diff --git a/404.html b/404.html index 9b883dd..7a27145 100644 --- a/404.html +++ b/404.html @@ -18,7 +18,7 @@ - +
- +
@@ -100,16 +100,16 @@

Page not found (404)

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/LICENSE.html b/LICENSE.html index b62a0a2..3f47840 100644 --- a/LICENSE.html +++ b/LICENSE.html @@ -3,7 +3,7 @@ - +
- +
@@ -268,15 +268,15 @@

How to Apply These Terms

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.0.

- - + + diff --git a/articles/clumped.html b/articles/clumped.html index 0b2b366..ab52c49 100644 --- a/articles/clumped.html +++ b/articles/clumped.html @@ -12,14 +12,13 @@ - - +
- +
@@ -84,7 +83,7 @@

Ilja J.

2024-05-03

- Source: vignettes/clumped.Rmd + Source: vignettes/clumped.Rmd
@@ -107,9 +106,8 @@

load the packages that we use#> filter, lag #> The following objects are masked from 'package:base': #> -#> intersect, setdiff, setequal, union

-
-  library(tidyr)     # for nesting/unnesting
+#>     intersect, setdiff, setequal, union
+  library(tidyr)     # for nesting/unnesting
   library(ggplot2)   # for plots!
 
   library(isoreader) # read in raw data
@@ -117,9 +115,8 @@ 
load the packages that we use#> Attaching package: 'isoreader'
 #> The following object is masked from 'package:stats':
 #> 
-#>     filter
-
-  library(clumpedr)  # this package! process clumped isotope data
+#> filter + library(clumpedr) # this package! process clumped isotope data

get your data from raw instrument data into R @@ -132,7 +129,7 @@

load data from a remote

Of course you can also just copy your files and paste them in a folder you desire.

-
+
 
It is nice to save a cache/backup as an R data structure file, which
 we can read in much faster.

-
+
 iso_save(dids, "out/dids.di.rds")

 

 

@@ -149,12 +146,12 @@ 
load from the cache
+
 dids  <- iso_read_dual_inlet("out/dids.di.rds")

 
I have made some standard data available here so as to run the tests,
 or a single did file for an ETH-3 standard.

 
See their documentation with the following code:

-
+
 ?standards
 ?eth3

 

@@ -164,11 +161,10 @@ 
process the data!
 
We save the file info separately, since we will have to refer to it
 for some plots.

-
+
 stdinfo <- iso_get_file_info(standards)
-#> Info: aggregating file info from 27 data file(s)

-
-glimpse(stdinfo)
+#> Info: aggregating file info from 27 data file(s)
+glimpse(stdinfo)
 #> Rows: 27
 #> Columns: 21
 #> $ file_id               <chr> "180814_75_IAM_1_ETH-3.did", "180814_75_IAM_10_I…
@@ -211,14 +207,13 @@ 
filter measurements of interestNote that I put the name of the newly generated object at the end
 here for this and future code chunks, so we print() the
 result for inspection.

-
+
 filt <- standards |>
   # we can subset to some files of interest (e.g., based on a regular expression)
   # in this case we subset to all the runs that have a "Clumped" method.
   iso_filter_files(grepl("Clumped.*met", Method))
-#> Info: applying file filter, keeping 27 of 27 files

-
-filt
+#> Info: applying file filter, keeping 27 of 27 files
+filt
 #> Data from 27 dual inlet iso files: 
 #> # A tibble: 27 × 6
 #>    file_id                file_path_ file_subpath raw_data file_info method_info
@@ -241,13 +236,12 @@ 
extract raw dataThen we extract the raw data. This gives it in a format where each
 row is one cycle of either standard or sample
 gas, with initensities 44–49 as columns.

-
+
 rawd <- filt |>
   # get all the raw data, per cycle from the dids
   iso_get_raw_data(include_file_info = "Analysis")
-#> Info: aggregating raw data from 27 data file(s), including file info '"Analysis"'

-
-rawd
+#> Info: aggregating raw data from 27 data file(s), including file info '"Analysis"'
+rawd
 #> # A tibble: 2,187 × 11
 #>    file_id Analysis type  cycle v44.mV v45.mV v46.mV v47.mV v48.mV v49.mV v54.mV
 #>    <chr>   <chr>    <chr> <int>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>
@@ -268,14 +262,13 @@ 
disable failed cycles
 
This disables any cycles that have a sudden drop in
 pressure/intensity.

-
+
 disc <- rawd |>
   mutate(dis_min = 500, dis_max = 50000, dis_fac = 3) |>
   find_bad_cycles(min = "dis_min", max = "dis_max",
                   fac = "dis_fac", relative_to = "init")
-#> Info: found 0 out of 27 acquisitions with a drop in pressure of mass 44.

-
-disc |> select(file_id, outlier_cycle_low:outlier_cycle)
+#> Info: found 0 out of 27 acquisitions with a drop in pressure of mass 44.
+disc |> select(file_id, outlier_cycle_low:outlier_cycle)
 #> # A tibble: 2,187 × 10
 #>    file_id        outlier_cycle_low outlier_cycle_high cycle_diff first_diff_fac
 #>    <chr>          <lgl>             <lgl>                   <dbl>          <dbl>
@@ -296,7 +289,7 @@ 
disable failed cycles
 
find initial intensities of each cycle
 

-
+
 inits <- get_inits(rawd)
 inits
 #> # A tibble: 27 × 4
@@ -319,12 +312,11 @@ 
background correction
 
Do a very simple background correction based on the half-cup mass
 54.

-
+
 bgds <- disc |>
   correct_backgrounds(factor = 0.82)
-#> Info: adding background based on half-mass with factor 0.82

-
-bgds |> select(file_id, v47.mV, v54.mV)
+#> Info: adding background based on half-mass with factor 0.82
+bgds |> select(file_id, v47.mV, v54.mV)
 #> # A tibble: 2,187 × 3
 #>    file_id                   v47.mV v54.mV
 #>    <chr>                      <dbl>  <dbl>
@@ -345,7 +337,7 @@ 
background correctionFor a background correction based on background scans performed
 before each run we have to get the raw scan data into R.

 
We can do this with:

-
+
   scns <- iso_read_scan("scan_file.scn", cache = TRUE, parallel = TRUE, quiet = FALSE)

 
Processing the background scan files in this way is beyond the scope
 of this vignette for now, since the functions that do the work are not
@@ -481,13 +473,12 @@ 
spread match
+
 sprd <- bgds |>
   spread_match(method = "normal")
 #> Info: reshaping data into wide format.
-#> Info: matching working gas intensities to sample gas, using method normal

-
-sprd |> select(file_id, r44:s49)
+#> Info: matching working gas intensities to sample gas, using method normal
+sprd |> select(file_id, r44:s49)
 #> # A tibble: 1,080 × 14
 #>    file_id       r44    r45    r46    r47   r48   r49   r54    s44    s45    s46
 #>    <chr>       <dbl>  <dbl>  <dbl>  <dbl> <dbl> <dbl> <dbl>  <dbl>  <dbl>  <dbl>
@@ -507,13 +498,12 @@ 
spread match
 
extract reference gas d13C and d18O values
 

-
+
 refd <- sprd |>
   append_ref_deltas(standards)
 #> Info: collapsing cycles, calculating sample summaries.
-#> Info: appending reference gas δ values from 27 data file(s)

-
-refd |> select(file_id, d13C_PDB_wg:d18O_PDBCO2_wg)
+#> Info: appending reference gas δ values from 27 data file(s)
+refd |> select(file_id, d13C_PDB_wg:d18O_PDBCO2_wg)
 #> # A tibble: 1,080 × 3
 #>    file_id                   d13C_PDB_wg d18O_PDBCO2_wg
 #>    <chr>                           <dbl>          <dbl>
@@ -534,15 +524,14 @@ 
calculate little delta’s a
 

 
Now we can go to the bread and butter of clumpedr, delta
 calculations!

-
+
 abd <- refd |>
   abundance_ratios(i44 = s44, i45 = s45, i46 = s46, i47 = s47, i48 = s48, i49 = s49) |>
   abundance_ratios(i44 = r44, i45 = r45, i46 = r46, i47 = r47, i48 = r48, i49 = r49,
                    R45 = R45_wg, R46 = R46_wg, R47 = R47_wg, R48 = R48_wg, R49 = R49_wg)
 #> Info: calculating abundance ratios R[i] = i / 44
-#> Info: calculating abundance ratios R[i] = i / 44

-
-abd |> select(file_id, R45:R49_wg)
+#> Info: calculating abundance ratios R[i] = i / 44
+abd |> select(file_id, R45:R49_wg)
 #> # A tibble: 1,080 × 11
 #>    file_id     R45   R46   R47   R48     R49 R45_wg R46_wg R47_wg R48_wg  R49_wg
 #>    <chr>     <dbl> <dbl> <dbl> <dbl>   <dbl>  <dbl>  <dbl>  <dbl>  <dbl>   <dbl>
@@ -557,12 +546,11 @@ 
calculate little delta’s a
 #>  9 180814_7…  1.19  1.40  1.58 0.131 -0.0159   1.18   1.39   1.56  0.128 -0.0159
 #> 10 180814_7…  1.19  1.40  1.58 0.131 -0.0160   1.18   1.39   1.55  0.128 -0.0159
 #> # ℹ 1,070 more rows

-
+
 dlts <- abd |>
   little_deltas()
-#> Info: calculating δ values with (Ri / Ri_wg - 1) * 1000

-
-# this contains some more columns, but just showing the ones of interest for now
+#> Info: calculating δ values with (Ri / Ri_wg - 1) * 1000
+# this contains some more columns, but just showing the ones of interest for now
 dlts |> select(file_id, d45:d49)
 #> # A tibble: 1,080 × 6
 #>    file_id                     d45   d46   d47   d48   d49
@@ -578,13 +566,12 @@ 
calculate little delta’s a
 #>  9 180814_75_IAM_1_ETH-3.did  4.76  11.3  15.5  24.1  1.00
 #> 10 180814_75_IAM_1_ETH-3.did  4.76  11.3  15.9  24.9  2.53
 #> # ℹ 1,070 more rows

-
+
 bigD <- dlts |>
   mutate(Mineralogy = "Calcite") |>
   bulk_and_clumping_deltas()
-#> Info: calculating δ¹³C, δ¹⁸O, and Δ's.

