003"),
alleq_tbl("236219M_LpW~WW_Mayz2003"),
alleq_tbl("236219J_LpW~WW_Mayz2003"))
## Farb1994
x <- bind_rows(x, alleq_tbl("236219_WW~TL_Farb1994"),
alleq_tbl("236219SA_WW~TL_Farb1994"),
alleq_tbl("236219A_WW~TL_Farb1994"),
alleq_tbl("236219M_WW~TL_Farb1994"),
alleq_tbl("236219F_WW~TL_Farb1994"),
alleq_tbl("236219SA_WW~CL_Farb1994"),
alleq_tbl("236219A_WW~CL_Farb1994"),
alleq_tbl("236219M_WW~CL_Farb1994"),
alleq_tbl("236219F_WW~CL_Farb1994"),
alleq_tbl("236217_WW~TL_Farb1994"),
alleq_tbl("236217SA_WW~TL_Farb1994"),
alleq_tbl("236217MI_WW~TL_Farb1994"),
alleq_tbl("236217MII_WW~TL_Farb1994"),
alleq_tbl("236217F_WW~TL_Farb1994"),
alleq_tbl("236217SF_WW~TL_Farb1994"),
alleq_tbl("236217SA_WW~CL_Farb1994"),
alleq_tbl("236217MI_WW~CL_Farb1994"),
alleq_tbl("236217MII_WW~CL_Farb1994"),
alleq_tbl("236217F_WW~CL_Farb1994"),
alleq_tbl("236217SF_WW~CL_Farb1994"))
## Melv2018
x <- bind_rows(x, alleq_tbl("236217F_TL~CL_Melv2018"),
alleq_tbl("236217M_TL~CL_Melv2018"))
x <- bind_rows(x, alleq_tbl("236216_TL~CL_PuJo1988"),
alleq_tbl("236217_TL~CL_PuJo1988"),
alleq_tbl("236219_ED~CL_FaMa2010"),
alleq_tbl("236219_ED~TL_FaMa2010"),
alleq_tbl("236219_ED~WW_FaMa2010"),
alleq_tbl("236219_CL~TL_FaMa2010"),
alleq_tbl("236219_WW~TL_FaMa2010"),
alleq_tbl("236219_WW~CL_FaMa2010"),
alleq_tbl("236219_LpWW~WW_FaMa2010"))
x <- bind_rows(x, alleq_tbl("236217SAJ_TL~CL_Farb1990"),
alleq_tbl("236217M1_TL~CL_Farb1990"),
alleq_tbl("236217M2_TL~CL_Farb1990"),
alleq_tbl("236217F_TL~CL_Farb1990"),
alleq_tbl("236219J_TL~CL_Farb1990"),
alleq_tbl("236219M_TL~CL_Farb1990"),
alleq_tbl("236219F_TL~CL_Farb1990"),
alleq_tbl("236219A_TL~CL_Farb1990"),
alleq_tbl("236219_TL~CL_Farb1990"))
## crustaceans
x <- bind_rows(x, alleq_tbl("369204_TL~CL_ArGo1991"),
alleq_tbl("369214_TL~CL_ArGo1991"),
alleq_tbl("515320_WW~TL_Rido1994"),
alleq_tbl("515320_WW~ED_Kuun1999"),
alleq_tbl("515320_DW~ED_Kuun1999"),
alleq_tbl("515320_AFDW~ED_Kuun1999"),
alleq_tbl("515320_WW~CL_Kuun1999"),
alleq_tbl("515320_DW~CL_Kuun1999"),
alleq_tbl("515320_AFDW~CL_Kuun1999"),
alleq_tbl("515320_WW~TL_Kuun1999"),
alleq_tbl("515320_CL~TL_Kuun1999"),
alleq_tbl("515320_ED~CL_Kuun1999"),
alleq_tbl("515320_DW~WW_Kuun1999"),
alleq_tbl("515320_AFDW~WW_Kuun1999"),
alleq_tbl("392346M_WW~CL_TaLo2006"),
alleq_tbl("392346F_WW~CL_TaLo2006"),
alleq_tbl("392346_WW~CL_TaLo2006"),
alleq_tbl("392346M_DW~CL_TaLo2006"),
alleq_tbl("392346F_DW~CL_TaLo2006"),
alleq_tbl("392346_DW~CL_TaLo2006"),
alleq_tbl("392886M_WW~CL_TaLo2006"),
alleq_tbl("392886F_WW~CL_TaLo2006"),
alleq_tbl("392886M_DW~CL_TaLo2006"),
alleq_tbl("392886F_DW~CL_TaLo2006"),
alleq_tbl("392346_TL~CL_TaLo2006"),
alleq_tbl("392346_ACW~CL_TaLo2006"),
alleq_tbl("392346_MCW~CL_TaLo2006"),
alleq_tbl("392346_RBW~CL_TaLo2006"),
alleq_tbl("392346_RL~CL_TaLo2006"),
alleq_tbl("392886_TL~CL_TaLo2006"),
alleq_tbl("392886_ACW~CL_TaLo2006"),
alleq_tbl("392886_MCW~CL_TaLo2006"),
alleq_tbl("392886_RBW~CL_TaLo2006"),
alleq_tbl("392886_RL~CL_TaLo2006"))
## ---
## Miscellaneous others
##
## Leptonychotes weddellii
x <- bind_rows(x,alleq_tbl("195932_WW_GaBu1988"))
## Chorismus antarcticus
x <- bind_rows(x,alleq_tbl("369214_WW_Lake2003"))
## also applicable to Notocrangon antarcticus
x <- bind_rows(x,alleq_tbl("369214_WW_Lake2003",
