From c85a47585722e56291c71b4955fda57ae0b7ef94 Mon Sep 17 00:00:00 2001 From: "Elizabeth R. Lawrence" Date: Fri, 6 Dec 2024 19:43:32 -0500 Subject: [PATCH] call webshot for buttons --- examples.md | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/examples.md b/examples.md index 9fa788a..67b61c5 100644 --- a/examples.md +++ b/examples.md @@ -102,6 +102,8 @@ The example for ENV-DATA collected with marine bird sightings/occurrences is bas For this dataset, human observation recorded individual bird sightings (thus, each specimen is a single occurrence). The dataset contains abiotic measurements (ENV-DATA) which are related to each individual sighting, instead of an entire sample. Therefore, we can create an Occurrence core with an eMoF extension that contain the abiotic environmental measurements or facts. ```{r echo=FALSE} +library(webshot) +library(downloadthis) downloadthis::download_link( link = "https://www.marine.csiro.au/ipt/archive.do?r=in2017_v02_wov&v=1.15", button_label = "Download dataset DwC-A .zip", @@ -150,6 +152,8 @@ knitr::include_graphics("images/ENV_example_CETUS.png") ``` ```{r echo=FALSE} +library(webshot) +library(downloadthis) downloadthis::download_link( link = "https://ipt.vliz.be/eurobis/archive.do?r=cetus_cetaceans&v=1.0", button_label = "Download dataset DwC-A .zip", @@ -214,6 +218,8 @@ And finally, the extendedMeasurementOrFact extension table has attributes of the This section deals with encoding survey and/or sighting data of sea turtles into Darwin Core using the ENV-DATA approach. Extracts from the actual dataset [Presence of sea turtles collected through Fixed-Line-Transect monitoring across the Western Mediterranean Sea (Civitavecchia-Barcelona route) between 2013 and 2017](https://ipt.vliz.be/eurobis/resource?r=cc_flt_cbar_13-17#anchor-description) are used as an example. ```{r echo=FALSE} +library(webshot) +library(downloadthis) downloadthis::download_link( link = "https://ipt.vliz.be/eurobis/archive.do?r=cc_flt_cbar_13-17&v=1.0", button_label = "Download dataset DwC-A .zip", @@ -284,6 +290,8 @@ In addition to the measurements recorded by the example dataset, other measureme This example deals with encoding phytoplankton observation data, including environmental data, into Darwin Core. Extracts from the actual dataset [LifeWatch observatory data: phytoplankton observations by imaging flow cytometry (FlowCam) in the Belgian Part of the North Sea](https://obis.org/dataset/956d618f-91dc-4930-a253-cdf80ddb9371), are used as an example. Phytoplankton data should adhere to guidelines by Martin-Cabrera et al., 2022: [Best practices and recommendations for plankton imaging data management: Ensuring effective data flow towards European data infrastructures. Version 1](http://dx.doi.org/10.25607/OBP-1742). Specific guidelines for the Occurrence and eMoF tables are documented in this publication, and we emphasize important fields in this example. ```{r echo=FALSE} +library(webshot) +library(downloadthis) downloadthis::download_link( link = "https://ipt.vliz.be/eurobis/archive.do?r=fyto&v=1.0", button_label = "Download dataset DwC-A .zip", @@ -344,6 +352,8 @@ The structure of the Event, Occurrence and extendedMeasurementOrFact extensions Here we align seagrass survey data to Darwin Core according to the ENV-DATA approach and using sections of the actual dataset [Seagrass Monitoring at Chengue Bay, Colombia](http://ipt.iobis.org/caribbeanobis/resource?r=seagrasssurvey_colombia) as an example. ```{r echo=FALSE} +library(webshot) +library(downloadthis) downloadthis::download_link( link = "https://ipt.iobis.org/caribbeanobis/archive.do?r=seagrasssurvey_colombia&v=1.6", button_label = "Download dataset DwC-A .zip", @@ -405,6 +415,8 @@ The eMoF table contains the measurement information and data of each occurrence. Here we will encode zooplankton observation and environmental data into Darwin Core. Extracts from the actual dataset [LifeWatch observatory data: zooplankton observations by imaging (ZooScan) in the Belgian Part of the North Sea](https://obis.org/dataset/afa5b0e8-826d-4433-b698-beb176ef7880), are used as an example. As with the phytoplankton example, zooplankton data should also adhere to guidelines by Martin-Cabrera et al., 2022: [Best practices and recommendations for plankton imaging data management: Ensuring effective data flow towards European data infrastructures. Version 1.](http://dx.doi.org/10.25607/OBP-1742). These Best Practices indicate that for imaging data like this example, the fields `identificationVerificationStatus` and `identifiedBy` are crucial to know whether the data has been validated, and by whom. `identificationReferences` is used to document the citation or algorithm software used in identification. When possible, `associatedMedia` should also be populated with the persistent URL of annotated images. ```{r echo=FALSE} +library(webshot) +library(downloadthis) downloadthis::download_link( link = "https://ipt.vliz.be/eurobis/archive.do?r=lifewatch_zooplankton&v=1.0", button_label = "Download dataset DwC-A .zip",