Update filtering vignette

luomus · Feb 29, 2024 · 078a43b · 078a43b
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diff --git a/docs/articles/v05_filtering.html b/docs/articles/v05_filtering.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -7,5 +7,5 @@ articles:
  v03_selecting_variables: v03_selecting_variables.html
  v04_metadata: v04_metadata.html
  v05_filtering: v05_filtering.html
-last_built: 2024-01-25T08:09Z
+last_built: 2024-02-29T07:54Z
 
diff --git a/docs/search.json b/docs/search.json
diff --git a/inst/vign/cache/date-filter_267c11bbb5f8c988c458866dc69475c0.RData b/inst/vign/cache/date-filter_267c11bbb5f8c988c458866dc69475c0.RData
diff --git a/...lter_2e06a9dacc9bcc9aa4429207a6e34852.rdb → ...lter_267c11bbb5f8c988c458866dc69475c0.rdb b/...lter_2e06a9dacc9bcc9aa4429207a6e34852.rdb → ...lter_267c11bbb5f8c988c458866dc69475c0.rdb
diff --git a/inst/vign/cache/date-filter_267c11bbb5f8c988c458866dc69475c0.rdx b/inst/vign/cache/date-filter_267c11bbb5f8c988c458866dc69475c0.rdx
diff --git a/inst/vign/cache/date-filter_2e06a9dacc9bcc9aa4429207a6e34852.RData b/inst/vign/cache/date-filter_2e06a9dacc9bcc9aa4429207a6e34852.RData
diff --git a/inst/vign/cache/date-filter_2e06a9dacc9bcc9aa4429207a6e34852.rdx b/inst/vign/cache/date-filter_2e06a9dacc9bcc9aa4429207a6e34852.rdx
diff --git a/inst/vign/cache/quality-filter_47b528602d64ac8fdea1c6b48aa7be32.RData b/inst/vign/cache/quality-filter_47b528602d64ac8fdea1c6b48aa7be32.RData
diff --git a/inst/vign/cache/quality-filter_47b528602d64ac8fdea1c6b48aa7be32.rdb b/inst/vign/cache/quality-filter_47b528602d64ac8fdea1c6b48aa7be32.rdb
diff --git a/inst/vign/cache/quality-filter_47b528602d64ac8fdea1c6b48aa7be32.rdx b/inst/vign/cache/quality-filter_47b528602d64ac8fdea1c6b48aa7be32.rdx
diff --git a/inst/vign/cache/quality-filter_bf22dddc37cecd3cf1188356b31745fe.RData b/inst/vign/cache/quality-filter_bf22dddc37cecd3cf1188356b31745fe.RData
diff --git a/inst/vign/cache/quality-filter_bf22dddc37cecd3cf1188356b31745fe.rdb b/inst/vign/cache/quality-filter_bf22dddc37cecd3cf1188356b31745fe.rdb
diff --git a/inst/vign/cache/quality-filter_bf22dddc37cecd3cf1188356b31745fe.rdx b/inst/vign/cache/quality-filter_bf22dddc37cecd3cf1188356b31745fe.rdx
diff --git a/inst/vign/v05_filtering.Rmd b/inst/vign/v05_filtering.Rmd
@@ -51,7 +51,7 @@ See `?filters` section "Location" for more details
 The event or import date of records can be used to filter occurrence data from
 FinBIF. The date filters can be a single year, month or date,
 ```{details date-filter}
-finbif_occurrence(filter = list(date_range_ym = c("2019-12")))
+finbif_occurrence(filter = list(date_range_ym = c("2020-12")))
 ```
 , or for record events, a range as a character vector.
 ```{details date-range-filter}
@@ -80,12 +80,12 @@ strict <- c(
  record_quality = "expert_verified"
 )
 permissive <- list(
- quality_issues = "both",
- record_reliability = c("reliable", "unassessed", "unreliable"),
+ wild_status = c("wild", "non_wild", "wild_unknown"),
  record_quality = c(
  "expert_verified", "community_verified", "unassessed", "uncertain",
  "erroneous"
- )
+ ),
+ abundance_min = 0
 )
 c(
  strict = finbif_occurrence(filter = strict, count_only = TRUE),

diff --git a/inst/vign/v05_filtering.md b/inst/vign/v05_filtering.md
@@ -71,7 +71,7 @@ The event or import date of records can be used to filter occurrence data from
 FinBIF. The date filters can be a single year, month or date,
 
