diff --git a/404.html b/404.html
index 0bdbf59..998ffea 100644
--- a/404.html
+++ b/404.html
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="https://cnr-ibba.github.io/r-smarter-api/index.html">smarterapi</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE.html b/LICENSE.html
index caba527..711c89a 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">smarterapi</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/geojson.html b/articles/geojson.html
index c86a723..d1227b3 100644
--- a/articles/geojson.html
+++ b/articles/geojson.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">smarterapi</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/index.html b/articles/index.html
index 8e9a3bb..7b6f4e1 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">smarterapi</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/smarterapi.html b/articles/smarterapi.html
index 1bf5574..9c071bf 100644
--- a/articles/smarterapi.html
+++ b/articles/smarterapi.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">smarterapi</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/variants.html b/articles/variants.html
index 788b14e..d0584a6 100644
--- a/articles/variants.html
+++ b/articles/variants.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">smarterapi</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/authors.html b/authors.html
index ccaa98b..f225395 100644
--- a/authors.html
+++ b/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">smarterapi</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -65,13 +65,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Cozzi P (2024).
 <em>smarterapi: Fetch SMARTER Data Through REST API</em>.
-R package version 0.2.0.9000, <a href="https://cnr-ibba.github.io/r-smarter-api/">https://cnr-ibba.github.io/r-smarter-api/</a>. 
+R package version 0.2.0, <a href="https://cnr-ibba.github.io/r-smarter-api/">https://cnr-ibba.github.io/r-smarter-api/</a>. 
 </p>
       <pre>@Manual{,
   title = {smarterapi: Fetch SMARTER Data Through REST API},
   author = {Paolo Cozzi},
   year = {2024},
-  note = {R package version 0.2.0.9000},
+  note = {R package version 0.2.0},
   url = {https://cnr-ibba.github.io/r-smarter-api/},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index f2f3099..363b9c9 100644
--- a/index.html
+++ b/index.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="index.html">smarterapi</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/pkgdown.yml b/pkgdown.yml
index d76ecf3..1c7b842 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -5,7 +5,7 @@ articles:
   geojson: geojson.html
   smarterapi: smarterapi.html
   variants: variants.html
-last_built: 2024-06-28T13:04Z
+last_built: 2024-06-28T13:18Z
 urls:
   reference: https://cnr-ibba.github.io/r-smarter-api/reference
   article: https://cnr-ibba.github.io/r-smarter-api/articles
diff --git a/reference/get_smarter_breeds.html b/reference/get_smarter_breeds.html
index 7584dd8..ef662ce 100644
--- a/reference/get_smarter_breeds.html
+++ b/reference/get_smarter_breeds.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">smarterapi</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_smarter_countries.html b/reference/get_smarter_countries.html
index 82ff307..6504786 100644
--- a/reference/get_smarter_countries.html
+++ b/reference/get_smarter_countries.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">smarterapi</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_smarter_datasets.html b/reference/get_smarter_datasets.html
index 7fc8b94..7366c02 100644
--- a/reference/get_smarter_datasets.html
+++ b/reference/get_smarter_datasets.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">smarterapi</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_smarter_genotypes.html b/reference/get_smarter_genotypes.html
index c4d4685..a8be380 100644
--- a/reference/get_smarter_genotypes.html
+++ b/reference/get_smarter_genotypes.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">smarterapi</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_smarter_geojson.html b/reference/get_smarter_geojson.html
index 6d75a5e..33e00f8 100644
--- a/reference/get_smarter_geojson.html
+++ b/reference/get_smarter_geojson.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">smarterapi</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_smarter_info.html b/reference/get_smarter_info.html
index 64e4258..57b72b3 100644
--- a/reference/get_smarter_info.html
+++ b/reference/get_smarter_info.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">smarterapi</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_smarter_samples.html b/reference/get_smarter_samples.html
index ba53787..7aa2f88 100644
--- a/reference/get_smarter_samples.html
+++ b/reference/get_smarter_samples.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">smarterapi</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_smarter_supportedchips.html b/reference/get_smarter_supportedchips.html
index 75e36c8..db8b92b 100644
--- a/reference/get_smarter_supportedchips.html
+++ b/reference/get_smarter_supportedchips.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">smarterapi</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_smarter_variants.html b/reference/get_smarter_variants.html
index 9d44397..4987a5c 100644
--- a/reference/get_smarter_variants.html
+++ b/reference/get_smarter_variants.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">smarterapi</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/index.html b/reference/index.html
index 59736eb..c38a46f 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">smarterapi</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/search.json b/search.json
index 7c885e1..af9e3a4 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
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If not, see <http://www.gnu.org/licenses/>. <program>  Copyright (C) <year>  <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/geojson.html","id":"get-data-using-parameters","dir":"Articles","previous_headings":"","what":"Get data using parameters","title":"Working with GeoJSON data","text":"can collect GeoJSON data using parameters, like using get_smarter_samples() function. function parse GeoJSON data return Simple Feature object, tibble object geometry column. example, try collect data Sheep hapmap background dataset: preview first rows hapmap_data object: Table continues Table continues ","code":"hapmap_dataset <- get_smarter_datasets(query = list(   species = \"Sheep\",   type = \"background\",   type = \"genotypes\",   search = \"hapmap\" )) hapmap_data <- get_smarter_geojson(species = \"Sheep\", query = list(   dataset = hapmap_dataset[\"_id.$oid\"][1],   country = \"Italy\" ))"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/geojson.html","id":"filter-data-using-spatial-queries","dir":"Articles","previous_headings":"","what":"Filter data using spatial queries","title":"Working with GeoJSON data","text":"alternative approach selecting samples exploits spatial queries. example, imported goat dataset geojson file qgis. created two polygons features correspondance samples want collect using GPS coordinates like following picture: exported two polygons shapefile. can spatial query st_intersects() order collect samples correspondance two areas interest: query done using get_smarter_geojson() function providing polygons argument: means can also provide sf object polygon argument. select country, using spatial queries:","code":"polygons_file <- system.file(\"extdata\", \"polygons.shp\", package = \"smarterapi\") polygons <- sf::st_read(polygons_file) goat_data <- get_smarter_geojson(\"Goat\", query = list(type = \"background\")) sel_sgbp <- sf::st_intersects(goat_data, polygons) sel_logical <- lengths(sel_sgbp) > 0 selected_goats <- goat_data[sel_logical, ] selected_goats <- get_smarter_geojson(   \"Goat\",   query = list(type = \"background\"),   polygons = polygons ) italy <- rnaturalearth::ne_countries(scale = \"medium\", returnclass = \"sf\") %>%   dplyr::filter(name == \"Italy\") italy_goats <- get_smarter_geojson(   \"Goat\",   query = list(type = \"background\"),   polygons = italy )"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/geojson.html","id":"convert-from-multipoints-to-point","dir":"Articles","previous_headings":"","what":"Convert from MULTIPOINTS to POINT","title":"Working with GeoJSON data","text":"get_smarter_geojson() methods returns sf MULTIPOINTS objects since multiple locations collected animal, example transhumant samples. However, simplicity, can focus analyses using one GPS coordinate, transforming MULTIPOINTS object POINT object: warnings see terminal tell considering first coordinate object MULTIPOINT collection.","code":"hapmap_data <- hapmap_data %>% sf::st_cast(\"POINT\", do_split = FALSE) hapmap_data #> Simple feature collection with 92 features and 11 fields #> Geometry type: POINT #> Dimension:     XY #> Bounding box:  xmin: 9.016667 ymin: 37 xmax: 18.16667 ymax: 40.81667 #> Geodetic CRS:  WGS 84 #> # A tibble: 92 × 12 #>    breed      breed_code chip_name    country dataset metadata original_id   sex #>    <chr>      <chr>      <chr>        <chr>   <chr>   <chr>    <chr>       <int> #>  1 Altamurana ALT        IlluminaOvi… Italy   \"{ \\\"$… \"{ \\\"lo… ALT1           NA #>  2 Altamurana ALT        IlluminaOvi… Italy   \"{ \\\"$… \"{ \\\"lo… ALT23          NA #>  3 Altamurana ALT        IlluminaOvi… Italy   \"{ \\\"$… \"{ \\\"lo… ALT10          NA #>  4 Altamurana ALT        IlluminaOvi… Italy   \"{ \\\"$… \"{ \\\"lo… ALT20          NA #>  5 Altamurana ALT        IlluminaOvi… Italy   \"{ \\\"$… \"{ \\\"lo… ALT21          NA #>  6 Altamurana ALT        IlluminaOvi… Italy   \"{ \\\"$… \"{ \\\"lo… ALT22          NA #>  7 Altamurana ALT        IlluminaOvi… Italy   \"{ \\\"$… \"{ \\\"lo… ALT15          NA #>  8 Altamurana ALT        IlluminaOvi… Italy   \"{ \\\"$… \"{ \\\"lo… ALT8           NA #>  9 Altamurana ALT        IlluminaOvi… Italy   \"{ \\\"$… \"{ \\\"lo… ALT16          NA #> 10 Altamurana ALT        IlluminaOvi… Italy   \"{ \\\"$… \"{ \\\"lo… ALT24          NA #> # ℹ 82 more rows #> # ℹ 4 more variables: smarter_id <chr>, species <chr>, type <chr>, #> #   geometry <POINT [°]>"},{"path":[]},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/geojson.html","id":"displaying-data-using-ggplot2","dir":"Articles","previous_headings":"Visualize SMARTER GPS data","what":"Displaying data using ggplot2","title":"Working with GeoJSON data","text":"sf data visualized using ggplot2. following examples derive countries rnaturalearth package, zoom plot selected points previous example:  See post nice introduction sf ggplot2.","code":"# determine a bounding box around our samples bbox <- sf::st_bbox(hapmap_data)  # collect the world countries as sf world <- rnaturalearth::ne_countries(scale = \"medium\", returnclass = \"sf\")  # plot the data: use the bounding box to zoom the plot on our samples ggplot2::ggplot() +   ggplot2::geom_sf(data = world, fill = \"antiquewhite\") +   ggplot2::geom_sf(data = hapmap_data, color = \"blue\", size = 5) +   ggspatial::annotation_scale(location = \"bl\", width_hint = 0.5) +   ggspatial::annotation_north_arrow(     location = \"bl\",     which_north = \"true\",     pad_x = ggplot2::unit(0.75, \"in\"),     pad_y = ggplot2::unit(0.5, \"in\"),     style = ggspatial::north_arrow_fancy_orienteering   ) +   ggspatial::coord_sf(     xlim = c(bbox$xmin, bbox$xmax),     ylim = c(bbox$ymin, bbox$ymax)   ) +   ggplot2::theme_bw() +   ggplot2::theme(plot.title = ggplot2::element_text(hjust = 0.5)) +   ggplot2::xlab(\"longitude\") + ggplot2::ylab(\"latitude\") +   ggplot2::ggtitle(\"Selected samples\")"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/geojson.html","id":"displaying-data-using-leaflet","dir":"Articles","previous_headings":"Visualize SMARTER GPS data","what":"Displaying data using leaflet","title":"Working with GeoJSON data","text":"Data visualized interactive way using R leaflet library: See Leaflet R documentation information.","code":"leaflet::leaflet(   data = hapmap_data,   