diff --git a/articles/bootstrapped_clumped_calibration.html b/articles/bootstrapped_clumped_calibration.html index e5eea82..d1baee0 100644 --- a/articles/bootstrapped_clumped_calibration.html +++ b/articles/bootstrapped_clumped_calibration.html @@ -93,9 +93,11 @@ theme_set(theme_bw()) library(clumpedcalib) set.seed(123) +
+

Bootstrapped York regression +

-

load calibration data and calculate bootstrapped York -regression +

load calibration data

Here I show this with a very small artificial set of calibration data. Be sure to replace with your own!

@@ -115,9 +117,13 @@

load c # or if you have your data saved as an CSV ## raw <- readr::read_csv("dat/example_calib.csv", -## col_names = c("X", "D47", "sd_X", "sd_D47")) - -# this is very much a toy example with only 100 bootstraps! +## col_names = c("X", "D47", "sd_X", "sd_D47"))

+
+
+

calculate bootstrapped York regression +

+
+# this is very much a toy example with only 100 bootstraps!
 calib <- clumped_calib_boot(raw, Nsim = 100) #|>
   # for the real deal, increase Nsim to something like 1e5 and save the results
   # for re-use
@@ -125,7 +131,7 @@ 
load c
 
 # then you can read these stored results like so:
 ## calib <- readr::read_csv("calib_clumped_boot.csv")
-
+
 raw |>
   ggplot(aes(x = X, y = D47)) +
   labs(x = 10^6 / T^2 ~ "(K)", y = Delta[47] ~ "(I-CDES)") +
@@ -143,11 +149,15 @@ 
load c
               alpha = .2, data = calib)
+
+
+

Apply it to your data +

load sample data

I’ve come up with some fake replicate-level data.

-
+
 dat <- tibble::tribble(
   ~ age, ~ bins, ~ d18O_PDB_vit, ~ d13C_PDB_vit, ~ D47_final, ~ outlier, ~ identifier_1, ~ broadid,
   15.2,1,12,13,0.6,FALSE,"smp1","other",
@@ -169,15 +179,11 @@ 
load sample data

 

 

-
calculate bootstrapped means and apply the temperature
-calibration
+
just give me the results!
 

-

-
just give me the results!
-

 
This is a simple wrapper function to quickly get the end result. If
 you want more control, see below.

-
+
 # calculate other "normal" summary stats if desired, like N
 oth <- dat |>
   group_by(bins) |>
@@ -201,7 +207,7 @@ 
just give me the results!#> Caused by warning in `sqrt()`:
 #> ! NaNs produced
 #> Joining with `by = join_by(bins)`

-
+
 # make a plot
 sum |>
   ggplot(aes(x = age, y = temp)) +
@@ -211,9 +217,9 @@ 
just give me the results!  geom_text(aes(label = paste("N =", n)), nudge_x = 1.5)

 

 

-

-
individual functions
-

+

+
more control
+

 
If you want to have more control, I recommend not using the above
 wrapper function, but in stead take it one step at a time:

 
    
@@ -235,7 +241,7 @@ 
    individual functions.
    
-
    +
     sim <- dat |>
   filter_outliers(group = bins) |>
   bootstrap_means(group = bins, # specify which columns to use
@@ -257,13 +263,9 @@ 
    individual functions#> ℹ In group 2: `bins = 2`.
 #> Caused by warning in `sqrt()`:
 #> ! NaNs produced
    
-
    
-

-

-
acknowledgements
-

 
We would like to thank Alvaro Fernandez for writing and sharing the
 Matlab code that inspired this R package.

+

 