-
-  # outlier on the cycle level now contains all the reasons for cycle outliers
+#> Info: calculating δ¹³C, δ¹⁸O, and Δ's.
+  # outlier on the cycle level now contains all the reasons for cycle outliers
 # it calculates more columns, but we show some of the new ones here:
 bigD |> select(file_id, R13_wg:R17, C12, C626, C628, C828, # some columns not shown here
                d18O_PDB, d13C_PDB, R47_stoch, D47_raw)
@@ -607,13 +594,12 @@ 
calculate little delta’s a
 

 
collapse cycles: calculate averages and standard deviations
 

-
+
 coll <- bigD |>
   collapse_cycles(cols = c(d13C_PDB, d18O_PDB, D47_raw), id = c(file_id, Analysis))
 #> Info: collapsing cycles, calculating sample summaries.
-#> defaulting to mean, sd, n, sem, and 95% cl

-
-  # in the future we may want to use this nicer nesting approach?
+#> defaulting to mean, sd, n, sem, and 95% cl
+  # in the future we may want to use this nicer nesting approach?
   # It doesn't calculate summaries yet though.
   # nest_cycle_data(bgs = NULL)
 coll |> select(file_id, d13C_PDB_mean, D47_raw_mean, D47_raw_cl)
@@ -637,7 +623,7 @@ 
append metadata
 
This just left_join()s the metadata based on
 file_id, so that we can use it for outlier removal etc.

-
+
 dati <- coll |>
   add_info(stdinfo, cols = c("file_root", "file_path", "file_subpath",
                              "file_datetime", "file_size", "Row",
@@ -648,9 +634,8 @@ 
append metadata                             "MS_integration_time.s")) |>
   add_info(inits, cols = c("s44_init", "r44_init"))
 #> Info: appending measurement information.
-#> Info: appending measurement information.

-
-dati |> select(file_id, file_root:r44_init)
+#> Info: appending measurement information.
+dati |> select(file_id, file_root:r44_init)
 #> # A tibble: 27 × 22
 #>    file_id  file_root file_path file_subpath file_datetime       file_size Row  
 #>    <chr>    <chr>     <chr>     <chr>        <dttm>                  <int> <chr>
@@ -678,15 +663,14 @@ 
remove outliers
 
Here we just filter outliers based on initial intensities.

-
+
 rout <- dati |>
   unnest(cols = cycle_data) |>
   find_init_outliers(init_low = 4000, init_high = 40000, init_diff = 3000) |>
   summarize_outlier()
 #> Info: identifying aliquots with 4000 > i44_init & i44_init < 40000, s44 - r44 > 3000.
-#> Info: creating a single `outlier` column, based on all "outlier_" columns.

-
-rout |> select(file_id, starts_with("outlier"))
+#> Info: creating a single `outlier` column, based on all "outlier_" columns.
+rout |> select(file_id, starts_with("outlier"))
 #> # A tibble: 1,080 × 17
 #>    file_id    outlier_cycle_low_r44 outlier_cycle_low_s44 outlier_cycle_high_r44
 #>    <chr>      <lgl>                 <lgl>                 <lgl>                 
@@ -711,7 +695,7 @@ 
remove outliers
 
empirical transfer function
 

-
+
 detf <- rout |>
   append_expected_values(std_names = c("ETH-1", "ETH-2", "ETH-3"),
                          # I-CDES values (make sure to double-check which ones you use!)
@@ -720,9 +704,8 @@ 
empirical transfer functionapply_etf()
 #> Info: Applying ETF to D47_raw using α = slope and β = intercept.
 #> Info: Calculating ETF with D47_raw_mean as a function of expected_D47 for each Preparation.
-#> Info: Appending expected values as expected_D47 for standards ETH-1 ETH-2 and ETH-3

-
-  ## or the three functions above combined into one function
+#> Info: Appending expected values as expected_D47 for standards ETH-1 ETH-2 and ETH-3
+  ## or the three functions above combined into one function
   ## empirical_transfer_function()
 detf |> select(file_id, expected_D47:D47_etf)
 #> # A tibble: 1,080 × 7
@@ -743,7 +726,7 @@ 
empirical transfer function
 
temperature calculation
 

-
+
 temp <- detf |>
   mutate(slope = 0.0397, intercept = 0.1518) |>
   temperature_calculation(D47 = D47_etf, slope = "slope", intercept = "intercept")
@@ -752,9 +735,8 @@ 
temperature calculation#> Warning: There was 1 warning in `mutate()`.
 #> ℹ In argument: `temperature = revcal(...)`.
 #> Caused by warning in `sqrt()`:
-#> ! NaNs produced

-
-temp |> select(file_id, D47_raw_mean, D47_etf, temperature)
+#> ! NaNs produced
+temp |> select(file_id, D47_raw_mean, D47_etf, temperature)
 #> # A tibble: 1,080 × 4
 #>    file_id                   D47_raw_mean  D47_etf temperature
 #>    <chr>                            <dbl>    <dbl>       <dbl>
@@ -783,7 +765,7 @@ 
plots and summary
+
 # create a tibble that holds heights for text annotations
 summ <- temp |>
   group_by(`Identifier 1`) |>
@@ -801,15 +783,13 @@ 
plots and summary
+
 stdinfo <- iso_get_file_info(standards)
-#> Info: aggregating file info from 27 data file(s)

-
-
+#> Info: aggregating file info from 27 data file(s)
+
 inits <- get_inits(iso_get_raw_data(standards, include_file_info = "Analysis"))
-#> Info: aggregating raw data from 27 data file(s), including file info '"Analysis"'

-
-
+#> Info: aggregating raw data from 27 data file(s), including file info '"Analysis"'
+
 standards |>
   iso_filter_files(grepl("Clumped.*met", Method)) |>
   iso_get_raw_data(include_file_info = "Analysis") |>
@@ -892,7 +872,7 @@ 
HINT: look at plots interactively
 
Note that it is very nice to look at this plot—or any of the future
 ones—interactively using ggplotly:

-
+
 plotly::toWebGL(plotly::ggplotly(dynamicTicks = TRUE))

 
This creates an interactive version of the last plot in your
 browser.

@@ -908,9 +888,7 @@ 
HINT: look at plots interactively

   

-
Site built with pkgdown 2.0.9.

+
Site built with pkgdown 2.1.0.

 

 
       
 

 
-  
 
 
-  
+
+
 
   
 
diff --git a/articles/index.html b/articles/index.html
index 5733fe7..cbde3d8 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -72,15 +72,15 @@ 
All vignettes

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/authors.html b/authors.html
index daf91fa..a250793 100644
--- a/authors.html
+++ b/authors.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -57,7 +57,7 @@
         
Authors and Citation

       

 
-      
+
       
  • 
           
    Ilja Kocken. Author, maintainer. 
           
    
@@ -66,21 +66,21 @@ 
    Authors and Citation
    
     
    
     
    
       
    Citation
    
-      Source: DESCRIPTION
+      Source: DESCRIPTION
     
    
     
    
 
 
     
    Kocken I (2024).
 clumpedr: Clumped Isotope Analysis in R.
-R package version 0.3.0.9000, https://github.com/isoverse/clumpedr. 
+R package version 0.3.0.9000, https://github.com/isoverse/clumpedr, https://clumpedr.isoverse.org/.
 
    
     
    @Manual{,
   title = {clumpedr: Clumped Isotope Analysis in R},
   author = {Ilja Kocken},
   year = {2024},
-  note = {R package version 0.3.0.9000},
-  url = {https://github.com/isoverse/clumpedr},
+  note = {R package version 0.3.0.9000, https://github.com/isoverse/clumpedr},
+  url = {https://clumpedr.isoverse.org/},
 }
    
 
   

@@ -94,15 +94,15 @@ 
Citation

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/index.html b/index.html
index f9c28ce..cf2230f 100644
--- a/index.html
+++ b/index.html
@@ -19,7 +19,7 @@
 
 
 
-    
+
 
     

       

 
 
-      
+
 
       

   

@@ -205,16 +205,16 @@ 
Dev status

 
 

   

-
Site built with pkgdown 2.0.9.