with_id="369204_WW_Lake2003",
taxon_name="Notocrangon antarcticus",
taxon_aphia_id=369204,
notes="Uses equation developed by Lake et al. for Chorismus antarcticus but noted as also applicable to Notocrangon antarcticus"))
## Tremtomus newnesi
x <- bind_rows(x,alleq_tbl("234628_WW~SL_EaDe1997"))
## energetics
## Electrona antarctica
x <- bind_rows(x,alleq_tbl("217697_EDDW~SL_VanD2006"),
alleq_tbl("217697_EDWW~SL_VanD2006"),
alleq_tbl("217697_EDDW~WW_VanD2006"),
alleq_tbl("217697_EDWW~WW_VanD2006"),
alleq_tbl("217697_EDDW~DW_VanD2006"),
alleq_tbl("217697_EDWW~DW_VanD2006"))
## Aethotaxis mitopteryx
x <- bind_rows(x,alleq_tbl("234660_LpDW~SL_FrHa1994"))
x <- bind_rows(x,alleq_tbl("234660_LpDW~WW_FrHa1994"))
x <- bind_rows(x,alleq_tbl("234660_WC~LpWW_FrHa1994"))
## Pleuragramma antarcticum 234721, proper name is Pleuragramma antarctica
x <- bind_rows(x,alleq_tbl("234721_LpDW~SL_FrHa1994"),
alleq_tbl("234721_WC~LpWW_FrHa1994"))
## Trematomus lepidorhinus
x <- bind_rows(x,alleq_tbl("234770_LpDW~SL_FrHa1994"),
alleq_tbl("234770_WC~LpWW_FrHa1994"))
## Bathydraco marri
x <- bind_rows(x,alleq_tbl("234816_WC~LpWW_FrHa1994"))
## Dolloidraco longedorsalis
x <- bind_rows(x,alleq_tbl("234696_WC~LpWW_FrHa1994"))
## from Vane2005
x <- bind_rows(x,alleq_tbl("234725_WW~TL_Vane2005"),
alleq_tbl("234725_TEC~TL_Vane2005"),
alleq_tbl("234797_WW~TL_Vane2005"),
alleq_tbl("234797_TEC~TL_Vane2005"),
alleq_tbl("234667_WW~TL_Vane2005"),
alleq_tbl("234667_TEC~TL_Vane2005"),
alleq_tbl("234678_WW~TL_Vane2005"),
alleq_tbl("234678_TEC~TL_Vane2005"),
alleq_tbl("234704_WW~TL_Vane2005"),
alleq_tbl("234704_TEC~TL_Vane2005"),
alleq_tbl("234700_WW~TL_Vane2005"),
alleq_tbl("234700_TEC~TL_Vane2005"),
alleq_tbl("313344_WW~TL_Vane2005"),
alleq_tbl("313344_TEC~TL_Vane2005"))
## from Dubi2012
x <- bind_rows(x, alleq_tbl("266542_WW~OAL_summer_Dubi2012"),
alleq_tbl("266545_WW~OAL_summer_Dubi2012"),
alleq_tbl("266542_WW~OAL_autumn_Dubi2012"),
alleq_tbl("266545_WW~OAL_autumn_Dubi2012"),
alleq_tbl("266542_WW~OAL_winter_Dubi2012"),
alleq_tbl("266545_WW~OAL_winter_Dubi2012"),
alleq_tbl("266542_DW~OAL_summer_Dubi2012"),
alleq_tbl("266545_DW~OAL_summer_Dubi2012"),
alleq_tbl("266542_DW~OAL_autumn_Dubi2012"),
alleq_tbl("266545_DW~OAL_autumn_Dubi2012"),
alleq_tbl("266542_DW~OAL_winter_Dubi2012"),
alleq_tbl("266545_DW~OAL_winter_Dubi2012"),
alleq_tbl("266542_CW~OAL_summer_Dubi2012"),
alleq_tbl("266545_CW~OAL_summer_Dubi2012"),
alleq_tbl("266545_CW~OAL_autumn_Dubi2012"),
alleq_tbl("266542_CW~OAL_winter_Dubi2012"),
alleq_tbl("266545_CW~OAL_winter_Dubi2012"),
alleq_tbl("137217_LpW~OAL_Dubi2012")
)
## from AhSh1998
x <- bind_rows(x, alleq_tbl("197217_AFDW~SHL_AhSh1998"),
alleq_tbl("197217_OCR~AFDW_AhSh1998"))
## from UrMe1998
x <- bind_rows(x, alleq_tbl("197217_SFDW~SHL_UrMe1998"),
alleq_tbl("197217_SFDW~SHL_postspawn_UrMe1998"),
alleq_tbl("197217_AFDW~SHL_UrMe1998"),
alleq_tbl("197217_AFDW~SFDW_UrMe1998"),
alleq_tbl("197217_SL~age_UrMe1998"))
## East2019
temp <- lapply(alleq_East2019(), function(z) alleq_tbl(thiseq = z)) ## all equations from this source
x <- bind_rows(x, bind_rows(temp))
x
}
allometric_equations <- build_allometry_df()