   
diff --git a/pkgdown.yml b/pkgdown.yml
index f068e4b..f06e1c5 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   bootstrapped_clumped_calibration: bootstrapped_clumped_calibration.html
-last_built: 2024-01-30T21:07Z
+last_built: 2024-01-30T21:13Z
 urls:
   reference: https://japhir.github.io/clumpedcalib/reference
   article: https://japhir.github.io/clumpedcalib/articles
diff --git a/search.json b/search.json
index c31cc7c..4aa0dd1 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
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Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see . GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read .","code":" Copyright (C)     This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see .   Copyright (C)    This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://japhir.github.io/clumpedcalib/articles/bootstrapped_clumped_calibration.html","id":"load-calibration-data-and-calculate-bootstrapped-york-regression","dir":"Articles","previous_headings":"","what":"load calibration data and calculate bootstrapped York regression","title":"Bootstraped Clumped Isotope Calibration","text":"show small artificial set calibration data. sure replace ! column names must identical X, D47, sd_X, sd_D47.","code":"raw <- tibble::tribble(   ~ X, ~ D47, ~ sd_X, ~ sd_D47,   11.25,0.607,0.062,0.007,   11.26,0.602,0.070,0.006,   11.26,0.603,0.069,0.005,   11.60,0.604,0.068,0.005,   12.81,0.674,0.091,.004,   13.28,0.672,0.092,0.012,   13.05,0.670,0.093,0.003,   )  # or if you have your data saved as an CSV ## raw <- readr::read_csv(\"dat/example_calib.csv\", ##                 col_names = c(\"X\", \"D47\", \"sd_X\", \"sd_D47\"))  # this is very much a toy example with only 100 bootstraps! calib <- clumped_calib_boot(raw, Nsim = 100) #|>   # for the real deal, increase Nsim to something like 1e5 and save the results   # for re-use   ## readr::write_csv(glue::glue(\"calib_clumped_boot.csv\"))  # then you can read these stored results like so: ## calib <- readr::read_csv(\"calib_clumped_boot.csv\") raw |>   ggplot(aes(x = X, y = D47)) +   labs(x = 10^6 / T^2 ~ \"(K)\", y = Delta[47] ~ \"(I-CDES)\") +   scale_x_continuous(sec.axis = sec_axis(     \"Temperature (°C)\",     trans = \\(x) sqrt(1e6 / x) - 273.15,     breaks = seq(0, 30, 5))) +   geom_point() +   geom_errorbar(aes(xmin = X - sd_X, xmax = X + sd_X)) +   geom_errorbar(aes(ymin = D47 - sd_D47, ymax = D47 + sd_D47)) +   # for now just draw all the lines since we're only sampling a few   # setting alpha lower allows you to overplot the draws   # don't forget to subset to just a few 100 though, otherwise it will be slow   geom_abline(aes(slope = slope, intercept = intercept),               alpha = .2, data = calib)"},{"path":"https://japhir.github.io/clumpedcalib/articles/bootstrapped_clumped_calibration.html","id":"load-sample-data","dir":"Articles","previous_headings":"","what":"load sample data","title":"Bootstraped Clumped Isotope Calibration","text":"’ve come fake replicate-level data.","code":"dat <- tibble::tribble(   ~ age, ~ bins, ~ d18O_PDB_vit, ~ d13C_PDB_vit, ~ D47_final, ~ outlier, ~ identifier_1, ~ broadid,   15.2,1,12,13,0.6,FALSE,\"smp1\",\"other\",   15.4,1,8,9,0.61,FALSE,\"smp1\",\"other\",   15.7,1,9,15,0.599,FALSE,\"smp2\",\"other\",   33.2,2,12,13,0.62,FALSE,\"smp3\",\"other\",   33.7,2,8,9,0.65,FALSE,\"smp4\",\"other\",   33.6,2,8,14,0.67,FALSE,\"smp5\",\"other\",   33.9,2,9,15,0.63,FALSE,\"smp5\",\"other\", )  # You can save your data to a CSV with the same column names and load it like so: ## dat <- readr::read_csv(\"fake_data.csv\")  pl_raw <- dat |>   ggplot(aes(x = age, y = D47_final, colour = factor(bins))) +   geom_point() pl_raw"},{"path":[]},{"path":"https://japhir.github.io/clumpedcalib/articles/bootstrapped_clumped_calibration.html","id":"just-give-me-the-results","dir":"Articles","previous_headings":"calculate bootstrapped means and apply the temperature calibration","what":"just give me the results!","title":"Bootstraped Clumped Isotope Calibration","text":"simple wrapper function quickly get end result. want control, see .","code":"# calculate other \"normal\" summary stats if desired, like N oth <- dat |>   group_by(bins) |>   summarize(n = n())  # calculate d18Osw and temp median and quantile interval sum <- apply_calib_and_d18O_boot(data = dat,                                  calib = calib,                                  group = bins,                                  Nsim = 100,                                  output = \"summary\") |>   # add N back in   left_join(oth) #> filter: no rows removed #> filter: no rows removed #> filter: no rows removed #> Warning: There was 1 warning in `dplyr::mutate()`. #> ℹ In argument: `d18Osw = d18Osw_calc(d18Occ = d18O, temp = temp, equation = #>   equation)`. #> ℹ In group 2: `bins = 2`. #> Caused by warning in `sqrt()`: #> ! NaNs produced #> Joining with `by = join_by(bins)` # make a plot sum |>   ggplot(aes(x = age, y = temp)) +   ggdist::geom_pointinterval(aes(ymin = temp.lower, ymax = temp.upper,                                  linewidth = factor(.width))) +   scale_linewidth_manual(values = c(\"0.68\" = 9, \"0.95\" = 2), guide = \"none\") +   geom_text(aes(label = paste(\"N =\", n)), nudge_x = 1.5)"},{"path":"https://japhir.github.io/clumpedcalib/articles/bootstrapped_clumped_calibration.html","id":"individual-functions","dir":"Articles","previous_headings":"calculate bootstrapped means and apply the temperature calibration","what":"individual functions","title":"Bootstraped Clumped Isotope Calibration","text":"want control, recommend using wrapper function, stead take one step time: filter_outliers(): says tin. bootstrap_means(): Calculate bootstrapped means sample bins. temp_d18Osw_calc(): Apply temperature calibration use clumped-derived temperature d18Occ–d18Osw–temperature relationship calculate d18Osw. our_summary(): Summarize calculating median 68% 95% confidence intervals mean. can overwrite filter_outliers() filtering function comment already cleaned data. assumes ’s logical column outlier character column broadid samples equal \"\".","code":"sim <- dat |>   filter_outliers(group = bins) |>   bootstrap_means(group = bins, # specify which columns to use                   age = age,                   d13C = d13C_PDB_vit,                   d18O = d18O_PDB_vit,                   D47 = D47_final,                   # obviously set Nsim way higher for real data!                   Nsim = 100) |>   # you can choose several d18Occ--d18Osw--temperature equations, see `equations_supported()`.   temp_d18Osw_calc(calib = calib, equation = \"KimONeil1997\", Nsim = 100) |>   our_summary(group = bins) #> filter: no rows removed #> filter: no rows removed #> filter: no rows removed #> Warning: There was 1 warning in `dplyr::mutate()`. #> ℹ In argument: `d18Osw = d18Osw_calc(d18Occ = d18O, temp = temp, equation = #>   equation)`. #> ℹ In group 2: `bins = 2`. #> Caused by warning in `sqrt()`: #> ! NaNs produced"},{"path":"https://japhir.github.io/clumpedcalib/articles/bootstrapped_clumped_calibration.html","id":"acknowledgements","dir":"Articles","previous_headings":"","what":"acknowledgements","title":"Bootstraped Clumped Isotope Calibration","text":"like thank Alvaro Fernandez writing sharing Matlab code inspired R package.","code":""},{"path":"https://japhir.github.io/clumpedcalib/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Ilja Kocken. Author, maintainer.","code":""},{"path":"https://japhir.github.io/clumpedcalib/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Kocken (2024). clumpedcalib: Calculate Apply Clumped Isotope Calibrations Using Bootstrapping. R package version 0.0.0.9000, https://japhir.github.io/clumpedcalib/.","code":"@Manual{,   title = {clumpedcalib: Calculate and Apply Clumped Isotope Calibrations Using Bootstrapping},   author = {Ilja Kocken},   year = {2024},   note = {R package version 0.0.0.9000},   url = {https://japhir.github.io/clumpedcalib/}, }"},{"path":"https://japhir.github.io/clumpedcalib/index.html","id":"clumpedcalib-calculate-and-apply-clumped-isotope-calibrations-using-bootstrapping","dir":"","previous_headings":"","what":"Calculate and Apply Clumped Isotope Calibrations Using Bootstrapping","title":"Calculate and Apply Clumped Isotope Calibrations Using Bootstrapping","text":"Written Ilja J. Kocken Feel free use stuff, long adhere file:LICENSE.md NOTE: just method use, ’m publishing actual calibration dataset ’m using ! Calculate bootstrapped York regression clumped isotope calibration data. clumped_calib_boot(). Calculate bootstrapped sample means age, d13C, d18O, D47. bootstrap_means(). Apply bootstrapped calibration calculate temperature d18Osw. temp_d18Osw_calc(). Summarize bootstrapped values calculate 68 95% CIs. our_summary(). Also comes classic d18Occ calibrations. See temp_calc(). well inverses, constraints temperature wish calculate d18Osw. See d18Osw_calc().","code":""},{"path":"https://japhir.github.io/clumpedcalib/index.html","id":"how-to-calculate-bootstrapped-averages-and-apply-a-clumped-isotope-specific-temperature-calibration","dir":"","previous_headings":"","what":"How to calculate bootstrapped averages and apply a clumped-isotope specific temperature calibration.","title":"Calculate and Apply Clumped Isotope Calibrations Using Bootstrapping","text":"use : Install package clumpedcalib, see #installation. Update input calibration data file:dat/example_calib.csv. Make sure column names include X, D47, sd_X, sd_D47. Add sample data replicate level. Check see like function calculates d18Osw. Currently, defaults Kim & O'Neil 1997 calibration, adjusted Bemis et al., 1998. want use wrapper function: create definition filter outliers filters bad measurements NA's data. Use wrapper function apply_calib_and_d18O_boot(), better yet: Walk example workflow step--step apply bulletpoint functions one--one. look functions better understand ’s happening. bootstrapped calibration idea based Matlab script written Alvaro Fernandez.","code":""},{"path":"https://japhir.github.io/clumpedcalib/index.html","id":"installation","dir":"","previous_headings":"","what":"installation","title":"Calculate and Apply Clumped Isotope Calibrations Using Bootstrapping","text":"install development package: can look functions copy like.","code":"remotes::install_github(\"japhir/clumpedcalib\")"},{"path":"https://japhir.github.io/clumpedcalib/reference/apply_calib_and_d18O_boot.