options = leaflet::leafletOptions(minZoom = 5, maxZoom = 10) ) %>%   leaflet::addTiles() %>%   leaflet::addMarkers(     clusterOptions = leaflet::markerClusterOptions(), label = ~smarter_id   )"},{"path":[]},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/geojson.html","id":"derive-elevation-data-using-elevatr","dir":"Articles","previous_headings":"Integrate data with external sources","what":"Derive elevation data using elevatr","title":"Working with GeoJSON data","text":"can collect elevation data using elevatr package. following functions returns input dataframe elevation elev_units additional columns: See elevatr vignette elevatr tutorial rspatialdata documentation information examples.","code":"prj_dd <- \"EPSG:4326\" hapmap_data_elev <- elevatr::get_elev_point(   hapmap_data,   prj = prj_dd,   src = \"aws\" )"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/geojson.html","id":"add-worldclim-data-from-rasters","dir":"Articles","previous_headings":"Integrate data with external sources","what":"Add worldclim data from rasters","title":"Working with GeoJSON data","text":"can collect data worldclim database using geodata package: package particular collect raster data different sources (see geodata reference manual information). example, collect raster lowest definition (10min =~ 340km) worldclim bioclimatic variables elevation. Raster images placed tempdir path. using terra::extract calculate values data, converting terra SpatialVectors: See raster extraction geocomputation R information.","code":"worldclim_bio <- geodata::worldclim_global(   var = \"bio\",   res = 10,   path = tempdir() ) bio_data <- terra::extract(worldclim_bio, terra::vect(hapmap_data))  worldclim_elev <- geodata::worldclim_global(   var = \"elev\",   res = 10,   path = tempdir() ) elev_data <- terra::extract(worldclim_elev, terra::vect(hapmap_data))  hapmap_data_worldclim <- cbind(hapmap_data, merge(elev_data, bio_data))"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"getting-started","dir":"Articles","previous_headings":"","what":"Getting started","title":"Using smarterapi","text":"Simply import smarterapi like R package:","code":"library(dplyr) library(smarterapi)"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"collect-info-about-versions","dir":"Articles","previous_headings":"","what":"Collect info about versions","title":"Using smarterapi","text":"smarter database continuously updated, example receiving new samples, genotypes, metadata something fixed updated, example new assembly added. order ensure reproducibility monitoring changes, genotypes metadata provided using versions: means ensure genotypes dataset metadata referring version. can check database version using get_smarter_info() method: version system specified genotype file dataset can download smarter FTP site: ensure working version, metadata genotypes: , may find samples genotype files referring -dated assembly version. see changelist version, please refer SMARTER-database HISTORY.rst file.","code":"info <- get_smarter_info() info$version #> [1] \"0.4.10\" info$last_updated #> [1] \"2024-05-29 02:41:35 UTC\" $ tree -L 2 SHEEP/ SHEEP/ └── OAR3     ├── archive     ├── SMARTER-OA-OAR3-top-0.4.10.md5     └── SMARTER-OA-OAR3-top-0.4.10.zip"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"querying-smarter-api","dir":"Articles","previous_headings":"","what":"Querying SMARTER API","title":"Using smarterapi","text":"smarterapi package structured handle requests/responses SMARTER API backend using R packages like httr jsonlite. general, functions accepts query=list() parameter, pass additional parameter API endpoint order filter results matching query. functions like get_smarter_samples() get_smarter_variants() requires additional parameters like species assembly version. function general return results data.frame: filter data using dplyr standard R methods filter data directly submitting proper query API. Please refer proper documentation understand parameters function expect. See also SMARTER-backend API web interface idea parameter allowed endpoint.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"collect-samples","dir":"Articles","previous_headings":"","what":"Collect samples","title":"Using smarterapi","text":"examples collecting samples. main function required collect sample get_smarter_samples(), helper function allow query /samples/goat /samples/sheep endpoints SMARTER-backend API. use functions better idea values use filter data. Remember parameters see different example can merged restrict query samples looking .","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"select-by-datasets","dir":"Articles","previous_headings":"Collect samples","what":"Select by datasets","title":"Using smarterapi","text":"Getting samples dataset quite easy, provide proper dataset_id get_smarter_samples() function. However, determine proper dataset_id using get_smarter_dataset() function, model /datasets endpoint. example, extract background genotypes datasets (data generated SMARTER project) pass proper type query argument. Since query argument list, can pass multiple parameters . parameters supports arrays, supply parameter name multiple times: one passed API endpoint Take time explore dataframe columns. two importants fields, first _id.$oid column, dataset_id want provide collect samples belonging dataset. second file column, archive name uploaded smarter database. example, background_goat_genotypes table looks like: collect adaptmap samples, can provide proper dataset_id get_smarter_samples() method. can add additional parameters, like country: previous case quite easy, want one dataset background_goat_genotypes dataframe, can simply paste value get_smarter_samples query. can handle multiple datasets? can transform proper column list renaming : can also use get_smarter_datasets() function reverse selection samples, example get samples one datasets: suppose, example, collect samples isheep datasets: last selection example relies dataset file contents: remember name file submitted dataset, can search datasets content: time two results returned, since one phenotypes dataset, genotypes. select genotypes, simply add type=genotypes query parameter.","code":"# select all genotypes datasets made before SMARTER project background_genotypes <- get_smarter_datasets(   query = list(type = \"background\", type = \"genotypes\") )  # same as before, but limiting to goat species background_goat_genotypes <- get_smarter_datasets(   query = list(     type = \"background\",     type = \"genotypes\",     species = \"Goat\"   ) ) # select the adaptmap id, which is in the first row of the dataframe adatpmap_id <- background_goat_genotypes[\"_id.$oid\"][1, 1] adaptmap_goats <- get_smarter_samples(   species = \"Goat\", query = list(dataset = adatpmap_id, country = \"Italy\") ) # get more datasets foreground_goat_genotypes <- get_smarter_datasets(   query = list(type = \"genotypes\", type = \"foreground\", species = \"Goat\") )  # construct the query arguments datasets <- as.list(foreground_goat_genotypes$\"_id.$oid\") names(datasets) <- rep(\"dataset\", length(datasets)) breeds <- list(breed_code = \"LNR\", breed_code = \"SKO\", breed_code = \"FSS\") query <- append(datasets, breeds)  # select samples: subset by breed code and datasets foreground_goat_samples <- get_smarter_samples(species = \"Goat\", query = query) # collect all foreground datasets having \"isheep\" in their name isheep_datasets <- get_smarter_datasets(   query = list(     type = \"foreground\",     type = \"genotypes\",     search = \"isheep\"   ) )  # collect ids for isheep datasets isheep_ids <- isheep_datasets$\"_id.$oid\"  # collect all foreground samples foreground_samples <- get_smarter_samples(   \"Sheep\", query = list(type = \"foreground\") )  # get rid of isheep_samples filtered_samples <- foreground_samples %>%   dplyr::filter(!`dataset_id.$oid` %in% isheep_ids) datasets <- get_smarter_datasets(query = list(search = \"adaptmap\"))"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"select-by-breed","dir":"Articles","previous_headings":"Collect samples","what":"Select by breed","title":"Using smarterapi","text":"can select samples relying breeds names breed codes. Breed names written languages come , order retrieve Île de France Fjällnäs breed samples, specify full breed name use search parameter get_smarter_breeds() model /breeds endpoint: Search breeds can return multiple values, example: Name codes can used select samples passing multiple arguments query: get samples merino breed name:","code":"breeds <- get_smarter_breeds(   query = list(     species = \"Sheep\",     search = \"de france\"   ) ) breeds <- get_smarter_breeds(   query = list(     species = \"Sheep\",     search = \"merino\"   ) ) selected_samples <- get_smarter_samples(species = \"Sheep\", query = list(   breed_code = \"MER\", breed_code = \"AME\" )) # construct the query arguments query <- as.list(breeds$code) names(query) <- rep(\"breed_code\", length(query))  # execute query merino_samples <- get_smarter_samples(species = \"Sheep\", query = query)"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"select-by-country","dir":"Articles","previous_headings":"Collect samples","what":"Select by country","title":"Using smarterapi","text":"can retrive samples countries. First get list available countries relying country name, extract samples using correct country name:","code":"italy <- get_smarter_countries(query = list(search = \"italy\"))  italian_background_sheeps <- get_smarter_samples(   species = \"Sheep\",   query = list(     country = italy$name[1]   ) )"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"select-by-chip","dir":"Articles","previous_headings":"Collect samples","what":"Select by chip","title":"Using smarterapi","text":"can select samples relying chip sequenced. search multiple chip types, collect samples belongs specified chip. First, collect list available chips certain species: collect samples relying chip name, example:","code":"sheep_chips <- get_smarter_supportedchips(query = list(species = \"Sheep\")) selected_samples <- get_smarter_samples(   species = \"Sheep\",   query = list(     chip_name = \"IlluminaOvineHDSNP\",     chip_name = \"AffymetrixAxiomOviCan\"   ) )"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"select-by-metadata","dir":"Articles","previous_headings":"Collect samples","what":"Select by metadata","title":"Using smarterapi","text":"Since metadata aren’t formatted way samples, difficult define single query can apply samples. moment, queries can apply metadata restricted presence absence. example, can collect samples GPS coordinates phenotypes (): , filter smarter_goats dataframe order collect samples want.","code":"smarter_goats <- get_smarter_samples(   species = \"Goat\",   query = list(     locations__exists = TRUE,     phenotype__exists = TRUE   ) )"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"refer-samples-to-their-original-publication","dir":"Articles","previous_headings":"","what":"Refer samples to their original publication","title":"Using smarterapi","text":"Suppose want refer samples original publication come : dataset dataframe doi column publication DOI stored. can use information collect publication information, need merge samples datasets dataframes order refer properly samples publication come . example :","code":"# collect all the genotypes datasets datasets <- get_smarter_datasets(   query = list(     species = \"Sheep\",     type = \"genotypes\"   ) )  # collect all the samples samples <- get_smarter_samples(   species = \"Sheep\", )  # merge datasets and samples using dplyr samples_with_doi <- dplyr::inner_join(   datasets,   samples,   by = dplyr::join_by(`_id.$oid` == `dataset_id.