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README.Rmd
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README.Rmd
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---
output:
github_document:
toc: no
toc_depth: 2
---
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
# MODIStsp <img src='man/figures/logo.png' align="right" height="139" />
<!-- badges: start -->
[](https://cran.r-project.org/package=MODIStsp)
[](https://cran.r-project.org/package=MODIStsp)
[](https://doi.org/10.5281/zenodo.1972039)
[](https://app.codecov.io/github/ropensci/MODIStsp?branch=master)
[](https://github.com/ropensci/software-review/issues/184)
<!-- badges: end -->
[`{MODIStsp}`](https://docs.ropensci.org/MODIStsp/) is a `R` package devoted to
automatizing the creation of time series of rasters derived from MODIS Land Products
data.
`{MODIStsp}` allows performing several preprocessing steps (e.g., download, mosaicing,
reprojection and resize) on MODIS data available within a given time period.
Users have the ability to select which specific layers of the original MODIS HDF
files they want to process. They also can select which additional Quality Indicators
should be extracted from the aggregated MODIS Quality Assurance layers and, in the
case of Surface Reflectance products, which Spectral Indexes should be computed
from the original reflectance bands. For each output layer, outputs are saved as
single-band raster files corresponding to each available acquisition date.
Virtual files allowing access to the entire time series as a single file can be
also created. All processing parameters can be easily selected with a user-friendly
GUI, although non-interactive execution exploiting a previously created Options
File is possible. Stand-alone execution outside an "R" environment is also possible,
allowing to use scheduled execution of MODIStsp to automatically update time series
related to a MODIS product and extent whenever a new image is available.
<a href="http://www.irea.cnr.it/en/"> <img src="man/figures/irea_logo.png" height="40" align="left" /></a>
<span style='font-style:italic;font-weight:bold;'>`{MODIStsp}` was developed by Lorenzo Busetto and Luigi Ranghetti,
[Institute of Remote Sensing of Environment](http://www.irea.cnr.it/en/) - National Research Council - Italy (CNR-IREA).
[It is dedicated to the memory of Lorenzo](https://docs.ropensci.org/MODIStsp/articles/lorenzo.html).</span>
## Citation
To cite `{MODIStsp}` please use:
L. Busetto, L. Ranghetti (2016) MODIStsp: An R package for automatic preprocessing of MODIS
Land Products time series, Computers & Geosciences, Volume 97, Pages
40-48, ISSN 0098-3004, https://doi.org/10.1016/j.cageo.2016.08.020, URL: https://github.com/ropensci/MODIStsp.
## Website
For more information, documentation and examples of use, __see also the `{MODIStsp}` website at [docs.ropensci.org/MODIStsp](https://docs.ropensci.org/MODIStsp/)__.
## Important News
- 29/10/2021 - `{MODIStsp}` (GitHub version 2.0.6.9000) supports products with version 061.
Version 006 will remain the default product version until its decommission
will be announced.
Version 061 can be specified through the argument `prod_version` of function
`MODIStsp()` or by selecting it in the GUI.
- 10/12/2020 - `{MODIStsp}` was resubmitted to CRAN after the maintainer's death.
Now `{MODIStsp}` is dedicated to Lorenzo Busetto (https://docs.ropensci.org/MODIStsp/articles/lorenzo).
- 01/09/2020 - `{MODIStsp}` 2.0.0 is out. Provides a new GUI interface based on Shiny, getting rid
of the archived dependencies on gWidgets/gWidgetsRGtk2. Also provides much easier usage from
the CLI, by allowing to set all processing arguments also from the CLI. __Note:__ due to the
introduced changes, options files created with previous versions of `{MODIStsp}` will no
longer work. Also, processing scripts using `{MODIStsp}` may need to be slightly adapted.