 ```r
-finbif_occurrence(filter = list(date_range_ym = c("2019-12")))
+finbif_occurrence(filter = list(date_range_ym = c("2020-12")))
 ```
 
 
@@ -81,30 +81,19 @@ finbif_occurrence(filter = list(date_range_ym = c("2019-12")))
 ```r
 
 #> Records downloaded: 10
-#> Records available: 20150
+#> Records available: 23847
 #> A data.frame [10 x 12]
-#> record_id scientific_name abundance lat_wgs84 lon_wgs84
-#> 1 …KE.921/LGE.627772/1470480 Pteromys volans (Li… NA 61.81362 25.75756
-#> 2 …JX.1054648#107 Pica pica (Linnaeus… 3 65.30543 25.70355
-#> 3 …JX.1054648#85 Poecile montanus (C… 1 65.30543 25.70355
-#> 4 …JX.1054648#103 Garrulus glandarius… 3 65.30543 25.70355
-#> 5 …JX.1054648#123 Passer montanus (Li… 3 65.30543 25.70355
-#> 6 …JX.1054648#149 Pyrrhula pyrrhula (… 1 65.30543 25.70355
-#> 7 …JX.1054648#93 Cyanistes caeruleus… 9 65.30543 25.70355
-#> 8 …JX.1054648#95 Parus major Linnaeu… 35 65.30543 25.70355
-#> 9 …JX.1054648#137 Carduelis flammea (… 2 65.30543 25.70355
-#> 10 …JX.1056695#107 Pica pica (Linnaeus… 6 62.7154 23.0893 
-#> date_time
-#> 1 2019-12-31 12:00:00
-#> 2 2019-12-31 10:20:00
-#> 3 2019-12-31 10:20:00
-#> 4 2019-12-31 10:20:00
-#> 5 2019-12-31 10:20:00
-#> 6 2019-12-31 10:20:00
-#> 7 2019-12-31 10:20:00
-#> 8 2019-12-31 10:20:00
-#> 9 2019-12-31 10:20:00
-#> 10 2019-12-31 10:15:00
+#> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time
+#> 1 …107 Pica pica (Linnaeus… 31 65.0027 25.49381 2020-12-31 10:20:00
+#> 2 …45 Larus argentatus Po… 1 65.0027 25.49381 2020-12-31 10:20:00
+#> 3 …153 Emberiza citrinella… 2 65.0027 25.49381 2020-12-31 10:20:00
+#> 4 …49 Columba livia domes… 33 65.0027 25.49381 2020-12-31 10:20:00
+#> 5 …117 Corvus corax Linnae… 1 65.0027 25.49381 2020-12-31 10:20:00
+#> 6 …111 Corvus monedula Lin… 7 65.0027 25.49381 2020-12-31 10:20:00
+#> 7 …161 Sciurus vulgaris Li… 1 65.0027 25.49381 2020-12-31 10:20:00
+#> 8 …123 Passer montanus (Li… 28 65.0027 25.49381 2020-12-31 10:20:00
+#> 9 …149 Pyrrhula pyrrhula (… 1 65.0027 25.49381 2020-12-31 10:20:00
+#> 10 …77 Turdus pilaris Linn… 1 65.0027 25.49381 2020-12-31 10:20:00
 #> ...with 0 more record and 6 more variables:
 #> coordinates_uncertainty, any_issues, requires_verification, requires_identification,
 #> record_reliability, record_quality
@@ -212,19 +201,19 @@ strict <- c(
  record_quality = "expert_verified"
 )
 permissive <- list(
- quality_issues = "both",
- record_reliability = c("reliable", "unassessed", "unreliable"),
+ wild_status = c("wild", "non_wild", "wild_unknown"),
  record_quality = c(
  "expert_verified", "community_verified", "unassessed", "uncertain",
  "erroneous"
- )
+ ),
+ abundance_min = 0
 )
 c(
  strict = finbif_occurrence(filter = strict, count_only = TRUE),
  permissive = finbif_occurrence(filter = permissive, count_only = TRUE)
 )
-#> Error: 1 error occurred:
-#> - Invalid name in record reliability: unassessed
+#>  strict permissive 
+#>  52654 51733557
 ```
 
 ## Collection

diff --git a/vignettes/v05_filtering.Rmd b/vignettes/v05_filtering.Rmd
@@ -71,7 +71,7 @@ The event or import date of records can be used to filter occurrence data from
 FinBIF. The date filters can be a single year, month or date,
 
