From 7210ac52bc2ab1e7402c4a5d79cb889ca18e9235 Mon Sep 17 00:00:00 2001 From: Michael Sumner Date: Thu, 14 May 2020 19:26:17 +1000 Subject: [PATCH 1/3] new packages --- task_view/antarctic.md | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/task_view/antarctic.md b/task_view/antarctic.md index ab04f2c..397e488 100644 --- a/task_view/antarctic.md +++ b/task_view/antarctic.md @@ -23,7 +23,7 @@ For more detail on R packages dealing with taxonomy in general, see the [rOpenSc Mapping is a very common task, and in an Antarctic/Southern Ocean context brings with it particular issues including dealing with projection properties at high latitudes, coping with data that crosses the 180°E line, adding commonly-desired features such as ocean fronts, management boundaries, sea ice extent, stations and other geographic features, and common contextual layers such as bathymetry. -- [SOmap](https://github.com/AustralianAntarcticDivision/SOmap) is in development, but aims to provide straightforward mapping functions for Southern Ocean (polar stereographic) maps, along with commonly-used management and contextual layers such as MPA boundaries and ocean fronts. +- [SOmap](https://github.com/AustralianAntarcticDivision/SOmap) is in development, but aims to provide straightforward mapping functions for Southern Ocean (polar stereographic) maps, along with commonly-used management and contextual layers such as MPA boundaries and ocean fronts. - [antanym](https://github.com/SCAR/antanym) provides geographic place name data from the SCAR Composite Gazetteer of Antarctica, with plans to extend the coverage to subantarctic and informal gazetteers at a later date. @@ -31,7 +31,14 @@ Mapping is a very common task, and in an Antarctic/Southern Ocean context brings - graticule creates graticule lines (lines of longitude and latitude) and labels for maps. -- palr provides colour palettes for data, based on some well known remotely sensed data sets for sea ice concentration, sea surface temperature and chlorophyll-*a*. +- palr provides colour palettes for data, based on some well known remotely sensed data sets for sea ice concentration, sea surface temperature and chlorophyll-*a*. Provides functions to convert raster *data* to raster *imagery* +based on palette-mapping. + +- anglr Gives direct access to generic 3D tools and provides a full suite of mesh-creation and 3D plotting functions. Suitable for use with a wide variety of spatial data including raster elevation models, trajectory data, polygonal surfaces, climate model output, and aerial photography. + +- ceramic Download imagery tiles to a standard cache and load the data into raster objects, allows direct access to elevation data and satellite imagery for large areas at low resolution. (Very high resolution is available in *terrestrial* areas, but mostly only at lower latitudes). + +- reproj Transform coordinates from a specified source to a specified target map projection. Suitable for use on generic data structures, or for creating custom transformation functions for formats not supported by mainstream tools. - there is some Antarctic-related mapping functionality in [prtools](https://github.com/pierreroudier/prtools), [atlasr](https://github.com/jiho/atlasr), [CCAMLRGIS](https://github.com/ccamlr/CCAMLRGIS), and [sospatial](https://github.com/AustralianAntarcticDivision/sospatial). @@ -74,3 +81,5 @@ Tracking of animals using satellite, GPS, or light-level geolocation tags is com Packages that may be of interest but don't yet fit neatly into another category. - [distancetocoast](https://github.com/mdsumner/distancetocoast) provides "distance to coastline" data for longitude and latitude coordinates. + +- lazyraster Read raster data at a specified resolution on-demand. Provides very