$oid`) ) %>%   dplyr::select(smarter_id, breed_code, breed.y, doi) %>%   dplyr::filter(!is.na(doi))  # count how many samples come from each publication samples_with_doi %>%   group_by(doi) %>%   summarise(counts = n())"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"collect-genotypes","dir":"Articles","previous_headings":"","what":"Collect genotypes","title":"Using smarterapi","text":"genotypes can’t retrieved using smarter-api available public FTP. need download files using FTP client like FileZilla lftp extract genotypes using plink. alternative, possible download genotypes using get_smarter_genotypes method package. method download genotypes FTP current releases selected species assembly return destination path downloaded archive: method download genotypes current working directory, directory specified dest_path argument. genotypes stored compressed .zip file, need de-compressed order used plink.","code":"downloaded_archive <- get_smarter_genotypes(   \"Sheep\",   \"OAR3\" )"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"subset-genotypes-relying-samples","dir":"Articles","previous_headings":"","what":"Subset genotypes relying samples","title":"Using smarterapi","text":"identified samples interest, can extract genotypes proper file using plink. First, write TSV file breed_code smarter_id columns. example, using samples selected dplyr: Next, need collect proper plink options order loose information plink file. parameters used generate genotype files tracked info endpoint. example, get parameters Sheep genotypes: finally can call plink providing sample list:","code":"selected_sheeps_ids <- italian_background_sheeps %>%   dplyr::select(     \"breed_code\", \"smarter_id\"   )  write.table(   selected_sheeps_ids,   file = \"selected_sheeps.txt\",   quote = FALSE,   sep = \"\\t\",   row.names = FALSE,   col.names = FALSE ) info <- get_smarter_info() plink_opts <- paste0(info$plink_specie_opt$Sheep, collapse = \" \") plink_opts #> [1] \"--chr-set 26 no-xy no-mt --allow-no-sex\" plink --chr-set 26 no-xy no-mt --allow-no-sex \\   --bfile SMARTER-OA-OAR3-top-0.4.10 \\   --keep selected_sheeps.txt \\   --out selected_sheeps-OAR3-top-0.4.10 \\   --make-bed"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/variants.html","id":"assembly-versions","dir":"Articles","previous_headings":"","what":"Assembly versions","title":"Working with SNPs","text":"One aim project manage genotypes different assembly version. means collect data different assemblies (due data generated), different sources (Affymetrix, Illumina, WGS) different file formats. Genotypes normalized order consistent accross data sources stored one genotype file specie. Currently four assembly versions managed, two sheep dataset two goat dataset. Information assemblies data sources can retrieved backend info endpoint get_smarter_info() function:","code":"info <- get_smarter_info() assemblies <- as.data.frame(t(as.data.frame(info$working_assemblies))) names(assemblies) <- c(\"name\", \"source\")"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/variants.html","id":"collect-data-from-an-assembly","dir":"Articles","previous_headings":"","what":"Collect data from an assembly","title":"Working with SNPs","text":"get_smarter_variants() two mandatory parameters, species assembly, accept additional parameters (see one variant endpoints information). example can search variants snp name rs id (latter exists): Table continues Table continues Please, refer get_smarter_info() working_assemblies idea assemblies supported SMARTER-database. Data come SNPchiMp v.3 like Sheep OAR3 assembly, support illumina forward attribute. example following SNP: Table continues Table continues T/C forward strand OAR3: means reversed probe aligned genome (infer bottom illumina strand attribute SNP). Genotypes SMARTER-database converted using illumina top coding convention, find SNP /G SMARTER-database reference sequence ’s T/C.","code":"snp <- get_smarter_variants(   species = \"Goat\",   assembly = \"ARS1\",   query = list(     name = \"snp12965-scaffold1499-3295573\"   ) ) snp <- get_smarter_variants(   species = \"Sheep\",   assembly = \"OAR3\",   query = list(     rs_id = \"rs10721092\"   ) )"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/variants.html","id":"fetch-variants-by-region","dir":"Articles","previous_headings":"","what":"Fetch Variants by region","title":"Working with SNPs","text":"Variants endpoint support query regions, using <chromosome>:<start>-<end> format, example: Table continues Table continues ","code":"variants <- get_smarter_variants(   species = \"Goat\",   assembly = \"ARS1\",   query = list(     region = \"1:1-100000\"   ) )"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/variants.html","id":"fetch-variants-by-chip-name","dir":"Articles","previous_headings":"","what":"Fetch Variants by chip name","title":"Working with SNPs","text":"can download variants certain chip: please consider require lot time memory, since store 600K SNPs smarter database. First, collect available chips SMARTER-database, example Sheep species: collect SNPs certain chip providing SMARTER chip name. Please, consider download 50K SNP chip take lot time","code":"sheep_chips <- get_smarter_supportedchips(query = list(species = \"Sheep\")) variants <- get_smarter_variants(   species = \"Sheep\",   assembly = \"OAR3\",   query = list(     chip_name = \"IlluminaOvineSNP50\"   ) )"},{"path":"https://cnr-ibba.github.io/r-smarter-api/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Paolo Cozzi. Author, maintainer.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Cozzi P (2024). smarterapi: Fetch SMARTER Data REST API. R package version 0.2.0.9000, https://cnr-ibba.github.io/r-smarter-api/.","code":"@Manual{,   title = {smarterapi: Fetch SMARTER Data Through REST API},   author = {Paolo Cozzi},   year = {2024},   note = {R package version 0.2.0.9000},   url = {https://cnr-ibba.github.io/r-smarter-api/}, }"},{"path":"https://cnr-ibba.github.io/r-smarter-api/index.html","id":"smarterapi","dir":"","previous_headings":"","what":"Fetch SMARTER Data Through REST API","title":"Fetch SMARTER Data Through REST API","text":"goal smarterapi collect data SMARTER REST API provide user dataframe. Get information online vignette.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Fetch SMARTER Data Through REST API","text":"smarterapi package available GitHub can installed source package alternative using devtools package, example: installation, can load package R session:","code":"# install devtools if needed # install.packages(\"devtools\") devtools::install_github(\"cnr-ibba/r-smarter-api\") # import this library to deal with the SMARTER API library(smarterapi)"},{"path":"https://cnr-ibba.github.io/r-smarter-api/index.html","id":"smarter-credentials","dir":"","previous_headings":"","what":"SMARTER credentials","title":"Fetch SMARTER Data Through REST API","text":"public release SMARTER data, ’s need provide credentials access data. used credentials access data, need install latest version smarterapi package.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/index.html","id":"querying-the-smarter-backend","dir":"","previous_headings":"","what":"Querying the SMARTER backend","title":"Fetch SMARTER Data Through REST API","text":"smarterapi provides set functions used fetch data SMARTER-backend endpoints described api documentation returning data.frame object. example, get_smarter_datasets lets query Datasets endpoint, get_smarter_samples able query parse Sample endpoints response. smarterapi function documented R can get help function like R functions. two types parameters required fetch data SMARTER-backend: species parameter, can Goat Sheep respectively goat sheep Samples Variants endpoints, query parameter can provided get_smarter_ function. species parameter mandatory order query endpoint specific Goat Sheep, query parameter optional need specified list() object order limit query data particular. example, need foreground genotypes datasets, can collect data like : require background goat samples, can like : full option list available endpoint available SMARTER-backend swagger documentation: option name use name described parameters, description parameter types can give hints exploit endpoint properly. instance, parameters described array objects can specified multiple times:","code":"datasets <- get_smarter_datasets(   query = list(type = \"genotypes\", type = \"foreground\")) goat_samples <- get_smarter_samples(   species = \"Goat\", query = list(type = \"background\")) > goat_breeds <- get_smarter_breeds(query = list(species=\"Goat\", search=\"land\")) > goat_breeds[c(\"name\",\"code\")]             name code 1      Rangeland  RAN 2       Landrace  LNR 3         Landin  LND 4 Icelandic goat  ICL  > goat_samples <- get_smarter_samples(     species = \"Goat\",      query = list(       breed_code=\"RAN\",        breed_code=\"LNR\",        breed_code=\"LND\",        breed_code=\"ICL\"     )   )"},{"path":"https://cnr-ibba.github.io/r-smarter-api/index.html","id":"examples","dir":"","previous_headings":"","what":"Examples","title":"Fetch SMARTER Data Through REST API","text":"basic example shows collect data SMARTER REST API Italian goats belonging Adaptmap dataset: examples vignettes, example collect data Variants endpoints work geographic coordinates.","code":"# collect the dataset by providing part of the name with the search option: # since we are forcing to collect only background genotypes, only one dataset # will be returned datasets <- get_smarter_datasets(   query = list(     species = \"Goat\",      search = \"adaptmap\",      type = \"genotypes\",      type = \"background\"     ) )  # get the dataset id adatpmap_id <- datasets[\"_id.$oid\"][1]  # collect all the italian goats from the adaptmap dataset. Using the dataset id # to filter out all the samples belonging to this dataset and the country option # to filter out only the italian samples for this dataset adaptmap_goats <- get_smarter_samples(   species = \"Goat\",    query = list(     dataset = adatpmap_id,      country = \"Italy\"   ) )"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_breeds.html","id":null,"dir":"Reference","previous_headings":"","what":"Get SMARTER Breeds — get_smarter_breeds","title":"Get SMARTER Breeds — get_smarter_breeds","text":"Fetch SMARTER REST API breeds endpoint returns results dataframe.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_breeds.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get SMARTER Breeds — get_smarter_breeds","text":"","code":"get_smarter_breeds(query = list())"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_breeds.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get SMARTER Breeds — get_smarter_breeds","text":"query list query arguments","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_breeds.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get SMARTER Breeds — get_smarter_breeds","text":"Returns dataframe selected breeds","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_breeds.html","id":"passing-additional-parameters","dir":"Reference","previous_headings":"","what":"Passing additional parameters","title":"Get SMARTER Breeds — get_smarter_breeds","text":"Breeds endpoint supports additional parameters making queries. Additional parameters need passed list using query parameter. example, get \"Sheep\" breeds need provide list(species=\"Sheep\") query parameter. Endpoint supports query breed code name. addition, can search using pattern search parameter. See  Swagger Breeds endpoint information breeds endpoint","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_breeds.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get SMARTER Breeds — get_smarter_breeds","text":"","code":"selected_breed <- get_smarter_breeds(query = list(code = \"TEX\"))  selected_breeds <- get_smarter_breeds(query = list(search = \"mer\")) if (FALSE) { all_breeds <- get_smarter_breeds() sheep_breeds <- get_smarter_breeds(query = list(species = \"Sheep\")) }"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_countries.html","id":null,"dir":"Reference","previous_headings":"","what":"Get SMARTER Countries — get_smarter_countries","title":"Get SMARTER Countries — get_smarter_countries","text":"Fetch SMARTER REST API countries endpoint returns results dataframe.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_countries.