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NeoNet

Thomas Huet, Niccolò Mazzucco, Miriam Cubas Morera, Juan Gibaja, F. Xavier Oms, António Faustino Carvalho, Ana Catarina Basilio, Elías López-Romero

NeoNet serves as a framework to study the transition from the Late Mesolithic to the Early Neolithic through spatio-temporal modeling of radiocarbon dates and by offering:

  1. curated datasets
  2. R functions and reference data
  3. interactive app


img-name img-name
Neonet radiocarbon datasets: "NeoNet Med" (North-Central Mediterranean, location) and "NeoNet Atl" (European South Atlantic river basin, location), here filtered by periods.

  • Studied periods

Studied periods are listed in the periods.tsv table:

period period_full_name color
EM Early Mesolithic #0000CF
MM Middle Mesolithic #1D1DFF
LM Late Mesolithic #3737FF
LMEN Late Mesolithic/Early Neolithic #6A6AFF
UM Undefined Mesolithic #8484FF
EN Early Neolithic #FF1B1B
EMN Early/Middle Neolithic #FF541B
MN Middle Neolithic #FF8D1B
LN Late Neolithic #FFC04D
UN Undefined Neolithic #E7E700

NeoNet datasets

These datasets are harvested by the c14bazAAR package, functions get_c14data("neonet") and get_c14data("neonetatl")

NeoNet app
mapping the Late Mesolithic/Early Neolithic transition

NeoNet app is an R Shiny application for mapping radiocarbon (C14). The application offers a mobile geographic window for date selection by location, various filters on chronology and date quality, a calibration window, and other tools to create a user-friendly interface supported by curated datasets of radiocarbon dates and archaeological contexts. NeoNet app is hosted on the server of the University of Pisa. This NeoNet app uses this radiocarbon dataset: https://doi.org/10.13131/archelogicadata-yb11-yb66 published as a data paper in the Journal of Open Archaeology Data and describe in this web document.

NeoNet app

NeoNet app dev

TODO

  • On export action (download button), export this metadata:
    • max SD
    • selected periods
    • dataset (Med, Atl) DOI
    • timestamp
    • bibliographical reference

NeoNet functions
radiocarbon management

NeoNet functions enable the handling of radiocarbon dates sourced from the dataset or exported from the interactive app. Current functions cover:

Data

Reference data

Data preparation

Starting by running these neo_*() functions to manage a new XLSX dataset. Sourcing functions:

source("R/neo_subset.R")
source("R/neo_bib.R")
source("R/neo_matlife.R")
source("R/neo_calib.R")
source("R/neo_merge.R")
source("R/neo_html.R")
source("R/neo_datamiss.R")
source("R/neo_datasum.R")
source("R/neo_doi.R")

Read the new dataset and bibliographic file

data.c14 <- paste0(getwd(), "/inst/extdata/", "NeoNet_atl_ELR (1).xlsx")
df.bib <- paste0(getwd(), "/inst/extdata/", "NeoNet_atl_ELR.bib")

Cleaning the dataset and making it conform to the published NeoNet dataset

df.c14 <- openxlsx::read.xlsx(data.c14)
df.c14 <- neo_subset(df.c14,
                     rm.C14Age = TRUE,
                     rm.Spatial = FALSE,
                     rm.Period = FALSE)
df.c14 <- neo_calib(df.c14)
neo_doi(df.c14)

Prepare the dataset for the Shiny application by merging it with NeoNet Med, calculating materil life duration, and HTML popup layouts

df.c14 <- neo_merge(df.c14 = df.c14, 
                    data.bib = data.bib, 
                    merge.bib = F)
df.c14 <- neo_matlife(df.c14)
df.c14 <- neo_html(df.c14)

Export the merged dataset

write.table(df.c14, "C:/Rprojects/neonet/R/app-dev/c14_dataset_med_x_atl.tsv",
            sep = "\t",
            row.names = FALSE)

Data report

Calculate basic statistics

neo_datasum(df.c14)

Calculate basic statistics: missing data

neo_datamiss(df.c14)


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Missing data (empty cells)

Data alignment

Retrieve dates coming from other databases (with the c14bazAAR R package) and mapped to be compliant with the Neonet format (..., LM, EN, ...) and functions, using neo_dbs_parse(), a mapping table (XLSX) created with neo_dbs_create_ref(), and neo_dbs_align():

source("R/neo_dbs_parse.R")
source("R/neo_dbs_align.R")