+
Site built with pkgdown 2.1.0.

 

 
       
 

 
-  
 
 
-  
+
+
 
   
 
diff --git a/news/index.html b/news/index.html
index e3a1888..a6e4a46 100644
--- a/news/index.html
+++ b/news/index.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

       
Changelog 

-      Source: NEWS.md
+      Source: NEWS.md
     

 
     

@@ -98,15 +98,15 @@ 
clump
 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/pkgdown.yml b/pkgdown.yml
index aa66688..bed3b2b 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,10 +1,9 @@
 pandoc: 3.1.11
-pkgdown: 2.0.9
+pkgdown: 2.1.0
 pkgdown_sha: ~
 articles:
   clumped: clumped.html
-last_built: 2024-05-20T21:56Z
+last_built: 2024-07-22T09:24Z
 urls:
   reference: http://clumpedr.isoverse.org/reference
   article: http://clumpedr.isoverse.org/articles
-
diff --git a/reference/Brand.html b/reference/Brand.html
new file mode 100644
index 0000000..9ffc202
--- /dev/null
+++ b/reference/Brand.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/reference/abundance_ratios.html b/reference/abundance_ratios.html
index 848072f..e63ed38 100644
--- a/reference/abundance_ratios.html
+++ b/reference/abundance_ratios.html
@@ -4,7 +4,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Calculate abundance ratio based on input intensities

-    Source: R/abundance_ratios.R
+    Source: R/abundance_ratios.R
     
     

 
@@ -85,31 +85,31 @@ 
Calculate abundance ratio based on input intensities

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble.

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
i44, i45, i46, i47, i48, i49

+
i44, i45, i46, i47, i48, i49

 
Name of mass x column. Defaults to sx.

 
 
-
R45, R46, R47, R48, R49

+
R45, R46, R47, R48, R49

 
Desired new name of the calculated ratio for mass x. Defaults to Rx.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

     

     
Value

-    
-
-
Same as .data but with new columns Rx.

+    
Same as .data but with new columns Rx.

     

 
     

@@ -140,15 +140,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/acid_fractionation.html b/reference/acid_fractionation.html
index ce53821..f17e7c4 100644
--- a/reference/acid_fractionation.html
+++ b/reference/acid_fractionation.html
@@ -7,7 +7,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Add acid fractionation

-    Source: R/acid_fractionation.R
+    Source: R/acid_fractionation.R
     
     

 
@@ -83,38 +83,38 @@ 
Add acid fractionation

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble.

 
 
-
aff

+
aff

 
Temperature-dependent acid fractionation projection from 70 \(^\circ\)C to
 25 \(^\circ\)C. Defaults to 0.062, which is the average of the values obtained by
 De Vlieze et al., 2015 and Murray et al., 2016. See Muller et al., 2017.

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
D47

+
D47

 
The column name of the \(\Delta_47\) values to use for the acid
 fractionation calculation.

 
 
-
D47_out

+
D47_out

 
The desired new column name.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

     

     
Value

-    
-
-
Same as .data but with new column, named for the value of parameter D47_out.

+    
Same as .data but with new column, named for the value of parameter D47_out.

     

     

     
References

@@ -128,7 +128,7 @@ 
References

 S. M. Bernasconi. Carbonate clumped isotope analyses with the
 long-integration dual-inlet (LIDI) workflow: scratching at the lower sample
 weight boundaries. Rapid Commun. Mass Spectrom. 2017, 31,
-1057--1066.

+1057–1066.

     

 
     

@@ -152,15 +152,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/add_info.html b/reference/add_info.html
index 3c840d9..4a00d66 100644
--- a/reference/add_info.html
+++ b/reference/add_info.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Add the information from the did files

-    Source: R/add_info.R
+    Source: R/add_info.R
     
     

 
@@ -68,38 +68,38 @@ 
Add the information from the did files

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble, resulting from
 collapse_cycles().

 
 
-
.info

+
.info

 
A tibble, resulting from
 clean_did_info().

 
 
-
cols

+
cols

 
A character vector with column names in info to add to the data.

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

     

     
Value

-    
-
-
Same as .data but with new columns in cols.

+    
Same as .data but with new columns in cols.

     

     

     
See also

     
dplyr::left_join() for the function that does the matching.

-
Other metadata cleaning functions: 
+
Other metadata cleaning functions:
 clean_did_info(),
 get_inits(),
 parse_info()

@@ -130,15 +130,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/append_expected_values.html b/reference/append_expected_values.html
index e106cda..467c470 100644
--- a/reference/append_expected_values.html
+++ b/reference/append_expected_values.html
@@ -1,10 +1,10 @@
 
 Append expected values — append_expected_values • clumpedr
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Append expected values

-    Source: R/append_expected_values.R
+    Source: R/append_expected_values.R
     
     

 
     

     
Append the expected values for the standards. Defaults to using
-ETH-1--ETH-3.

+ETH-1–ETH-3.

     

 
     

@@ -78,39 +78,39 @@ 
Append expected values

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble.

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
std_names

+
std_names

 
Names of the standards.

 
 
-
std_values

+
std_values

 
Expected values of the standards. Defaults to Bernasconi et al., 2021.

 
 
-
exp

+
exp

 
Name of the new column that will hold expected values.

 
 
-
by

+
by

 
Name of the standard/sample identifier column.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

     

     
Value

-    
-
-
Same as .data but with new column in exp.

+    
Same as .data but with new column in exp.

     

     

     
References

@@ -125,7 +125,7 @@ 
References

     

     

     
See also

-    
Other empirical transfer functions: 
+    
Other empirical transfer functions:
 apply_etf(),
 calculate_etf(),
 empirical_transfer_function()

@@ -170,15 +170,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/append_ref_deltas.html b/reference/append_ref_deltas.html
index 117a375..73f16e1 100644
--- a/reference/append_ref_deltas.html
+++ b/reference/append_ref_deltas.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Append reference gas delta values

-    Source: R/reference_gas_delta.R
+    Source: R/reference_gas_delta.R
     
     

 
@@ -75,35 +75,35 @@ 
Append reference gas delta values

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble to append the delta values to.

 
 
-
.did

+
.did

 
An iso file, resulting from isoreader::iso_read_dual_inlet().

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
d13C_PDB_wg

+
d13C_PDB_wg

 
\(\delta^{13}C\) reference gas value to overwrite.

 
 
-
d18O_PDBCO2_wg

+
d18O_PDBCO2_wg

 
\(\delta^{18}O\) reference gas value to overwrite.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

     

     
Value

-    
-
-
Same as .data but with new columns d13C_PDB_wg and d18O_PDBCO2_wg.

+    
Same as .data but with new columns d13C_PDB_wg and d18O_PDBCO2_wg.

     

 
     

@@ -142,15 +142,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/apply_etf.html b/reference/apply_etf.html
index c4bde70..c18ae15 100644
--- a/reference/apply_etf.html
+++ b/reference/apply_etf.html
@@ -4,7 +4,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Apply the ETF

-    Source: R/apply_etf.R
+    Source: R/apply_etf.R
     
     

 
@@ -78,31 +78,33 @@ 
Apply the ETF

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble containing column D47.

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
intercept

+
intercept

 
The column name with the ETF intercept.

 
 
-
slope

+
slope

 
The column name with the ETF slope.

 
 
-
raw

+
raw

 
The column with raw values to apply the ETF to.

 
 
-
out

+
out

 
The new column name.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

@@ -115,7 +117,7 @@ 
Details

     

     

     
See also

-    
Other empirical transfer functions: 
+    
Other empirical transfer functions:
 append_expected_values(),
 calculate_etf(),
 empirical_transfer_function()

@@ -133,15 +135,15 @@ 
See also

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/brand.parameters.html b/reference/brand.parameters.html
new file mode 100644
index 0000000..9ffc202
--- /dev/null
+++ b/reference/brand.parameters.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/reference/brand_parameters.html b/reference/brand_parameters.html
new file mode 100644
index 0000000..9ffc202
--- /dev/null
+++ b/reference/brand_parameters.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/reference/bulk_and_clumping_deltas.html b/reference/bulk_and_clumping_deltas.html
index 73578a7..ea9155c 100644
--- a/reference/bulk_and_clumping_deltas.html
+++ b/reference/bulk_and_clumping_deltas.html
@@ -4,7 +4,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Compute \(\delta^{13}\)C, \(\delta^{18}\)O \(\Delta_{47}\), \(\Delta_{48}\), and \(\Delta_{49}\) values

-    Source: R/bulk_and_clumping_deltas.R
+    Source: R/bulk_and_clumping_deltas.R
     
     

 
@@ -85,82 +85,82 @@ 
Compute \(\delta^{13}\)C, \(\delta^{18}\)O \(\Delta_{47}\), \(\Delta_{48}\),
 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble containing s44-s49, r44-r49,
 R45-R49, R45_wg-R49_wg, d45-d49, and working gas compositions d13C_PDB_wg and
 d18OPDBCO2_wg.

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
d45

+
d45

 
Column name of d45.