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get SMARTER Countries — get_smarter_countries","text":"","code":"get_smarter_countries(query = list())"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_countries.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get SMARTER Countries — get_smarter_countries","text":"query list query arguments","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_countries.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get SMARTER Countries — get_smarter_countries","text":"Returns dataframe selected countries","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_countries.html","id":"passing-additional-parameters","dir":"Reference","previous_headings":"","what":"Passing additional parameters","title":"Get SMARTER Countries — get_smarter_countries","text":"Contries endpoint supports additional parameters making queries. Additional parameters need passed list using query parameter. example, get countries \"Sheeps\" need provide list(species=\"Sheep\") query parameter. Endpoint supports searches two tree ISO codes using alpha_2 alpha3 parameters respectively. addition, can search using pattern search parameter. See  Swagger Countries endpoint information breeds endpoint","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_countries.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get SMARTER Countries — get_smarter_countries","text":"","code":"italy <- get_smarter_countries(query = list(name = \"Italy\")) france <- get_smarter_countries(query = list(alpha_2 = \"FR\"))  if (FALSE) { # get countries where there are sheeps sheep_countries <- get_smarter_countries(query = list(species = \"Sheep\")) }"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_datasets.html","id":null,"dir":"Reference","previous_headings":"","what":"Get SMARTER Datasets — get_smarter_datasets","title":"Get SMARTER Datasets — get_smarter_datasets","text":"Fetch SMARTER REST API datasets endpoint returns results dataframe.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_datasets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get SMARTER Datasets — get_smarter_datasets","text":"","code":"get_smarter_datasets(query = list())"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_datasets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get SMARTER Datasets — get_smarter_datasets","text":"query list query arguments","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_datasets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get SMARTER Datasets — get_smarter_datasets","text":"Returns dataframe selected datasets","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_datasets.html","id":"passing-additional-parameters","dir":"Reference","previous_headings":"","what":"Passing additional parameters","title":"Get SMARTER Datasets — get_smarter_datasets","text":"Datasets endpoint supports additional parameters making queries. Additional parameters need passed list using query parameter. example, get \"Sheep\" datasets need provide list(species=\"Sheep\") query parameter. Endpoint supports query type chip_name. addition, can search using pattern file contents search parameter. See  Swagger Datasets endpoint information datasets endpoint","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_datasets.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get SMARTER Datasets — get_smarter_datasets","text":"","code":"genotypes_foreground <- get_smarter_datasets(   query = list(type = \"foreground\", type = \"genotypes\") )  adaptmap_genotypes <- get_smarter_datasets(   query = list(species = \"Goat\", search = \"adaptmap\", type = \"genotypes\") ) if (FALSE) {  all_datasets <- get_smarter_datasets() }"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_genotypes.html","id":null,"dir":"Reference","previous_headings":"","what":"Get SMARTER Genotypes — get_smarter_genotypes","title":"Get SMARTER Genotypes — get_smarter_genotypes","text":"Retrieve genotypes data SMARTER database. information supported assemblies returned (see get_smarter_info information).","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_genotypes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get SMARTER Genotypes — get_smarter_genotypes","text":"","code":"get_smarter_genotypes(species, assembly, dest_path = NULL)"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_genotypes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get SMARTER Genotypes — get_smarter_genotypes","text":"species smarter species (\"Goat\", \"Sheep\") assembly smarter working assembly species dest_path path file downloaded. NULL, file downloaded current working directory","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_genotypes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get SMARTER Genotypes — get_smarter_genotypes","text":"character string path downloaded file returned","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_genotypes.html","id":"about-smarter-supported-assemblies","dir":"Reference","previous_headings":"","what":"About SMARTER supported assemblies","title":"Get SMARTER Genotypes — get_smarter_genotypes","text":"Currently SMARTER supports OAR3 OAR4 assemblies Sheep CHI1 ARS1 assemblies goat. Genotypes provided PLINK binary format, compressed zip file.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_genotypes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get SMARTER Genotypes — get_smarter_genotypes","text":"","code":"if (FALSE) { # get genotypes for sheep OAR3 in current directory get_smarter_genotypes(species = \"Sheep\", assembly = \"OAR3\") }"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_geojson.html","id":null,"dir":"Reference","previous_headings":"","what":"Get SMARTER GeoJSON Samples — get_smarter_geojson","title":"Get SMARTER GeoJSON Samples — get_smarter_geojson","text":"Fetch SMARTER REST API samples GPS coordinates return simple features.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_geojson.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get SMARTER GeoJSON Samples — get_smarter_geojson","text":"","code":"get_smarter_geojson(species, query = list(), polygons = NULL)"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_geojson.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get SMARTER GeoJSON Samples — get_smarter_geojson","text":"species smarter species (\"Goat\", \"Sheep\") query list query arguments polygons sf object polygons filter samples","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_geojson.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get SMARTER GeoJSON Samples — get_smarter_geojson","text":"sf data object","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_geojson.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get SMARTER GeoJSON Samples — get_smarter_geojson","text":"","code":"if (FALSE) { # required to execute pipe operations and draw examples library(dplyr) library(leaflet)  # get goat samples with GPS coordinates as sf object goat_data <- get_smarter_geojson(   species = \"Goat\",   query = list(     type = \"background\",     country = \"Italy\"   ) )  # leaflet doesn't handle MULTIPOINT data (https://github.com/rstudio/leaflet/issues/352) # Cast them into point considering only the first objects # (https://r-spatial.github.io/sf/reference/st_cast.html) goat_data <- goat_data %>% sf::st_cast(\"POINT\", do_split=FALSE)  # draw samples in a leaflet map using markerCluser leaflet(data = goat_data) %>%   leaflet::addTiles() %>%   leaflet::addMarkers(     clusterOptions = leaflet::markerClusterOptions(), label = ~smarter_id   ) }"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Get SMARTER Info — get_smarter_info","title":"Get SMARTER Info — get_smarter_info","text":"Collect information smarter database status returns values list","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get SMARTER Info — get_smarter_info","text":"","code":"get_smarter_info()"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get SMARTER Info — get_smarter_info","text":"list object SMARTER database information","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_info.html","id":"about-smarter-database-info-endpoint","dir":"Reference","previous_headings":"","what":"About SMARTER database info endpoint","title":"Get SMARTER Info — get_smarter_info","text":"info endpoint contains information status database information required understand genotypes updated . example, SMARTER database current version last_updated recent genotype file, retrive information samples included genotype file. case, download recent copy SMARTER database FTP site. plink_specie nested list contains plink species options used generate genotype data. want modify genotype file compatible SMARTER database may want use specie options","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get SMARTER Info — get_smarter_info","text":"","code":"smarter_status <- get_smarter_info() smarter_version <- smarter_status$version"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_samples.html","id":null,"dir":"Reference","previous_headings":"","what":"Get SMARTER Samples — get_smarter_samples","title":"Get SMARTER Samples — get_smarter_samples","text":"Fetch SMARTER REST API samples endpoint returns results dataframe.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_samples.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get SMARTER Samples — get_smarter_samples","text":"","code":"get_smarter_samples(species, query = list())"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_samples.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get SMARTER Samples — get_smarter_samples","text":"species smarter species (\"Goat\", \"Sheep\") query list query arguments","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_samples.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get SMARTER Samples — get_smarter_samples","text":"Returns dataframe selected samples","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_samples.html","id":"passing-additional-parameters","dir":"Reference","previous_headings":"","what":"Passing additional parameters","title":"Get SMARTER Samples — get_smarter_samples","text":"Samples endpoint supports additional parameters making queries. Additional parameters need passed list using query parameter. example, get \"foreground\" samples need provide list(type=\"foreground\") query parameter. Endpoint supports lot parameters can provided multiple times See  Swagger Samples endpoint information samples endpoint","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_samples.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get SMARTER Samples — get_smarter_samples","text":"","code":"italian_sheeps <- get_smarter_samples(   \"Sheep\",   query = list(country = \"Italy\") )  merino_sheeps <- get_smarter_samples(\"Sheep\", query = list(breed = \"Merino\"))  selected_goats <- get_smarter_samples(   \"Goat\",   query = list(country = \"Italy\", breed_code = \"ORO\", breed_code = \"GAR\") ) if (FALSE) {  foreground_goats <- get_smarter_samples(   \"Goat\",   query = list(type = \"foreground\") )  all_sheep_samples <- get_smarter_samples(\"Sheep\") }"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_supportedchips.html","id":null,"dir":"Reference","previous_headings":"","what":"Get SMARTER Supported Chips — get_smarter_supportedchips","title":"Get SMARTER Supported Chips — get_smarter_supportedchips","text":"Collect information chip data currently managed SMARTER database.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_supportedchips.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get SMARTER Supported Chips — get_smarter_supportedchips","text":"","code":"get_smarter_supportedchips(query = list())"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_supportedchips.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get SMARTER Supported Chips — get_smarter_supportedchips","text":"query list query arguments","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_supportedchips.