# spatial and chronological limits
where <- sf::st_read("https://raw.githubusercontent.com/zoometh/neonet/main/doc/talks/2024-simep/roi.geojson", quiet = TRUE)
when <- c(-9000, -4000) # in cal BC

# parameters
l.dbs <- c("calpal", "medafricarbon", "agrichange", "bda", "calpal", "radon", "katsianis") 
col.c14baz <- c("sourcedb", "site", "labnr", "c14age", "c14std", "period", "culture", "lon", "lat")

# collect the dates form different DBs, standardize the cultural period layout, filter on 'when' and 'where'
df <- neo_dbs_parse(l.dbs = l.dbs,
                    chr.interval.uncalBC = when, 
                    roi = where,
                    col.c14baz = col.c14baz)
df.c14 <- neo_dbs_align(df,
                        mapping.file = "C:/Rprojects/neonet/doc/ref_table_per.xlsx")

Alignments are done using the mapping file ref_table_per.xlsx, a default parameter in neo_dbs_align().

Mapping file

The XLSX file ref_table_per.xlsx has been created using:

df <- neo_dbs_parse(l.dbs = l.dbs,
                    chr.interval.uncalBC = when, 
                    roi = where,
                    col.c14baz = col.c14baz)

# create the mapping file
neo_dbs_create_ref(df.all.res = df,
                   root.path = "C:/Rprojects/neonet/results",
                   outFile = "df_ref_per.xlsx")

This mapping file ref_table_per.xlsx is a reference table to map cultural assessment coming from external DBs, collected throug c14bazAAR, to the Neonet one (..., LM, EN, ...) format. This XLSX file has to be updated manually by specialists.


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Equivalences between third part databases cultural assessment (columns 'period' and 'culture') and Neonet classes (column 'class')

For example:

df.c14 <- neo_dbs_align(df,
                        mapping.file = "C:/Rprojects/neonet/doc/ref_table_per.xlsx")
head(df.c14)

Gives a dataframe where all fields have been renamed to be parsed with the Neonet functions. Among this mapping the column 'Period' with, for example, MM Middle Mesolithic) maps the bda period = Mésolithique 1 and culture = Capsien ancien or Capsien typique (columns 'db_period' and 'db_culture'):

sourcedb SiteName LabCode C14Age C14SD db_period db_culture Period lon lat
bda Mechta el Arbi Poz-92231 6600 80 Mésolithique 1 Capsien ancien MM 6.130900 36.09940
bda Mechta el Arbi Poz-92232 6250 130 Mésolithique 1 Capsien ancien MM 6.130900 36.09940
bda Mechta el Arbi Poz-92230 3500 120 Mésolithique 1 Capsien ancien MM 6.130900 36.09940
bda Kef Zoura D UOC-2925 7787 48 Mésolithique 1 Capsien typique MM 7.682121 35.04205
bda Bortal Fakher L-240A 6930 200 Mésolithique 1 Capsien typique MM 8.176087 34.35480
bda Relilaï (B) Gif-1714 7760 180 Mésolithique 1 Capsien typique MM 7.694694 35.04480

Outlier dates

To filter aberrant dates, a combination of different function allow to retrieve the current information (once mapped to the Neonet layout) of these potential outliers and their original information (from their source database).


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Here the dates 260 (circled in red), 396 and 345 seem aberrant

To check the info of the date numbered 260, do:

source("R/neo_find_date.R")
source("R/neo_dbs_info_date.R")

abber.date <- neo_find_date(df = isochr$data, print.it = FALSE, idf.dates = 260)
ad <- neo_dbs_info_date(df.c14 = df.c14, LabCode = abber.date$labcode)

Gives:

[1] "Reads a 'sf' dataframe"
[1] "Layout for 'aberrant dates' format:"
neonetatl	Sac-1676	El Retamar	-6263	EN	None	None 

