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iNaturalist_traits

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Plant trait maps produced using iNaturalist citizen science data

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[![DOI](https://zenodo.org/badge/455158085.svg)](https://zenodo.org/badge/latestdoi/455158085)

# Citizen science plant observations encode global trait patterns

This repository hosts additional material accompanying the publication:

Wolf, S. and Mahecha, M. D. and Sabatini, F. M. and Wirth, C. and Bruelheide, H. and Kattge, J. and Moreno Martínez, Á. and Mora, K. and Kattenborn, T., *Citizen science plant observations encode global trait patterns*. Nat Ecol Evol (2022). https://doi.org/10.1038/s41559-022-01904-x

1. The entire workflow documentation: https://sojwolf.github.io/iNaturalist_traits/
  2. GeoTiff trait maps based on iNaturalist observations and sPlotOpen observations, respectively
  3. How to create updated trait maps

## Trait maps

### Versions

The maps available here were generated using iNaturalist observations downloaded on January 4, 2022 (https://doi.org/10.15468/dl.34tjre) and sPlotOpen version 52 (https://idata.idiv.de/ddm/Data/ShowData/3474?version=52).

If you would like to update the iNaturalist maps using the most recent TRY (trait) and iNaturalist data, please refer to the section **Create updated trait maps** below.

1. iNaturalist

1. 0.5 degrees

1. ln
              2. exp(ln)

2. 2 degrees

1. ln
              2. exp(ln)

2. sPlotOpen

1. 0.5 degrees

1. ln
              2. exp(ln)

2. 2 degrees

1. ln
              2. exp(ln)

### Load in Python

Get file names:

```python
from os import listdir
from os.path import isfile, join

path = "iNaturalist_traits-main/iNat_maps/2_deg/ln/"
files = [f for f in listdir(path) if isfile(join(path, f))]
files.sort()
```
Load all trait maps as xarray:
```python
from import xarray as xr

def cubeFile(file):
    name = file.replace(".tif","")
    sr = xr.open_dataset(path + file,engine = "rasterio",chunks = 1024).sel(band = 1)
    sr = sr.assign_coords({"variable":name})
    return sr

da = xr.concat([cubeFile(x) for x in files],dim = "variable")
```
Select a specific band:
```
da.band_data.sel(variable = "iNat_Leaf.Area_2_ln")
```
Convert to data frame

```python
df = da_2.band_data.to_dataset().to_dataframe().reset_index()
df_spread = df.pivot(index= ['x','y'],columns='variable',values='band_data').reset_index()
```

### Load in R

To load one trait map:

```
library(raster)

plant_height <- raster("iNat_Plant.Height_05deg_expln.tif")

trait_stack <- list.files(pattern = "05deg_expln.tif")
trait_stack <- stack(all_maps)
```

## Create updated trait maps

If you would like to use the most recent vascular plant data, instead of the maps provided here, the following instructions will guide you.

### Download iNaturalist database

Open the following link and click ‘Rerun Query’:

https://doi.org/10.15468/dl.34tjre

Request the download: Click on "Download" and sign into/generate your account. For this analysis the ‘simple’ version is sufficient (roughly 10 GB). This will also generate a new DOI that you can cite. You will receive a download link via e-mail as soon as the download is ready (usually after about 15 minutes).

### Download TRY data

To download data from the TRY database, create an account at https://www.try-db.org/de.

When asked which traits you would like to download, type in the following list. This filters TRY data for our traits of interest:

```
3113, 3117, 4, 13, 14, 15, 3106, 26, 27, 47, 50, 56, 78, 138, 163, 169, 237, 282
```

Continue without species list and choose open trait data only. You will receive a download link via e-mail after about one or two days.

The iNaturalist and TRY downloads will contain files that look something like this:

iNaturalist_filename: ```0354963-210914110416597.csv```

TRY_filename: ```19287.txt```

### Link iNaturalist and TRY and generate trait maps

Download the ```make_traitmaps/``` folder from this repository and execute the containing python script to generate 0.5 and 2 degree maps. Make sure the R script make_iNat_traitmaps.R is also in the directory.

```
python make_traitmaps.py -n iNaturalist_filename -t TRY_filename
```

This script does not apply fuzzy name matching, since it adds around 1% more data. If you want to add a fuzzy match or want more information, please refer to the workflow documentation at https://sojwolf.github.io/iNaturalist_traits/.
After running the script, you can remove the file ```iNat_TRY_log.csv``` if you do not need information on each observation for your analysis.

### Requirements

**Python packages**:

For handling data frames and (multidimensional) arrays:
  - ```pandas```
  - ```numpy```

For system interface:
  - ```getopt```
  - ```sys```

**R packages**:

For making rasters and exporting GeoTiffs:
  - ```raster```
  - ```rgdal```

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