GRENE_ei_EcoBiodiv_MAPHATJP_dataset


IDENTIFICATION INFORMATION

Name GRENE_ei_EcoBiodiv_MAPHATJP_dataset
Edition 0.9
Abbreviation MAPHATJP
Metadata Identifier GRENE_ei_EcoBiodiv_MAPHATJP20181216224345-en

CONTACT

CONTACT on DATASET

Name Osamu
Organization The University of Tokyo
Address 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
TEL +81-3-5454-4305
FAX +81-3-5454-4305
E-mail osamu@darwin.c.u-tokyo.ac.jp

DOCUMENT AUTHOR

Name Osamu
Organization The University of Tokyo
E-mail osamu@darwin.c.u-tokyo.ac.jp

DATASET CREATOR

Name Masayuki U. Saito
Organization Tokyo University of Agriculture and Technology
E-mail saito.ume@gmail.com

DATE OF THIS DOCUMENT

2018-12-16

DATE OF DATASET

  • creation : 2016-03-18

  • revision : 2016-04-01

DATASET OVERVIEW

Abstract

This is the model projection data of potential habitats for 1188 Japanese plant species. The spatial resolution of the data is the standard Japanese third-order mesh composed approximately 1 km × 1 km cells. To estimate the distribution of potential habitats, the presence data of plants extracted from a vegetation survey carried out from 2000 to 2012 by the Ministry of the Environment is used as a response variable. Mean annual temperature, total summer (May to September) and winter precipitation (December to March), topographic wetness index (TWI), geomorphological classification (lowland, hill and mountain), each presence-absence of volcanic product, limestone and ultrabasic rock, each proportion of secondary vegetation, plantation, agricultural area and urban area are used as environmental predictors. All response variables and environmental predictors are prepared in the standard Japanese third-order mesh. Only proportions of land use (secondary vegetation, plantation, agricultural area and urban area) are caluculated from each target cell and its 8 neighboring cells. MaxEnt software (http://www.cs.princeton.edu/∼schapire/maxent/) is used for modelling habitat distribution of each plant species.

Topic Category(ISO19139)

  • environment

  • biota

Temporal Extent

Begin Date 2000-__-__
End Date 2012-__-__

Geographic Bounding Box

North bound latitude 45.508
West bound longitude 122.875
Eastbound longitude 145.762
South bound latitude 24.000

Grid

Dimension Name Dimension Size (slice number of the dimension) Resolution Unit
row 1 30 (second)
column 1 45 (second)

Keywords

Keywords on Dataset

Keyword Type Keyword Keyword thesaurus Name
place Asia > Eastern Asia > Japan Country
theme Ecosystems, Biodiversity GEOSS
theme Biodiversity GEO_COP

Online Resource

Distribution Information

name version specification
CSV RFC 4180
GeoTIFF TIFF 6.0

DATA PROCESSING

Data Processing (1)

General Explanation of the data producer's knowledge about the lineage of a dataset

Environmental variables used in the dataset.

01. mean annual temperature: calculated form WorldClim v1.4 (Hijmans et al., 2005).

02. total summer precipitation (May to September): calculated form WorldClim v1.4 (Hijmans et al., 2005).

03. total winter precipitation (December to March): calculated form WorldClim v1.4 (Hijmans et al., 2005).

04. topographic wetness index (TWI): calculated from 50 m cell elevation data obtained from the Geographical Survey Institute (2001).

05. geomorphological classification (three categories: lowland, hill and mountain): reclassified from the land classification of a third-order mesh by Wakamatsu et al. (2005).

06. presence-absence of volcanic product: extracted from land classification mesh data compiled by the Ministry of Land, Infrastructure, Transport and Tourism (1979).

07. presence-absence of limestone: extracted from land classification mesh data compiled by the Ministry of Land, Infrastructure, Transport and Tourism (1979).

08. presence-absence of ultrabasic rock: extracted from land classification mesh data compiled by the Ministry of Land, Infrastructure, Transport and Tourism (1979).

09. proportion of secondary vegetation: extracted from the vegetation map compliled by the Ministry of the Environment (1999) that was reclassified by the criteria of Ogawa et al. (2013) and Akasaka et al. (2014). Proportion is caluculated from 3 x 3 cells (a target cell and the 8 adjacent cells immediately surrounding it).

10. proportion of plantation: extracted from the vegetation map compliled by the Ministry of the Environment (1999) that was reclassified by the criteria of Ogawa et al. (2013) and Akasaka et al. (2014). Proportion is caluculated from 3 x 3 cells (a target cell and the 8 adjacent cells immediately surrounding it).

11. proportion of agricultural area: extracted from the vegetation map compliled by the Ministry of the Environment (1999) that was reclassified by the criteria of Ogawa et al. (2013) and Akasaka et al. (2014). Proportion is caluculated from 3 x 3 cells (a target cell and the 8 adjacent cells immediately surrounding it).

12. proportion of urban area: extracted from the vegetation map compliled by the Ministry of the Environment (1999) that was reclassified by the criteria of Ogawa et al. (2013) and Akasaka et al. (2014). Proportion is caluculated from 3 x 3 cells (a target cell and the 8 adjacent cells immediately surrounding it).

Response variable used in the dataset.

01. plant occurrence: extracted from the result of the 6th and 7th vegetation survey (2000-2012) conducted by the Ministry of the Environment. 1188 plant species present at more than 50 sites are targeted. YList (Yonekura and Kajita, 2003) is used as a Taxonomic authority file (TAF) of Japanese vernacular and scentific name of each plant species.

USE CONSTRAINTS

Data Policy by Data Provider

The dataset is published under the Creative Commons License Attribution-ShareAlike 4.0 (CC BY-SA 4.0).

ACKNOWLEDGEMENT

Dataset Acknowledgement

Please cite as follows when you want to use the dataset: Saito M.U., Kurashima O., Ito M., 2016. Maps of potential habitats for Japanese plant species. Available at http://gnetum.c.u-tokyo.ac.jp/maphatjp/.


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This project is supported by "Data Integration & Analysis System" funded by MEXT, Japan
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