 
 
-
d46

+
d46

 
Column name of d46.

 
 
-
d47

+
d47

 
Column name of d47.

 
 
-
d48

+
d48

 
Column name of d48.

 
 
-
d49

+
d49

 
Column name of d49.

 
 
-
R13_PDB

+
R13_PDB

 
The R13 value of the PDB reference. Defaults to 0.01118, from
 Chang and Li, 1990.

 
 
-
R18_PDB

+
R18_PDB

 
The R18 value of the PDB reference. Defaults to 1.008751,
 from Coplen et al., 1983.

 
 
-
R17_PDBCO2

+
R17_PDBCO2

 
The R17 value of PDB (g). Defaults to 0.0003931, from
 Assonov and Brenninkmeijer 2003, re-scaled by Brand, 2010.

 
 
-
R18_PDBCO2

+
R18_PDBCO2

 
The R18 value of PDB (g). Defaults to 0.00208839, derrived
 from Baertschi, 1976, calculated by Brand 2010 eq. 2.

 
 
-
lambda

+
lambda

 
Isotopic fractionation of \(^{17}\)O. Defaults to 0.528,
 from Barkan and Luz, 2005.

 
 
-
D17O

+
D17O

 
The difference between the expected \(\delta^{17}\)O
 (\(\delta^{18}\)O\(-\lambda*\delta^{18}\)O)
 and the actual \(\delta^{17}\)O value.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

     

     
Value

-    
-
-
Same as .data but with new columns R45-R49, a lot of intermediate steps, and D47_raw.

+    
Same as .data but with new columns R45-R49, a lot of intermediate steps, and D47_raw.

     

     

     
References

     
Daeron, M., Blamart, D., Peral, M., & Affek, H. P., Absolute
 isotopic abundance ratios and the accuracy of \(\Delta_{47}\)
-measurements, Chemical Geology 2016, 442, 83--96.
+measurements, Chemical Geology 2016, 442, 83–96.
 doi:10.1016/j.chemgeo.2016.08.014

     

 
@@ -190,15 +190,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/calculate_etf.html b/reference/calculate_etf.html
index 25afa7a..a1be638 100644
--- a/reference/calculate_etf.html
+++ b/reference/calculate_etf.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Calculate the Empirical Transfer Function

-    Source: R/calculate_etf.R
+    Source: R/calculate_etf.R
     
     

 
@@ -80,60 +80,60 @@ 
Calculate the Empirical Transfer Function

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble.

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
raw

+
raw

 
Column name of raw \(\Delta_{47}\) values.

 
 
-
exp

+
exp

 
Column name of expected \(\Delta_{47}\) values.

 
 
-
session

+
session

 
The column name to group analyses by. Defaults to
 Preparation.

 
 
-
etf

+
etf

 
The column name of the new model.

 
 
-
etf_coefs

+
etf_coefs

 
The column name with the coefficients of the model.

 
 
-
slope

+
slope

 
The column name of the new slope.

 
 
-
intercept

+
intercept

 
The column name of the new intercept.

 
 
-
parallel

+
parallel

 
Whether or not (default) to process this in parallel, using package furrr.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

     

     
Value

-    
-
-
Same as .data with new columns etf, etf_coefs, slope, and intercept.

+    
Same as .data with new columns etf, etf_coefs, slope, and intercept.

     

     

     
See also

-    
Other empirical transfer functions: 
+    
Other empirical transfer functions:
 append_expected_values(),
 apply_etf(),
 empirical_transfer_function()

@@ -151,15 +151,15 @@ 
See also

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/clean_did_info.html b/reference/clean_did_info.html
index 6905c39..3785bed 100644
--- a/reference/clean_did_info.html
+++ b/reference/clean_did_info.html
@@ -4,7 +4,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Clean up the did file info

-    Source: R/clean_did_info.R
+    Source: R/clean_did_info.R
     
     

 
@@ -77,27 +77,29 @@ 
Clean up the did file info

 
     

     
Arguments

-    
.did

+
+
+
.did

 
An iso file, resulting from isoreader::iso_read_dual_inlet().

 
 
-
masspec

+
masspec

 
The name of the mass spectrometer to append.

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
std_names

+
std_names

 
Character vector of the standard names to find in Identifier 1.

 
 
-
oth_name

+
oth_name

 
Single general name to assign to non-standard "other" measurements.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

@@ -105,7 +107,7 @@ 
Arguments

     
See also

     
isoreader::iso_read_dual_inlet()

 
isoreader::iso_get_file_info()

-
Other metadata cleaning functions: 
+
Other metadata cleaning functions:
 add_info(),
 get_inits(),
 parse_info()

@@ -123,15 +125,15 @@ 
See also

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/clumpedr-package.html b/reference/clumpedr-package.html
index 22bb8f4..e936a14 100644
--- a/reference/clumpedr-package.html
+++ b/reference/clumpedr-package.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Clumped isotope analysis in R

-    Source: R/clumpedr-package.R
+    Source: R/clumpedr-package.R
     
     

 
@@ -69,7 +69,7 @@ 
Details

     

     

     
Package options

-    
+
 
 
The functions in this package listen to the quiet option.

     

@@ -96,15 +96,15 @@ 
Author

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/clumpedr.html b/reference/clumpedr.html
new file mode 100644
index 0000000..6b8a15c
--- /dev/null
+++ b/reference/clumpedr.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/reference/clumpedr.parameters.html b/reference/clumpedr.parameters.html
new file mode 100644
index 0000000..9ffc202
--- /dev/null
+++ b/reference/clumpedr.parameters.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/reference/clumpedr.params.html b/reference/clumpedr.params.html
new file mode 100644
index 0000000..9ffc202
--- /dev/null
+++ b/reference/clumpedr.params.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/reference/clumpedr_get_default_parameters.html b/reference/clumpedr_get_default_parameters.html
index 3aad9dd..b8f9fb0 100644
--- a/reference/clumpedr_get_default_parameters.html
+++ b/reference/clumpedr_get_default_parameters.html
@@ -10,7 +10,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Get the current default parameters

-    Source: R/settings.R
+    Source: R/settings.R
     
     

 
@@ -93,15 +93,15 @@ 
Get the current default parameters

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/collapse_cycles.html b/reference/collapse_cycles.html
index 133054b..b44ce21 100644
--- a/reference/collapse_cycles.html
+++ b/reference/collapse_cycles.html
@@ -4,7 +4,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Collapse the cycles of the raw measurements

-    Source: R/collapse_cycles.R
+    Source: R/collapse_cycles.R
     
     

 
@@ -80,40 +80,42 @@ 
Collapse the cycles of the raw measurements

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble resulting from bulk_and_clumping_deltas().

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
cols

+
cols

 
Columns to calculate summaries for.

 
 
-
id

+
id

 
Index columns that will be excluded from nesting. Defaults tofile_id.

 
 
-
outlier

+
outlier

 
The column containing outlier information.

 
 
-
funs

+
funs

 
List of summary functions to apply. Defaults to mean, sd, n, sem, 95% cl.

 
 
-
alpha

+
alpha

 
The confidence level for the summary functions.

 
 
-
na.rm

+
na.rm

 
a logical value indicating wheter NA values should be stripped
 before the computation proceeds.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

@@ -130,15 +132,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/correct_backgrounds.html b/reference/correct_backgrounds.html
index f29a670..e291b28 100644
--- a/reference/correct_backgrounds.html
+++ b/reference/correct_backgrounds.html
@@ -4,7 +4,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Background corrections

-    Source: R/correct_backgrounds.R
+    Source: R/correct_backgrounds.R
     
     

 
@@ -77,35 +77,35 @@ 
Background corrections

 
     

     
Arguments

-    
.data

+
+
+
.data

 
The dataframe with raw iso files.

 
 
-
factor

+
factor

 
Factor by which to multiply the half-cup before subtraction.

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
i47

+
i47

 
Column with mass 47 intensities to correct. Defaults to v47.mV.

 
 
-
i54

+
i54

 
Column with mass 47.5 intensities to use for correction. Defaults to v54.mV.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

     

     
Value

-    
-
-
Same as .data but with altered i47 column.

+    
Same as .data but with altered i47 column.

     

 
     

@@ -148,15 +148,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/default.parameters.html b/reference/default.parameters.html
new file mode 100644
index 0000000..9ffc202
--- /dev/null
+++ b/reference/default.parameters.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/reference/default.params.html b/reference/default.params.html
index 12c74d7..54d6200 100644
--- a/reference/default.params.html
+++ b/reference/default.params.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Default parameters

-    Source: R/defaults.R
+    Source: R/defaults.R
     
     

 
@@ -65,46 +65,48 @@ 
Default parameters

 
     

     
Arguments

-    
R13_PDB

+
+
+
R13_PDB

 
The R13 value of the PDB reference. Defaults to 0.01118, from
 Chang and Li, 1990.

 
 
-
R18_PDB

+
R18_PDB

 
The R18 value of the PDB reference. Defaults to 1.008751,
 from Coplen et al., 1983.

 
 
-
R17_PDBCO2

+
R17_PDBCO2

 
The R17 value of PDB (g). Defaults to 0.0003931, from
 Assonov and Brenninkmeijer 2003, re-scaled by Brand, 2010.

