special-uor / embsecbio

The Eastern Mediterranean-Black Sea-Caspian-Corridor region and biome reconstructions database.

EMBSeCBIO

The goal of EMBSeCBIO is to provide functions to work with the Eastern Mediterranean-Black Sea-Caspian-Corridor region and biome reconstructions database.

Installation

You can(not) install the released version of EMBSeCBIO from CRAN with:

# install.packages("embsecbio")

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("special-uor/embsecbio")

Example

Obtain the top 10 sites and their corresponding metadata:

`%>%` <- magrittr::`%>%`
embsecbio::site %>%
  dplyr::slice(1:10) %>%
  knitr::kable()

ID_SITE	site_name	latitude	longitude	elevation	site_type	basin_size	catch_size
2	Sakhare	41.58	45.32	800	lacustrine, playa	small (0.01-1 km2)	small (<10 km2)
3	Kumisi	41.58	44.83	469	lacustrine, natural open-water, tectonic lake	medium (1.1-50 km2)	small (<10 km2)
4	Tsavkisi	41.68	44.72	1100	terrestrial, mire, bog	small (0.01-1 km2)	small (<10 km2)
5	Imera	41.65	44.22	1610	terrestrial, mire, bog	small (0.01-1 km2)	small (<10 km2)
6	Aligol	41.63	44.02	1550	terrestrial, mire, bog	small (0.01-1 km2)	small (<10 km2)
7	Ispani-II	41.87	41.80	2	terrestrial, mire, bog, raised bog	medium (1.1-50 km2)	small (<10 km2)
8	Lake Urmia	37.50	45.50	1297	lacustrine, natural open-water	very large (>500 km2)	large (>500 km2)
9	Adange	43.31	41.33	1750	fluvial	small (0.01-1 km2)	small (<10 km2)
10	Amtkel	43.27	41.31	1830	fluvial	small (0.01-1 km2)	small (<10 km2)
11	Gagra 471	43.28	40.27	0	fluvial	small (0.01-1 km2)	small (<10 km2)

Obtain the top 10 entities and their corresponding metadata:

`%>%` <- magrittr::`%>%`
embsecbio::entity %>%
  dplyr::slice(1:10) %>%
  knitr::kable()

ID_ENTITY	ID_SITE	entity_name	latitude	longitude	elevation	source	entity_type	mod_or_0ka_class	comments
2	2	Sakhare core 1	41.58	45.32	800	EMBSECBIO	core	PCT	if sample age = modern
3	3	Kumisi core 1	41.58	44.83	469	EMBSECBIO	core	PCT	if sample age = modern
4	4	Tsavkisi core 1	41.68	44.72	1100	EMBSECBIO	core	PCT	if sample age = modern
5	5	Imera core 1	41.65	44.22	1610	EMBSECBIO	core	PCT	if sample age = modern
6	6	Aligol core 1	41.63	44.02	1550	NOAA	core	PCT	if sample age = modern
7	7	Ispani II core 1	41.87	41.80	2	EMBSECBIO	peat core	PCT	if sample age = modern
8	8	Urmia core 20	37.50	45.50	1297	NOAA	core	PCT	if sample age = modern
9	9	Adange core 1	43.31	41.33	1750	NOAA	core	PCT	if sample age = modern
10	10	Amtkel core 1	43.27	41.31	1830	NOAA	core	PCT	if sample age = modern
11	11	Gagra #471	43.28	40.27	0	NOAA	profile or section	PCT	if sample age = modern

Find entities linked to sites:

`%>%` <- magrittr::`%>%`
ents <- embsecbio::site %>%
  dplyr::slice(1:4) %>%
  embsecbio::get_entities()

ents %>%
  knitr::kable()

ID_ENTITY	ID_SITE	entity_name	latitude	longitude	elevation	source	entity_type	mod_or_0ka_class	comments
2	2	Sakhare core 1	41.58	45.32	800	EMBSECBIO	core	PCT	if sample age = modern
3	3	Kumisi core 1	41.58	44.83	469	EMBSECBIO	core	PCT	if sample age = modern
4	4	Tsavkisi core 1	41.68	44.72	1100	EMBSECBIO	core	PCT	if sample age = modern
5	5	Imera core 1	41.65	44.22	1610	EMBSECBIO	core	PCT	if sample age = modern
1169	2	Sakhare-2	41.58	45.32	800	EMBSECBIO	surface sample	SS	NA
1170	2	Sakhare-3	41.58	45.32	800	EMBSECBIO	surface sample	SS	NA
1171	2	Sakhare-4	41.58	45.32	800	EMBSECBIO	surface sample	SS	NA
1172	3	Kumisi-2	41.58	44.83	469	EMBSECBIO	surface sample	SS	NA
1173	3	Kumisi-3	41.58	44.83	469	EMBSECBIO	surface sample	SS	NA
1174	3	Kumisi-4	41.58	44.83	469	EMBSECBIO	surface sample	SS	NA
1175	4	Tsavkisi-1	41.68	44.72	1100	EMBSECBIO	surface sample	SS	NA
1176	4	Tsavkisi-2	41.68	44.72	1100	EMBSECBIO	surface sample	SS	NA
1177	4	Tsavkisi-3	41.68	44.72	1100	EMBSECBIO	surface sample	SS	NA
1178	4	Tsavkisi-4	41.68	44.72	1100	EMBSECBIO	surface sample	SS	NA
1186	5	Imera-1	41.65	44.22	1610	EMBSECBIO	sediment sample	SS	NA
1187	5	Imera-2	41.65	44.22	1610	EMBSECBIO	sediment sample	SS	NA
1188	5	Imera-3	41.65	44.22	1610	EMBSECBIO	sediment sample	SS	NA
1189	5	Imera-4	41.65	44.22	1610	EMBSECBIO	sediment sample	SS	NA
1197	2	Sakhare-1	41.58	45.32	800	EMBSECBIO	surface sample	SS	NA

Datasets

1. Harrison, Sandy and Marinova, Elena (2017): EMBSeCBIO modern pollen biomisation. University of Reading. Dataset. http://dx.doi.org/10.17864/1947.109