quick 'overview' access to very large raster data sets, by specifying a region of interest and/or an output grid size. From 06b86d61a2618664c2a415117df4ecbfa7374f36 Mon Sep 17 00:00:00 2001 From: Michael Sumner Date: Thu, 14 May 2020 20:15:57 +1000 Subject: [PATCH 2/3] pkgs, change SpatTemp task view to Tracking --- task_view/antarctic.md | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/task_view/antarctic.md b/task_view/antarctic.md index 397e488..bed7b9d 100644 --- a/task_view/antarctic.md +++ b/task_view/antarctic.md @@ -63,6 +63,8 @@ based on palette-mapping. - robis for marine data, rgbif for global biodiversity data. spocc wraps these and other occurrence data providers with a consistent interface (but not necessarily the full functionality of provider-specific packages, where they exist). +- rbgm Facilities for working with box-geometry model (BGM) files of the Atlantis whole-of-ecosystem model. Functions to read from BGM files directly, preserving internal topology, as well as helper functions to generate spatial data from these mesh forms. + - [obistools](https://github.com/iobis/obistools) and scrubr for quality-checking occurrence data. - a package for the data behind the [Mapping Application for Penguin Populations and Projected Dynamics (MAPPPD)](http://www.penguinmap.com/) is in planning: contact [Grant Humphries](mailto:grwhumphries@blackbawks.net). @@ -71,8 +73,10 @@ based on palette-mapping. ### Animal tracking -Tracking of animals using satellite, GPS, or light-level geolocation tags is common, and there are many R packages that can help with this. See the [spatiotemporal task view](https://cloud.r-project.org/web/views/SpatioTemporal.html) for a more complete list. Of particular interest may be: +Tracking of animals using satellite, GPS, or light-level geolocation tags is common, and there are many R packages that can help with this. See the [tracking task view](https://cloud.r-project.org/web/views/Tracking.html) for a more complete list. Of particular interest may be: + traipse A collection of commonly used tools for animal movement and other tracking data. Variously distance, angle, bearing, distance-to, bearing-to and speed are provided for geographic data that can be used directly or within 'tidyverse' syntax. + - [TwilightFree](https://github.com/ABindoff/TwilightFree) provides a method for processing light-level geolocation data that is robust to noise (sensor shading and obscuration) and may be particularly suitable for Southern Ocean applications. @@ -83,3 +87,5 @@ Packages that may be of interest but don't yet fit neatly into another category. - [distancetocoast](https://github.com/mdsumner/distancetocoast) provides "distance to coastline" data for longitude and latitude coordinates. - lazyraster Read raster data at a specified resolution on-demand. Provides very quick 'overview' access to very large raster data sets, by specifying a region of interest and/or an output grid size. + +- tidync Tidy tools to explore the contents of 'NetCDF' file or URL, presented as variables organized by grid with a database-like interface. From 8c41d80c63f00dcb497801108a7100c12a5222cc Mon Sep 17 00:00:00 2001 From: Michael Sumner Date: Thu, 14 May 2020 21:05:15 +1000 Subject: [PATCH 3/3] make working --- task_view/Antarctic.ctv | 26 +++++++++--- task_view/Antarctic.html | 85 ++++++++++++++++++++++++++++++++++------ task_view/README.md | 74 ++++++++++++++++++++++++++++------ task_view/antarctic.md | 1 - 4 files changed, 154 insertions(+), 32 deletions(-) diff --git a/task_view/Antarctic.ctv b/task_view/Antarctic.ctv index 1c6bfbe..c46647c 100644 --- a/task_view/Antarctic.ctv +++ b/task_view/Antarctic.ctv @@ -2,7 +2,7 @@ Antarctic Antarctic and Southern Ocean Science Ben Raymond - 2019-02-18 + 2020-05-14