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate bootstrapped means with temperature and d18Osw — apply_calib_and_d18O_boot","title":"Calculate bootstrapped means with temperature and d18Osw — apply_calib_and_d18O_boot","text":"age, d18O, d13C, D47, calculate temperature d18Osw.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/apply_calib_and_d18O_boot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate bootstrapped means with temperature and d18Osw — apply_calib_and_d18O_boot","text":"","code":"apply_calib_and_d18O_boot(   data,   calib,   group,   output = \"summary\",   equation = NULL,   Nsim = NULL )"},{"path":"https://japhir.github.io/clumpedcalib/reference/apply_calib_and_d18O_boot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate bootstrapped means with temperature and d18Osw — apply_calib_and_d18O_boot","text":"data dataframe columns outlier, broadid calib dataframe draws bootstrapped (Bayesian) temperature regression. columns slope intercept. group Column name groups. output Character vector specifying whether return \"summary\" \"raw\" bootstrapped samples. equation Character vector equation use. Defaults Kim & O'Neil, 1997. Nsim number bootstraps want run. Defaults number rows calib.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/bootstrap_means.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate bootstrapped means for each group in a dataframe — bootstrap_means","title":"Calculate bootstrapped means for each group in a dataframe — bootstrap_means","text":"Calculate bootstrapped means group dataframe","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/bootstrap_means.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate bootstrapped means for each group in a dataframe — bootstrap_means","text":"","code":"bootstrap_means(data, group, age, d13C, d18O, D47, Nsim = 1e+05)"},{"path":"https://japhir.github.io/clumpedcalib/reference/bootstrap_means.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate bootstrapped means for each group in a dataframe — bootstrap_means","text":"data dataframe tibble columns outlier, broadid (\"\" samples), D47_final, d18O_PDB_vit, d13C_PDB_vit, grouping column. group column name data character factor column contains binning information want calculate bootstrapped averages . age column name data sample ages. d13C column name data carbon isotope values. d18O column name data oxygen isotope values. D47 column name data clumped isotope values. Nsim number bootstraps want run. Defaults number rows calib.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/bootstrap_means.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate bootstrapped means for each group in a dataframe — bootstrap_means","text":"tibble bootstrapped slope-intercept pair.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/clumped_calib_boot.html","id":null,"dir":"Reference","previous_headings":"","what":"Bootstrapped clumped isotope calibration — clumped_calib_boot","title":"Bootstrapped clumped isotope calibration — clumped_calib_boot","text":"Bootstrapped clumped isotope calibration","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/clumped_calib_boot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Bootstrapped clumped isotope calibration — clumped_calib_boot","text":"","code":"clumped_calib_boot(data, Nsim = 1e+05)"},{"path":"https://japhir.github.io/clumpedcalib/reference/clumped_calib_boot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Bootstrapped clumped isotope calibration — clumped_calib_boot","text":"data data.frame columns D47, X, sd_X, sd_D47. X stands commonly-used temperature scale, 10^6 / T^2 T K. Nsim Number simulations bootstrapping.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/clumped_calib_boot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Bootstrapped clumped isotope calibration — clumped_calib_boot","text":"tibble bootstrapped slope--intercept pairs.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/clumpedcalib-package.html","id":null,"dir":"Reference","previous_headings":"","what":"clumpedcalib: Calculate and Apply Clumped Isotope Calibrations Using Bootstrapping — clumpedcalib-package","title":"clumpedcalib: Calculate and Apply Clumped Isotope Calibrations Using Bootstrapping — clumpedcalib-package","text":"Calculate bootstrapped York regression clumped isotope calibration data. Calculate bootstrapped sample means age, d13C, d18O, D47. Apply bootstrapped calibration calculate temperature d18Osw.","code":""},{"path":[]},{"path":"https://japhir.github.io/clumpedcalib/reference/clumpedcalib-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"clumpedcalib: Calculate and Apply Clumped Isotope Calibrations Using Bootstrapping — clumpedcalib-package","text":"Maintainer: Ilja Kocken .j.kocken@uu.nl (ORCID)","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/d18Osw_calc.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate the d18Osw from the d18Occ and temperature — d18Osw_calc","title":"Calculate the d18Osw from the d18Occ and temperature — d18Osw_calc","text":"Defaults Kim & O'neil 1997 modified Bemis et al., 1998.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/d18Osw_calc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate the d18Osw from the d18Occ and temperature — d18Osw_calc","text":"","code":"d18Osw_calc(d18Occ, temperature, equation = NULL)"},{"path":"https://japhir.github.io/clumpedcalib/reference/d18Osw_calc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate the d18Osw from the d18Occ and temperature — d18Osw_calc","text":"d18Occ oxygen isotope composition carbonate VPDB. temperature formation temperature (°C). equation Character vector equation use. Defaults Kim & O'Neil, 1997.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/d18Osw_calc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate the d18Osw from the d18Occ and temperature — d18Osw_calc","text":"oxygen isotope composition sea water VSMOW.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/d18Osw_calc.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate the d18Osw from the d18Occ and temperature — d18Osw_calc","text":"Shackleton, N. J. (1974). Attainment isotopic equilibrium ocean water benthic foraminifera genus Uvigerina: Isotopic changes ocean last glacial. Colloques Internationaux Du CNRS, 219, 203–209. Erez, J., & Luz, B. (1983). Experimental paleotemperature equation planktonic foraminifera. Geochimica et Cosmochimica Acta, 47(6), 1025–1031. https://doi.org/10.1016/0016-7037(83)90232-6 Kim, S.-T., & O’Neil, J. R. (1997). Equilibrium nonequilibrium oxygen isotope effects synthetic carbonates. Geochimica et Cosmochimica Acta, 61(16), 3461–3475. https://doi.org/10.1016/S0016-7037(97)00169-5 Bemis, B. E., Spero, H. J., Bijma, J., & Lea, D. W. (1998). Reevaluation oxygen isotopic composition planktonic foraminifera: Experimental results revised paleotemperature equations. Paleoceanography, 13(2), 150–160. https://doi.org/10.1029/98PA00070 Marchitto, T. M., Curry, W. B., Lynch-Stieglitz, J., Bryan, S. P., Cobb, K. M., & Lund, D. C. (2014). Improved oxygen isotope temperature calibrations cosmopolitan benthic foraminifera. Geochimica et Cosmochimica Acta, 130, 1–11. https://doi.org/10.1016/j.gca.2013.12.034","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/d18Osw_calc.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate the d18Osw from the d18Occ and temperature — d18Osw_calc","text":"Ilja J. Kocken","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/d18Osw_calc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate the d18Osw from the d18Occ and temperature — d18Osw_calc","text":"","code":"d18Osw_calc(3, 2, \"KimONeil1997\") #> [1] 0.02724298"},{"path":"https://japhir.github.io/clumpedcalib/reference/equation_supported.