Where neonetatl is the source DB, Sac-1676 is the labnum, El Retamar the site name, -6263 the weighted mean (cal BC), EN the period (Early Neolithic), None the culture (no data) and the second None a place holder for a description explaining why this date has been discarted. If the archaeological documentation shows that date Sac-1676 (aka 260) is wrong (mixed assemblage, possibly coming from another layer, etc.). The last line neonetatl Sac-1676 El Retamar -6263 EN None None can be pasted as it into the c14_aberrant_dates.tsv file. More info can be found for this date, reusing the ad dataframe. Running the following functions helps to contextualize the date.

source("R/neo_dbs_info_date_src.R")

neo_dbs_info_date_src(db = ad$sourcedb,
                      LabCode = ad$LabCode)

Gives:

   sourcedb sourcedb_version    labnr c14age c14std       site    feature period material species country      lat
1 neonetatl       2023-12-08 Sac-1676   7400    100 El Retamar Conchero 6     EN    shell    <NA>   Spain 36.57873
        lon                    shortref
1 -6.226273 Cantillo-Duarte et al. 2010

The list of aberrant dates, for example c14_aberrant_dates.tsv, is used to discard some dates with the neo_dbs_rm_date() function

source("R/neo_dbs_rm_date.R")

df_filtered <- neo_dbs_rm_date(df.c14)

By default, dates having a dash prefix in their sourcedb column will be skipped (ex: -radon)


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Screenshot of the 'c14_to_remove.tsv' table

A template script to run this operation: run_outliers.R

Wrong coordinates

Site coordinates can be wrong, for example for the Jordian site of Sabha (Xronos | Google maps). Curated coordinates are listed in the c14_corrected_coordinates.tsv file and handle by the neo_dbs_coord_dates() function.

Correct Site names

When aggregate different databases, using ce c14bazAAR package, two same sites can have different site names (ex: Pollera and Grotta della Pollera). To avoid these mismatches, the function neo_dbs_sitename_dates() uses the mapping table c14_corrected_sitenames.tsv

source("R/neo_dbs_sitename_dates.R")
df.c14 <- neo_dbs_sitename_dates(df.c14)

SPD plot

Plot the summed probabilty densities (SPD) of the two datasets, once df.c14 calculated. The function neo_spd() calls neo_spdplot(). The latter has been adapted from rcarbon::plot.stackCalSPD.R, to fetch NeoNet default period colors.

library(rcarbon)

source("R/neo_spd.R")
source("R/neo_spdplot.R")

neo_spd(df.c14 = df.c14)


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NeoNet dataset SPD with default period colors

neo_spd() can be run on a GeoJSON file exported from the NeoNet app (see "export dates" in the web document. For example neonet-data-2023-09-24.geojson, see also: isochrones

neo_spd(df.c14 = "https://raw.githubusercontent.com/zoometh/neonet/main/results/neonet-data-2023-09-24.geojson",
        export = T)

In the same way, SPD can be done for KCC

source("R/neo_spd.R")
source("R/neo_spdplot.R")
source("R/neo_kcc_extract.R")
kcc.file <- c("koppen_6k.tif", "koppen_7k.tif", "koppen_8k.tif",
              "koppen_9k.tif", "koppen_10k.tif", "koppen_11k.tif")
df_cc <- neo_kcc_extract(df.c14 = df_filtered,
                         kcc.file = kcc.file)
neo_spd(df.c14 = df_cc, color.on = "kcc")

Isochrones

Create a map with isochrone contours to model the spread of Neolithic using the neo_isochr() function.

Example

The file neonet-data-2023-09-24.geojson is an export from the NeoNet app (see "export dates" in the web document). This GeoJSON file can be curated in a GIS (ex: removing aberrant dates) before running the following functions (neo_isochr, neo_spd, etc.).


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Screen capture of the NeoNet app before the export of the `neonet-data-2023-09-24.geojson` file: Early Neolithic (EN) dates only having a SD ≤ 50, and calBC interval between -7000 and -3000

The output is a map with isochrones calculated on the median of calibrated dates.

library(rcarbon)

source("R/neo_isochr.R")
source("R/neo_spd.R")
source("R/neo_calib.R")

neo_isochr(df.c14 = "https://raw.githubusercontent.com/zoometh/neonet/main/results/neonet-data-2023-09-24.geojson", 
           show.lbl = FALSE)

Where neo_calib() calculate the cal BC min and max (i.e, calibrates), and the medidan (with 'intcal20' and the Bchron R package)


