https changeover

.github/workflows/R-Git-Check.yml

@@ -26,7 +26,6 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ridigbio
 Title: Interface to the iDigBio Data API
 Version: 0.3.9
-Date: 2024-7-02
+Date: 2024-8-19
 Encoding: UTF-8
 Authors@R: c(person("Francois", "Michonneau", comment="Original Author", role=c("aut", "cph"),
   email="[email protected]"),
@@ -22,7 +22,7 @@ Description: An interface to iDigBio's search API that allows downloading
   such as the metadata end points return lists of information. iDigBio is a US
   project focused on digitizing and serving museum specimen collections on the
   web. See <https://www.idigbio.org> for information on iDigBio.
-URL: https://github.com/iDigBio/ridigbio, http://idigbio.github.io/ridigbio/
+URL: https://github.com/iDigBio/ridigbio, https://idigbio.github.io/ridigbio/
 BugReports: https://github.com/iDigBio/ridigbio/issues
 Depends:
   R (>= 3.0.1)
@@ -33,7 +33,8 @@ Imports:
   jsonlite,
   leaflet,
   kableExtra,
-  tidyverse
+  tidyverse,
+  cowplot
 License: MIT + file LICENSE
 LazyData: true
 Suggests:

R/base.R

@@ -7,9 +7,9 @@
 ##' @author Francois Michonneau
 idig_url <- function(dev = FALSE) {
   if (dev) {
-    "http://beta-search.idigbio.org"
+    "https://beta-search.idigbio.org"
   } else {
-    "http://search.idigbio.org"
+    "https://search.idigbio.org"
   }
 }
 
@@ -134,4 +134,5 @@ ignore_unused_imports <- function() {
   leaflet::`%>%`()
   kableExtra::kable()
   tidyverse::tidyverse_logo()
+  cowplot::theme_minimal_grid()
 }

R/idig_search_media.R

@@ -29,17 +29,17 @@
 ##' \item{dqs: Data quality score assigned by iDigBio.}   
 ##' \item{etag: Tag assigned by iDigBio.}         
 ##' \item{flags: Data quality flag assigned by iDigBio.}          
-##' \item{[format](http://purl.org/dc/terms/format) }          
+##' \item{[format](https://purl.org/dc/terms/format) }          
 ##' \item{hasSpecimen: TRUE or FALSE, indicates if there is an associated record for this media.}          
 ##' \item{[licenselogourl](https://ac.tdwg.org/termlist/#ac_licenseLogoURL)}          
 ##' \item{mediatype: Media object type.}          
-##' \item{[modified](http://purl.org/dc/terms/modified)}          
+##' \item{[modified](https://purl.org/dc/terms/modified)}          
 ##' \item{recordids: List of UUID for associated records.}          
 ##' \item{records: UUID for the associated record.}          
 ##' \item{recordset: Record set ID assigned by iDigBio.}          
-##' \item{[rights](http://purl.org/dc/terms/rights)}          
-##' \item{[tag](http://rs.tdwg.org/ac/terms/tag)}           
-##' \item{[type](http://purl.org/dc/terms/type)}          
+##' \item{[rights](https://purl.org/dc/terms/rights)}          
+##' \item{[tag](https://rs.tdwg.org/ac/terms/tag)}           
+##' \item{[type](https://purl.org/dc/terms/type)}          
 ##' \item{uuid: Unique identifier assigned by iDigBio.}          
 ##' \item{version: Media record version assigned by iDigBio.}          
 ##' \item{[webstatement](https://developer.adobe.com/xmp/docs/XMPNamespaces/xmpRights/)}          

R/idig_search_records.R

@@ -92,12 +92,12 @@
 ##' \itemize{
 ##' \item{UUID: Unique identifier assigned by iDigBio.}   
 ##' \item{[occurrenceID](https://dwc.tdwg.org/list/#dwc_occurrenceID)}  
-##' \item{[catalognumber](http://rs.tdwg.org/dwc/terms/catalogNumber)}   
-##' \item{[family](http://rs.tdwg.org/dwc/terms/family) - may be reassigned by iDigBio}   
+##' \item{[catalognumber](https://rs.tdwg.org/dwc/terms/catalogNumber)}   
+##' \item{[family](https://rs.tdwg.org/dwc/terms/family) - may be reassigned by iDigBio}   
 ##' \item{[genus](https://dwc.tdwg.org/list/#dwc_genus) - may be reassigned by iDigBio}   
-##' \item{[scientificname](http://rs.tdwg.org/dwc/terms/scientificName) - may be reassigned by iDigBio}   
-##' \item{[country](http://rs.tdwg.org/dwc/terms/country) - may be modified by iDigBio}   
-##' \item{[stateprovince](http://rs.tdwg.org/dwc/terms/stateProvince) }   
+##' \item{[scientificname](https://rs.tdwg.org/dwc/terms/scientificName) - may be reassigned by iDigBio}   
+##' \item{[country](https://rs.tdwg.org/dwc/terms/country) - may be modified by iDigBio}   
+##' \item{[stateprovince](https://rs.tdwg.org/dwc/terms/stateProvince) }   
 ##' \item{geopoint: Assigned by iDigBio.}     
 ##' \item{[data.dwc:eventDate](https://dwc.tdwg.org/list/#dwc_eventDate)}   
 ##' \item{[data.dwc:year](https://dwc.tdwg.org/list/#dwc_year)}   

README.md

@@ -40,14 +40,14 @@ sudo apt install libcurl4
 ## Getting Started
 There are several articles that can help get you started:
 
-* [Introduction to ridigbio](http://idigbio.github.io/ridigbio/articles/BasicUsage.html)
-* [Record API Demo](http://idigbio.github.io/ridigbio/articles/RecordAPIDemo.html)
-* [Media API Demo](http://idigbio.github.io/ridigbio/articles/MediaAPIDemo.html)
-* [Fields in ridigibio](http://idigbio.github.io/ridigbio/articles/Fields.html)
-* [Tissue Samples Locator Demo](http://idigbio.github.io/ridigbio/articles/FindTissue.html)
-* [Identification of Modified Data](http://idigbio.github.io/ridigbio/articles/ModifiedDataID.html)
-* [Identification of Suspicious Coordinates](http://idigbio.github.io/ridigbio/articles/BadCoordinateID.html)
-* [Identification of Data Flags](http://idigbio.github.io/ridigbio/articles/IDDataFlags.html)
+* [Introduction to ridigbio](https://idigbio.github.io/ridigbio/articles/BasicUsage.html)
+* [Record API Demo](https://idigbio.github.io/ridigbio/articles/RecordAPIDemo.html)
+* [Media API Demo](https://idigbio.github.io/ridigbio/articles/MediaAPIDemo.html)
+* [Fields in ridigibio](https://idigbio.github.io/ridigbio/articles/Fields.html)
+* [Tissue Samples Locator Demo](https://idigbio.github.io/ridigbio/articles/FindTissue.html)
+* [Identification of Modified Data](https://idigbio.github.io/ridigbio/articles/ModifiedDataID.html)
+* [Identification of Suspicious Coordinates](https://idigbio.github.io/ridigbio/articles/BadCoordinateID.html)
+* [Identification of Data Flags](https://idigbio.github.io/ridigbio/articles/IDDataFlags.html)
 
 
 Most iDigBio users are interested in downloading occurrence records:

_pkgdown.yml

@@ -1,4 +1,4 @@
-url: http://idigbio.github.io/ridigbio/
+url: https://idigbio.github.io/ridigbio/
 template:
   bootstrap: 5
   params:

vignettes/BadCoordinateID.Rmd

@@ -30,11 +30,13 @@ library(kableExtra)
 
 # Load libraries for visualizing geographic data
 library(leaflet)
+
+library(cowplot)
 ```
 
 ## Write a query to search for specimen records
 
-First, let's find all the specimen records for the data quality flag we are interested in. Do this using the `idig_search_records` function from the `ridigbio` package. You can learn more about this function from the [iDigBio API documentation](https://github.com/iDigBio/idigbio-search-api/wiki) and [ridigbio documentation](https://cran.r-project.org/web/packages/ridigbio/ridigbio.pdf). In this example, we want to start by searching for specimens flagged with "rev_geocode_corrected."
+First, let's find all the specimen records for the data quality flag we are interested in. Do this using the `idig_search_records` function from the `ridigbio` package. You can learn more about this function from the [iDigBio API documentation](https://github.com/iDigBio/idigbio-search-api/wiki) and [ridigbio documentation](https://cran.r-project.org/package=ridigbio/ridigbio.pdf). In this example, we want to start by searching for specimens flagged with "rev_geocode_corrected."
 
 ```{r}
 # Edit the fields (e.g. `flags`) and values (e.g. "rev_geocode_corrected") in
@@ -134,7 +136,7 @@ map <- df_rev_geocode_lat_sign[1:10,] %>%
 
 We can visualize this data on a map to better understand what the data quality flag is telling us. For example, in the map below you can see the effect of accidentally reversing the latitude on three example georeferenced specimen records.
 
-```{r echo = FALSE}
+```{r echo = FALSE, out.width = '100%'}
 map
 ```
 
@@ -178,8 +180,16 @@ percentFlagged <- sum(spmByColl$n)/totalInstSpm*100
 
 For example, we can ask how many specimen records from which collections at the Natural History Museum of Los Angeles (LACM) have been flagged as "rev_geocode_corrected" by iDigBio. *As an aside, although this graph highlights the number of specimen records with data quality issues, these represent only `r round(percentFlagged, 2)`% of the total specimen records published by LACM.*
 
-```{r echo = FALSE}
-graph_spmByColl
+```{r out.width="700px", echo = FALSE}
+graph_spmByColl <- graph_spmByColl +
+                   theme_minimal_grid() +
+                   theme(
+                       text = element_text(size = 22),
+                       axis.text = element_text(size = 22),
+                       plot.title = element_text(size = 22, face = "bold")
+                   )
+
+knitr::include_graphics(save_plot("plot.png", graph_spmByColl, base_height = 10, base_width = 24))
 ```
 
 We can also explore what *other* data quality flags these specimen records have been flagged with.
@@ -202,7 +212,7 @@ df_flagAssoc <- df_flagCoord %>%
   arrange(category, desc(n))
 