- 09/05/2020 - `{MODIStsp}` 1.4.0 is out. Switches to use of GDAL3/PROJ6 WKTs for projection representation and usage of `{sf}` for all internal work on vector data. Adds support for products MCD19A1 and MCD19A2 products.
- 07/06/2019 - `{MODIStsp}` 1.3.9 is out. Fixes a bug causing crashes on MOD14A1 product, adds support for product MCD12Q2 and removes support for no longer available version 5 of some products.
- 05/03/2019 - `{MODIStsp}` 1.3.8 is out. Fixes an issue causing incorrect application of scale/offset values on GDAL versions > 2.3 (https://github.com/ropensci/MODIStsp/issues/163) and adds support for products MOD21A1D.006, MOD21A1N.006 and MOD21A2.006.
- 29/11/2018 - We recently discovered a nasty bug in the computation of some custom spectral indices (those including additions / subtractions on reflectance values, such as in (b1_NIR+0.1) / b2_Red. See [here](https://docs.ropensci.org/MODIStsp/articles/discovered_bug.html) for further details. The bug is fixed as of version 1.3.7.
- 07/08/2018 - We are glad to report that `{MODIStsp}` is now included in the
[rOpenSci](https://ropensci.org/about/) packages ecosystem. We thank reviewers
Leah Wasser and Jeffrey Hanson for their valuable reviews, which helped us to
further improve the package.
- 10/07/2018 - `{MODIStsp}` v. 1.3.6 is out (check out the [Release Notes](https://github.com/ropensci/MODIStsp/releases/tag/1.3.6) for further details).
- 20/06/2018 - `{MODIStsp}` v. 1.3.5 is out (check out the [Release Notes](https://github.com/ropensci/MODIStsp/releases/tag/v1.3.5) for further details).
- 11/04/2018 - Due to new NASA Policies the MODIS FTP servers were shut down
starting, April 2, 2018. **FTP download is therefore no longer working** and will
be removed in the next MODIStsp version.
- 11/04/2018 - [**Decommissioning of MODIS Version 5 Land Data Products**]( https://lpdaac.usgs.gov/news/decommissioning-modis-version-51-land-cover-type-data-products-january-7-2019/). As per NASA notice above, MODIS v005 products are going to be
decommissioned, and will soon be no longer available for download. Support for those
products will be removed in the next MODIStsp version.
- 11/08/2017 - `{MODIStsp}` 1.3.3 was released today. It provides improvements in
processing speed, as well as the usual bug fixes
(thanks to all the users that signaled problems). Check the [Release Notes](https://github.com/ropensci/MODIStsp/releases/tag/v1.3.3) for further details.
- 25/07/2017 - As of today, **most of the content related to `{MODIStsp}` has been
moved to our new website at [docs.ropensci.org/MODIStsp](https://docs.ropensci.org/MODIStsp/)
**, which provides a much better user interface and ease of access to MODIStsp-related
information. From now on, please **consult the new website for detailed and updated
information on the package**.
- Also our previous FAQ page on GitHub containing info for solving common
installation, downloading and processing problems and issues was discontinued
and **migrated at [docs.ropensci.org/MODIStsp/articles/faq.html](https://docs.ropensci.org/MODIStsp/articles/faq.html)**.
## Problems and Issues
- Please **report any issues** you may encounter in our [issues page on github <i class="fa fa-github-square" aria-hidden="true"></i>](https://github.com/ropensci/MODIStsp/issues).
## <i class="fa fa-desktop" aria-hidden="true"></i> System Requirements
`{MODIStsp}` requires [`R`](https://cran.r-project.org) v >= 3.6.3.