 ```r
-finbif_occurrence(filter = list(date_range_ym = c("2019-12")))
+finbif_occurrence(filter = list(date_range_ym = c("2020-12")))
 ```
 
 
@@ -81,30 +81,19 @@ finbif_occurrence(filter = list(date_range_ym = c("2019-12")))
 ```r
 
 #> Records downloaded: 10
-#> Records available: 20150
+#> Records available: 23847
 #> A data.frame [10 x 12]
-#> record_id scientific_name abundance lat_wgs84 lon_wgs84
-#> 1 …KE.921/LGE.627772/1470480 Pteromys volans (Li… NA 61.81362 25.75756
-#> 2 …JX.1054648#107 Pica pica (Linnaeus… 3 65.30543 25.70355
-#> 3 …JX.1054648#85 Poecile montanus (C… 1 65.30543 25.70355
-#> 4 …JX.1054648#103 Garrulus glandarius… 3 65.30543 25.70355
-#> 5 …JX.1054648#123 Passer montanus (Li… 3 65.30543 25.70355
-#> 6 …JX.1054648#149 Pyrrhula pyrrhula (… 1 65.30543 25.70355
-#> 7 …JX.1054648#93 Cyanistes caeruleus… 9 65.30543 25.70355
-#> 8 …JX.1054648#95 Parus major Linnaeu… 35 65.30543 25.70355
-#> 9 …JX.1054648#137 Carduelis flammea (… 2 65.30543 25.70355
-#> 10 …JX.1056695#107 Pica pica (Linnaeus… 6 62.7154 23.0893 
-#> date_time
-#> 1 2019-12-31 12:00:00
-#> 2 2019-12-31 10:20:00
-#> 3 2019-12-31 10:20:00
-#> 4 2019-12-31 10:20:00
-#> 5 2019-12-31 10:20:00
-#> 6 2019-12-31 10:20:00
-#> 7 2019-12-31 10:20:00
-#> 8 2019-12-31 10:20:00
-#> 9 2019-12-31 10:20:00
-#> 10 2019-12-31 10:15:00
+#> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time
+#> 1 …107 Pica pica (Linnaeus… 31 65.0027 25.49381 2020-12-31 10:20:00
+#> 2 …45 Larus argentatus Po… 1 65.0027 25.49381 2020-12-31 10:20:00
+#> 3 …153 Emberiza citrinella… 2 65.0027 25.49381 2020-12-31 10:20:00
+#> 4 …49 Columba livia domes… 33 65.0027 25.49381 2020-12-31 10:20:00
+#> 5 …117 Corvus corax Linnae… 1 65.0027 25.49381 2020-12-31 10:20:00
+#> 6 …111 Corvus monedula Lin… 7 65.0027 25.49381 2020-12-31 10:20:00
+#> 7 …161 Sciurus vulgaris Li… 1 65.0027 25.49381 2020-12-31 10:20:00
+#> 8 …123 Passer montanus (Li… 28 65.0027 25.49381 2020-12-31 10:20:00
+#> 9 …149 Pyrrhula pyrrhula (… 1 65.0027 25.49381 2020-12-31 10:20:00
+#> 10 …77 Turdus pilaris Linn… 1 65.0027 25.49381 2020-12-31 10:20:00
 #> ...with 0 more record and 6 more variables:
 #> coordinates_uncertainty, any_issues, requires_verification, requires_identification,
 #> record_reliability, record_quality
@@ -212,19 +201,19 @@ strict <- c(
  record_quality = "expert_verified"
 )
 permissive <- list(
- quality_issues = "both",
- record_reliability = c("reliable", "unassessed", "unreliable"),
+ wild_status = c("wild", "non_wild", "wild_unknown"),
  record_quality = c(
  "expert_verified", "community_verified", "unassessed", "uncertain",
  "erroneous"
- )
+ ),
+ abundance_min = 0
 )
 c(
  strict = finbif_occurrence(filter = strict, count_only = TRUE),
  permissive = finbif_occurrence(filter = permissive, count_only = TRUE)
 )
-#> Error: 1 error occurred:
-#> - Invalid name in record reliability: unassessed
+#>  strict permissive 
+#>  52654 51733557
 ```
 
 ## Collection