diff --git a/ms/data_readme.Rmd b/ms/data_readme.Rmd index 63e9345..6eee967 100644 --- a/ms/data_readme.Rmd +++ b/ms/data_readme.Rmd @@ -167,9 +167,9 @@ Description of methods used for collection/generation of data: A list of native, non-hybrid fern specimens housed at the herbarium of the Museum of Science and Nature, Japan was converted to a community data matrix at -four grain sizes (grid-cells spanning Japan, each 0.1, 0.2, 0.3, or 0.4 degrees -per side). The 0.2 degree grain size was selected for further analysis based on -redundancy (ratio of number of specimens to number of taxa per cell). +four grain sizes (square grid-cells spanning Japan, each 10, 20, 30, or 40 km +per side). The 20 km degree grain size was selected for further analysis based +on redundancy (ratio of number of specimens to number of taxa per cell). All taxon names are based on the Green List (http://www.rdplants.org/gl/; English version available at @@ -265,7 +265,7 @@ assert(ja_climate_data, not_na, everything(), success_fun = success_logical) `r fs::path_file(ja_climate_data_file)`: Climate data in Japan downloaded from WorldClim database (https://worldclim.org/data/v1.4/formats.html). Raw data were downloaded at the 2.5 minute scale. The intersection of the raw climate data -with 0.2 degree grid-cells (japan_ferns_shape_full.gpkg) were identified, +with 20 km × 20 km grid-cells (japan_ferns_shape_full.gpkg) were identified, then average value for each climatic variable was calculated for each grid-cell. Number of variables: `r ncol(ja_climate_data)` @@ -302,8 +302,8 @@ assert(japan_ferns_comm_full, not_na, everything(), success_fun = success_logica ``` `r fs::path_file(japan_ferns_comm_full_file)`: Community matrix (species x sites -matrix) of native, non-hybrid ferns in Japan. Sites correspond to 0.2 degree x -0.2 degree grid-cells covering Japan. For location of grid-cells, see +matrix) of native, non-hybrid ferns in Japan. Sites correspond to 20 km x +20 km grid-cells covering Japan. For location of grid-cells, see japan_ferns_shape_full.gpkg. Full dataset including all grid-cells (none excluded due to low redundancy). @@ -422,7 +422,7 @@ Variable list: make_data_desc( tribble( ~col, ~desc, - "res", "Degree of resolution (grid-cell side length), from 0.1 to 0.4 degrees", + "res", "Degree of resolution (grid-cell side length), from 10 to 40 km (in m)", "grids", "Name of grid-cell", "richness", "Number of taxa occurring in grid-cell", "abundance", "Number of specimens occurring in grid-cell", @@ -444,14 +444,14 @@ assert(japan_ferns_shape_full, not_na, everything(), success_fun = success_logic `r fs::path_file(japan_ferns_shape_full_file)`: Location of grid-cells (sites) for native, non-hybrid ferns in Japan in GeoPackage format. Compiled from raw -specimen data by binning specimens into 0.2 degree grid-cells across Japan. Full -dataset including all grid-cells (none excluded due to low redundancy). +specimen data by binning specimens into 20 km × 20 km grid-cells across Japan. +Full dataset including all grid-cells (none excluded due to low redundancy). Number of variables: `r ncol(japan_ferns_shape_full)` Number of cases/rows: `r nrow(japan_ferns_shape_full)` -Coordinate reference system: JGD2000 +Coordinate reference system: Mollweide (+proj=moll +lon_0=135) Variable list: