# import temperature preference parameters
library(tidyverse)
taxa.temperature.prefs <- readr::read_delim("data-raw/temperature-parameters.csv", delim = ";") %>%
dplyr::mutate(Tmin = ifelse(is.na(Tmin), -Inf, Tmin),
Tmax = ifelse(is.na(Tmax), Inf, Tmax),
ID = paste(Taxon, Source, sep = " "))
#usethis::use_data(taxa.temperature.prefs, overwrite = T)
l09_cnsts_dic <- list(sacculifer = c(0.3, 2155, 289.3, 304.4, 94385, 171209),
bulloides = c(0.25, 6482, 280, 298.5, 295374, 159618),
pachy_d = c(0.13, 6584, 277.8, 293.7, 300239, 110583),
siphonifera = c(0.17, 7105, 284.9, 301.8, 349991, 130852),
universa = c(0.23, 626, 289.8, 304, 30953, 249412),
pachy_s = c(0.37, 6584, 999, 279.8, 0, 59491),
dutertrei = c(0.1, 6876, 280.1, 298.8, 210746, 57855),
ruber = c(0.24, 1086, 292.3, 303.4, 53765, 165490))
l09_maxgrowth_dic <- list(sacculifer = 0.369316159643382, bulloides = 0.317097315352481,
siphonifera = 0.279187426094619, pachy_d = 0.109441954385795,
universa = 0.240849035558603, pachy_s = 0.0488642301133836,
dutertrei = 0.109516330927052, ruber = 0.260441142387609)
# Calibration parameters
## MgCa
### Create table combining estimates vcov matrices with publishd parameters from Anand et al. 2003
MgCa.foram.pars <- climproxycalibration::MgCa.foram.pars
tbl3 <- climproxycalibration::anand.table.3
MgCa.foram.pars.df <- plyr::ldply(MgCa.foram.pars, function(x) {
data.frame(slope = x$means[1],
intercept = x$means[2],
vcov = I(list(x$vcov)))}
, .id = "Species") %>%
mutate(Species = as.character(Species))
MgCa.foram.pars.df[1, "Species"] <- "Ten planktonic species_350-500"
MgCa.foram.pars.Anand <- left_join(MgCa.foram.pars.df, tbl3[c(1, 22:36),], by = "Species") %>%
tbl_df() %>%
rename(calibration = Species) %>%
mutate(calibration.type = "MgCa") %>%
mutate(slope = ifelse(is.na(A), slope, A),
intercept = ifelse(is.na(B), intercept, log(B))) %>%
select(calibration.type, calibration, slope, intercept, vcov, Notes)
Uk37.pars.df <- tibble(
calibration.type = "Uk37",
calibration = "Mueller global",
slope = 0.033,
intercept = 0.044,
vcov = list(structure(
structure(c(1.46053818728255e-07, -2.80815422746781e-06,
-2.80815422746781e-06, 6.06536807458765e-05),
.Dim = c(2L, 2L)),
.Dimnames = list(c("slope", "intercept"),
c("slope", "intercept"))
)))
calibration.parameters <- bind_rows(MgCa.foram.pars.Anand, Uk37.pars.df)
# Uk37.pars <- list(mueller.uk37 = structure(list(
# means = structure(
# # Set to Eq. 30, Table 1. Müller et al (1998)
# c(0.033, 0.044),
# .Names = c("slope", "intercept")
# ),
# vcov = structure(
# structure(c(1.46053818728255e-07, -2.80815422746781e-06,
# -2.80815422746781e-06, 6.06536807458765e-05),
# .Dim = c(2L, 2L)),
# .Dimnames = list(c("slope", "intercept"),
# c("slope", "intercept"))
# )
# ),
# .Names = c("means", "vcov")))
# CalibrationParameters <- list(MgCa = climproxycalibration::MgCa.foram.pars,
# Uk37 = Uk37.pars)
#devtools::use_data(Uk37.pars, overwrite == TRUE)
#devtools::use_data(MgCa.foram.pars, overwrite == TRUE)
#usethis::use_data(calibration.parameters, overwrite == TRUE)
#usethis::use_data(CalibrationParameters, overwrite == TRUE)
usethis::use_data(calibration.parameters, taxa.temperature.prefs, l09_cnsts_dic, l09_maxgrowth_dic,
internal = TRUE, overwrite = TRUE)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.