A crop type dataset for consistent land cover classification in Central Asia

Land cover is a key variable in the context of climate change. In particular, crop type information is essential to understand the spatial distribution of water usage and anticipate the risk of water scarcity and the consequent danger of food insecurity. This applies to arid regions such as the Aral Sea Basin (ASB), Central Asia, where agriculture relies heavily on irrigation. Here, remote sensing is valuable to map crop types, but its quality depends on consistent ground-truth data. Yet, in the ASB, such data are missing. Addressing this issue, we collected thousands of polygons on crop types, 97.7% of which in Uzbekistan and the remaining in Tajikistan. We collected 8,196 samples between 2015 and 2018, 213 in 2011 and 26 in 2008. Our data compile samples for 40 crop types and is dominated by “cotton” (40%) and “wheat”, (25%). These data were meticulously validated using expert knowledge and remote sensing data and relied on transferable, open-source workflows that will assure the consistency of future sampling campaigns. Measurement(s) crop type • land cover • Uncertainty • Normalized Difference Vegetation Index Technology Type(s) GPS navigation system • satellite imaging • computational modeling technique Factor Type(s) year of data collection • crop type label Sample Characteristic - Environment agricultural field Sample Characteristic - Location Uzbekistan • Tajikistan Measurement(s) crop type • land cover • Uncertainty • Normalized Difference Vegetation Index Technology Type(s) GPS navigation system • satellite imaging • computational modeling technique Factor Type(s) year of data collection • crop type label Sample Characteristic - Environment agricultural field Sample Characteristic - Location Uzbekistan • Tajikistan Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.12613775


Background & Summary
Land cover change is a key driver of climate change 1,2 . It contributes to regional 3 and global 4 warming which creates the risk for severe consequences for, among others, water 5,6 and food 7,8 security. Therefore, land cover is an essential decision support variable 9 that supports decision makers, helping develop local, national, and international management policies 10,11 .
Land cover information is particularly important in arid regions such as the Aral Sea Basin (ASB) in Central Asia. Here, agriculture depends heavily on irrigation 12,13 , a crucial element in answering the dietary needs of a growing population 14 . Simultaneously, food security is threatened by water scarcity, a phenomenon created by the over-exploration of water resources and climate change [15][16][17] . This transforms the region into a geo-political hotspot where international, water-driven conflicts are possible 18,19 unless mitigated by sustainable water management 20 . Therefore, the stability of the Central Asia region demands the development of sustainable agricultural practices. To achieve this, accurate information on the spatial and temporal distribution of land cover is required, especially that on crop types. Since different crops types have unique irrigation requirements 21 , knowing their temporal and spatial distribution helps optimize water usage and avoid land degradation 22,23 .
To map the distribution of crops, remote sensing is a popular and powerful tool. It allows us to map agricultural land cover promptly and efficiently, supporting several global, agricultural monitoring application 24,25 . Still, while remote sensing technologies are powerful, they depend on reliable ground-truth data. When dealing with applications such as land cover mapping, ground-truth data teach us how to distinguish classes and helps us validate their accuracy. However, access to reliable ground information on crops in data scarce regions such as Central Asia is limited. Here, existing field data on crop types is reduced to national surveys that are only available in aggregated tables of questionable quality 26 . In response to this data gap, we compiled a database of 8,435 validated samples on crop types collected within several irrigated cropland areas (Fig. 1a). Of these samples, 97.7% were collected in Uzbekistan and the remaining in Tajikistan. We collected 26 samples in 2008, 213 in 2011 and 8,196 between 2015 and 2018. These data cover 40 classes, 65% of which correspond to "cotton" and "wheat", reflecting their dominance in the region 27 . "Cotton" is the biggest contributor to this proportion with 40% of the total (Fig. 1d).
We collected these ground-truth data in the scope of the project Central Asia Waters (CAWa, CAWa, www. cawa-project.net) in an effort to provide consistent, timely land cover information on crop types for efficient water management in Central Asia. These data are an input required by the Water Use Efficiency Monitor in Central Asia (WUEMoCA) web service (http://wuemoca.net/app/) and will help improve data services in the region. Consequently, our sample dataset will increase in volume as soon as new field campaigns take place.

