Neotoma to LiPD

This vignette demonstrates a function to translate LiPD to Neotoma

The example file (site) used is Bambili 2. Bambili 2 is loaded using Neotoma and first translated to LiPD. This makes for a simple use case

B <- neotoma2::get_sites(sitename = "Bambili 2")
D <- neotoma2::get_downloads(B)

## ..

L <- lipdR:::neotoma2lipd(D)

summary(L)

## ################################################################################################
## Bambili2.Lzine.2019
## neotomaSiteId_23664
## v.1.0.0
## ################################################################################################
## 
## ### Archive Type ###
## unknown
## 
## ### Geographic Metadata ###
## Bambili 2 (5.925018N, 10.242784E), 2323 masl
## 
## ### Publications (printing first 1 citations of  1  total) ###
## 
## Lézine, A.-M., K. Izumi, M. Kageyama, and G. Achoundong. 2019. A 90,000-year record of Afromontane forest responses to climate change. Science 363(6423):177-181. [DOI: 10.1126/science.aav6821] 
## 
## ### Paleo Data ###
## 
## Summary data for object 1, Measurement Table 1 of 1:
## Measurement table contains 141 observations of 206 variables
## 
## # A tibble: 4 × 207
##   ` `    depth  age   Celtis_pollen Hypericum_pollen Fabaceaeundiff_pollen
##   <chr>  <chr>  <chr> <chr>         <chr>            <chr>                
## 1 units  cm     NA    NISP          NISP             NISP                 
## 2 min    154.5  20312 1             1                1                    
## 3 median 607    53111 4             5                3                    
## 4 max    1259.5 88932 15            22               12                   
## # ℹ 201 more variables: Myrica_pollen <chr>,
## #   CombretaceaeMelastomataceaeundiff_pollen <chr>,
## #   Dyschoristetype_pollen <chr>, VitellariatypeVparadoxa_pollen <chr>,
## #   Polypodiumtype_spore <chr>, Cyatheatype_spore <chr>,
## #   Ilexmitis_pollen <chr>, EmbeliatypeEschimperi_pollen <chr>,
## #   Vernonieaeundiff_pollen <chr>, Oleacapensistype_pollen <chr>,
## #   Ascolepis_pollen <chr>, NuxiatypeNcongesta_pollen <chr>, …
## 
## ### Chron Data ###
## 
## Summary data for object 1, Measurement Table 1 of 1:
## Measurement table contains 16 observations of 10 variables
## 
## # A tibble: 5 × 11
##   ` `      depth depth_top depth_bottom thickness age   ageOld ageYoung age_type
##   <chr>    <chr> <chr>     <chr>        <chr>     <chr> <chr>  <chr>    <chr>   
## 1 units    cm    cm        cm           cm        yr BP yr BP  yr BP    unitless
## 2 descrip… midp… top depth bottom depth sample t… cale… older… younger… type of…
## 3 min      199.5 Inf       Inf          NA        22225 22873  21577    Biostra…
## 4 median   402   NA        NA           NA        40633 34584  33020    Radioca…
## 5 max      1239… -Inf      -Inf         NA        88350 51467  42882    Radioca…
## # ℹ 2 more variables: ageUnc <chr>, neotomaChronConrolId <chr>

Dave Edge

2023-01-09