This article is about R packages that are relevant to Antarctic and Southern Ocean science. It includes packages in various states of maturity, including some in planning or very early stages of development.

Antarctic and Southern Ocean science covers a diverse range of topics within the geosciences, life sciences, physical sciences, and humanities and social sciences. This article is not intended to be an exhaustive list of packages that are relevant to all of those fields, but rather a synopsis of packages that are for one reason or another of particular interest to Antarctic and Southern Ocean researchers. The definition of “particular interest” is of course largely arbitrary. Packages listed here are generally expected to be at a useful stage of development, or if not, are seeking engagement/input from the wider community.

@@ -21,9 +21,12 @@

  • SOmap is in development, but aims to provide straightforward mapping functions for Southern Ocean (polar stereographic) maps, along with commonly-used management and contextual layers such as MPA boundaries and ocean fronts.

  • antanym provides geographic place name data from the SCAR Composite Gazetteer of Antarctica, with plans to extend the coverage to subantarctic and informal gazetteers at a later date.

    • -

  • orsifronts provides the commonly-used Orsi et al. (1995) definitions of the major Southern Ocean fronts.

    • +

  • orsifronts provides the commonly-used Orsi et al. (1995) definitions of the major Southern Ocean fronts.

  • graticule creates graticule lines (lines of longitude and latitude) and labels for maps.

    • -

  • palr provides colour palettes for data, based on some well known remotely sensed data sets for sea ice concentration, sea surface temperature and chlorophyll-a.

    • +

  • palr provides colour palettes for data, based on some well known remotely sensed data sets for sea ice concentration, sea surface temperature and chlorophyll-a. Provides functions to convert raster data to raster imagery based on palette-mapping.

    • +

  • anglr Gives direct access to generic 3D tools and provides a full suite of mesh-creation and 3D plotting functions. Suitable for use with a wide variety of spatial data including raster elevation models, trajectory data, polygonal surfaces, climate model output, and aerial photography.

    • +

  • ceramic Download imagery tiles to a standard cache and load the data into raster objects, allows direct access to elevation data and satellite imagery for large areas at low resolution. (Very high resolution is available in terrestrial areas, but mostly only at lower latitudes).

    • +

  • reproj Transform coordinates from a specified source to a specified target map projection. Suitable for use on generic data structures, or for creating custom transformation functions for formats not supported by mainstream tools.

  • there is some Antarctic-related mapping functionality in prtools, atlasr, CCAMLRGIS, and sospatial.

Environmental Data

@@ -34,34 +37,43 @@

Oceanography

    -

  • satellite reflectance data are a common basis for estimating chlorophyll-a and other phytoplankton parameters at ocean-basin scales. Global products are widely available; however, Southern-Ocean specific algorithms are likely to provide better estimates in these regions. croc implements the Johnson et al. (2013) Southern Ocean algorithm.

    • +

  • satellite reflectance data are a common basis for estimating chlorophyll-a and other phytoplankton parameters at ocean-basin scales. Global products are widely available; however, Southern-Ocean specific algorithms are likely to provide better estimates in these regions. croc implements the Johnson et al. (2013) Southern Ocean algorithm.

  • more broadly, oce provides a wide range of tools for reading, processing, and displaying oceanographic data, including measurements from Argo floats and CTD casts, sectional data, sea-level time series, and coastline and topographic data.

  • fda.oce provides functional data analysis of oceanographic profiles for front detection, water mass identification, unsupervised or supervised classification, model comparison, data calibration, and more.

Biodiversity data

  • robis for marine data, rgbif for global biodiversity data. spocc wraps these and other occurrence data providers with a consistent interface (but not necessarily the full functionality of provider-specific packages, where they exist).

    • +

  • rbgm Facilities for working with box-geometry model (BGM) files of the Atlantis whole-of-ecosystem model. Functions to read from BGM files directly, preserving internal topology, as well as helper functions to generate spatial data from these mesh forms.

  • obistools and scrubr for quality-checking occurrence data.

  • a package for the data behind the Mapping Application for Penguin Populations and Projected Dynamics (MAPPPD) is in planning: contact Grant Humphries.

  • diet data sohungry and allometric equations solong

Animal tracking

-

Tracking of animals using satellite, GPS, or light-level geolocation tags is common, and there are many R packages that can help with this. See the spatiotemporal task view for a more complete list. Of particular interest may be:

+

Tracking of animals using satellite, GPS, or light-level geolocation tags is common, and there are many R packages that can help with this. See the tracking task view for a more complete list. Of particular interest may be:

+

traipse A collection of commonly used tools for animal movement and other tracking data. Variously distance, angle, bearing, distance-to, bearing-to and speed are provided for geographic data that can be used directly or within ‘tidyverse’ syntax.

  • TwilightFree provides a method for processing light-level geolocation data that is robust to noise (sensor shading and obscuration) and may be particularly suitable for Southern Ocean applications.

Miscellaneous

Packages that may be of interest but don’t yet fit neatly into another category.

    -
  • distancetocoast provides “distance to coastline” data for longitude and latitude coordinates.
    • +

  • distancetocoast provides “distance to coastline” data for longitude and latitude coordinates.