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get SMARTER Supported Chips — get_smarter_supportedchips","text":"Returns dataframe selected chips","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_supportedchips.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get SMARTER Supported Chips — get_smarter_supportedchips","text":"","code":"chips <- get_smarter_supportedchips() if (FALSE) { # collect data on chips get_smarter_supportedchips()  # retrieve samples relying on chip used samples <- get_smarter_samples(   species = \"Sheep\",   query = list(chip_name = \"AffymetrixAxiomOviCan\") ) }"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_variants.html","id":null,"dir":"Reference","previous_headings":"","what":"Get SMARTER Variants — get_smarter_variants","title":"Get SMARTER Variants — get_smarter_variants","text":"Retrieve information SMARTER SNPs. information supported assemblies returned (see get_smarter_info information).","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_variants.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get SMARTER Variants — get_smarter_variants","text":"","code":"get_smarter_variants(species, assembly, query = list())"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_variants.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get SMARTER Variants — get_smarter_variants","text":"species smarter species (\"Goat\", \"Sheep\") assembly smarter working assembly species query list query arguments","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_variants.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get SMARTER Variants — get_smarter_variants","text":"Returns dataframe selected variants","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_variants.html","id":"about-smarter-supported-assemblies","dir":"Reference","previous_headings":"","what":"About SMARTER supported assemblies","title":"Get SMARTER Variants — get_smarter_variants","text":"Currently SMARTER supports OAR3 OAR4 assemblies Sheep CHI1 ARS1 assemblies goat. assembly, evidences used create smarter database returned. Retrieving variant certain assembly species require time memory.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_variants.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get SMARTER Variants — get_smarter_variants","text":"","code":"# get variants by region (chrom:start-end) variants <- get_smarter_variants(   species = \"Goat\",   assembly = \"ARS1\",   query = list(region = \"1:1-100000\") ) if (FALSE) { # get available assemblies from info endpoint names(get_smarter_info()$working_assemblies)  # collect variants from goat ARS1 endpoint (takes a lot of time) ars1_variant <- get_smarter_variants(   species = \"Goat\",   assembly = \"ARS1\" ) }"}]
+[{"path":"https://cnr-ibba.github.io/r-smarter-api/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. 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Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see <http://www.gnu.org/licenses/>. GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read <http://www.gnu.org/philosophy/--lgpl.html>.","code":"<one line to give the program's name and a brief idea of what it does.> Copyright (C) <year>  <name of author>  This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>. <program>  Copyright (C) <year>  <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/geojson.html","id":"get-data-using-parameters","dir":"Articles","previous_headings":"","what":"Get data using parameters","title":"Working with GeoJSON data","text":"can collect GeoJSON data using parameters, like using get_smarter_samples() function. function parse GeoJSON data return Simple Feature object, tibble object geometry column. example, try collect data Sheep hapmap background dataset: preview first rows hapmap_data object: Table continues Table continues ","code":"hapmap_dataset <- get_smarter_datasets(query = list(   species = \"Sheep\",   type = \"background\",   type = \"genotypes\",   search = \"hapmap\" )) hapmap_data <- get_smarter_geojson(species = \"Sheep\", query = list(   dataset = hapmap_dataset[\"_id.$oid\"][1],   country = \"Italy\" ))"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/geojson.html","id":"filter-data-using-spatial-queries","dir":"Articles","previous_headings":"","what":"Filter data using spatial queries","title":"Working with GeoJSON data","text":"alternative approach selecting samples exploits spatial queries. example, imported goat dataset geojson file qgis. created two polygons features correspondance samples want collect using GPS coordinates like following picture: exported two polygons shapefile. can spatial query st_intersects() order collect samples correspondance two areas interest: query done using get_smarter_geojson() function providing polygons argument: means can also provide sf object polygon argument. select country, using spatial queries:","code":"polygons_file <- system.file(\"extdata\", \"polygons.shp\", package = \"smarterapi\") polygons <- sf::st_read(polygons_file) goat_data <- get_smarter_geojson(\"Goat\", query = list(type = \"background\")) sel_sgbp <- sf::st_intersects(goat_data, polygons) sel_logical <- lengths(sel_sgbp) > 0 selected_goats <- goat_data[sel_logical, ] selected_goats <- get_smarter_geojson(   \"Goat\",   query = list(type = \"background\"),   polygons = polygons ) italy <- rnaturalearth::ne_countries(scale = \"medium\", returnclass = \"sf\") %>%   dplyr::filter(name == \"Italy\") italy_goats <- get_smarter_geojson(   \"Goat\",   query = list(type = \"background\"),   polygons = italy )"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/geojson.html","id":"convert-from-multipoints-to-point","dir":"Articles","previous_headings":"","what":"Convert from MULTIPOINTS to POINT","title":"Working with GeoJSON data","text":"get_smarter_geojson() methods returns sf MULTIPOINTS objects since multiple locations collected animal, example transhumant samples. However, simplicity, can focus analyses using one GPS coordinate, transforming MULTIPOINTS object POINT object: warnings see terminal tell considering first coordinate object MULTIPOINT collection.","code":"hapmap_data <- hapmap_data %>% sf::st_cast(\"POINT\", do_split = FALSE) hapmap_data #> Simple feature collection with 92 features and 11 fields #> Geometry type: POINT #> Dimension:     XY #> Bounding box:  xmin: 9.016667 ymin: 37 xmax: 18.16667 ymax: 40.81667 #> Geodetic CRS:  WGS 84 #> # A tibble: 92 × 12 #>    breed      breed_code chip_name    country dataset metadata original_id   sex #>    <chr>      <chr>      <chr>        <chr>   <chr>   <chr>    <chr>       <int> #>  1 Altamurana ALT        IlluminaOvi… Italy   \"{ \\\"$… \"{ \\\"lo… ALT1           NA #>  2 Altamurana ALT        IlluminaOvi… Italy   \"{ \\\"$… \"{ \\\"lo… ALT23          NA #>  3 Altamurana ALT        IlluminaOvi… Italy   \"{ \\\"$… \"{ \\\"lo… ALT10          NA #>  4 Altamurana ALT        IlluminaOvi… Italy   \"{ \\\"$… \"{ \\\"lo… ALT20          NA #>  5 Altamurana ALT        IlluminaOvi… Italy   \"{ \\\"$… \"{ \\\"lo… ALT21          NA #>  6 Altamurana ALT        IlluminaOvi… Italy   \"{ \\\"$… \"{ \\\"lo… ALT22          NA #>  7 Altamurana ALT        IlluminaOvi… Italy   \"{ \\\"$… \"{ \\\"lo… ALT15          NA #>  8 Altamurana ALT        IlluminaOvi… Italy   \"{ \\\"$… \"{ \\\"lo… ALT8           NA #>  9 Altamurana ALT        IlluminaOvi… Italy   \"{ \\\"$… \"{ \\\"lo… ALT16          NA #> 10 Altamurana ALT        IlluminaOvi… Italy   \"{ \\\"$… \"{ \\\"lo… ALT24          NA #> # ℹ 82 more rows #> # ℹ 4 more variables: smarter_id <chr>, species <chr>, type <chr>, #> #   geometry <POINT [°]>"},{"path":[]},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/geojson.html","id":"displaying-data-using-ggplot2","dir":"Articles","previous_headings":"Visualize SMARTER GPS data","what":"Displaying data using ggplot2","title":"Working with GeoJSON data","text":"sf data visualized using ggplot2. following examples derive countries rnaturalearth package, zoom plot selected points previous example:  See post nice introduction sf ggplot2.","code":"# determine a bounding box around our samples bbox <- sf::st_bbox(hapmap_data)  # collect the world countries as sf world <- rnaturalearth::ne_countries(scale = \"medium\", returnclass = \"sf\")  # plot the data: use the bounding box to zoom the plot on our samples ggplot2::ggplot() +   ggplot2::geom_sf(data = world, fill = \"antiquewhite\") +   ggplot2::geom_sf(data = hapmap_data, color = \"blue\", size = 5) +   ggspatial::annotation_scale(location = \"bl\", width_hint = 0.5) +   ggspatial::annotation_north_arrow(     location = \"bl\",     which_north = \"true\",     pad_x = ggplot2::unit(0.75, \"in\"),     pad_y = ggplot2::unit(0.5, \"in\"),     style = ggspatial::north_arrow_fancy_orienteering   ) +   ggspatial::coord_sf(     xlim = c(bbox$xmin, bbox$xmax),     ylim = c(bbox$ymin, bbox$ymax)   ) +   ggplot2::theme_bw() +   ggplot2::theme(plot.title = ggplot2::element_text(hjust = 0.5)) +   ggplot2::xlab(\"longitude\") + ggplot2::ylab(\"latitude\") +   ggplot2::ggtitle(\"Selected samples\")"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/geojson.html","id":"displaying-data-using-leaflet","dir":"Articles","previous_headings":"Visualize SMARTER GPS data","what":"Displaying data using leaflet","title":"Working with GeoJSON data","text":"Data visualized interactive way using R leaflet library: See Leaflet R documentation information.","code":"leaflet::leaflet(   data = hapmap_data,   options = leaflet::leafletOptions(minZoom = 5, maxZoom = 10) ) %>%   leaflet::addTiles() %>%   leaflet::addMarkers(     clusterOptions = leaflet::markerClusterOptions(), label = ~smarter_id   )"},{"path":[]},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/geojson.html","id":"derive-elevation-data-using-elevatr","dir":"Articles","previous_headings":"Integrate data with external sources","what":"Derive elevation data using elevatr","title":"Working with GeoJSON data","text":"can collect elevation data using elevatr package. following functions returns input dataframe elevation elev_units additional columns: See elevatr vignette elevatr tutorial rspatialdata documentation information examples.","code":"prj_dd <- \"EPSG:4326\" hapmap_data_elev <- elevatr::get_elev_point(   hapmap_data,   prj = prj_dd,   src = \"aws\" )"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/geojson.html","id":"add-worldclim-data-from-rasters","dir":"Articles","previous_headings":"Integrate data with external sources","what":"Add worldclim data from rasters","title":"Working with GeoJSON data","text":"can collect data worldclim database using geodata package: package particular collect raster data different sources (see geodata reference manual information). example, collect raster lowest definition (10min =~ 340km) worldclim bioclimatic variables elevation. Raster images placed tempdir path. using terra::extract calculate values data, converting terra SpatialVectors: See raster extraction geocomputation R information.","code":"worldclim_bio <- geodata::worldclim_global(   var = \"bio\",   res = 10,   path = tempdir() ) bio_data <- terra::extract(worldclim_bio, terra::vect(hapmap_data))  worldclim_elev <- geodata::worldclim_global(   var = \"elev\",   res = 10,   path = tempdir() ) elev_data <- terra::extract(worldclim_elev, terra::vect(hapmap_data))  hapmap_data_worldclim <- cbind(hapmap_data, merge(elev_data, bio_data))"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"getting-started","dir":"Articles","previous_headings":"","what":"Getting started","title":"Using smarterapi","text":"Simply import smarterapi like R package:","code":"library(dplyr) library(smarterapi)"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"collect-info-about-versions","dir":"Articles","previous_headings":"","what":"Collect info about versions","title":"Using smarterapi","text":"smarter database continuously updated, example receiving new samples, genotypes, metadata something fixed updated, example new assembly added. order ensure reproducibility monitoring changes, genotypes metadata provided using versions: means ensure genotypes dataset metadata referring version. can check database version using get_smarter_info() method: version system specified genotype file dataset can download smarter FTP site: ensure working version, metadata genotypes: , may find samples genotype files referring -dated assembly version. see changelist version, please refer SMARTER-database HISTORY.rst file.","code":"info <- get_smarter_info() info$version #> [1] \"0.4.10\" info$last_updated #> [1] \"2024-05-29 02:41:35 UTC\" $ tree -L 2 SHEEP/ SHEEP/ └── OAR3     ├── archive     ├── SMARTER-OA-OAR3-top-0.4.10.md5     └── SMARTER-OA-OAR3-top-0.4.10.zip"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"querying-smarter-api","dir":"Articles","previous_headings":"","what":"Querying SMARTER API","title":"Using smarterapi","text":"smarterapi package structured handle requests/responses SMARTER API backend using R packages like httr jsonlite. general, functions accepts query=list() parameter, pass additional parameter API endpoint order filter results matching query. functions like get_smarter_samples() get_smarter_variants() requires additional parameters like species assembly version. function general return results data.frame: filter data using dplyr standard R methods filter data directly submitting proper query API. Please refer proper documentation understand parameters function expect. See also SMARTER-backend API web interface idea parameter allowed endpoint.