____________________________________________________________________________________
# Installation Instructions
## <i class="fa fa-windows" aria-hidden="true"></i> Installing on Windows
You can install the stable version of `{MODIStsp}` from CRAN:
`install.packages("MODIStsp")`
, or the development version (containing the latest improvements and bug fixes)
from GitHub:
```{r, eval=FALSE, message=FALSE, warning=FALSE, include=TRUE}
install.packages("remotes")
library(remotes)
install_github("ropensci/MODIStsp")
```
## <i class="fa fa-linux" aria-hidden="true"></i> Installing on Linux Systems
To install `{MODIStsp}` on Linux, you need to be able to install the `{sf}` package,
which requires several dependencies. See [here](https://github.com/r-spatial/sf#installing)
if you have trouble installing `{sf}`.
Then, you can install the stable version of MODIStsp from CRAN:
```{r, eval=FALSE, message=FALSE, warning=FALSE, include=TRUE}
install.packages("MODIStsp")
```
, or the development version (containing the latest improvements and bug fixes)
from GitHub:
```{r, eval=FALSE, message=FALSE, warning=FALSE, include=TRUE}
library(devtools)
install_github("ropensci/MODIStsp")
```
## <i class="fa fa-apple" aria-hidden="true"></i> Installing on Mac
To install `{MODIStsp}` on Mac, you need to be able to install the `{sf}` package,
which requires several dependencies. See [here](https://github.com/r-spatial/sf#installing)
if you have trouble installing `{sf}`.
Then, you can install the stable version of `{MODIStsp}` from CRAN:
```{r, eval=FALSE, message=FALSE, warning=FALSE, include=TRUE}
install.packages("MODIStsp")
```
, or the development version (containing the latest improvements and bug fixes)
from GitHub:
```{r, eval=FALSE, message=FALSE, warning=FALSE, include=TRUE}
library(devtools)
install_github("ropensci/MODIStsp")
```
# Usage
The easiest way to use `{MODIStsp}` is to use its powerful GUI (Graphical User Interface)
for selection of processing options, and then run the processing.
To open the GUI, load the package and launch the MODIStsp function, with no parameters:
```{r, eval=FALSE, message=FALSE, warning=FALSE, include=TRUE, caption=FALSE}
library(MODIStsp)
MODIStsp()
```
This **opens a Shiny GUI** from which processing options can be specified (and eventually
saved or loaded). After specifying all required parameters, clicking on "Start"
will start
the processing (see [here](https://docs.ropensci.org/MODIStsp/articles/interactive_execution.html)
for more detailed instructions).
`{MODIStsp}` can also be launched in non-interactive mode within an `R` session or
script by setting the optional `GUI` parameter to FALSE, and the `opts_file`
parameter to the path of a previously saved JSON Options file. This allows to
exploit `{MODIStsp}` functionalities within generic "R" processing scripts.
```{r, eval=FALSE}
library(MODIStsp)
# --> Specify the path to a valid options file saved in advance from MODIStsp GUI
opts_file <- "X:/yourpath/youroptions.json"
# --> Launch the processing
MODIStsp(gui = FALSE, opts_file = opts_file)
```
Finally, `{MODIStsp}` can be run by manually specifying all processing arguments,
or by overwriting some of the arguments contained in a saved json file in the call
to the package, such as in:
```{r, eval=FALSE}
library(MODIStsp)
# --> Specify the path to a valid options file saved in advance from MODIStsp GUI
opts_file <- "X:/yourpath/youroptions.json"
# --> Launch the processing
MODIStsp(gui = FALSE,
opts_file = opts_file,
start_date = "2020.05.01",
end_date = "2020.08.01",
spatmeth = "file",
spafile = "X:/path_to/spatial_extent_file.gpkg")
```
, where we are overwriting the options related to spatial and temporal extent
contained in the options file with new values. This allows easily running
processing based on the same main options (e.g., product layers, output format, etc.)
but changing on the fly the desired ones.
See [here](https://docs.ropensci.org/MODIStsp/articles/noninteractive_execution.html)
for more detailed instructions and examples.
# Code of Conduct
Please note that this package is released with a [Contributor Code of Conduct](https://ropensci.org/code-of-conduct/).
By contributing to this project, you agree to abide by its terms.