## todo: check each row that taxon_name and taxon_aphia_id match (or are expected mismatches, at least)
## todo: move these tests to testthat
## check worrms aphia_id
## unique ids
assert_that(!any(duplicated(allometric_equations$equation_id)))
## unique rows
## check that all eqs return a tibble/df with a_v col at least
chk <- vapply(seq_len(nrow(allometric_equations)),function(z) {
tmp <- allometric_equations[z,]$equation[[1]](0)
is.data.frame(tmp) && "allometric_value" %in% names(tmp)},
FUN.VALUE=TRUE)
assert_that(all(chk))
## more checks
assert_that(all(grepl("WW",allometric_equations$equation_id[allometric_equations$return_property=="wet weight"])))
assert_that(all(grepl("ML",allometric_equations$equation_id[allometric_equations$return_property=="mantle length"])))
## check that masses look ok
idx <- grepl("WiMc1990", allometric_equations$equation_id) & allometric_equations$return_property == "wet weight" & vapply(seq_len(nrow(allometric_equations)), function(z) identical(allometric_equations[z, ]$inputs[[1]]$property, "standard length"), FUN.VALUE = TRUE)
tmp <- vapply(which(idx),function(z) allometric_equations[z, ]$equation[[1]](100)$allometric_value,FUN.VALUE = 1)
assert_that(!any(abs(tmp)<1 | abs(tmp)>50))
## SL from OL
idx <- grepl("WiMc1990", allometric_equations$equation_id) & allometric_equations$return_property == "standard length" & vapply(seq_len(nrow(allometric_equations)), function(z) identical(allometric_equations[z, ]$inputs[[1]]$property, "otolith length"), FUN.VALUE = TRUE)
tmp <- vapply(which(idx),function(z)allometric_equations[z, ]$equation[[1]](4)$allometric_value,FUN.VALUE = 1)
assert_that(!any(abs(tmp)<50 | abs(tmp)>500))
## SL from OW
idx <- grepl("WiMc1990",allometric_equations$equation_id) & allometric_equations$return_property=="standard length" & vapply(seq_len(nrow(allometric_equations)),function(z) identical(allometric_equations[z,]$inputs[[1]]$property, "otolith width"), FUN.VALUE=TRUE)
tmp <- vapply(which(idx),function(z)allometric_equations[z,]$equation[[1]](4)$allometric_value,FUN.VALUE = 1)
assert_that(!any(abs(tmp)<50 | abs(tmp)>1000))
## taxonomy check
utn <- allometric_equations %>% mutate(noted_invalid = grepl("Accepted taxon name is", .data$notes)) %>% distinct(.data$taxon_name, .data$taxon_aphia_id, .data$noted_invalid) %>% dplyr::arrange(.data$taxon_name)
if (any(duplicated(utn$taxon_name))) stop("There must be at least one invalid taxon that is not noted as invalid")
chk <- utn %>% rowwise %>% mutate(taxon_aphia_id_new = { tmp <- search_worms(.data$taxon_name); if (nrow(tmp) == 1) tmp$AphiaID else NA_integer_ }) %>% ungroup %>% as.data.frame
##chk %>% dplyr::filter(.data$taxon_aphia_id != .data$taxon_aphia_id_new | is.na(.data$taxon_aphia_id_new)) %>% count(.data$taxon_name, .data$taxon_aphia_id, .data$noted_invalid, .data$taxon_aphia_id_new)
chk %>% dplyr::filter(.data$taxon_aphia_id != .data$taxon_aphia_id_new | is.na(.data$taxon_aphia_id_new)) %>% count(.data$taxon_name, .data$taxon_aphia_id, .data$noted_invalid, .data$taxon_aphia_id_new) %>% dplyr::filter(!noted_invalid)
## usethis::use_data(allometric_equations, internal = FALSE, overwrite = TRUE)
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