 
 
-
R18_PDBCO2

+
R18_PDBCO2

 
The R18 value of PDB (g). Defaults to 0.00208839, derrived
 from Baertschi, 1976, calculated by Brand 2010 eq. 2.

 
 
-
lambda

+
lambda

 
Isotopic fractionation of \(^{17}\)O. Defaults to 0.528,
 from Barkan and Luz, 2005.

 
 
-
D17O

+
D17O

 
The difference between the expected \(\delta^{17}\)O
 (\(\delta^{18}\)O\(-\lambda*\delta^{18}\)O)
 and the actual \(\delta^{17}\)O value.

 
 
-
D47

+
D47

 
TODO: look up

 
 
-
D48

+
D48

 
TODO: look up

 
 
-
D49

+
D49

 
TODO: look up

 
 

@@ -126,7 +128,7 @@ 
References

 \(^{17}\)O interference in \(\delta^{13}\)C measurements when
 analyzing CO\(_{2}\) with stable isotope mass spectrometry (IUPAC
 Technical Report). Pure and Applied Chemistry, 2010, 82(8),
-1719--1733. doi:10.1351/PAC-REP-09-01-05

+1719–1733. doi:10.1351/PAC-REP-09-01-05

     

 
   

@@ -141,15 +143,15 @@ 
References

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/delta_values.html b/reference/delta_values.html
index bce37ac..a0110bf 100644
--- a/reference/delta_values.html
+++ b/reference/delta_values.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Calculate abundance ratios, \(\delta^{18}\)O, \(\delta^{13}\)C, \(\delta\)'s, and raw \(\Delta\) values

-    Source: R/delta_values.R
+    Source: R/delta_values.R
     
     

 
@@ -68,16 +68,18 @@ 
Calculate abundance ratios, \(\delta^{18}\)O, \(\delta^{13}\)C, \(\delta\)'s
 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble, resulting from
 correct_backgrounds().

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

@@ -99,15 +101,15 @@ 
Details

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/empirical_transfer_function.html b/reference/empirical_transfer_function.html
index c8a0a75..117584e 100644
--- a/reference/empirical_transfer_function.html
+++ b/reference/empirical_transfer_function.html
@@ -5,7 +5,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Empirical Transfer Function

-    Source: R/empirical_transfer_function.R
+    Source: R/empirical_transfer_function.R
     
     

 
@@ -89,68 +89,70 @@ 
Empirical Transfer Function

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble resulting from collapse_cycles().

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
std_names

+
std_names

 
Names of the standards.

 
 
-
std_values

+
std_values

 
Expected values of the standards. Defaults to Bernasconi et al., 2021.

 
 
-
raw

+
raw

 
Column name of raw \(\Delta_{47}\) values.

 
 
-
exp

+
exp

 
Name of the new column that will hold expected values.

 
 
-
session

+
session

 
The column name to group analyses by. Defaults to
 Preparation.

 
 
-
id1

+
id1

 
Column name of Identifier 1 (default).

 
 
-
etf

+
etf

 
The column name of the new model.

 
 
-
etf_coefs

+
etf_coefs

 
The column name with the coefficients of the model.

 
 
-
slope

+
slope

 
The column name of the new slope.

 
 
-
intercept

+
intercept

 
The column name of the new intercept.

 
 
-
out

+
out

 
The new column name.

 
 
-
outlier

+
outlier

 
Column name of outlier (default).

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 
-
parallel

+
parallel

 
Whether or not (default) to process this in parallel, using package furrr.

 
 

@@ -161,7 +163,7 @@ 
Details

     

     

     
See also

-    
Other empirical transfer functions: 
+    
Other empirical transfer functions:
 append_expected_values(),
 apply_etf(),
 calculate_etf()

@@ -179,15 +181,15 @@ 
See also

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/eth3.html b/reference/eth3.html
index f2c2115..30345b2 100644
--- a/reference/eth3.html
+++ b/reference/eth3.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Single ETH-3 standard did file

-    Source: R/data.R
+    Source: R/data.R
     
     

 
@@ -83,15 +83,15 @@ 
Format

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/find_bad_cycles.html b/reference/find_bad_cycles.html
index 13da273..31a4692 100644
--- a/reference/find_bad_cycles.html
+++ b/reference/find_bad_cycles.html
@@ -7,7 +7,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Find bad cycles based on several criteria.

-    Source: R/find_bad_cycles.R
+    Source: R/find_bad_cycles.R
     
     

 
@@ -86,50 +86,50 @@ 
Find bad cycles based on several criteria.

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble, resulting from
 isoreader::iso_get_raw_data().

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
min

+
min

 
Minimum intensity level for good cycles. Defaults to 1,500 mV.

 
 
-
max

+
max

 
Maximum intensity level for good cycles. Defaults to 50,000 mV.

 
 
-
fac

+
fac

 
Factor for how much larger the current drop should be than the
 one specified in relative_to.

 
 
-
v44

+
v44

 
Column name of mass 44.

 
 
-
cycle

+
cycle

 
Column name of the column with the measurement cycle number.

 
 
-
relative_to

+
relative_to

 
cycle Drop detection occurs relative to either the first
 cycle ("init", default) or to the previous cycle ("prev").

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

     

     
Value

-    
-
-
Same as .data but with some new columns that allow us to disable
+    
Same as .data but with some new columns that allow us to disable
 certain cycles/whole samples.

     

     

@@ -182,15 +182,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/find_init_outliers.html b/reference/find_init_outliers.html
index 6c5e114..16fbe1b 100644
--- a/reference/find_init_outliers.html
+++ b/reference/find_init_outliers.html
@@ -6,7 +6,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Find measurements that have wrong initial intensities.

-    Source: R/find_outliers.R
+    Source: R/find_outliers.R
     
     

 
@@ -74,27 +74,29 @@ 
Find measurements that have wrong initial intensities.

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble with raw Delta values and file information.

 
 
-
init_low

+
init_low

 
Column in .data with minimum initial intensity threshold for mass 44.

 
 
-
init_high

+
init_high

 
Column in .data with maximum initial intensity threshold for mass 44.

 
 
-
init_diff

+
init_diff

 
Column in .data with maximum initial difference in mass 44 threshold between standard and sample gas.

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

@@ -111,15 +113,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/find_internal_sd_outlier.html b/reference/find_internal_sd_outlier.html
index 07dfd07..7a19ea5 100644
--- a/reference/find_internal_sd_outlier.html
+++ b/reference/find_internal_sd_outlier.html
@@ -4,7 +4,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Find internal standard deviation outliers.

-    Source: R/find_outliers.R
+    Source: R/find_outliers.R
     
     

 
@@ -76,23 +76,25 @@ 
Find internal standard deviation outliers.

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble with raw Delta values and file information.

 
 
-
internal_sd

+
internal_sd

 
The internal standard deviation cutoff value.

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
D47

+
D47

 
The column to calculate the internal sd value for.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

@@ -109,15 +111,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/find_outliers.html b/reference/find_outliers.html
index f424d61..90b1371 100644
--- a/reference/find_outliers.html
+++ b/reference/find_outliers.html
@@ -10,7 +10,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Find outliers

-    Source: R/find_outliers.R
+    Source: R/find_outliers.R
     
     

 
@@ -94,59 +94,61 @@ 
Find outliers

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble with raw Delta values and file information.

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
init_low

+
init_low

 
Minimum initial intensity threshold for mass 44.

 
 
-
init_high

+
init_high

 
Maximum initial intensity threshold for mass 44.

 
 
-
init_diff

+
init_diff

 
Maximum initial difference in mass 44 threshold between standard and sample gas.

 
 
-
param49_off

+
param49_off

 
Where param_49 > this value is considered an outlier.

 
 
-
internal_sd

+
internal_sd

 
The internal standard deviation outlier cutoff.

 
 
-
n_min

+
n_min

 
Minimum number of aliquots within session to calculate threshold.

 
 
-
n_id1

+
n_id1

 
Minimum number of aliquots within session to calculate threshold within group.

 
 
-
nsd_off

+
nsd_off

 
Number of standard deviations away from the mean threshold.

 
 
-
D47

+
D47

 
The column with \(\Delta_{47}\) values.

 
 
-
session

+
session

 
Column name that defines correction session.

 
 
-
id1

+
id1

 
Column name of the sample/standard identifier.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

@@ -163,15 +165,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/find_param49_outliers.html b/reference/find_param49_outliers.html
index 8f3e72e..57d6faa 100644
--- a/reference/find_param49_outliers.html
+++ b/reference/find_param49_outliers.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Find param 49 outliers.

-    Source: R/find_outliers.R
+    Source: R/find_outliers.R
     
     

 
@@ -68,19 +68,21 @@ 
Find param 49 outliers.

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble with raw Delta values and file information.

 
 
-
param49_off

+
param49_off

 
The absolute cutoff value for the parameter 49 value.

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

@@ -97,15 +99,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/find_session_id1_outlier.html b/reference/find_session_id1_outlier.html
index a47097b..c14cdf7 100644
--- a/reference/find_session_id1_outlier.html
+++ b/reference/find_session_id1_outlier.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Find session outliers by sample/standard type.