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"collect-samples","dir":"Articles","previous_headings":"","what":"Collect samples","title":"Using smarterapi","text":"examples collecting samples. main function required collect sample get_smarter_samples(), helper function allow query /samples/goat /samples/sheep endpoints SMARTER-backend API. use functions better idea values use filter data. Remember parameters see different example can merged restrict query samples looking .","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"select-by-datasets","dir":"Articles","previous_headings":"Collect samples","what":"Select by datasets","title":"Using smarterapi","text":"Getting samples dataset quite easy, provide proper dataset_id get_smarter_samples() function. However, determine proper dataset_id using get_smarter_dataset() function, model /datasets endpoint. example, extract background genotypes datasets (data generated SMARTER project) pass proper type query argument. Since query argument list, can pass multiple parameters . parameters supports arrays, supply parameter name multiple times: one passed API endpoint Take time explore dataframe columns. two importants fields, first _id.$oid column, dataset_id want provide collect samples belonging dataset. second file column, archive name uploaded smarter database. example, background_goat_genotypes table looks like: collect adaptmap samples, can provide proper dataset_id get_smarter_samples() method. can add additional parameters, like country: previous case quite easy, want one dataset background_goat_genotypes dataframe, can simply paste value get_smarter_samples query. can handle multiple datasets? can transform proper column list renaming : can also use get_smarter_datasets() function reverse selection samples, example get samples one datasets: suppose, example, collect samples isheep datasets: last selection example relies dataset file contents: remember name file submitted dataset, can search datasets content: time two results returned, since one phenotypes dataset, genotypes. select genotypes, simply add type=genotypes query parameter.","code":"# select all genotypes datasets made before SMARTER project background_genotypes <- get_smarter_datasets(   query = list(type = \"background\", type = \"genotypes\") )  # same as before, but limiting to goat species background_goat_genotypes <- get_smarter_datasets(   query = list(     type = \"background\",     type = \"genotypes\",     species = \"Goat\"   ) ) # select the adaptmap id, which is in the first row of the dataframe adatpmap_id <- background_goat_genotypes[\"_id.$oid\"][1, 1] adaptmap_goats <- get_smarter_samples(   species = \"Goat\", query = list(dataset = adatpmap_id, country = \"Italy\") ) # get more datasets foreground_goat_genotypes <- get_smarter_datasets(   query = list(type = \"genotypes\", type = \"foreground\", species = \"Goat\") )  # construct the query arguments datasets <- as.list(foreground_goat_genotypes$\"_id.$oid\") names(datasets) <- rep(\"dataset\", length(datasets)) breeds <- list(breed_code = \"LNR\", breed_code = \"SKO\", breed_code = \"FSS\") query <- append(datasets, breeds)  # select samples: subset by breed code and datasets foreground_goat_samples <- get_smarter_samples(species = \"Goat\", query = query) # collect all foreground datasets having \"isheep\" in their name isheep_datasets <- get_smarter_datasets(   query = list(     type = \"foreground\",     type = \"genotypes\",     search = \"isheep\"   ) )  # collect ids for isheep datasets isheep_ids <- isheep_datasets$\"_id.$oid\"  # collect all foreground samples foreground_samples <- get_smarter_samples(   \"Sheep\", query = list(type = \"foreground\") )  # get rid of isheep_samples filtered_samples <- foreground_samples %>%   dplyr::filter(!`dataset_id.$oid` %in% isheep_ids) datasets <- get_smarter_datasets(query = list(search = \"adaptmap\"))"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"select-by-breed","dir":"Articles","previous_headings":"Collect samples","what":"Select by breed","title":"Using smarterapi","text":"can select samples relying breeds names breed codes. Breed names written languages come , order retrieve Île de France Fjällnäs breed samples, specify full breed name use search parameter get_smarter_breeds() model /breeds endpoint: Search breeds can return multiple values, example: Name codes can used select samples passing multiple arguments query: get samples merino breed name:","code":"breeds <- get_smarter_breeds(   query = list(     species = \"Sheep\",     search = \"de france\"   ) ) breeds <- get_smarter_breeds(   query = list(     species = \"Sheep\",     search = \"merino\"   ) ) selected_samples <- get_smarter_samples(species = \"Sheep\", query = list(   breed_code = \"MER\", breed_code = \"AME\" )) # construct the query arguments query <- as.list(breeds$code) names(query) <- rep(\"breed_code\", length(query))  # execute query merino_samples <- get_smarter_samples(species = \"Sheep\", query = query)"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"select-by-country","dir":"Articles","previous_headings":"Collect samples","what":"Select by country","title":"Using smarterapi","text":"can retrive samples countries. First get list available countries relying country name, extract samples using correct country name:","code":"italy <- get_smarter_countries(query = list(search = \"italy\"))  italian_background_sheeps <- get_smarter_samples(   species = \"Sheep\",   query = list(     country = italy$name[1]   ) )"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"select-by-chip","dir":"Articles","previous_headings":"Collect samples","what":"Select by chip","title":"Using smarterapi","text":"can select samples relying chip sequenced. search multiple chip types, collect samples belongs specified chip. First, collect list available chips certain species: collect samples relying chip name, example:","code":"sheep_chips <- get_smarter_supportedchips(query = list(species = \"Sheep\")) selected_samples <- get_smarter_samples(   species = \"Sheep\",   query = list(     chip_name = \"IlluminaOvineHDSNP\",     chip_name = \"AffymetrixAxiomOviCan\"   ) )"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"select-by-metadata","dir":"Articles","previous_headings":"Collect samples","what":"Select by metadata","title":"Using smarterapi","text":"Since metadata aren’t formatted way samples, difficult define single query can apply samples. moment, queries can apply metadata restricted presence absence. example, can collect samples GPS coordinates phenotypes (): , filter smarter_goats dataframe order collect samples want.","code":"smarter_goats <- get_smarter_samples(   species = \"Goat\",   query = list(     locations__exists = TRUE,     phenotype__exists = TRUE   ) )"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"refer-samples-to-their-original-publication","dir":"Articles","previous_headings":"","what":"Refer samples to their original publication","title":"Using smarterapi","text":"Suppose want refer samples original publication come : dataset dataframe doi column publication DOI stored. can use information collect publication information, need merge samples datasets dataframes order refer properly samples publication come . example :","code":"# collect all the genotypes datasets datasets <- get_smarter_datasets(   query = list(     species = \"Sheep\",     type = \"genotypes\"   ) )  # collect all the samples samples <- get_smarter_samples(   species = \"Sheep\", )  # merge datasets and samples using dplyr samples_with_doi <- dplyr::inner_join(   datasets,   samples,   by = dplyr::join_by(`_id.$oid` == `dataset_id.$oid`) ) %>%   dplyr::select(smarter_id, breed_code, breed.y, doi) %>%   dplyr::filter(!is.na(doi))  # count how many samples come from each publication samples_with_doi %>%   group_by(doi) %>%   summarise(counts = n())"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"collect-genotypes","dir":"Articles","previous_headings":"","what":"Collect genotypes","title":"Using smarterapi","text":"genotypes can’t retrieved using smarter-api available public FTP. need download files using FTP client like FileZilla lftp extract genotypes using plink. alternative, possible download genotypes using get_smarter_genotypes method package. method download genotypes FTP current releases selected species assembly return destination path downloaded archive: method download genotypes current working directory, directory specified dest_path argument. genotypes stored compressed .zip file, need de-compressed order used plink.","code":"downloaded_archive <- get_smarter_genotypes(   \"Sheep\",   \"OAR3\" )"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/smarterapi.html","id":"subset-genotypes-relying-samples","dir":"Articles","previous_headings":"","what":"Subset genotypes relying samples","title":"Using smarterapi","text":"identified samples interest, can extract genotypes proper file using plink. First, write TSV file breed_code smarter_id columns. example, using samples selected dplyr: Next, need collect proper plink options order loose information plink file. parameters used generate genotype files tracked info endpoint. example, get parameters Sheep genotypes: finally can call plink providing sample list:","code":"selected_sheeps_ids <- italian_background_sheeps %>%   dplyr::select(     \"breed_code\", \"smarter_id\"   )  write.table(   selected_sheeps_ids,   file = \"selected_sheeps.txt\",   quote = FALSE,   sep = \"\\t\",   row.names = FALSE,   col.names = FALSE ) info <- get_smarter_info() plink_opts <- paste0(info$plink_specie_opt$Sheep, collapse = \" \") plink_opts #> [1] \"--chr-set 26 no-xy no-mt --allow-no-sex\" plink --chr-set 26 no-xy no-mt --allow-no-sex \\   --bfile SMARTER-OA-OAR3-top-0.4.10 \\   --keep selected_sheeps.txt \\   --out selected_sheeps-OAR3-top-0.4.10 \\   --make-bed"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/variants.html","id":"assembly-versions","dir":"Articles","previous_headings":"","what":"Assembly versions","title":"Working with SNPs","text":"One aim project manage genotypes different assembly version. means collect data different assemblies (due data generated), different sources (Affymetrix, Illumina, WGS) different file formats. Genotypes normalized order consistent accross data sources stored one genotype file specie. Currently four assembly versions managed, two sheep dataset two goat dataset. Information assemblies data sources can retrieved backend info endpoint get_smarter_info() function:","code":"info <- get_smarter_info() assemblies <- as.data.frame(t(as.data.frame(info$working_assemblies))) names(assemblies) <- c(\"name\", \"source\")"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/variants.html","id":"collect-data-from-an-assembly","dir":"Articles","previous_headings":"","what":"Collect data from an assembly","title":"Working with SNPs","text":"get_smarter_variants() two mandatory parameters, species assembly, accept additional parameters (see one variant endpoints information). example can search variants snp name rs id (latter exists): Table continues Table continues Please, refer get_smarter_info() working_assemblies idea assemblies supported SMARTER-database. Data come SNPchiMp v.3 like Sheep OAR3 assembly, support illumina forward attribute. example following SNP: Table continues Table continues T/C forward strand OAR3: means reversed probe aligned genome (infer bottom illumina strand attribute SNP). Genotypes SMARTER-database converted using illumina top coding convention, find SNP /G SMARTER-database reference sequence ’s T/C.","code":"snp <- get_smarter_variants(   species = \"Goat\",   assembly = \"ARS1\",   query = list(     name = \"snp12965-scaffold1499-3295573\"   ) ) snp <- get_smarter_variants(   species = \"Sheep\",   assembly = \"OAR3\",   query = list(     rs_id = \"rs10721092\"   ) )"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/variants.html","id":"fetch-variants-by-region","dir":"Articles","previous_headings":"","what":"Fetch Variants by region","title":"Working with SNPs","text":"Variants endpoint support query regions, using <chromosome>:<start>-<end> format, example: Table continues Table continues ","code":"variants <- get_smarter_variants(   species = \"Goat\",   assembly = \"ARS1\",   query = list(     region = \"1:1-100000\"   ) )"},{"path":"https://cnr-ibba.github.io/r-smarter-api/articles/variants.html","id":"fetch-variants-by-chip-name","dir":"Articles","previous_headings":"","what":"Fetch Variants by chip name","title":"Working with SNPs","text":"can download variants certain chip: please consider require lot time memory, since store 600K SNPs smarter database. First, collect available chips SMARTER-database, example Sheep species: collect SNPs certain chip providing SMARTER chip name. Please, consider download 50K SNP chip take lot time","code":"sheep_chips <- get_smarter_supportedchips(query = list(species = \"Sheep\")) variants <- get_smarter_variants(   species = \"Sheep\",   assembly = \"OAR3\",   query = list(     chip_name = \"IlluminaOvineSNP50\"   ) )"},{"path":"https://cnr-ibba.github.io/r-smarter-api/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Paolo Cozzi. Author, maintainer.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Cozzi P (2024). smarterapi: Fetch SMARTER Data REST API. R package version 0.2.0, https://cnr-ibba.github.io/r-smarter-api/.","code":"@Manual{,   title = {smarterapi: Fetch SMARTER Data Through REST API},   author = {Paolo Cozzi},   year = {2024},   note = {R package version 0.2.0},   url = {https://cnr-ibba.github.io/r-smarter-api/}, }"},{"path":"https://cnr-ibba.github.io/r-smarter-api/index.html","id":"smarterapi","dir":"","previous_headings":"","what":"Fetch SMARTER Data Through REST API","title":"Fetch SMARTER Data Through REST API","text":"goal smarterapi collect data SMARTER REST API provide user dataframe. Get information online vignette.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Fetch SMARTER Data Through REST API","text":"smarterapi package available GitHub can installed source package alternative using devtools package, example: installation, can load package R session:","code":"# install devtools if needed # install.packages(\"devtools\") devtools::install_github(\"cnr-ibba/r-smarter-api\") # import this library to deal with the SMARTER API library(smarterapi)"},{"path":"https://cnr-ibba.github.io/r-smarter-api/index.html","id":"smarter-credentials","dir":"","previous_headings":"","what":"SMARTER credentials","title":"Fetch SMARTER Data Through REST API","text":"public release SMARTER data, ’s need provide credentials access data. used credentials access data, need install latest version smarterapi package.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/index.html","id":"querying-the-smarter-backend","dir":"","previous_headings":"","what":"Querying the SMARTER backend","title":"Fetch SMARTER Data Through REST API","text":"smarterapi provides set functions used fetch data SMARTER-backend endpoints described api documentation returning data.frame object. example, get_smarter_datasets lets query Datasets endpoint, get_smarter_samples able query parse Sample endpoints response. smarterapi function documented R can get help function like R functions. two types parameters required fetch data SMARTER-backend: species parameter, can Goat Sheep respectively goat sheep Samples Variants endpoints, query parameter can provided get_smarter_ function. species parameter mandatory order query endpoint specific Goat Sheep, query parameter optional need specified list() object order limit query data particular. example, need foreground genotypes datasets, can collect data like : require background goat samples, can like : full option list available endpoint available SMARTER-backend swagger documentation: option name use name described parameters, description parameter types can give hints exploit endpoint properly. instance, parameters described array objects can specified multiple times:","code":"datasets <- get_smarter_datasets(   query = list(type = \"genotypes\", type = \"foreground\")) goat_samples <- get_smarter_samples(   species = \"Goat\", query = list(type = \"background\")) > goat_breeds <- get_smarter_breeds(query = list(species=\"Goat\", search=\"land\")) > goat_breeds[c(\"name\",\"code\")]             name code 1      Rangeland  RAN 2       Landrace  LNR 3         Landin  LND 4 Icelandic goat  ICL  > goat_samples <- get_smarter_samples(     species = \"Goat\",      query = list(       breed_code=\"RAN\",        breed_code=\"LNR\",        breed_code=\"LND\",        breed_code=\"ICL\"     )   )"},{"path":"https://cnr-ibba.github.io/r-smarter-api/index.html","id":"examples","dir":"","previous_headings":"","what":"Examples","title":"Fetch SMARTER Data Through REST API","text":"basic example shows collect data SMARTER REST API Italian goats belonging Adaptmap dataset: examples vignettes, example collect data Variants endpoints work geographic coordinates.","code":"# collect the dataset by providing part of the name with the search option: # since we are forcing to collect only background genotypes, only one dataset # will be returned datasets <- get_smarter_datasets(   query = list(     species = \"Goat\",      search = \"adaptmap\",      type = \"genotypes\",      type = \"background\"     ) )  # get the dataset id adatpmap_id <- datasets[\"_id.$oid\"][1]  # collect all the italian goats from the adaptmap dataset. Using the dataset id # to filter out all the samples belonging to this dataset and the country option # to filter out only the italian samples for this dataset adaptmap_goats <- get_smarter_samples(   species = \"Goat\",    query = list(     dataset = adatpmap_id,      country = \"Italy\"   ) )"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_breeds.html","id":null,"dir":"Reference","previous_headings":"","what":"Get SMARTER Breeds — get_smarter_breeds","title":"Get SMARTER Breeds — get_smarter_breeds","text":"Fetch SMARTER REST API breeds endpoint returns results dataframe.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_breeds.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get SMARTER Breeds — get_smarter_breeds","text":"","code":"get_smarter_breeds(query = list())"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_breeds.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get SMARTER Breeds — get_smarter_breeds","text":"query list query arguments","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_breeds.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get SMARTER Breeds — get_smarter_breeds","text":"Returns dataframe selected breeds","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_breeds.html","id":"passing-additional-parameters","dir":"Reference","previous_headings":"","what":"Passing additional parameters","title":"Get SMARTER Breeds — get_smarter_breeds","text":"Breeds endpoint supports additional parameters making queries. Additional parameters need passed list using query parameter. example, get \"Sheep\" breeds need provide list(species=\"Sheep\") query parameter. Endpoint supports query breed code name. addition, can search using pattern search parameter. See  Swagger Breeds endpoint information breeds endpoint","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_breeds.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get SMARTER Breeds — get_smarter_breeds","text":"","code":"selected_breed <- get_smarter_breeds(query = list(code = \"TEX\"))  selected_breeds <- get_smarter_breeds(query = list(search = \"mer\")) if (FALSE) { all_breeds <- get_smarter_breeds() sheep_breeds <- get_smarter_breeds(query = list(species = \"Sheep\")) }"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_countries.html","id":null,"dir":"Reference","previous_headings":"","what":"Get SMARTER Countries — get_smarter_countries","title":"Get SMARTER Countries — get_smarter_countries","text":"Fetch SMARTER REST API countries endpoint returns results dataframe.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_countries.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get SMARTER Countries — get_smarter_countries","text":"","code":"get_smarter_countries(query = list())"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_countries.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get SMARTER Countries — get_smarter_countries","text":"query list query arguments","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_countries.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get SMARTER Countries — get_smarter_countries","text":"Returns dataframe selected countries","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_countries.html","id":"passing-additional-parameters","dir":"Reference","previous_headings":"","what":"Passing additional parameters","title":"Get SMARTER Countries — get_smarter_countries","text":"Contries endpoint supports additional parameters making queries. Additional parameters need passed list using query parameter. example, get countries \"Sheeps\" need provide list(species=\"Sheep\") query parameter. Endpoint supports searches two tree ISO codes using alpha_2 alpha3 parameters respectively. addition, can search using pattern search parameter. See  Swagger Countries endpoint information breeds endpoint","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_countries.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get SMARTER Countries — get_smarter_countries","text":"","code":"italy <- get_smarter_countries(query = list(name = \"Italy\")) france <- get_smarter_countries(query = list(alpha_2 = \"FR\"))  if (FALSE) { # get countries where there are sheeps sheep_countries <- get_smarter_countries(query = list(species = \"Sheep\")) }"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_datasets.html","id":null,"dir":"Reference","previous_headings":"","what":"Get SMARTER Datasets — get_smarter_datasets","title":"Get SMARTER Datasets — get_smarter_datasets","text":"Fetch SMARTER REST API datasets endpoint returns results dataframe.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_datasets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get SMARTER Datasets — get_smarter_datasets","text":"","code":"get_smarter_datasets(query = list())"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_datasets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get SMARTER Datasets — get_smarter_datasets","text":"query list query arguments","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_datasets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get SMARTER Datasets — get_smarter_datasets","text":"Returns dataframe selected datasets","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_datasets.html","id":"passing-additional-parameters","dir":"Reference","previous_headings":"","what":"Passing additional parameters","title":"Get SMARTER Datasets — get_smarter_datasets","text":"Datasets endpoint supports additional parameters making queries. Additional parameters need passed list using query parameter. example, get \"Sheep\" datasets need provide list(species=\"Sheep\") query parameter. Endpoint supports query type chip_name. addition, can search using pattern file contents search parameter. See  Swagger Datasets endpoint information datasets endpoint","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_datasets.