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Output map from the `neonet-data-2023-09-24.geojson`

Interpolation

Isochrones are created from the interpolation map:

source("R/neo_isochr_inter_map.R")
inter.map <- neo_isochr_inter_map(isochr$inter)
inter.map
## Not Run
# ggplot2::ggsave(paste0(root.path, "img/", "isochrones-barriere-Italy-EN-inter-map.png"), inter.map, width = 7, height = 7)


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Weighted medians interpolated

EN and LM

The same function can be used symetrically: instead of plotting the earliest dates of the Neolithic (EN), one can also plot the latest dates of the Paleolithic (or Late Mesolithic, LM)

myc14data <- "https://raw.githubusercontent.com/zoometh/neonet/main/results/1_AOI_France_E-W.geojson"
neo_isochr(df.c14 = myc14data, mapname = "France_EW")
neo_isochr(df.c14 = myc14data, mapname = "France_EW", selected.per = c("LM"))


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Output maps from the `1_AOI_France_E-W.geojson`: earliest Neolithic dates and latest Paleolithic dates

Koppen

KCC, Koppen Climate Classification, Koeppen Climate Classification

The Neonet framework and online app integrate Koppen Climate Classification (KCC) for 6,000 BP to 10,000 BP.

Classes

Koppen classification uses five broad classes:

code climate colors
A* Tropical #0000FF #0078FF #46AAF
B* Arid #FF0000 #FF9696 #F5A500 #FFDC64
C* Temperate #FFFF00 #C8C800 #969600 #96FF96 #64C864 #329632 #C8FF50 #64FF50 #32C800
D* Cold #FF00FF #C800C8 #963296 #966496 #AAAF #5A78DC #4B50B4 #320087 #00FFFF #37C8FF #007D7D #00465F
E* Polar #B2B2B2 #666666

And, there are 30 basic classes

code num value hexa color color
Af 1 Tropical, rainforest 0000FF #0000FF
Am 2 Tropical, monsoon 0078FF #0078FF
Aw 3 Tropical, savannah 46AAF #46AAF
BWh 4 Arid, desert, hot FF0000 #FF0000
BWk 5 Arid, desert, cold FF9696 #FF9696
BSh 6 Arid, steppe, hot F5A500 #F5A500
BSk 7 Arid, steppe, cold FFDC64 #FFDC64
Csa 8 Temperate, dry summer, hot summer FFFF00 #FFFF00
Csb 9 Temperate, dry summer, warm summer C8C800 #C8C800
Csc 10 Temperate, dry summer, cold summer 969600 #969600
Cwa 11 Temperate, dry winter, hot summer 96FF96 #96FF96
Cwb 12 Temperate, dry winter, warm summer 64C864 #64C864
Cwc 13 Temperate, dry winter, cold summer 329632 #329632
Cfa 14 Temperate, no dry season, hot summer C8FF50 #C8FF50
Cfb 15 Temperate, no dry season, warm summer 64FF50 #64FF50
Cfc 16 Temperate, no dry season, cold summer 32C800 #32C800
Dsa 17 Cold, dry summer, hot summer FF00FF #FF00FF
Dsb 18 Cold, dry summer, warm summer C800C8 #C800C8
Dsc 19 Cold, dry summer, cold summer 963296 #963296
Dsd 20 Cold, dry summer, very cold winter 966496 #966496
Dwa 21 Cold, dry winter, hot summer AAAF #AAAF
Dwb 22 Cold, dry winter, warm summer 5A78DC #5A78DC
Dwc 23 Cold, dry winter, cold summer 4B50B4 #4B50B4
Dwd 24 Cold, dry winter, very cold winter 320087 #320087
Dfa 25 Cold, no dry season, hot summer 00FFFF #00FFFF
Dfb 26 Cold, no dry season, warm summer 37C8FF #37C8FF
Dfc 27 Cold, no dry season, cold summer 007D7D #007D7D
Dfd 28 Cold, no dry season, very cold winter 00465F #00465F
ET 29 Polar, tundra B2B2B2 #B2B2B2
EF 30 Polar, frost 666666 #666666

The Koppen Climate Classes (KCC) are listed here

Koppen functions

Koppen functions are designed not only for the Neonet dataset, but also for all radiocarbon dataset respecting the minimum data stracture (site, labcode, x, y, etc.).