-    Source: R/find_outliers.R
+    Source: R/find_outliers.R
     
     

 
@@ -77,35 +77,37 @@ 
Find session outliers by sample/standard type.

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble with raw Delta values and file information.

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
n_id1

+
n_id1

 
The minimum number of measurements of the sample/standard in the session needed to calculate an offset from the median.

 
 
-
nsd_off

+
nsd_off

 
The number of standard deviations away from the median.

 
 
-
D47

+
D47

 
The column to calculate the internal sd value for.

 
 
-
session

+
session

 
The session for which to calculate the standard deviation and median values.

 
 
-
id1

+
id1

 
The column that defines the sample/standard name.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

@@ -122,15 +124,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/find_session_outlier.html b/reference/find_session_outlier.html
index 891198c..cc0b2c6 100644
--- a/reference/find_session_outlier.html
+++ b/reference/find_session_outlier.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Find session outliers.

-    Source: R/find_outliers.R
+    Source: R/find_outliers.R
     
     

 
@@ -77,35 +77,37 @@ 
Find session outliers.

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble with raw Delta values and file information.

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
n

+
n

 
The minimum number of measurements in the session needed to calculate an offset from the median.

 
 
-
nsd_off

+
nsd_off

 
The number of standard deviations away from the median.

 
 
-
D47

+
D47

 
The column to calculate the internal sd value for.

 
 
-
outlier_session

+
outlier_session

 
Column name of new output column.

 
 
-
session

+
session

 
The session for which to calculate the standard deviation and median values.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

@@ -122,15 +124,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/get_inits.html b/reference/get_inits.html
index b4538e2..53e07f8 100644
--- a/reference/get_inits.html
+++ b/reference/get_inits.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Get initial intensities of specified mass

-    Source: R/clean_did_info.R
+    Source: R/clean_did_info.R
     
     

 
@@ -68,19 +68,19 @@ 
Get initial intensities of specified mass

 
     

     
Arguments

-    
.did

+
+
+
.did

 
The raw data, resulting from isoreader::iso_get_raw_data().

 
 

     

     
Value

-    
-
-
A new tibble with columns file_id, s44_init, and r44_init

+    
A new tibble with columns file_id, s44_init, and r44_init

     

     

     
See also

-    
Other metadata cleaning functions: 
+    
Other metadata cleaning functions:
 add_info(),
 clean_did_info(),
 parse_info()

@@ -119,15 +119,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/get_ref_delta.html b/reference/get_ref_delta.html
index 185ca4d..f1b4f84 100644
--- a/reference/get_ref_delta.html
+++ b/reference/get_ref_delta.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Get reference gas delta values

-    Source: R/reference_gas_delta.R
+    Source: R/reference_gas_delta.R
     
     

 
@@ -68,7 +68,9 @@ 
Get reference gas delta values

 
     

     
Arguments

-    
.did

+
+
+
.did

 
An iso file, resulting from isoreader::iso_read_dual_inlet().

 
 

@@ -85,15 +87,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/index.html b/reference/index.html
index f485d76..b8db366 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -1,9 +1,9 @@
 
-Function reference • clumpedrPackage index • clumpedr
-    
+
 
     

       

   

 

 
-      
+
 
       

   

@@ -229,15 +229,15 @@ 
All functions 
 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/isobar_ratios.html b/reference/isobar_ratios.html
index 847dc32..f7a5c37 100644
--- a/reference/isobar_ratios.html
+++ b/reference/isobar_ratios.html
@@ -6,7 +6,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Compute isotopic ratios

-    Source: R/isobar_ratios.R
+    Source: R/isobar_ratios.R
     
     

 
@@ -91,72 +91,74 @@ 
Compute isotopic ratios

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble with columns R13 and R18.

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
R13

+
R13

 
The column name for R13.

 
 
-
R18

+
R18

 
The column name for R18.

 
 
-
R45

+
R45

 
The output column name for R45.

 
 
-
R46

+
R46

 
The output column name for R46.

 
 
-
R47

+
R47

 
The output column name for R47.

 
 
-
R48

+
R48

 
The output column name for R48.

 
 
-
R49

+
R49

 
The output column name for R49.

 
 
-
R17_PDBCO2

+
R17_PDBCO2

 
The R17 value of PDB (g). Defaults to 0.0003931, from
 Assonov and Brenninkmeijer 2003, re-scaled by Brand, 2010.

 
 
-
R18_PDBCO2

+
R18_PDBCO2

 
The R18 value of PDB (g). Defaults to 0.00208839, derrived
 from Baertschi, 1976, calculated by Brand 2010 eq. 2.

 
 
-
lambda

+
lambda

 
Isotopic fractionation of \(^{17}\)O. Defaults to 0.528,
 from Barkan and Luz, 2005.

 
 
-
D17O

+
D17O

 
The difference between the expected \(\delta^{17}\)O
 (\(\delta^{18}\)O\(-\lambda*\delta^{18}\)O)
 and the actual \(\delta^{17}\)O value.

 
 
-
D47

+
D47

 
TODO: look up

 
 
-
D48

+
D48

 
TODO: look up

 
 
-
D49

+
D49

 
TODO: look up

 
 

@@ -164,7 +166,7 @@ 
Arguments

     
References

     
Daeron, M., Blamart, D., Peral, M., & Affek, H. P., Absolute
 isotopic abundance ratios and the accuracy of \(\Delta_{47}\)
-measurements, Chemical Geology 2016, 442, 83--96.
+measurements, Chemical Geology 2016, 442, 83–96.
 doi:10.1016/j.chemgeo.2016.08.014

     

 
@@ -180,15 +182,15 @@ 
References

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/little_deltas.html b/reference/little_deltas.html
index cab76b5..3641a74 100644
--- a/reference/little_deltas.html
+++ b/reference/little_deltas.html
@@ -4,7 +4,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Calculate little deltas from abundance ratios

-    Source: R/little_deltas.R
+    Source: R/little_deltas.R
     
     

 
@@ -70,23 +70,23 @@ 
Calculate little deltas from abundance ratios

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble with abundance ratios.

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

     

     
Value

-    
-
-
Same as .data but with new columns d45-d49.

+    
Same as .data but with new columns d45-d49.

     

 
     

@@ -112,15 +112,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/match_intensities.html b/reference/match_intensities.html
index d27a4d5..de8b12b 100644
--- a/reference/match_intensities.html
+++ b/reference/match_intensities.html
@@ -4,7 +4,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Match the reference gas intensity to that of the sample gas

-    Source: R/spread_match.R
+    Source: R/spread_match.R
     
     

 
@@ -76,25 +76,27 @@ 
Match the reference gas intensity to that of the sample gas

 
     

     
Arguments

-    
.data

-
A tibble with s44--s49 and r44--r49; output of
+
+
+
.data

+
A tibble with s44–s49 and r44–r49; output of
 spread_intensities().

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
method

+
method

 
"linterp" for linear interpolation, or "normal" for
 conventional bracketing of sample gas.

 
 
-
masses

+
masses

 
The masses to generate r and s columns from.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

@@ -111,15 +113,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/nest_cycle_data.html b/reference/nest_cycle_data.html
index 95686ef..650f91d 100644
--- a/reference/nest_cycle_data.html
+++ b/reference/nest_cycle_data.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
nest cycle data

-    Source: R/collapse_cycles.R
+    Source: R/collapse_cycles.R
     
     

 
@@ -92,83 +92,83 @@ 
nest cycle data

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble resulting from bulk_and_clumping_deltas().

 
 
-
...

+
...

 
Additional chacter vectors to nest by.

 
 
-
masses

+
masses

 
The masses that are present in the mass spectrometer. Defaults to 44:49 and 54.

 
 
-
ratios

+
ratios

 
Ratio columns, based on masses.

 
 
-
outlier_cycles

+
outlier_cycles

 
Columns with outlier_cycle information.

 
 
-
outliers

+
outliers

 
Other outlier-related columns.

 
 
-
cycle_drop

+
cycle_drop

 
Columns related to detecing cycle drops.

 
 
-
bgs

+
bgs

 
Backgrounds.

 
 
-
bg_corrected

+
bg_corrected

 
Background-corrected raw intensities per cup.

 
 
-
Rs

+
Rs

 
R values.

 
 
-
deltas

+
deltas

 
delta values.

 
 
-
isotopes

+
isotopes

 
C values.

 
 
-
params

+
params

 
Taylor polynomial parameters.

 
 
-
stochastic

+
stochastic

 
Stochastic R values.

 
 
-
flags

+
flags

 
Flag columns.

 
 
-
Deltas

+
Deltas

 
Big delta values.

 
 
-
p49

+
p49

 
Param 49.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

     

     
Value

-    
-
-
A summary of .data,

+    
A summary of .data,

     

     

     
Details

@@ -188,15 +188,15 @@ 
Details

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/parse_info.html b/reference/parse_info.html
index d5c299f..06a9c8f 100644
--- a/reference/parse_info.html
+++ b/reference/parse_info.html
@@ -4,7 +4,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Parse info into appropriate types.