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get SMARTER Datasets — get_smarter_datasets","text":"","code":"genotypes_foreground <- get_smarter_datasets(   query = list(type = \"foreground\", type = \"genotypes\") )  adaptmap_genotypes <- get_smarter_datasets(   query = list(species = \"Goat\", search = \"adaptmap\", type = \"genotypes\") ) if (FALSE) {  all_datasets <- get_smarter_datasets() }"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_genotypes.html","id":null,"dir":"Reference","previous_headings":"","what":"Get SMARTER Genotypes — get_smarter_genotypes","title":"Get SMARTER Genotypes — get_smarter_genotypes","text":"Retrieve genotypes data SMARTER database. information supported assemblies returned (see get_smarter_info information).","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_genotypes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get SMARTER Genotypes — get_smarter_genotypes","text":"","code":"get_smarter_genotypes(species, assembly, dest_path = NULL)"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_genotypes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get SMARTER Genotypes — get_smarter_genotypes","text":"species smarter species (\"Goat\", \"Sheep\") assembly smarter working assembly species dest_path path file downloaded. NULL, file downloaded current working directory","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_genotypes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get SMARTER Genotypes — get_smarter_genotypes","text":"character string path downloaded file returned","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_genotypes.html","id":"about-smarter-supported-assemblies","dir":"Reference","previous_headings":"","what":"About SMARTER supported assemblies","title":"Get SMARTER Genotypes — get_smarter_genotypes","text":"Currently SMARTER supports OAR3 OAR4 assemblies Sheep CHI1 ARS1 assemblies goat. Genotypes provided PLINK binary format, compressed zip file.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_genotypes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get SMARTER Genotypes — get_smarter_genotypes","text":"","code":"if (FALSE) { # get genotypes for sheep OAR3 in current directory get_smarter_genotypes(species = \"Sheep\", assembly = \"OAR3\") }"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_geojson.html","id":null,"dir":"Reference","previous_headings":"","what":"Get SMARTER GeoJSON Samples — get_smarter_geojson","title":"Get SMARTER GeoJSON Samples — get_smarter_geojson","text":"Fetch SMARTER REST API samples GPS coordinates return simple features.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_geojson.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get SMARTER GeoJSON Samples — get_smarter_geojson","text":"","code":"get_smarter_geojson(species, query = list(), polygons = NULL)"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_geojson.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get SMARTER GeoJSON Samples — get_smarter_geojson","text":"species smarter species (\"Goat\", \"Sheep\") query list query arguments polygons sf object polygons filter samples","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_geojson.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get SMARTER GeoJSON Samples — get_smarter_geojson","text":"sf data object","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_geojson.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get SMARTER GeoJSON Samples — get_smarter_geojson","text":"","code":"if (FALSE) { # required to execute pipe operations and draw examples library(dplyr) library(leaflet)  # get goat samples with GPS coordinates as sf object goat_data <- get_smarter_geojson(   species = \"Goat\",   query = list(     type = \"background\",     country = \"Italy\"   ) )  # leaflet doesn't handle MULTIPOINT data (https://github.com/rstudio/leaflet/issues/352) # Cast them into point considering only the first objects # (https://r-spatial.github.io/sf/reference/st_cast.html) goat_data <- goat_data %>% sf::st_cast(\"POINT\", do_split=FALSE)  # draw samples in a leaflet map using markerCluser leaflet(data = goat_data) %>%   leaflet::addTiles() %>%   leaflet::addMarkers(     clusterOptions = leaflet::markerClusterOptions(), label = ~smarter_id   ) }"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Get SMARTER Info — get_smarter_info","title":"Get SMARTER Info — get_smarter_info","text":"Collect information smarter database status returns values list","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get SMARTER Info — get_smarter_info","text":"","code":"get_smarter_info()"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get SMARTER Info — get_smarter_info","text":"list object SMARTER database information","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_info.html","id":"about-smarter-database-info-endpoint","dir":"Reference","previous_headings":"","what":"About SMARTER database info endpoint","title":"Get SMARTER Info — get_smarter_info","text":"info endpoint contains information status database information required understand genotypes updated . example, SMARTER database current version last_updated recent genotype file, retrive information samples included genotype file. case, download recent copy SMARTER database FTP site. plink_specie nested list contains plink species options used generate genotype data. want modify genotype file compatible SMARTER database may want use specie options","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get SMARTER Info — get_smarter_info","text":"","code":"smarter_status <- get_smarter_info() smarter_version <- smarter_status$version"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_samples.html","id":null,"dir":"Reference","previous_headings":"","what":"Get SMARTER Samples — get_smarter_samples","title":"Get SMARTER Samples — get_smarter_samples","text":"Fetch SMARTER REST API samples endpoint returns results dataframe.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_samples.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get SMARTER Samples — get_smarter_samples","text":"","code":"get_smarter_samples(species, query = list())"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_samples.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get SMARTER Samples — get_smarter_samples","text":"species smarter species (\"Goat\", \"Sheep\") query list query arguments","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_samples.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get SMARTER Samples — get_smarter_samples","text":"Returns dataframe selected samples","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_samples.html","id":"passing-additional-parameters","dir":"Reference","previous_headings":"","what":"Passing additional parameters","title":"Get SMARTER Samples — get_smarter_samples","text":"Samples endpoint supports additional parameters making queries. Additional parameters need passed list using query parameter. example, get \"foreground\" samples need provide list(type=\"foreground\") query parameter. Endpoint supports lot parameters can provided multiple times See  Swagger Samples endpoint information samples endpoint","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_samples.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get SMARTER Samples — get_smarter_samples","text":"","code":"italian_sheeps <- get_smarter_samples(   \"Sheep\",   query = list(country = \"Italy\") )  merino_sheeps <- get_smarter_samples(\"Sheep\", query = list(breed = \"Merino\"))  selected_goats <- get_smarter_samples(   \"Goat\",   query = list(country = \"Italy\", breed_code = \"ORO\", breed_code = \"GAR\") ) if (FALSE) {  foreground_goats <- get_smarter_samples(   \"Goat\",   query = list(type = \"foreground\") )  all_sheep_samples <- get_smarter_samples(\"Sheep\") }"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_supportedchips.html","id":null,"dir":"Reference","previous_headings":"","what":"Get SMARTER Supported Chips — get_smarter_supportedchips","title":"Get SMARTER Supported Chips — get_smarter_supportedchips","text":"Collect information chip data currently managed SMARTER database.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_supportedchips.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get SMARTER Supported Chips — get_smarter_supportedchips","text":"","code":"get_smarter_supportedchips(query = list())"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_supportedchips.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get SMARTER Supported Chips — get_smarter_supportedchips","text":"query list query arguments","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_supportedchips.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get SMARTER Supported Chips — get_smarter_supportedchips","text":"Returns dataframe selected chips","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_supportedchips.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get SMARTER Supported Chips — get_smarter_supportedchips","text":"","code":"chips <- get_smarter_supportedchips() if (FALSE) { # collect data on chips get_smarter_supportedchips()  # retrieve samples relying on chip used samples <- get_smarter_samples(   species = \"Sheep\",   query = list(chip_name = \"AffymetrixAxiomOviCan\") ) }"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_variants.html","id":null,"dir":"Reference","previous_headings":"","what":"Get SMARTER Variants — get_smarter_variants","title":"Get SMARTER Variants — get_smarter_variants","text":"Retrieve information SMARTER SNPs. information supported assemblies returned (see get_smarter_info information).","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_variants.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get SMARTER Variants — get_smarter_variants","text":"","code":"get_smarter_variants(species, assembly, query = list())"},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_variants.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get SMARTER Variants — get_smarter_variants","text":"species smarter species (\"Goat\", \"Sheep\") assembly smarter working assembly species query list query arguments","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_variants.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get SMARTER Variants — get_smarter_variants","text":"Returns dataframe selected variants","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_variants.html","id":"about-smarter-supported-assemblies","dir":"Reference","previous_headings":"","what":"About SMARTER supported assemblies","title":"Get SMARTER Variants — get_smarter_variants","text":"Currently SMARTER supports OAR3 OAR4 assemblies Sheep CHI1 ARS1 assemblies goat. assembly, evidences used create smarter database returned. Retrieving variant certain assembly species require time memory.","code":""},{"path":"https://cnr-ibba.github.io/r-smarter-api/reference/get_smarter_variants.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get SMARTER Variants — get_smarter_variants","text":"","code":"# get variants by region (chrom:start-end) variants <- get_smarter_variants(   species = \"Goat\",   assembly = \"ARS1\",   query = list(region = \"1:1-100000\") ) if (FALSE) { # get available assemblies from info endpoint names(get_smarter_info()$working_assemblies)  # collect variants from goat ARS1 endpoint (takes a lot of time) ars1_variant <- get_smarter_variants(   species = \"Goat\",   assembly = \"ARS1\" ) }"}]