Create KCC maps

The app integrates Koppen Climate Classification (KCC) for 6,000 BP to 10,000 BP created with the R pastclim package and the neo_kcc_create() function.


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The Koppen Climate Classification calculated for 8,000 BP (8k) with the pastclim R package and hosted on a GeoServer

Neonet functions help to blend pastclim KCC and radiocarbon dates.

# install the packages pastclim and terra
devtools::install_github("EvolEcolGroup/pastclim", ref="dev")
library(pastclim)
library(terra)

# set paths and create maps
outDir <- "C:/Rprojects/neonet/doc/data/clim/"
pastclim::set_data_path(path_to_nc = outDir)

source("R/neo_kcc_create.R")
neo_kcc_create()

Creates these KCC GeoTiffs:

KCC are created as GeoTiffs using the R pastclim package

Geotiff image description
img-name koppen_11k download
img-name koppen_10k download
img-name koppen_9k download
img-name koppen_8k download
img-name koppen_7k download
img-name koppen_6k download

Past Koppen Climate Classification calculated in Kyears BP with the pastclim R package

Extract

This set of functions creates an interactive dataset of df.c14 dates and the climates to which they belong.

kcc.file <- c("koppen_6k.tif", "koppen_7k.tif", "koppen_8k.tif",
              "koppen_9k.tif", "koppen_10k.tif", "koppen_11k.tif")
source("R/neo_kcc_extract.R")
df_kcc <- neo_kcc_extract(df.c14 = df.c14, kcc.file = kcc.file)
source("R/neo_kcc_extract_longformat.R")
df_kcc_long <- neo_kcc_extract_longformat(df_kcc)
source("R/neo_dbs_info_dates_datatable.R")
dt.out <- neo_dbs_info_dates_datatable(df.c14 = df_kcc_long,
                                       fields = c("SiteName", "code", "Period", "median", "map", "LabCode", "db_period", "db_culture", "sourcedb", "X", "Y", "color"),
                                       font.size = "16pt")
## Not Run
# htmlwidgets::saveWidget(dt.out, "C:/Rprojects/neonet/doc/talks/2024-simep/img/dates_kcc.html")

Map

The neo_kcc_map() creates a KCC map with a layer of dates above

source("R/config.R") # default variables: column names mapping, colors, etc.

df <- c14bazAAR::get_c14data("neonet")
df <- sf::st_as_sf(df, coords = c("lon", "lat"), crs = 4326)
neo_kcc_map(df.c14 = df,
            kcc = "C:/Rprojects/neonet/doc/data/clim/koppen_7k.tif",
            export = TRUE,
            fileOut = "neonet_kcc.png" )

Gives:


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The neonet dataset over the KCC 7k

To assess what were the climates classes that where inhabited in the past, during the Late Mesolithic (LM) and Middle Mesolithic (MM) based on previous dates

df.c14 <- neo_calib(df.c14)
df.c14 <- sf::st_as_sf(df.c14, coords = c("lon", "lat"), crs = 4326)
kcc.file <- c("koppen_6k.tif", "koppen_7k.tif", "koppen_8k.tif",
              "koppen_9k.tif", "koppen_10k.tif", "koppen_11k.tif")
df_cc <- neo_kcc_extract(df.c14 = df.c14, kcc.file = kcc.file)
col.req <- gsub(pattern = ".tif", "", kcc.file)
neo_kcc_plotbar(df_cc = df_cc, 
                kcc.file = c("koppen_8k.tif", "koppen_9k.tif"),
                col.req = col.req,
                selected.per = c("EN"),
                title = "Neolithic: transition btw 7,000 and 6,000 BC",
                legend.show = FALSE)

Gives:


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KCC occupied during the EN between 7,000 and 6,000 BC (9 ka and 8 ka BP) with counts of sites belonging to these time slices

The neo_kcc_extract() function collects the KCC values (climates) of each date.

NeoNet strati

NeoNet-strati is an online R Shiny interactive app to record the stratigraphy of NeoNet's archaeological sites in an editable dataframe based on LabCode identifiers.