-    Source: R/clean_did_info.R
+    Source: R/clean_did_info.R
     
     

 
@@ -77,33 +77,35 @@ 
Parse info into appropriate types.

 
     

     
Arguments

-    
.did

+
+
+
.did

 
An iso file, resulting from isoreader::iso_read_dual_inlet().

 
 
-
masspec

+
masspec

 
The name of the mass spectrometer to append.

 
 
-
std_names

+
std_names

 
Character vector of the standard names to find in Identifier 1.

 
 
-
oth_name

+
oth_name

 
Single general name to assign to non-standard "other" measurements.

 
 
-
broadid_name

+
broadid_name

 
The name of the new broadid column.

 
 
-
id1

+
id1

 
The column with sample and standard names.

 
 

     

     
See also

-    
Other metadata cleaning functions: 
+    
Other metadata cleaning functions:
 add_info(),
 clean_did_info(),
 get_inits()

@@ -121,15 +123,15 @@ 
See also

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/pipe.html b/reference/pipe.html
index ece67f3..9f19fe8 100644
--- a/reference/pipe.html
+++ b/reference/pipe.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Pipe operator

-    Source: R/utils-pipe.R
+    Source: R/utils-pipe.R
     
     

 
@@ -79,15 +79,15 @@ 
Pipe operator

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/remove_outliers.html b/reference/remove_outliers.html
index a0b95e8..9837471 100644
--- a/reference/remove_outliers.html
+++ b/reference/remove_outliers.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Remove outliers

-    Source: R/remove_outliers.R
+    Source: R/remove_outliers.R
     
     

 
@@ -83,61 +83,63 @@ 
Remove outliers

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble, resulting from
 collapse_cycles().

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
init_low

+
init_low

 
Minimum initial intensity threshold for mass 44.

 
 
-
init_high

+
init_high

 
Maximum initial intensity threshold for mass 44.

 
 
-
init_diff

+
init_diff

 
Maximum initial difference in mass 44 threshold between standard and sample gas.

 
 
-
param49_off

+
param49_off

 
Where param_49 > this value is considered an outlier.

 
 
-
internal_sd

+
internal_sd

 
The internal standard deviation outlier cutoff.

 
 
-
n_min

+
n_min

 
Minimum number of aliquots within session to calculate threshold.

 
 
-
n_id1

+
n_id1

 
Minimum number of aliquots within session to calculate threshold within group.

 
 
-
nsd_off

+
nsd_off

 
The number of standard deviations away from the median
 Preparation of the standards.

 
 
-
D47

+
D47

 
The column with \(\Delta_47\) values. Defaults to D47_raw_mean.

 
 
-
session

+
session

 
Column name that defines correction session.

 
 
-
id1

+
id1

 
Column name of the sample/standard identifier.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

@@ -162,15 +164,15 @@ 
Details

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/revcal.html b/reference/revcal.html
index 8c1c2ac..33571b8 100644
--- a/reference/revcal.html
+++ b/reference/revcal.html
@@ -7,7 +7,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Reverse temperature calibration

-    Source: R/calibration.R
+    Source: R/calibration.R
     
     

 
@@ -83,36 +83,36 @@ 
Reverse temperature calibration

 
     

     
Arguments

-    
D47

+
+
+
D47

 
The \(\Delta_{47}\) value.

 
 
-
slope

+
slope

 
The slope of the regression.

 
 
-
intercept

+
intercept

 
The intercept of the regression.

 
 
-
slpcnf

+
slpcnf

 
The confidence of the slope of the regression.

 
 
-
intcnf

+
intcnf

 
The confidence of the intercept of the regression.

 
 
-
ignorecnf

+
ignorecnf

 
Whether or not to ignore the confidence of the temperature
 calibration.

 
 

     

     
Value

-    
-
-
A tibble with input \(\Delta_{47}\) and estimated Tc value
+    
A tibble with input \(\Delta_{47}\) and estimated Tc value
 with lower and upper bounds.

     

     

@@ -137,15 +137,15 @@ 
See also

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/spread_intensities.html b/reference/spread_intensities.html
index ddb8627..2010bdb 100644
--- a/reference/spread_intensities.html
+++ b/reference/spread_intensities.html
@@ -5,7 +5,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Spread intensities from iso_read format into wide format.

-    Source: R/spread_match.R
+    Source: R/spread_match.R
     
     

 
@@ -79,35 +79,35 @@ 
Spread intensities from iso_read format into wide format.

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble containing mass intensities per cycle.

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
ids

+
ids

 
Identifying columns that we'll group by.

 
 
-
our_cols

+
our_cols

 
Columns with data values that need to be reshaped. Defaults to v44.mV to v54.mV.

 
 
-
names_pattern

+
names_pattern

 
Regular expression passed to [tidyr::pivot_longer].

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

     

     
Value

-    
-
-
A tibble with the sample and reference
+    
A tibble with the sample and reference
 gasses side-by-side as s44-s49 and r44-r49.

     

 
@@ -123,15 +123,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/spread_match.html b/reference/spread_match.html
index 18463b1..827aa13 100644
--- a/reference/spread_match.html
+++ b/reference/spread_match.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Spread and match sample gas and reference gas.

-    Source: R/spread_match.R
+    Source: R/spread_match.R
     
     

 
@@ -74,24 +74,26 @@ 
Spread and match sample gas and reference gas.

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble, resulting from isoreader::iso_get_raw_data().

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
method

+
method

 
"linterp" for linear interpolation, or "normal" for
 conventional bracketing of sample gas.

 
 
-
masses

+
masses

 
The masses to generate r and s columns from.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

@@ -108,15 +110,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/standards.html b/reference/standards.html
index d4d8a47..6f278c9 100644
--- a/reference/standards.html
+++ b/reference/standards.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
27 Dual Inlet did files

-    Source: R/data.R
+    Source: R/data.R
     
     

 
@@ -83,15 +83,15 @@ 
Format

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/summarise_outlier.html b/reference/summarise_outlier.html
index b9832e3..9c82bbf 100644
--- a/reference/summarise_outlier.html
+++ b/reference/summarise_outlier.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Summarise the outlier columns.

-    Source: R/find_outliers.R
+    Source: R/find_outliers.R
     
     

 
@@ -68,19 +68,21 @@ 
Summarise the outlier columns.

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble with raw Delta values and file information.

 
 
-
out_column

+
out_column

 
The name of the outlier column.

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

@@ -97,15 +99,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/summarize_outlier.html b/reference/summarize_outlier.html
index 8b13f7f..e4bb947 100644
--- a/reference/summarize_outlier.html
+++ b/reference/summarize_outlier.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Summarize the outlier columns.

-    Source: R/find_outliers.R
+    Source: R/find_outliers.R
     
     

 
@@ -68,19 +68,21 @@ 
Summarize the outlier columns.

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble with raw Delta values and file information.

 
 
-
out_column

+
out_column

 
The name of the outlier column.

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

@@ -97,15 +99,15 @@ 
Arguments

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/tempcal.html b/reference/tempcal.html
index 35f2dab..c30cbf3 100644
--- a/reference/tempcal.html
+++ b/reference/tempcal.html
@@ -5,7 +5,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Temperature calibration

-    Source: R/calibration.R
+    Source: R/calibration.R
     
     

 
@@ -79,36 +79,36 @@ 
Temperature calibration

 
     

     
Arguments

-    
Tc

+
+
+
Tc

 
The temperature in \(^{\circ}\)C.

 
 
-
slope

+
slope

 
The slope of the regression.

 
 
-
intercept

+
intercept

 
The intercept of the regression.

 
 
-
slpcnf

+
slpcnf

 
The confidence of the slope of the regression.

 
 
-
intcnf

+
intcnf

 
The confidence of the intercept of the regression.

 
 
-
ignorecnf

+
ignorecnf

 
Whether or not to ignore the confidence of the temperature
 calibration.

 
 

     

     
Value

-    
-
-
A tibble with input Tc and estimated
+    
A tibble with input Tc and estimated
 \(\Delta_47\) value with lower and upper bounds.

     

     

@@ -122,7 +122,7 @@ 
References

 C. Vasconcelos, P. Agrinier, A. Katz, B. H. Passey, J. M. Ferry, J.
 Bourrand. Calibration of the dolomite clumped isotope thermometer from 25
 to 350 \(^\circ\)C, and implications for a universal calibration for all (Ca, Mg,
-Fe)CO\({}_3\) carbonates. 2017, 200, 255--279.

+Fe)CO\({}_3\) carbonates. 2017, 200, 255–279.

     

     

     
See also

@@ -141,15 +141,15 @@ 
See also

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/temperature_axis.html b/reference/temperature_axis.html
index 78c4e2e..8be5cfe 100644
--- a/reference/temperature_axis.html
+++ b/reference/temperature_axis.html
@@ -4,7 +4,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Generate a formula for a secondary temperature y-axis

-    Source: R/utils.R
+    Source: R/utils.R
     
     

 
@@ -70,11 +70,13 @@ 
Generate a formula for a secondary temperature y-axis

 
     

     
Arguments

-    
slope

+
+
+
slope

 
The slope of the calibration.

 
 
-
intercept

+
intercept

 
The intercept of the calibration.