Methods
Sample collection. Initially, our crop sample database was composed by points collected with Geographic Positioning Systems (GPS). Most were retrieved close to roads, expressing the poor accessibility within between fields. We collected a single GPS point for each field when either its centre or edges were accessible. When the access to a field was completely obstructed, we collected several GPS points along its borders to aid in its later distinction. After the field survey, we drew polygons around the respective fields through image interpretation. We relied on multi-temporal, very high-resolution satellite imagery from Google Earth (GE). While drawing the extent of each sample, we circumvented non-vegetated areas, excluded samples from fields with only mixed-crops (e.g. urban gardens). Moreover, we excluded samples with no valid GE Data, either due to the lack of observations or due to heavy cloud-cover. The first two criteria address the issue of mixed pixels. While GE shows us a clear demarcation between e.g. a crop and a building within a field, this is often unclear when using satellite data. Satellite sensors commonly used for land cover classification, such as Landsat and the Moderate Resolution Spectroradiometer (MODIS), miss such details due to their coarse spatial resolution. Therefore, when the area within a pixel is composed by different land cover types (i.e. mixed-pixels, Fig. 2a,b), we obtain an unclear spectral signature that will negatively influence the training and validation of a land cover classification. The third criteria avoids uncertainties in our dataset related to land cover change. When drawing polygons, we looked for images within the same year and as close as possible to the sampling date. When no image was available, we considered images within 1 year of the growing season, collected both before and after, given no visible change of the field borders. The polygons vary greatly in size, with areas ranging between 5 m 2 and 484,507 m 2 . Roughly 75% of samples have an area below 100,000 m 2 (10 ha).
Detection of double cropping. Our field campaigns were conducted during mid to late summer, which allowed us to observe early-year cultivation patterns. However, in some locations, crop rotation is a common practice and single observations can misinform land cover mapping applications. To address this, we visually inspected the temporal variability of each sample to identify and interpret second harvest events. To do so, we used all available collection 1 Landsat Data (i.e. Landsat 4, 5, 7 and 8) for each of the sampling years (+/−2 Image @ 2020 Google, Maxar Technologies , and exemplifies the spatial detail of these data within the Fergana, Uzbekistan, collected on a field-by-field basis. These samples depict different crop types which compose distinct phenological class groups (d). "Winter" crops are solely represented by winter-wheat while "summer" combines "cotton", "rice" and "maize" and "permanent" combines "orchards, "vineyards" and "alfalfa". "Fallow" is described by samples from unused agricultural land, lacking a clear phenological peak. Crop types that lacked a characteristic phenological behaviour (e.g. potatoes, onions) were labelled as "unclear". "Double" corresponds to "winter" crops that were followed by a "summer" crop after the first harvest.
www.nature.com/scientificdata www.nature.com/scientificdata/ months). Then, for each sampling site, we estimated the Normalized Difference Vegetation Index (NDVI) and masked cloud and shadows using the pixel quality information provided with the data. Finally, we derived an equidistant time series linearly interpolated every 16 days with consideration for the acquisition date of each pixel. When interpolating missing values, we searched for pixels acquired within 60 days before and after the target date. This was meant to avoid the over generalization of the time series, preserving relevant phenological patterns.
Then, for each sample polygon, we extracted an average NDVI time-series for the corresponding sampling year. When computing the average, we considered the NDVI heterogeneity within each pixel. First, we used pol-y2sample() from the fieldRS R package (https://CRAN.R-project.org/package=fieldRS) to convert each polygon into points, where each point is a pixel that overlaps with the polygon. Additionally, the function reports on the percent overlap between a pixel and the polygon (Fig. 3). These data are used by extractTS() from the CAWaR package (https://cran.r-project.org/package=CAWaR), which derives an average for each time-step weighed by the percent cover of each pixel. This step accounts for mixed-pixel effects. At the edges of a field, a pixel may be composed by different crop types and contaminate the observed spectral signature when computing a simple average.
After deriving the NDVI profiles for each polygon, we visually inspected them to detect double cropping events, expressed as two peaks in the NDVI time-series. When this phenomenon occurred, we interpreted the second peak with the support of local experts, as well as our own knowledge on the phenological behaviour of each crop. We supported our visual assessment with median profiles for each crop type derived with the ana-lyzeTS() function from CAWaR, derived on a regional basis. Using the median, we exclude temporal outliers related to abnormal growth patterns and the mislabelling of samples. During our assessment, when the second phenological peak displayed a known pattern, we relabelled our samples accordingly. For example, if the first phenological peak (which we sampled on the field) corresponded to "wheat" and the second to "cotton", we relabelled our sample as "wheat-cotton". Following this process, we grouped our samples into phenological classes based on their NDVI curves (Fig. 4). When an interpretation was not possible due to data gaps or noise, we relabelled our sample as e.g. "wheat-other". Samples to which we could not assign a phenological class objectively were labelled as "unclear".