    • +

  • lazyraster Read raster data at a specified resolution on-demand. Provides very quick ‘overview’ access to very large raster data sets, by specifying a region of interest and/or an output grid size.

    • +

  • tidync Tidy tools to explore the contents of ‘NetCDF’ file or URL, presented as variables organized by grid with a database-like interface.

 + anglr + ceramic graticule + lazyraster oce orsifronts palr raster + rbgm + reproj rerddap rgbif robis @@ -69,6 +81,8 @@ scrubr spocc taxize + tidync + traipse worrms diff --git a/task_view/Antarctic.html b/task_view/Antarctic.html index a436f23..e4cbbfb 100644 --- a/task_view/Antarctic.html +++ b/task_view/Antarctic.html @@ -6,11 +6,11 @@ - + - + @@ -95,7 +95,7 @@

  • orsifronts - provides the commonly-used Orsi et al. (1995) definitions of the major Southern Ocean fronts. + provides the commonly-used Orsi et al. (1995) definitions of the major Southern Ocean fronts.

  • @@ -110,7 +110,37 @@

    provides colour palettes for data, based on some well known remotely sensed data sets for sea ice concentration, sea surface temperature and chlorophyll- a - . + . Provides functions to convert raster + + data + + to raster + + imagery + + based on palette-mapping. +

    +

    • +
  • +

    +anglr + Gives direct access to generic 3D tools and provides a full suite of mesh-creation and 3D plotting functions. Suitable for use with a wide variety of spatial data including raster elevation models, trajectory data, polygonal surfaces, climate model output, and aerial photography. +

    +
    • +
  • +

    +ceramic + Download imagery tiles to a standard cache and load the data into raster objects, allows direct access to elevation data and satellite imagery for large areas at low resolution. (Very high resolution is available in + + terrestrial + + areas, but mostly only at lower latitudes). +

    +
    • +
  • +

    +reproj + Transform coordinates from a specified source to a specified target map projection. Suitable for use on generic data structures, or for creating custom transformation functions for formats not supported by mainstream tools.

  • @@ -187,7 +217,7 @@

    croc - implements the Johnson et al. (2013) Southern Ocean algorithm. + implements the Johnson et al. (2013) Southern Ocean algorithm.

  • @@ -222,6 +252,12 @@

  • +rbgm + Facilities for working with box-geometry model (BGM) files of the Atlantis whole-of-ecosystem model. Functions to read from BGM files directly, preserving internal topology, as well as helper functions to generate spatial data from these mesh forms. +

    +
    • +
  • +

    obistools @@ -260,11 +296,15 @@

    Tracking of animals using satellite, GPS, or light-level geolocation tags is common, and there are many R packages that can help with this. See the - - spatiotemporal task view + + tracking task view for a more complete list. Of particular interest may be:

    +

    +traipse + A collection of commonly used tools for animal movement and other tracking data. Variously distance, angle, bearing, distance-to, bearing-to and speed are provided for geographic data that can be used directly or within ‘tidyverse’ syntax. +

    • @@ -281,21 +321,40 @@

      • - - distancetocoast - - provides “distance to coastline” data for longitude and latitude coordinates. +

        + + distancetocoast + + provides “distance to coastline” data for longitude and latitude coordinates. +

        +
        • +
      • +

        +lazyraster + Read raster data at a specified resolution on-demand. Provides very quick ‘overview’ access to very large raster data sets, by specifying a region of interest and/or an output grid size. +

        +
        • +
      • +

        +tidync + Tidy tools to explore the contents of ‘NetCDF’ file or URL, presented as variables organized by grid with a database-like interface. +

      CRAN packages:

