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DESCRIPTION

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@@ -27,7 +27,7 @@ Description: An end-to-end toolkit for land use and land cover classification
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random forests, extreme gradient boosting, multi-layer perceptrons,
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temporal convolutional neural networks proposed by Pelletier et al (2019) <doi:10.3390/rs11050523>,
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residual networks by Fawaz et al (2019) <doi:10.1007/s10618-019-00619-1>, and temporal attention encoders
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by Garnot and Landrieu (2020) <arXiv:2007.00586>.
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by Garnot and Landrieu (2020) <doi:10.48550/arXiv.2007.00586>.
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Performs efficient classification of big Earth observation data cubes and includes
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functions for post-classification smoothing based on Bayesian inference, and
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methods for uncertainty assessment. Enables best

R/api_kohonen.R

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for (i in 1:nclasses) {
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outmat[which(as.integer(yvec) == i), i] <- 1
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}
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outmat
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}
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contributing.md

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# Contributing to the sits R package
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- We welcome all contributors to sits package!
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Please submit questions, bug reports, and requests in the [issues tracker](https://github.com/e-sensing/sits/issues).
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If you plan to contribute code, go ahead! Fork the repo and submit a pull request. A few notes:
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We welcome all contributors to sits package! Please submit questions, bug reports, and requests in the [issues tracker](https://github.com/e-sensing/sits/issues). If you plan to contribute code, go ahead! Fork the repo and submit a pull request. A few notes:
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- This package is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By participating in this project you agree to abide by its terms.
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- If you have large changes, please open an issue first to discuss.
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- This package generally uses the [rOpenSci packaging guidelines](https://github.com/ropensci/onboarding/blob/master/packaging_guide.md) for style and structure.
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- Documentation is generated by **roxygen2**. Please write documentation in code files and let it auto-generate documentation files.
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- For more substantial contributions, consider adding a new section to one of the chapters of the SITS book (https://e-sensing.github.io/sitsbook/), which has been written in R markdown and whose source is available in the [sitsbook repository](https://github.com/e-sensing/sitsbook).
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- We aim for testing that has high coverage and is robust. Include tests with
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any major contribution to code.
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- We aim for testing that has high coverage and is robust. Include tests with any major contribution to code.
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- We particularly welcome additions in two areas: new STAC-based image repositories and new raster machine learning/deep learning algorithms. Please see more details below.
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## General structure of sits code.
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- New functions that build on the `sits` API should follow the general principles below.
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New functions that build on the `sits` API should follow the general principles below.
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### API design
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The sits `code` relies on the packages of the `tidyverse` to work with tables and list. We use `dplyr` and `tidyr` for data selection and wrangling, `purrr` and `slider` for loops on lists and table, `lubridate` to handle dates and times.
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### Adherence to the `sits` data types
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- The `sits` package in built on top of three data types: time series tibble, data cubes and models. Most `sits` functions have one or more of these types as inputs and one of them as return values.
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- Each STAC catalogue is different. The STAC specification allows providers to implement their data descriptions with specific information. For this reason, the generic API described in `api_source.R` needs to be specialized for each provider. Whenever a provider needs specific implementations of parts of the STAC protocol, we include them in separate files. For example, `api_source_mpc.R` implements specific quirks of the MPC platform. Similarly, specific support for CDSE (Copernicus Data Space Environment) is available in `api_source_cdse.R`.
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- In summary, before including a new data provider, study the code that has been implemented.
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### Supporting new Machine Learning and Deep Learning algorithms
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- In general terms, ML/DL algorithms in `sits` are encapsulated as closures which are the output of the `sits_train()` function. In line with the established practices in **R**, each closure contains a function that classifies input values, as well as information on the samples used to train the model.

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