Fig. 2
Comparison of field samples. Image (a) shows a typical example of a communitarian urban garden. The land parcel is divided between several individuals and used to plant multiple types of crops, including fruit trees. Such cases are hard to interpret with remote sensing due to mixed pixel effects. Image (b) depicts a field where crops share the managed areas with buildings. Excluding the building is essential to accurately depict the spectral signature of the cultivated area. Image (c) shows an ideal case, where the field was cultivated with a single crop with no additional structures within it. Due to their homogeneity, such fields help discriminate crop specific spectral signatures. www.nature.com/scientificdata www.nature.com/scientificdata/

Data Records
Our data are provided through figshare 28 and is and contains three main files: CAWa_cropTypes_samples.shp (Table 1) containing the file samples; CAWa_cropType_polygon-info.csv (Table 2) containing quality information on each sample; CAWa_cropType_time-series.csv (Table 3) containing the sample-specific NDVI time-series used in the detection of double cropping events. The entries in CAWa_PolygonInfo.csv and CAWa_cropType_ time-series.csv have the same sorting as the entries in CAWa_cropTypes.shp making them interoperable. To ease the combination of these data, we provide an RDS file named CAWa_cropType.rds, which compiles all resources through a list object usable in R (Table 4).

Technical Validation
To guaranty the consistency of our ground-truth data, we first checked class labels for misspellings using labelCheck() from fieldRS. The function provided us with a list of unique classes within a pre-defined table structure meant for manual editing. We visually assesse each unique label looking for misspelling and needed class aggregations (e.g. "fruit trees" and "apple trees" merged as "orchard"). Then, we provided the table with corrected labels to labelCheck() to automatically correct the originals. We repeated this process after the detection of double cropping events to find labelling errors introduced during the visual assessment of temporal profiles.  Fig. 4 Comparison of phenological classes. Comparison of profiles for different phenological class groups. This information is used as a reference to re-classify crop types based on their respective NDVI profiles. "Winter" includes only winter wheat, which is planted in the last months of the year. "Summer" includes e.g. cotton and maize, which are planted at the begging of the year and usually harvested in mid-to late-summer. "Double" describes the existence of crop rotation (i.e. two phenological peaks) while "Permanent" depicts persistent agricultural practices, such as orchards.  www.nature.com/scientificdata www.nature.com/scientificdata/ Additionally, during the visual assessment, we clearly mislabelled samples. These relate e.g. to cotton samples labelled as wheat that had visible summer peak in the NDVI. Here, we used our knowledge on crop-specific phenology behaviour, and the reference plots derived by analyzeTS() to consolidated our expectation on the shape of the temporal NDVI profile for a given class.

Usage Notes
We developed this dataset to map the distribution of crop types in irrigation systems of the Aral Sea Basin in Central Asia. However, the use of these data can be extended. In the scope of land cover mapping, our data can support existing mapping services such as the Climate Change Initiative (CCI) land cover data (https://www. esa-landcover-cci.org/) as it complements spatial and temporal data gap in a large agricultural system. Since our samples are provided as polygons, users can freely adjust them to different satellite sensors. When dealing with high-resolution sensors, our pixel-based sampling approach can be used to translate our database into larger number of samples with associated information on pixel homogeneity. This information is an essential element in evaluating the consistency of land cover mapping applications within and between classes. On the other hand, when using mid and low-resolution satellite data, the sample homogeneity data provided with our product can be used as a metric of uncertainty.
Practitioners interested in collecting new samples might also profit from our data. In particular, users can rely on the NDVI time-series associated to each sample -as well as the samples themselves -as a reference when interpreting remotely-sensed data.

Code availability
The code used in the processing of our ground-truth data is open-source and was published in the Comprehensive R Archive Network (CRAN). The workflow for the processing of ground-truth data are available online in the form of an html vignette (https://CRAN.R-project.org/package=CAWaR/vignettes/CAWaR.html) and can be tested using example ground-truth data provided within the corresponding R package.

Column
Format Description 1, …, 353 Numeric NDVI for a given day of year (given by the column name) Table 3. Content of "CAWa_cropType_time-series.csv". These data contain the weighted-mean NDVI timeseries used in the validation of the crop-type labels initially assigned to each sample during the respective field surveys. For each row, corresponding to a unique sample, the 23 columns provide equidistant NDVI values with a 16-day interval. The name of each column informs on the day of the year in which the respective sample was collected.
List element name R Class Description samples SpatialPolygonsDataFrame Content described in Table 1 Info Data.Frame Content described in Table 2 ndvi Data.Frame Content described in Table 3   Table 4. Content of "CAWa_CropType_samples.rds". The data described in Tables 1-3 are combined into an RDS file, which is an R specific file format. When read into R, the input data are organized in a list composed by three elements as described in the present table.