 
 

@@ -113,15 +115,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/temperature_calculation.html b/reference/temperature_calculation.html
index f7e1dd1..22ee45a 100644
--- a/reference/temperature_calculation.html
+++ b/reference/temperature_calculation.html
@@ -5,7 +5,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
Calculate the temperatures

-    Source: R/temperature_calculation.R
+    Source: R/temperature_calculation.R
     
     

 
@@ -80,31 +80,33 @@ 
Calculate the temperatures

 
     

     
Arguments

-    
.data

+
+
+
.data

 
A tibble, resulting from acid_fractionation().

 
 
-
...

+
...

 
These dots are for future extensions and must be empty.

 
 
-
D47

+
D47

 
The column name of the \(\Delta_{47}\) values to use as input.

 
 
-
temp

+
temp

 
The column name of the output temperature.

 
 
-
slope

+
slope

 
Character(1) column name with the slope.

 
 
-
intercept

+
intercept

 
Character(1) column name with the intercept.

 
 
-
quiet

+
quiet

 
If TRUE, print info messages. If NULL (default) listens to options(clumpedr.quiet)

 
 

@@ -126,15 +128,15 @@ 
See also

 

 
 

-  
Site built with pkgdown 2.0.9.

+  
Site built with pkgdown 2.1.0.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/sitemap.xml b/sitemap.xml
index fdbcc87..942faf7 100644
--- a/sitemap.xml
+++ b/sitemap.xml
@@ -1,153 +1,53 @@
-
-
-  
-    http://clumpedr.isoverse.org/404.html
-  
-  
-    http://clumpedr.isoverse.org/LICENSE.html
-  
-  
-    http://clumpedr.isoverse.org/articles/clumped.html
-  
-  
-    http://clumpedr.isoverse.org/articles/index.html
-  
-  
-    http://clumpedr.isoverse.org/authors.html
-  
-  
-    http://clumpedr.isoverse.org/index.html
-  
-  
-    http://clumpedr.isoverse.org/news/index.html
-  
-  
-    http://clumpedr.isoverse.org/reference/abundance_ratios.html
-  
-  
-    http://clumpedr.isoverse.org/reference/acid_fractionation.html
-  
-  
-    http://clumpedr.isoverse.org/reference/add_info.html
-  
-  
-    http://clumpedr.isoverse.org/reference/append_expected_values.html
-  
-  
-    http://clumpedr.isoverse.org/reference/append_ref_deltas.html
-  
-  
-    http://clumpedr.isoverse.org/reference/apply_etf.html
-  
-  
-    http://clumpedr.isoverse.org/reference/bulk_and_clumping_deltas.html
-  
-  
-    http://clumpedr.isoverse.org/reference/calculate_etf.html
-  
-  
-    http://clumpedr.isoverse.org/reference/clean_did_info.html
-  
-  
-    http://clumpedr.isoverse.org/reference/clumpedr-package.html
-  
-  
-    http://clumpedr.isoverse.org/reference/clumpedr_get_default_parameters.html
-  
-  
-    http://clumpedr.isoverse.org/reference/collapse_cycles.html
-  
-  
-    http://clumpedr.isoverse.org/reference/correct_backgrounds.html
-  
-  
-    http://clumpedr.isoverse.org/reference/default.params.html
-  
-  
-    http://clumpedr.isoverse.org/reference/delta_values.html
-  
-  
-    http://clumpedr.isoverse.org/reference/empirical_transfer_function.html
-  
-  
-    http://clumpedr.isoverse.org/reference/eth3.html
-  
-  
-    http://clumpedr.isoverse.org/reference/find_bad_cycles.html
-  
-  
-    http://clumpedr.isoverse.org/reference/find_init_outliers.html
-  
-  
-    http://clumpedr.isoverse.org/reference/find_internal_sd_outlier.html
-  
-  
-    http://clumpedr.isoverse.org/reference/find_outliers.html
-  
-  
-    http://clumpedr.isoverse.org/reference/find_param49_outliers.html
-  
-  
-    http://clumpedr.isoverse.org/reference/find_session_id1_outlier.html
-  
-  
-    http://clumpedr.isoverse.org/reference/find_session_outlier.html
-  
-  
-    http://clumpedr.isoverse.org/reference/get_inits.html
-  
-  
-    http://clumpedr.isoverse.org/reference/get_ref_delta.html
-  
-  
-    http://clumpedr.isoverse.org/reference/index.html
-  
-  
-    http://clumpedr.isoverse.org/reference/isobar_ratios.html
-  
-  
-    http://clumpedr.isoverse.org/reference/little_deltas.html
-  
-  
-    http://clumpedr.isoverse.org/reference/match_intensities.html
-  
-  
-    http://clumpedr.isoverse.org/reference/nest_cycle_data.html
-  
-  
-    http://clumpedr.isoverse.org/reference/parse_info.html
-  
-  
-    http://clumpedr.isoverse.org/reference/pipe.html
-  
-  
-    http://clumpedr.isoverse.org/reference/remove_outliers.html
-  
-  
-    http://clumpedr.isoverse.org/reference/revcal.html
-  
-  
-    http://clumpedr.isoverse.org/reference/spread_intensities.html
-  
-  
-    http://clumpedr.isoverse.org/reference/spread_match.html
-  
-  
-    http://clumpedr.isoverse.org/reference/standards.html
-  
-  
-    http://clumpedr.isoverse.org/reference/summarise_outlier.html
-  
-  
-    http://clumpedr.isoverse.org/reference/summarize_outlier.html
-  
-  
-    http://clumpedr.isoverse.org/reference/tempcal.html
-  
-  
-    http://clumpedr.isoverse.org/reference/temperature_axis.html
-  
-  
-    http://clumpedr.isoverse.org/reference/temperature_calculation.html
-  
+
+http://clumpedr.isoverse.org/404.html
+http://clumpedr.isoverse.org/LICENSE.html
+http://clumpedr.isoverse.org/articles/clumped.html
+http://clumpedr.isoverse.org/articles/index.html
+http://clumpedr.isoverse.org/authors.html
+http://clumpedr.isoverse.org/index.html
+http://clumpedr.isoverse.org/news/index.html
+http://clumpedr.isoverse.org/reference/abundance_ratios.html
+http://clumpedr.isoverse.org/reference/acid_fractionation.html
+http://clumpedr.isoverse.org/reference/add_info.html
+http://clumpedr.isoverse.org/reference/append_expected_values.html
+http://clumpedr.isoverse.org/reference/append_ref_deltas.html
+http://clumpedr.isoverse.org/reference/apply_etf.html
+http://clumpedr.isoverse.org/reference/bulk_and_clumping_deltas.html
+http://clumpedr.isoverse.org/reference/calculate_etf.html
+http://clumpedr.isoverse.org/reference/clean_did_info.html
+http://clumpedr.isoverse.org/reference/clumpedr-package.html
+http://clumpedr.isoverse.org/reference/clumpedr_get_default_parameters.html
+http://clumpedr.isoverse.org/reference/collapse_cycles.html
+http://clumpedr.isoverse.org/reference/correct_backgrounds.html
+http://clumpedr.isoverse.org/reference/default.params.html
+http://clumpedr.isoverse.org/reference/delta_values.html
+http://clumpedr.isoverse.org/reference/empirical_transfer_function.html
+http://clumpedr.isoverse.org/reference/eth3.html
+http://clumpedr.isoverse.org/reference/find_bad_cycles.html
+http://clumpedr.isoverse.org/reference/find_init_outliers.html
+http://clumpedr.isoverse.org/reference/find_internal_sd_outlier.html
+http://clumpedr.isoverse.org/reference/find_outliers.html
+http://clumpedr.isoverse.org/reference/find_param49_outliers.html
+http://clumpedr.isoverse.org/reference/find_session_id1_outlier.html
+http://clumpedr.isoverse.org/reference/find_session_outlier.html
+http://clumpedr.isoverse.org/reference/get_inits.html
+http://clumpedr.isoverse.org/reference/get_ref_delta.html
+http://clumpedr.isoverse.org/reference/index.html
+http://clumpedr.isoverse.org/reference/isobar_ratios.html
+http://clumpedr.isoverse.org/reference/little_deltas.html
+http://clumpedr.isoverse.org/reference/match_intensities.html
+http://clumpedr.isoverse.org/reference/nest_cycle_data.html
+http://clumpedr.isoverse.org/reference/parse_info.html
+http://clumpedr.isoverse.org/reference/pipe.html
+http://clumpedr.isoverse.org/reference/remove_outliers.html
+http://clumpedr.isoverse.org/reference/revcal.html
+http://clumpedr.isoverse.org/reference/spread_intensities.html
+http://clumpedr.isoverse.org/reference/spread_match.html
+http://clumpedr.isoverse.org/reference/standards.html
+http://clumpedr.isoverse.org/reference/summarise_outlier.html
+http://clumpedr.isoverse.org/reference/summarize_outlier.html
+http://clumpedr.isoverse.org/reference/tempcal.html
+http://clumpedr.isoverse.org/reference/temperature_axis.html
+http://clumpedr.isoverse.org/reference/temperature_calculation.html
 
+