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if the provided equation is supported — equation_supported","title":"Check if the provided equation is supported — equation_supported","text":"Also parses equation name internal simplified code. See supported_equations() References equations currently supported.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/equation_supported.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if the provided equation is supported — equation_supported","text":"","code":"equation_supported(equation)"},{"path":"https://japhir.github.io/clumpedcalib/reference/equation_supported.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if the provided equation is supported — equation_supported","text":"equation Character vector equation reference. Must one supported_equations().","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/equation_supported.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if the provided equation is supported — equation_supported","text":"Character vector cleaned equation reference. Gives error currently supported.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/equation_supported.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Check if the provided equation is supported — equation_supported","text":"Shackleton, N. J. (1974). Attainment isotopic equilibrium ocean water benthic foraminifera genus Uvigerina: Isotopic changes ocean last glacial. Colloques Internationaux Du CNRS, 219, 203–209. Erez, J., & Luz, B. (1983). Experimental paleotemperature equation planktonic foraminifera. Geochimica et Cosmochimica Acta, 47(6), 1025–1031. https://doi.org/10.1016/0016-7037(83)90232-6 Kim, S.-T., & O’Neil, J. R. (1997). Equilibrium nonequilibrium oxygen isotope effects synthetic carbonates. Geochimica et Cosmochimica Acta, 61(16), 3461–3475. https://doi.org/10.1016/S0016-7037(97)00169-5 Bemis, B. E., Spero, H. J., Bijma, J., & Lea, D. W. (1998). Reevaluation oxygen isotopic composition planktonic foraminifera: Experimental results revised paleotemperature equations. Paleoceanography, 13(2), 150–160. https://doi.org/10.1029/98PA00070 Marchitto, T. M., Curry, W. B., Lynch-Stieglitz, J., Bryan, S. P., Cobb, K. M., & Lund, D. C. (2014). Improved oxygen isotope temperature calibrations cosmopolitan benthic foraminifera. Geochimica et Cosmochimica Acta, 130, 1–11. https://doi.org/10.1016/j.gca.2013.12.034","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/filter_outliers.html","id":null,"dir":"Reference","previous_headings":"","what":"Filter clumped isotope outliers — filter_outliers","title":"Filter clumped isotope outliers — filter_outliers","text":"Filter clumped isotope outliers","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/filter_outliers.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Filter clumped isotope outliers — filter_outliers","text":"","code":"filter_outliers(data, group)"},{"path":"https://japhir.github.io/clumpedcalib/reference/filter_outliers.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Filter clumped isotope outliers — filter_outliers","text":"data dataframe columns outlier, broadid group Column name groups.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/filter_outliers.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Filter clumped isotope outliers — filter_outliers","text":"dataframe outliers, standards, NAs filtered .","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/general_bemis_d18Osw.html","id":null,"dir":"Reference","previous_headings":"","what":"General Bemis et al., 1998 Table 1, inverted — general_bemis_d18Osw","title":"General Bemis et al., 1998 Table 1, inverted — general_bemis_d18Osw","text":"\\(\\delta_{w} = \\frac{\\sqrt{-4ac + b^{2} + 4cT} + b + 2cT}{2c} - d\\)","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/general_bemis_d18Osw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"General Bemis et al., 1998 Table 1, inverted — general_bemis_d18Osw","text":"","code":"general_bemis_d18Osw(d18Occ, temperature, a, b, c, d)"},{"path":"https://japhir.github.io/clumpedcalib/reference/general_bemis_d18Osw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"General Bemis et al., 1998 Table 1, inverted — general_bemis_d18Osw","text":"d18Occ \\(\\delta^{18}O\\) calcite VPDB. temperature Input temperature. Intercept. b Slope. c Slope quadratic term. d conversion correction VSMOW VPDB.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/general_bemis_d18Osw.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"General Bemis et al., 1998 Table 1, inverted — general_bemis_d18Osw","text":"calculated \\(\\delta^{18}O\\) value VSMOW.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/general_bemis_d18Osw.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"General Bemis et al., 1998 Table 1, inverted — general_bemis_d18Osw","text":"Bemis, B. E., Spero, H. J., Bijma, J., & Lea, D. W. (1998). Reevaluation oxygen isotopic composition planktonic foraminifera: Experimental results revised paleotemperature equations. Paleoceanography, 13(2), 150–160. https://doi.org/10.1029/98PA00070","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/general_bemis_temp.html","id":null,"dir":"Reference","previous_headings":"","what":"General Bemis et al. 1998 table 1 — general_bemis_temp","title":"General Bemis et al. 1998 table 1 — general_bemis_temp","text":"\\(T (°C) = + b(\\delta_{c} - \\delta_{w}) + c(\\delta_{c}- \\delta_{w})^{2}\\)","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/general_bemis_temp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"General Bemis et al. 1998 table 1 — general_bemis_temp","text":"","code":"general_bemis_temp(d18Occ, d18Osw, a, b, c, d)"},{"path":"https://japhir.github.io/clumpedcalib/reference/general_bemis_temp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"General Bemis et al. 1998 table 1 — general_bemis_temp","text":"d18Occ \\(\\delta^{18}O\\) calcite VPDB. d18Osw \\(\\delta^{18}O\\) sea water VSMOW. Intercept. b Slope. c Slope quadratic term. d conversion correction VSMOW VPDB.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/general_bemis_temp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"General Bemis et al. 1998 table 1 — general_bemis_temp","text":"calculated temperature °C.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/general_bemis_temp.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"General Bemis et al. 1998 table 1 — general_bemis_temp","text":"Bemis, B. E., Spero, H. J., Bijma, J., & Lea, D. W. (1998). Reevaluation oxygen isotopic composition planktonic foraminifera: Experimental results revised paleotemperature equations. Paleoceanography, 13(2), 150–160. https://doi.org/10.1029/98PA00070","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/our_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize the bootstrapped values into a mean, sd, and the 68% and 95% CIs — our_summary","title":"Summarize the bootstrapped values into a mean, sd, and the 68% and 95% CIs — our_summary","text":"Summarize bootstrapped values mean, sd, 68% 95% CIs","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/our_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize the bootstrapped values into a mean, sd, and the 68% and 95% CIs — our_summary","text":"","code":"our_summary(boot, group)"},{"path":"https://japhir.github.io/clumpedcalib/reference/our_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize the bootstrapped values into a mean, sd, and the 68% and 95% CIs — our_summary","text":"boot Output apply_calib_and_d18O_boot() group group summarize .","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/supported_equations.html","id":null,"dir":"Reference","previous_headings":"","what":"Supported d18Osw, d18Occ, temperature relationship equations. — supported_equations","title":"Supported d18Osw, d18Occ, temperature relationship equations. — supported_equations","text":"Defaults Kim & O'neil 1997 modified Bemis et al., 1998.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/supported_equations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Supported d18Osw, d18Occ, temperature relationship equations. — supported_equations","text":"","code":"supported_equations()"},{"path":"https://japhir.github.io/clumpedcalib/reference/supported_equations.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Supported d18Osw, d18Occ, temperature relationship equations. — supported_equations","text":"Shackleton, N. J. (1974). Attainment isotopic equilibrium ocean water benthic foraminifera genus Uvigerina: Isotopic changes ocean last glacial. Colloques Internationaux Du CNRS, 219, 203–209. Erez, J., & Luz, B. (1983). Experimental paleotemperature equation planktonic foraminifera. Geochimica et Cosmochimica Acta, 47(6), 1025–1031. https://doi.org/10.1016/0016-7037(83)90232-6 Kim, S.