      Related links:

      diff --git a/task_view/README.md b/task_view/README.md index 35de125..41b9de5 100644 --- a/task_view/README.md +++ b/task_view/README.md @@ -18,8 +18,8 @@ here are generally expected to be at a useful stage of development, or if not, are seeking engagement/input from the wider community. Contributions are welcome\! Please [submit an -issue](https://github.com/SCAR/ropensci/issues), or make a contribution -(see the [contribution guidelines](CONTRIBUTING.md)). If you have an +issue](https://github.com/SCAR/ropensci/issues) , or make a contribution +(see the [contribution guidelines](CONTRIBUTING.md) ). If you have an issue with one of the packages discussed below, please contact the maintainer of that package. @@ -50,7 +50,7 @@ development for working with RAS (visualising and predicting the growth in taxonomic diversity over time). For more detail on R packages dealing with taxonomy in general, see the -[rOpenSci taxonomy task view](https://github.com/ropensci/taxonomy). +[rOpenSci taxonomy task view](https://github.com/ropensci/taxonomy) . ### Mapping @@ -73,7 +73,7 @@ features, and common contextual layers such as bathymetry. at a later date. - [orsifronts](https://cran.rstudio.com/web/packages/orsifronts/index.html) provides the - commonly-used Orsi et al. (1995) definitions of the major Southern + commonly-used Orsi et al. (1995) definitions of the major Southern Ocean fronts. - [graticule](https://cran.rstudio.com/web/packages/graticule/index.html) creates graticule @@ -82,12 +82,33 @@ features, and common contextual layers such as bathymetry. - [palr](https://cran.rstudio.com/web/packages/palr/index.html) provides colour palettes for data, based on some well known remotely sensed data sets for sea ice concentration, sea surface temperature and chlorophyll- *a* . + Provides functions to convert raster *data* to raster *imagery* + based on palette-mapping. + + - [anglr](https://cran.rstudio.com/web/packages/anglr/index.html) Gives direct access to generic + 3D tools and provides a full suite of mesh-creation and 3D plotting + functions. Suitable for use with a wide variety of spatial data + including raster elevation models, trajectory data, polygonal + surfaces, climate model output, and aerial photography. + + - [ceramic](https://cran.rstudio.com/web/packages/ceramic/index.html) Download imagery tiles to + a standard cache and load the data into raster objects, allows + direct access to elevation data and satellite imagery for large + areas at low resolution. (Very high resolution is available in + *terrestrial* areas, but mostly only at lower latitudes). + + - [reproj](https://cran.rstudio.com/web/packages/reproj/index.html) Transform coordinates from a + specified source to a specified target map projection. Suitable for + use on generic data structures, or for creating custom + transformation functions for formats not supported by mainstream + tools. - there is some Antarctic-related mapping functionality in - [prtools](https://github.com/pierreroudier/prtools), - [atlasr](https://github.com/jiho/atlasr), - [CCAMLRGIS](https://github.com/ccamlr/CCAMLRGIS), and - [sospatial](https://github.com/AustralianAntarcticDivision/sospatial). + [prtools](https://github.com/pierreroudier/prtools) , + [atlasr](https://github.com/jiho/atlasr) , + [CCAMLRGIS](https://github.com/ccamlr/CCAMLRGIS) , and + [sospatial](https://github.com/AustralianAntarcticDivision/sospatial) + . ### Environmental Data @@ -120,7 +141,7 @@ features, and common contextual layers such as bathymetry. scales. Global products are widely available; however, Southern-Ocean specific algorithms are likely to provide better estimates in these regions. [croc](https://github.com/sosoc/croc) - implements the Johnson et al. (2013) Southern Ocean algorithm. + implements the Johnson et al. (2013) Southern Ocean algorithm. - more broadly, [oce](https://cran.rstudio.com/web/packages/oce/index.html) provides a wide range of tools for reading, processing, and displaying oceanographic @@ -142,6 +163,12 @@ features, and common contextual layers such as bathymetry. necessarily the full functionality of provider-specific packages, where they exist). + - [rbgm](https://cran.rstudio.com/web/packages/rbgm/index.html) Facilities for working with + box-geometry model (BGM) files of the Atlantis