NeoNet-strati app

flowchart TD
    A[NeoNet dataset] --is read by--> B{{<a href='https://trainingidn.shinyapps.io/neonet-strati'>neonet-strati</a>}}:::neonetshiny;
    B --edit<br>site stratigraphy--> B;
    B --export<br>site stratigraphy<br>file--> C[<a href='https://github.com/historical-time/data-samples/blob/main/neonet/Roc%20du%20Dourgne_2023-07-30.csv'>Roc du Dourgne_2023-07-30.csv</a>];
    C --is read by--> D{{<a href='https://github.com/historical-time/caa23/blob/main/neonet/functions/neo_strat.R'>neonet_strat</a>}}:::neonetfunct;
    D --export --> E[maps<br>charts<br>listings<br>...];
    classDef neonetfunct fill:#e3c071;
    classDef neonetshiny fill:#71e37c;
Loading

Strati app and strati analysis overall Workflow

App interface

The app is composed by different panels: a site to be recorded (Site Stratigraphy panel), and the complete dataset (All sites panel). A site name is copied from All sites panel to Site Stratigraphy panel.

Site Stratigraphy panel

Plot a selected site in an editable table to record its stratigraphical relationships.

img-name
Panel "Site Stratigraphy" editable dataframe. By default the app opens on "Pokrovnik"

All sites panel

Show the complete NeoNet dataset. A site can be selected by searching it in the selection search bar (top-right) and copying its name (Site Name column). Here Roc du Dourgne, highlighted in blue.


img-name
Panel "All sites". Selection of the "Roc du Dourgne" site


img-name
"Roc du Dourgne" site sorted on its "PhaseCode"

The stratigraphical relations can be added into the "After" column, and thereafter exported in CSV

img-name
"Roc du Dourgne" stratgraphical relationships (column "After") after edition

For example, "Roc du Dourgne" relationships are:

LabCode After Period PhaseCode C14Age C14SD
MC-1101 MC-1102 EN C5 5050 100
MC-1102 MC-1103 EN C5 6170 100
MC-1103 MC-1105 EN C6 5100 80
MC-1104 MC-1105 EN C6 6470 100
MC-1105 MC-1107 EN C6 5550 80
MC-1107 LM C7 6850 100
MC-781 EN C6 5000 170
MC-782 LM Layer 7 5770 170

The first row can be read as: "the layer containing radiocarbon date MC-1101 comes after the layer containing radiocarbon date MC-1102".

Once the site stratigraphy recorded, save the changes by downloading the dataset pressing the button (top-left) as a CSV file. The output file name is the site name and the current date (ex: Roc du Dourgne_2024-04-12.csv).

Strati analysis

The file exported from the NeoNet strati app can be read by the neo_strati() function (see Harris Matrix)

Harris Matrix

The output CSV file exported by NeoNet-strati can be read by the neo_strat() function. For example, ploting the C14Age and the PhaseCode.

neo_strat(inData = 'https://raw.githubusercontent.com/historical-time/data-samples/main/neonet/Roc du Dourgne_2023-07-30.csv',
          outLabel = c("C14Age"))
neo_strat(inData = 'https://raw.githubusercontent.com/historical-time/data-samples/main/neonet/Roc du Dourgne_2023-07-30.csv',
          outLabel = c("PhaseCode"))

Gives:

img-name img-name
"Roc du Dourgne" stratgraphical relationships using LabCode identifiers, ordered on the "LabCode" column, displaying the C14Age (left) and the LabCode (right)

Changing the outLabel to Period allows to color on periods using the default period colors (see the web document)

neo_strat(inData = 'https://raw.githubusercontent.com/historical-time/data-samples/main/neonet/Roc du Dourgne_2023-07-30.csv',
          outLabel = c("Period"))

Gives:

img-name
"Roc du Dourgne" stratgraphical relationships using LabCode identifiers, ordered on the "LabCode" column

Leafrog alignment

Using neo_leapfrog(DT = T) to merge dataframe from NeoNet and Leapfrog on common C14 LabCode values: https://historical-time.github.io/caa23/neonet/results/NN_and_LF.html


Screen capture of [NN_and_LF.html](https://historical-time.github.io/caa23/neonet/results/NN_and_LF.html)

Sibling projects

There are mainy IT-based projects dealing with radiocarbon dates, such as the comprehensive platform Xronos, the radiocarbon aggregator C14bazAAR, and many others, see the open-archaeo site

Documentation

Communication