 # Visualize associated data quality flags
-ggplot(df_flagAssoc, aes(x = reorder(flags, -percent), y = percent, fill = category)) +
+graph_spmByColl <- ggplot(df_flagAssoc, aes(x = reorder(flags, -percent), y = percent, fill = category)) +
   geom_col() +
   theme(axis.title.x = element_text(face = "bold"),
         axis.text.x = element_text(angle = 75, hjust = 1),
@@ -215,3 +225,15 @@ ggplot(df_flagAssoc, aes(x = reorder(flags, -percent), y = percent, fill = categ
        title = "LACM records flagged for geo-coordinate issues are also flagged for...",
        fill = "flag category")
 ```
+```{r out.width="700px", echo = FALSE}
+graph_spmByColl <- graph_spmByColl +
+                   theme_minimal_grid() +
+                   theme(
+                       text = element_text(size = 22),
+                       axis.text = element_text(size = 22),
+                       axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1),
+                       plot.title = element_text(size = 22, face = "bold")
+                   )
+
+knitr::include_graphics(save_plot("plot2.png", graph_spmByColl, base_height = 10, base_width = 24))
+```

vignettes/BasicUsage.Rmd

@@ -19,7 +19,7 @@ In this demo we will cover how to:
 
 ## Getting Started
 
-First, you must install the ridigbio package. If you are new to R and R studio, please refer to our QUBES module to get started: Introduction to R with Biodiversity Data, [doi:10.25334/84FC-TE88](htpps://www.doi.org/10.25334/84FC-TE88) .
+First, you must install the ridigbio package. If you are new to R and R studio, please refer to our QUBES module to get started: Introduction to R with Biodiversity Data, [doi:10.25334/84FC-TE88](https://www.doi.org/10.25334/84FC-TE88) .
 
 The lastest version of our R package can be installed via CRAN. 
 ```{r eval=FALSE, include=TRUE}
@@ -49,21 +49,21 @@ When fields are not specified, default columns include the following:
 | Column | Description |
 | ----------- | ----------- |
 | uuid | Universally Unique IDentifier assigned by iDigBio  |
-| occurrenceid |identifier for the occurrence, 	http://rs.tdwg.org/dwc/terms/occurrenceID| 
-| catalognumber |identifier for the record within the collection, http://rs.tdwg.org/dwc/terms/catalogNumber|
-| family | scientific name of the family, http://rs.tdwg.org/dwc/terms/family|
-| genus | scientific name of the genus, http://rs.tdwg.org/dwc/terms/genus |
-| scientificname | scientific name, http://rs.tdwg.org/dwc/terms/scientificName |
-| country | country, 	http://rs.tdwg.org/dwc/terms/country |
-| stateprovince |name of the next smaller administrative region than country, http://rs.tdwg.org/dwc/terms/stateProvince|
-| geopoint.lon | equivalent to decimalLongitude, 	http://rs.tdwg.org/dwc/terms/decimalLongitude|
-| geopoint.lat | equivalent to decimalLatitude,http://rs.tdwg.org/dwc/terms/decimalLatitude |
+| occurrenceid |identifier for the occurrence, 	https://rs.tdwg.org/dwc/terms/occurrenceID| 
+| catalognumber |identifier for the record within the collection, https://rs.tdwg.org/dwc/terms/catalogNumber|
+| family | scientific name of the family, https://rs.tdwg.org/dwc/terms/family|
+| genus | scientific name of the genus, https://rs.tdwg.org/dwc/terms/genus |
+| scientificname | scientific name, https://rs.tdwg.org/dwc/terms/scientificName |
+| country | country, 	https://rs.tdwg.org/dwc/terms/country |
+| stateprovince |name of the next smaller administrative region than country, https://rs.tdwg.org/dwc/terms/stateProvince|
+| geopoint.lon | equivalent to decimalLongitude, 	https://rs.tdwg.org/dwc/terms/decimalLongitude|
+| geopoint.lat | equivalent to decimalLatitude,https://rs.tdwg.org/dwc/terms/decimalLatitude |
 | datecollected | [Modified field and could lack biological meaning](https://github.com/iDigBio/idb-backend/issues/229) |
 | data.dwc:eventDate | equivalent to eventDate, https://dwc.tdwg.org/list/#dwc_eventDate |
 | data.dwc:year | year of collection event, https://dwc.tdwg.org/list/#dwc_year |
 | data.dwc:month | month of collection event, https://dwc.tdwg.org/list/#dwc_month |
 | data.dwc:day | day of collection event | (https://dwc.tdwg.org/list/#dwc_day |
-| collector | equivalent to recordedBy,	http://rs.tdwg.org/dwc/terms/recordedBy |
+| collector | equivalent to recordedBy,	https://rs.tdwg.org/dwc/terms/recordedBy |
 | recordset | indicates the iDigBio recordset the observation belongs too! |
 
 
@@ -121,17 +121,17 @@ When fields are not specified, default columns include the following:
 | dqs | data quality score assigned by iDigBio |
 | etag | tag assigned by iDigBio |
 | flags | data quality flag assigned by iDigBio |
-| format | media format, http://purl.org/dc/terms/format |
+| format | media format, https://purl.org/dc/terms/format |
 | hasSpecimen | TRUE or FALSE, indicates if there is an associated record for this media |
 | licenselogourl  | media license, https://ac.tdwg.org/termlist/#ac_licenseLogoURL) |
 | mediatype  | media object type |
-| modified | date modified, http://purl.org/dc/terms/modified  |
+| modified | date modified, https://purl.org/dc/terms/modified  |
 | recordids | list of UUID for associated records |
 |  records  | UUID for the associated record. Use this field to connect Record downloads with Media downloads |
 |  recordset  | indicates the iDigBio recordset the observation belongs too! |
-| rights | media rights, http://purl.org/dc/terms/rights  |
-| tag  | general keywords or tags, http://rs.tdwg.org/ac/terms/tag  |
-| type | media type, http://purl.org/dc/terms/type |
+| rights | media rights, https://purl.org/dc/terms/rights  |
+| tag  | general keywords or tags, https://rs.tdwg.org/ac/terms/tag  |
+| type | media type, https://purl.org/dc/terms/type |
 |  uuid | Universally Unique IDentifier assigned by iDigBio  |
 | version  | media record version assigned by iDigBio |
 | webstatement  | media rights, https://developer.adobe.com/xmp/docs/XMPNamespaces/xmpRights/ |