-T., & O’Neil, J. R. (1997). Equilibrium nonequilibrium oxygen isotope effects synthetic carbonates. Geochimica et Cosmochimica Acta, 61(16), 3461–3475. https://doi.org/10.1016/S0016-7037(97)00169-5 Bemis, B. E., Spero, H. J., Bijma, J., & Lea, D. W. (1998). Reevaluation oxygen isotopic composition planktonic foraminifera: Experimental results revised paleotemperature equations. Paleoceanography, 13(2), 150–160. https://doi.org/10.1029/98PA00070 Marchitto, T. M., Curry, W. B., Lynch-Stieglitz, J., Bryan, S. P., Cobb, K. M., & Lund, D. C. (2014). Improved oxygen isotope temperature calibrations cosmopolitan benthic foraminifera. Geochimica et Cosmochimica Acta, 130, 1–11. https://doi.org/10.1016/j.gca.2013.12.034","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/supported_equations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Supported d18Osw, d18Occ, temperature relationship equations. — supported_equations","text":"","code":"supported_equations() #> [1] \"Shackleton1974\" \"ErezLuz1983\"    \"KimONeil1997\"   \"Marchitto2014\""},{"path":"https://japhir.github.io/clumpedcalib/reference/temp_calc.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate the temperature from d18Occ and the d18Osw — temp_calc","title":"Calculate the temperature from d18Occ and the d18Osw — temp_calc","text":"Defaults relationship Kim & O'neil 1997, updated Bemis et al., 1998.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/temp_calc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate the temperature from d18Occ and the d18Osw — temp_calc","text":"","code":"temp_calc(d18Occ, d18Osw, equation = NULL)"},{"path":"https://japhir.github.io/clumpedcalib/reference/temp_calc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate the temperature from d18Occ and the d18Osw — temp_calc","text":"d18Occ oxygen isotope composition carbonate VPDB. d18Osw oxygen isotope composition sea water VSMOW equation Character vector equation use. Defaults Kim & O'Neil, 1997.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/temp_calc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate the temperature from d18Occ and the d18Osw — temp_calc","text":"temperature degrees Celsius.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/temp_calc.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate the temperature from d18Occ and the d18Osw — temp_calc","text":"Shackleton, N. J. (1974). Attainment isotopic equilibrium ocean water benthic foraminifera genus Uvigerina: Isotopic changes ocean last glacial. Colloques Internationaux Du CNRS, 219, 203–209. Erez, J., & Luz, B. (1983). Experimental paleotemperature equation planktonic foraminifera. Geochimica et Cosmochimica Acta, 47(6), 1025–1031. https://doi.org/10.1016/0016-7037(83)90232-6 Kim, S.-T., & O’Neil, J. R. (1997). Equilibrium nonequilibrium oxygen isotope effects synthetic carbonates. Geochimica et Cosmochimica Acta, 61(16), 3461–3475. https://doi.org/10.1016/S0016-7037(97)00169-5 Bemis, B. E., Spero, H. J., Bijma, J., & Lea, D. W. (1998). Reevaluation oxygen isotopic composition planktonic foraminifera: Experimental results revised paleotemperature equations. Paleoceanography, 13(2), 150–160. https://doi.org/10.1029/98PA00070 Marchitto, T. M., Curry, W. B., Lynch-Stieglitz, J., Bryan, S. P., Cobb, K. M., & Lund, D. C. (2014). Improved oxygen isotope temperature calibrations cosmopolitan benthic foraminifera. Geochimica et Cosmochimica Acta, 130, 1–11. https://doi.org/10.1016/j.gca.2013.12.034","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/temp_calc.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate the temperature from d18Occ and the d18Osw — temp_calc","text":"Ilja J. Kocken","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/temp_calc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate the temperature from d18Occ and the d18Osw — temp_calc","text":"","code":"temp_calc(3, 0, \"KimONeil1997\") #> [1] 1.889561"},{"path":"https://japhir.github.io/clumpedcalib/reference/temp_d18Osw_calc.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate temperature and d18Osw — temp_d18Osw_calc","title":"Calculate temperature and d18Osw — temp_d18Osw_calc","text":"bootstrapped samples bootstrapped set slope--intercept pairs.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/temp_d18Osw_calc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate temperature and d18Osw — temp_d18Osw_calc","text":"","code":"temp_d18Osw_calc(boot, calib, equation = NULL, Nsim = NULL)"},{"path":"https://japhir.github.io/clumpedcalib/reference/temp_d18Osw_calc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate temperature and d18Osw — temp_d18Osw_calc","text":"boot tibble bootstrapped slope-intercept pairs, output bootstrap_means(). calib dataframe draws bootstrapped (Bayesian) temperature regression. columns slope intercept. equation Character vector equation use. Defaults Kim & O'Neil, 1997.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/temp_d18Osw_calc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate temperature and d18Osw — temp_d18Osw_calc","text":"boot additional columns temp d18Osw.","code":""}]
+[{"path":"https://japhir.github.io/clumpedcalib/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc.  Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://japhir.github.io/clumpedcalib/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. 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Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://japhir.github.io/clumpedcalib/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see . GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read .","code":" Copyright (C)     This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see .   Copyright (C)    This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":[]},{"path":"https://japhir.github.io/clumpedcalib/articles/bootstrapped_clumped_calibration.html","id":"load-calibration-data","dir":"Articles","previous_headings":"Bootstrapped York regression","what":"load calibration data","title":"Bootstraped Clumped Isotope Calibration","text":"show small artificial set calibration data. sure replace ! column names must identical X, D47, sd_X, sd_D47.","code":"raw <- tibble::tribble(   ~ X, ~ D47, ~ sd_X, ~ sd_D47,   11.25,0.607,0.062,0.007,   11.26,0.602,0.070,0.006,   11.26,0.603,0.069,0.005,   11.60,0.604,0.068,0.005,   12.81,0.674,0.091,.004,   13.28,0.672,0.092,0.012,   13.05,0.670,0.093,0.003,   )  # or if you have your data saved as an CSV ## raw <- readr::read_csv(\"dat/example_calib.csv\", ##                 col_names = c(\"X\", \"D47\", \"sd_X\", \"sd_D47\"))"},{"path":"https://japhir.github.io/clumpedcalib/articles/bootstrapped_clumped_calibration.html","id":"calculate-bootstrapped-york-regression","dir":"Articles","previous_headings":"Bootstrapped York regression","what":"calculate bootstrapped York regression","title":"Bootstraped Clumped Isotope Calibration","text":"","code":"# this is very much a toy example with only 100 bootstraps! calib <- clumped_calib_boot(raw, Nsim = 100) #|>   # for the real deal, increase Nsim to something like 1e5 and save the results   # for re-use   ## readr::write_csv(glue::glue(\"calib_clumped_boot.csv\"))  # then you can read these stored results like so: ## calib <- readr::read_csv(\"calib_clumped_boot.csv\") raw |>   ggplot(aes(x = X, y = D47)) +   labs(x = 10^6 / T^2 ~ \"(K)\", y = Delta[47] ~ \"(I-CDES)\") +   scale_x_continuous(sec.axis = sec_axis(     \"Temperature (°C)\",     trans = \\(x) sqrt(1e6 / x) - 273.15,     breaks = seq(0, 30, 5))) +   geom_point() +   geom_errorbar(aes(xmin = X - sd_X, xmax = X + sd_X)) +   geom_errorbar(aes(ymin = D47 - sd_D47, ymax = D47 + sd_D47)) +   # for now just draw all the lines since we're only sampling a few   # setting alpha lower allows you to overplot the draws   # don't forget to subset to just a few 100 though, otherwise it will be slow   geom_abline(aes(slope = slope, intercept = intercept),               alpha = .2, data = calib)"},{"path":[]},{"path":"https://japhir.github.io/clumpedcalib/articles/bootstrapped_clumped_calibration.html","id":"load-sample-data","dir":"Articles","previous_headings":"Apply it to your data","what":"load sample data","title":"Bootstraped Clumped Isotope Calibration","text":"’ve come fake replicate-level data.","code":"dat <- tibble::tribble(   ~ age, ~ bins, ~ d18O_PDB_vit, ~ d13C_PDB_vit, ~ D47_final, ~ outlier, ~ identifier_1, ~ broadid,   15.2,1,12,13,0.6,FALSE,\"smp1\",\"other\",   15.4,1,8,9,0.61,FALSE,\"smp1\",\"other\",   15.7,1,9,15,0.599,FALSE,\"smp2\",\"other\",   33.2,2,12,13,0.62,FALSE,\"smp3\",\"other\",   33.7,2,8,9,0.65,FALSE,\"smp4\",\"other\",   33.6,2,8,14,0.67,FALSE,\"smp5\",\"other\",   33.9,2,9,15,0.63,FALSE,\"smp5\",\"other\", )  # You can save your data to a CSV with the same column names and load it like so: ## dat <- readr::read_csv(\"fake_data.csv\")  pl_raw <- dat |>   ggplot(aes(x = age, y = D47_final, colour = factor(bins))) +   geom_point() pl_raw"},{"path":"https://japhir.github.io/clumpedcalib/articles/bootstrapped_clumped_calibration.html","id":"just-give-me-the-results","dir":"Articles","previous_headings":"Apply it to your data","what":"just give me the results!","title":"Bootstraped Clumped Isotope Calibration","text":"simple wrapper function quickly get end result. want control, see .","code":"# calculate other \"normal\" summary stats if desired, like N oth <- dat |>   group_by(bins) |>   summarize(n = n())  # calculate d18Osw and temp median and quantile interval sum <- apply_calib_and_d18O_boot(data = dat,                                  calib = calib,                                  group = bins,                                  Nsim = 100,                                  output = \"summary\") |>   # add N back in   left_join(oth) #> filter: no rows removed #> filter: no rows removed #> filter: no rows removed #> Warning: There was 1 warning in `dplyr::mutate()`. #> ℹ In argument: `d18Osw = d18Osw_calc(d18Occ = d18O, temp = temp, equation = #>   equation)`. #> ℹ In group 2: `bins = 2`. #> Caused by warning in `sqrt()`: #> ! NaNs produced #> Joining with `by = join_by(bins)` # make a plot sum |>   ggplot(aes(x = age, y = temp)) +   ggdist::geom_pointinterval(aes(ymin = temp.lower, ymax = temp.upper,                                  linewidth = factor(.width))) +   scale_linewidth_manual(values = c(\"0.68\" = 9, \"0.95\" = 2), guide = \"none\") +   geom_text(aes(label = paste(\"N =\", n)), nudge_x = 1.5)"},{"path":"https://japhir.github.io/clumpedcalib/articles/bootstrapped_clumped_calibration.html","id":"more-control","dir":"Articles","previous_headings":"Apply it to your data","what":"more control","title":"Bootstraped Clumped Isotope Calibration","text":"want control, recommend using wrapper function, stead take one step time: filter_outliers(): says tin. bootstrap_means(): Calculate bootstrapped means sample bins. temp_d18Osw_calc(): Apply temperature calibration use clumped-derived temperature d18Occ–d18Osw–temperature relationship calculate d18Osw. our_summary(): Summarize calculating median 68% 95% confidence intervals mean. can overwrite filter_outliers() filtering function comment already cleaned data. assumes ’s logical column outlier character column broadid samples equal \"\". like thank Alvaro Fernandez writing sharing Matlab code inspired R package.","code":"sim <- dat |>   filter_outliers(group = bins) |>   bootstrap_means(group = bins, # specify which columns to use                   age = age,                   d13C = d13C_PDB_vit,                   d18O = d18O_PDB_vit,                   D47 = D47_final,                   # obviously set Nsim way higher for real data!                   Nsim = 100) |>   # you can choose several d18Occ--d18Osw--temperature equations, see `equations_supported()`.   temp_d18Osw_calc(calib = calib, equation = \"KimONeil1997\", Nsim = 100) |>   our_summary(group = bins) #> filter: no rows removed #> filter: no rows removed #> filter: no rows removed #> Warning: There was 1 warning in `dplyr::mutate()`. #> ℹ In argument: `d18Osw = d18Osw_calc(d18Occ = d18O, temp = temp, equation = #>   equation)`. #> ℹ In group 2: `bins = 2`. #> Caused by warning in `sqrt()`: #> ! NaNs produced"},{"path":"https://japhir.github.io/clumpedcalib/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Ilja Kocken. Author, maintainer.","code":""},{"path":"https://japhir.github.io/clumpedcalib/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Kocken (2024). clumpedcalib: Calculate Apply Clumped Isotope Calibrations Using Bootstrapping. R package version 0.0.0.9000, https://japhir.github.io/clumpedcalib/.","code":"@Manual{,   title = {clumpedcalib: Calculate and Apply Clumped Isotope Calibrations Using Bootstrapping},   author = {Ilja Kocken},   year = {2024},   note = {R package version 0.0.0.9000},   url = {https://japhir.github.io/clumpedcalib/}, }"},{"path":"https://japhir.github.io/clumpedcalib/index.html","id":"clumpedcalib-calculate-and-apply-clumped-isotope-calibrations-using-bootstrapping","dir":"","previous_headings":"","what":"Calculate and Apply Clumped Isotope Calibrations Using Bootstrapping","title":"Calculate and Apply Clumped Isotope Calibrations Using Bootstrapping","text":"Written Ilja J. Kocken Feel free use stuff, long adhere file:LICENSE.md NOTE: just method use, ’m publishing actual calibration dataset ’m using ! Calculate bootstrapped York regression clumped isotope calibration data. clumped_calib_boot(). Calculate bootstrapped sample means age, d13C, d18O, D47. bootstrap_means(). Apply bootstrapped calibration calculate temperature d18Osw. temp_d18Osw_calc(). Summarize bootstrapped values calculate 68 95% CIs. our_summary(). Also comes classic d18Occ calibrations. See temp_calc(). well inverses, constraints temperature wish calculate d18Osw. See d18Osw_calc().","code":""},{"path":"https://japhir.github.io/clumpedcalib/index.html","id":"how-to-calculate-bootstrapped-averages-and-apply-a-clumped-isotope-specific-temperature-calibration","dir":"","previous_headings":"","what":"How to calculate bootstrapped averages and apply a clumped-isotope specific temperature calibration.","title":"Calculate and Apply Clumped Isotope Calibrations Using Bootstrapping","text":"use : Install package clumpedcalib, see #installation. Update input calibration data file:dat/example_calib.csv. Make sure column names include X, D47, sd_X, sd_D47. Add sample data replicate level. Check see like function calculates d18Osw. Currently, defaults Kim & O'Neil 1997 calibration, adjusted Bemis et al., 1998. want use wrapper function: create definition filter outliers filters bad measurements NA's data. Use wrapper function apply_calib_and_d18O_boot(), better yet: Walk example workflow step--step apply bulletpoint functions one--one. look functions better understand ’s happening. bootstrapped calibration idea based Matlab script written Alvaro Fernandez.","code":""},{"path":"https://japhir.github.io/clumpedcalib/index.html","id":"installation","dir":"","previous_headings":"","what":"installation","title":"Calculate and Apply Clumped Isotope Calibrations Using Bootstrapping","text":"install development package: can look functions copy like.","code":"remotes::install_github(\"japhir/clumpedcalib\")"},{"path":"https://japhir.github.io/clumpedcalib/reference/apply_calib_and_d18O_boot.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate bootstrapped means with temperature and d18Osw — apply_calib_and_d18O_boot","title":"Calculate bootstrapped means with temperature and d18Osw — apply_calib_and_d18O_boot","text":"age, d18O, d13C, D47, calculate temperature d18Osw.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/apply_calib_and_d18O_boot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate bootstrapped means with temperature and d18Osw — apply_calib_and_d18O_boot","text":"","code":"apply_calib_and_d18O_boot(   data,   calib,   group,   output = \"summary\",   equation = NULL,   Nsim = NULL )"},{"path":"https://japhir.github.io/clumpedcalib/reference/apply_calib_and_d18O_boot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate bootstrapped means with temperature and d18Osw — apply_calib_and_d18O_boot","text":"data dataframe columns outlier, broadid calib dataframe draws bootstrapped (Bayesian) temperature regression. columns slope intercept. group Column name groups. output Character vector specifying whether return \"summary\" \"raw\" bootstrapped samples. equation Character vector equation use. Defaults Kim & O'Neil, 1997. Nsim number bootstraps want run. Defaults number rows calib.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/bootstrap_means.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate bootstrapped means for each group in a dataframe — bootstrap_means","title":"Calculate bootstrapped means for each group in a dataframe — bootstrap_means","text":"Calculate bootstrapped means group dataframe","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/bootstrap_means.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate bootstrapped means for each group in a dataframe — bootstrap_means","text":"","code":"bootstrap_means(data, group, age, d13C, d18O, D47, Nsim = 1e+05)"},{"path":"https://japhir.github.io/clumpedcalib/reference/bootstrap_means.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate bootstrapped means for each group in a dataframe — bootstrap_means","text":"data dataframe tibble columns outlier, broadid (\"\" samples), D47_final, d18O_PDB_vit, d13C_PDB_vit, grouping column. group column name data character factor column contains binning information want calculate bootstrapped averages . age column name data sample ages. d13C column name data carbon isotope values. d18O column name data oxygen isotope values. D47 column name data clumped isotope values. Nsim number bootstraps want run. Defaults number rows calib.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/bootstrap_means.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate bootstrapped means for each group in a dataframe — bootstrap_means","text":"tibble bootstrapped slope-intercept pair.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/clumped_calib_boot.html","id":null,"dir":"Reference","previous_headings":"","what":"Bootstrapped clumped isotope calibration — clumped_calib_boot","title":"Bootstrapped clumped isotope calibration — clumped_calib_boot","text":"Bootstrapped clumped isotope calibration","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/clumped_calib_boot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Bootstrapped clumped isotope calibration — clumped_calib_boot","text":"","code":"clumped_calib_boot(data, Nsim = 1e+05)"},{"path":"https://japhir.github.io/clumpedcalib/reference/clumped_calib_boot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Bootstrapped clumped isotope calibration — clumped_calib_boot","text":"data data.frame columns D47, X, sd_X, sd_D47. X stands commonly-used temperature scale, 10^6 / T^2 T K. Nsim Number simulations bootstrapping.