whole-of-ecosystem + model. Functions to read from BGM files directly, preserving + internal topology, as well as helper functions to generate spatial + data from these mesh forms. + - [obistools](https://github.com/iobis/obistools) and [scrubr](https://cran.rstudio.com/web/packages/scrubr/index.html) for quality-checking occurrence data. @@ -149,7 +176,7 @@ features, and common contextual layers such as bathymetry. - a package for the data behind the [Mapping Application for Penguin Populations and Projected Dynamics (MAPPPD)](http://www.penguinmap.com/) is in planning: contact [Grant - Humphries](mailto:grwhumphries@blackbawks.net). + Humphries](mailto:grwhumphries@blackbawks.net) . - diet data [sohungry](https://github.com/SCAR/sohungry) and allometric equations [solong](https://github.com/SCAR/solong) @@ -158,9 +185,14 @@ features, and common contextual layers such as bathymetry. Tracking of animals using satellite, GPS, or light-level geolocation tags is common, and there are many R packages that can help with this. -See the [spatiotemporal task -view](https://cloud.r-project.org/web/views/SpatioTemporal.html) for a -more complete list. Of particular interest may be: +See the [tracking task +view](https://cloud.r-project.org/web/views/Tracking.html) for a more +complete list. Of particular interest may be: + +[traipse](https://cran.rstudio.com/web/packages/traipse/index.html) A collection of commonly used +tools for animal movement and other tracking data. Variously distance, +angle, bearing, distance-to, bearing-to and speed are provided for +geographic data that can be used directly or within ‘tidyverse’ syntax. - [TwilightFree](https://github.com/ABindoff/TwilightFree) provides a method for processing light-level geolocation data that is robust to @@ -176,15 +208,29 @@ category. provides “distance to coastline” data for longitude and latitude coordinates. + - [lazyraster](https://cran.rstudio.com/web/packages/lazyraster/index.html) Read raster data at + a specified resolution on-demand. Provides very quick ‘overview’ + access to very large raster data sets, by specifying a region of + interest and/or an output grid size. + + - [tidync](https://cran.rstudio.com/web/packages/tidync/index.html) Tidy tools to explore the + contents of ‘NetCDF’ file or URL, presented as variables organized + by grid with a database-like interface. + ### CRAN packages: + - [anglr](https://cran.rstudio.com/web/packages/anglr/index.html) + - [ceramic](https://cran.rstudio.com/web/packages/ceramic/index.html) - [graticule](https://cran.rstudio.com/web/packages/graticule/index.html) + - [lazyraster](https://cran.rstudio.com/web/packages/lazyraster/index.html) - [oce](https://cran.rstudio.com/web/packages/oce/index.html) - [orsifronts](https://cran.rstudio.com/web/packages/orsifronts/index.html) - [palr](https://cran.rstudio.com/web/packages/palr/index.html) - [raster](https://cran.rstudio.com/web/packages/raster/index.html) + - [rbgm](https://cran.rstudio.com/web/packages/rbgm/index.html) + - [reproj](https://cran.rstudio.com/web/packages/reproj/index.html) - [rerddap](https://cran.rstudio.com/web/packages/rerddap/index.html) - [rgbif](https://cran.rstudio.com/web/packages/rgbif/index.html) - [robis](https://cran.rstudio.com/web/packages/robis/index.html) @@ -192,6 +238,8 @@ category. - [scrubr](https://cran.rstudio.com/web/packages/scrubr/index.html) - [spocc](https://cran.rstudio.com/web/packages/spocc/index.html) - [taxize](https://cran.rstudio.com/web/packages/taxize/index.html) + - [tidync](https://cran.rstudio.com/web/packages/tidync/index.html) + - [traipse](https://cran.rstudio.com/web/packages/traipse/index.html) - [worrms](https://cran.rstudio.com/web/packages/worrms/index.html) ### Related links: diff --git a/task_view/antarctic.md b/task_view/antarctic.md index bed7b9d..0661473 100644 --- a/task_view/antarctic.md +++ b/task_view/antarctic.md @@ -79,7 +79,6 @@ Tracking of animals using satellite, GPS, or light-level geolocation tags is com - [TwilightFree](https://github.com/ABindoff/TwilightFree) provides a method for processing light-level geolocation data that is robust to noise (sensor shading and obscuration) and may be particularly suitable for Southern Ocean applications. - ### Miscellaneous Packages that may be of interest but don't yet fit neatly into another category.