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/clumped_calib_boot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Bootstrapped clumped isotope calibration — clumped_calib_boot","text":"tibble bootstrapped slope--intercept pairs.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/clumpedcalib-package.html","id":null,"dir":"Reference","previous_headings":"","what":"clumpedcalib: Calculate and Apply Clumped Isotope Calibrations Using Bootstrapping — clumpedcalib-package","title":"clumpedcalib: Calculate and Apply Clumped Isotope Calibrations Using Bootstrapping — clumpedcalib-package","text":"Calculate bootstrapped York regression clumped isotope calibration data. Calculate bootstrapped sample means age, d13C, d18O, D47. Apply bootstrapped calibration calculate temperature d18Osw.","code":""},{"path":[]},{"path":"https://japhir.github.io/clumpedcalib/reference/clumpedcalib-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"clumpedcalib: Calculate and Apply Clumped Isotope Calibrations Using Bootstrapping — clumpedcalib-package","text":"Maintainer: Ilja Kocken .j.kocken@uu.nl (ORCID)","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/d18Osw_calc.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate the d18Osw from the d18Occ and temperature — d18Osw_calc","title":"Calculate the d18Osw from the d18Occ and temperature — d18Osw_calc","text":"Defaults Kim & O'neil 1997 modified Bemis et al., 1998.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/d18Osw_calc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate the d18Osw from the d18Occ and temperature — d18Osw_calc","text":"","code":"d18Osw_calc(d18Occ, temperature, equation = NULL)"},{"path":"https://japhir.github.io/clumpedcalib/reference/d18Osw_calc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate the d18Osw from the d18Occ and temperature — d18Osw_calc","text":"d18Occ oxygen isotope composition carbonate VPDB. temperature formation temperature (°C). equation Character vector equation use. Defaults Kim & O'Neil, 1997.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/d18Osw_calc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate the d18Osw from the d18Occ and temperature — d18Osw_calc","text":"oxygen isotope composition sea water VSMOW.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/d18Osw_calc.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate the d18Osw from the d18Occ and temperature — d18Osw_calc","text":"Shackleton, N. J. (1974). Attainment isotopic equilibrium ocean water benthic foraminifera genus Uvigerina: Isotopic changes ocean last glacial. Colloques Internationaux Du CNRS, 219, 203–209. Erez, J., & Luz, B. (1983). Experimental paleotemperature equation planktonic foraminifera. Geochimica et Cosmochimica Acta, 47(6), 1025–1031. https://doi.org/10.1016/0016-7037(83)90232-6 Kim, S.-T., & O’Neil, J. R. (1997). Equilibrium nonequilibrium oxygen isotope effects synthetic carbonates. Geochimica et Cosmochimica Acta, 61(16), 3461–3475. https://doi.org/10.1016/S0016-7037(97)00169-5 Bemis, B. E., Spero, H. J., Bijma, J., & Lea, D. W. (1998). Reevaluation oxygen isotopic composition planktonic foraminifera: Experimental results revised paleotemperature equations. Paleoceanography, 13(2), 150–160. https://doi.org/10.1029/98PA00070 Marchitto, T. M., Curry, W. B., Lynch-Stieglitz, J., Bryan, S. P., Cobb, K. M., & Lund, D. C. (2014). Improved oxygen isotope temperature calibrations cosmopolitan benthic foraminifera. Geochimica et Cosmochimica Acta, 130, 1–11. https://doi.org/10.1016/j.gca.2013.12.034","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/d18Osw_calc.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate the d18Osw from the d18Occ and temperature — d18Osw_calc","text":"Ilja J. Kocken","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/d18Osw_calc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate the d18Osw from the d18Occ and temperature — d18Osw_calc","text":"","code":"d18Osw_calc(3, 2, \"KimONeil1997\") #> [1] 0.02724298"},{"path":"https://japhir.github.io/clumpedcalib/reference/equation_supported.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if the provided equation is supported — equation_supported","title":"Check if the provided equation is supported — equation_supported","text":"Also parses equation name internal simplified code. See supported_equations() References equations currently supported.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/equation_supported.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if the provided equation is supported — equation_supported","text":"","code":"equation_supported(equation)"},{"path":"https://japhir.github.io/clumpedcalib/reference/equation_supported.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if the provided equation is supported — equation_supported","text":"equation Character vector equation reference. Must one supported_equations().","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/equation_supported.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if the provided equation is supported — equation_supported","text":"Character vector cleaned equation reference. Gives error currently supported.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/equation_supported.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Check if the provided equation is supported — equation_supported","text":"Shackleton, N. J. (1974). Attainment isotopic equilibrium ocean water benthic foraminifera genus Uvigerina: Isotopic changes ocean last glacial. Colloques Internationaux Du CNRS, 219, 203–209. Erez, J., & Luz, B. (1983). Experimental paleotemperature equation planktonic foraminifera. Geochimica et Cosmochimica Acta, 47(6), 1025–1031. https://doi.org/10.1016/0016-7037(83)90232-6 Kim, S.-T., & O’Neil, J. R. (1997). Equilibrium nonequilibrium oxygen isotope effects synthetic carbonates. Geochimica et Cosmochimica Acta, 61(16), 3461–3475. https://doi.org/10.1016/S0016-7037(97)00169-5 Bemis, B. E., Spero, H. J., Bijma, J., & Lea, D. W. (1998). Reevaluation oxygen isotopic composition planktonic foraminifera: Experimental results revised paleotemperature equations. Paleoceanography, 13(2), 150–160. https://doi.org/10.1029/98PA00070 Marchitto, T. M., Curry, W. B., Lynch-Stieglitz, J., Bryan, S. P., Cobb, K. M., & Lund, D. C. (2014). Improved oxygen isotope temperature calibrations cosmopolitan benthic foraminifera. Geochimica et Cosmochimica Acta, 130, 1–11. https://doi.org/10.1016/j.gca.2013.12.034","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/filter_outliers.html","id":null,"dir":"Reference","previous_headings":"","what":"Filter clumped isotope outliers — filter_outliers","title":"Filter clumped isotope outliers — filter_outliers","text":"Filter clumped isotope outliers","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/filter_outliers.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Filter clumped isotope outliers — filter_outliers","text":"","code":"filter_outliers(data, group)"},{"path":"https://japhir.github.io/clumpedcalib/reference/filter_outliers.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Filter clumped isotope outliers — filter_outliers","text":"data dataframe columns outlier, broadid group Column name groups.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/filter_outliers.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Filter clumped isotope outliers — filter_outliers","text":"dataframe outliers, standards, NAs filtered .","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/general_bemis_d18Osw.html","id":null,"dir":"Reference","previous_headings":"","what":"General Bemis et al., 1998 Table 1, inverted — general_bemis_d18Osw","title":"General Bemis et al., 1998 Table 1, inverted — general_bemis_d18Osw","text":"\\(\\delta_{w} = \\frac{\\sqrt{-4ac + b^{2} + 4cT} + b + 2cT}{2c} - d\\)","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/general_bemis_d18Osw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"General Bemis et al., 1998 Table 1, inverted — general_bemis_d18Osw","text":"","code":"general_bemis_d18Osw(d18Occ, temperature, a, b, c, d)"},{"path":"https://japhir.github.io/clumpedcalib/reference/general_bemis_d18Osw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"General Bemis et al., 1998 Table 1, inverted — general_bemis_d18Osw","text":"d18Occ \\(\\delta^{18}O\\) calcite VPDB. temperature Input temperature. Intercept. b Slope. c Slope quadratic term. d conversion correction VSMOW VPDB.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/general_bemis_d18Osw.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"General Bemis et al., 1998 Table 1, inverted — general_bemis_d18Osw","text":"calculated \\(\\delta^{18}O\\) value VSMOW.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/general_bemis_d18Osw.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"General Bemis et al., 1998 Table 1, inverted — general_bemis_d18Osw","text":"Bemis, B. E., Spero, H. J., Bijma, J., & Lea, D. W. (1998). Reevaluation oxygen isotopic composition planktonic foraminifera: Experimental results revised paleotemperature equations. Paleoceanography, 13(2), 150–160. https://doi.org/10.1029/98PA00070","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/general_bemis_temp.html","id":null,"dir":"Reference","previous_headings":"","what":"General Bemis et al. 1998 table 1 — general_bemis_temp","title":"General Bemis et al. 1998 table 1 — general_bemis_temp","text":"\\(T (°C) = + b(\\delta_{c} - \\delta_{w}) + c(\\delta_{c}- \\delta_{w})^{2}\\)","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/general_bemis_temp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"General Bemis et al. 1998 table 1 — general_bemis_temp","text":"","code":"general_bemis_temp(d18Occ, d18Osw, a, b, c, d)"},{"path":"https://japhir.github.io/clumpedcalib/reference/general_bemis_temp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"General Bemis et al. 1998 table 1 — general_bemis_temp","text":"d18Occ \\(\\delta^{18}O\\) calcite VPDB. d18Osw \\(\\delta^{18}O\\) sea water VSMOW. Intercept. b Slope. c Slope quadratic term. d conversion correction VSMOW VPDB.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/general_bemis_temp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"General Bemis et al. 1998 table 1 — general_bemis_temp","text":"calculated temperature °C.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/general_bemis_temp.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"General Bemis et al. 1998 table 1 — general_bemis_temp","text":"Bemis, B. E., Spero, H. J., Bijma, J., & Lea, D. W. (1998). Reevaluation oxygen isotopic composition planktonic foraminifera: Experimental results revised paleotemperature equations. Paleoceanography, 13(2), 150–160. https://doi.org/10.1029/98PA00070","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/our_summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize the bootstrapped values into a mean, sd, and the 68% and 95% CIs — our_summary","title":"Summarize the bootstrapped values into a mean, sd, and the 68% and 95% CIs — our_summary","text":"Summarize bootstrapped values mean, sd, 68% 95% CIs","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/our_summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize the bootstrapped values into a mean, sd, and the 68% and 95% CIs — our_summary","text":"","code":"our_summary(boot, group)"},{"path":"https://japhir.github.io/clumpedcalib/reference/our_summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize the bootstrapped values into a mean, sd, and the 68% and 95% CIs — our_summary","text":"boot Output apply_calib_and_d18O_boot() group group summarize .","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/supported_equations.html","id":null,"dir":"Reference","previous_headings":"","what":"Supported d18Osw, d18Occ, temperature relationship equations. — supported_equations","title":"Supported d18Osw, d18Occ, temperature relationship equations. — supported_equations","text":"Defaults Kim & O'neil 1997 modified Bemis et al., 1998.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/supported_equations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Supported d18Osw, d18Occ, temperature relationship equations. — supported_equations","text":"","code":"supported_equations()"},{"path":"https://japhir.github.io/clumpedcalib/reference/supported_equations.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Supported d18Osw, d18Occ, temperature relationship equations. — supported_equations","text":"Shackleton, N. J. (1974). Attainment isotopic equilibrium ocean water benthic foraminifera genus Uvigerina: Isotopic changes ocean last glacial. Colloques Internationaux Du CNRS, 219, 203–209. Erez, J., & Luz, B. (1983). Experimental paleotemperature equation planktonic foraminifera. Geochimica et Cosmochimica Acta, 47(6), 1025–1031. https://doi.org/10.1016/0016-7037(83)90232-6 Kim, S.-T., & O’Neil, J. R. (1997). Equilibrium nonequilibrium oxygen isotope effects synthetic carbonates. Geochimica et Cosmochimica Acta, 61(16), 3461–3475. https://doi.org/10.1016/S0016-7037(97)00169-5 Bemis, B. E., Spero, H. J., Bijma, J., & Lea, D. W. (1998). Reevaluation oxygen isotopic composition planktonic foraminifera: Experimental results revised paleotemperature equations. Paleoceanography, 13(2), 150–160. https://doi.org/10.1029/98PA00070 Marchitto, T. M., Curry, W. B., Lynch-Stieglitz, J., Bryan, S. P., Cobb, K. M., & Lund, D. C. (2014). Improved oxygen isotope temperature calibrations cosmopolitan benthic foraminifera. Geochimica et Cosmochimica Acta, 130, 1–11. https://doi.org/10.1016/j.gca.2013.12.034","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/supported_equations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Supported d18Osw, d18Occ, temperature relationship equations. — supported_equations","text":"","code":"supported_equations() #> [1] \"Shackleton1974\" \"ErezLuz1983\"    \"KimONeil1997\"   \"Marchitto2014\""},{"path":"https://japhir.github.io/clumpedcalib/reference/temp_calc.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate the temperature from d18Occ and the d18Osw — temp_calc","title":"Calculate the temperature from d18Occ and the d18Osw — temp_calc","text":"Defaults relationship Kim & O'neil 1997, updated Bemis et al., 1998.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/temp_calc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate the temperature from d18Occ and the d18Osw — temp_calc","text":"","code":"temp_calc(d18Occ, d18Osw, equation = NULL)"},{"path":"https://japhir.github.io/clumpedcalib/reference/temp_calc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate the temperature from d18Occ and the d18Osw — temp_calc","text":"d18Occ oxygen isotope composition carbonate VPDB. d18Osw oxygen isotope composition sea water VSMOW equation Character vector equation use. Defaults Kim & O'Neil, 1997.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/temp_calc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate the temperature from d18Occ and the d18Osw — temp_calc","text":"temperature degrees Celsius.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/temp_calc.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate the temperature from d18Occ and the d18Osw — temp_calc","text":"Shackleton, N. J. (1974). Attainment isotopic equilibrium ocean water benthic foraminifera genus Uvigerina: Isotopic changes ocean last glacial. Colloques Internationaux Du CNRS, 219, 203–209. Erez, J., & Luz, B. (1983). Experimental paleotemperature equation planktonic foraminifera. Geochimica et Cosmochimica Acta, 47(6), 1025–1031. https://doi.org/10.1016/0016-7037(83)90232-6 Kim, S.-T., & O’Neil, J. R. (1997). Equilibrium nonequilibrium oxygen isotope effects synthetic carbonates. Geochimica et Cosmochimica Acta, 61(16), 3461–3475. https://doi.org/10.1016/S0016-7037(97)00169-5 Bemis, B. E., Spero, H. J., Bijma, J., & Lea, D. W. (1998). Reevaluation oxygen isotopic composition planktonic foraminifera: Experimental results revised paleotemperature equations. Paleoceanography, 13(2), 150–160. https://doi.org/10.1029/98PA00070 Marchitto, T. M., Curry, W. B., Lynch-Stieglitz, J., Bryan, S. P., Cobb, K. M., & Lund, D. C. (2014). Improved oxygen isotope temperature calibrations cosmopolitan benthic foraminifera. Geochimica et Cosmochimica Acta, 130, 1–11. https://doi.org/10.1016/j.gca.2013.12.034","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/temp_calc.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate the temperature from d18Occ and the d18Osw — temp_calc","text":"Ilja J. Kocken","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/temp_calc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate the temperature from d18Occ and the d18Osw — temp_calc","text":"","code":"temp_calc(3, 0, \"KimONeil1997\") #> [1] 1.889561"},{"path":"https://japhir.github.io/clumpedcalib/reference/temp_d18Osw_calc.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate temperature and d18Osw — temp_d18Osw_calc","title":"Calculate temperature and d18Osw — temp_d18Osw_calc","text":"bootstrapped samples bootstrapped set slope--intercept pairs.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/temp_d18Osw_calc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate temperature and d18Osw — temp_d18Osw_calc","text":"","code":"temp_d18Osw_calc(boot, calib, equation = NULL, Nsim = NULL)"},{"path":"https://japhir.github.io/clumpedcalib/reference/temp_d18Osw_calc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate temperature and d18Osw — temp_d18Osw_calc","text":"boot tibble bootstrapped slope-intercept pairs, output bootstrap_means(). calib dataframe draws bootstrapped (Bayesian) temperature regression. columns slope intercept. equation Character vector equation use. Defaults Kim & O'Neil, 1997.","code":""},{"path":"https://japhir.github.io/clumpedcalib/reference/temp_d18Osw_calc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate temperature and d18Osw — temp_d18Osw_calc","text":"boot additional columns temp d18Osw.","code":""}]