Create a snapshot of the data linked to entities. Including metadata, climate & vegetation reconstructions and pollen counts.
snapshot(x, ...)
# S3 method for MariaDBConnection
snapshot(x, ..., ID_ENTITY, ID_SITE, entity_name, site_name, quiet = TRUE)
# S3 method for character
snapshot(x, ..., use_site_name = FALSE)
# S3 method for numeric
snapshot(x, ..., use_id_site = FALSE)
# S3 method for tbl_df
snapshot(x, ...)
# S3 method for tbl
snapshot(x, ...)
# S3 method for data.frame
snapshot(x, ...)
# S3 method for default
snapshot(x, ...)This object accepts different classes. If the given object is
a database connection, then extracts data from the database using the
ID_SITE, ID_ENTITY or entity_name (these should be provided after
the connection object). Alternatively, if the given object is a vector,
then it will retrieve the records from an internal snapshot of the
database, included in this package.
Optional parameters.
Optional, if ID_SITE, entity_name or site_name are
provided.
Optional, if ID_ENTITY, entity_name or site_name are
provided.
Optional, if ID_SITE, ID_ENTITY or site_name are
provided.
Optional, if ID_SITE, ID_ENTITY or entity_name are
provided.
Boolean flag to indicate if queries should be displayed.
Boolean flag to indicate whether to search using
entity_name (default) or site_name, using the values in x.
Boolean flag to indicate whether to search using
ID_ENTITY (default) or ID_SITE, using the values in x.
List with the individual tables.
if (FALSE) {
conn <- dabr::open_conn_mysql(dbname = "SMPDSv2",
password = rstudioapi::askForPassword())
# Using the entity name
snp1 <- smpds::snapshot(conn, entity_name = "juodonys_core")
snp1
# Using the site name
snp2 <- smpds::snapshot(conn, site_name = "Petresiunai")
snp2
# Using the ID_ENTITY
snp3 <- smpds::snapshot(conn, ID_ENTITY = 1)
snp3
# Using the ID_SITE
snp4 <- smpds::snapshot(conn, ID_SITE = 2)
snp4
}
# Using the entity name
snp1 <- smpds::snapshot("juodonys_core")
snp1
#> # A tibble: 1 × 6
#> ID_SITE ID_ENTITY ID_SAMPLE site_name entity_name pollen_counts$clean
#> <int> <int> <int> <chr> <chr> <int>
#> 1 3890 7901 1 Juodonys juodonys_core 1
#> # … with 2 more variables: pollen_counts$intermediate <int>, $amalgamated <int>
# Using the site name
snp2 <- smpds::snapshot("Petresiunai", use_site_name = TRUE)
snp2
#> # A tibble: 1 × 6
#> ID_SITE ID_ENTITY ID_SAMPLE site_name entity_name pollen_counts$clean
#> <int> <int> <int> <chr> <chr> <int>
#> 1 6690 14229 2 Petresiunai petresiunai_121 1
#> # … with 2 more variables: pollen_counts$intermediate <int>, $amalgamated <int>
# Using the ID_ENTITY
snp1 <- smpds::snapshot(1)
snp1
#> # A tibble: 1 × 6
#> ID_SITE ID_ENTITY ID_SAMPLE site_name entity_name pollen_counts$clean
#> <int> <int> <int> <chr> <chr> <int>
#> 1 1 1 9709 05-Mo 05-Mo 1
#> # … with 2 more variables: pollen_counts$intermediate <int>, $amalgamated <int>
# Using the ID_SITE
snp2 <- smpds::snapshot(2, use_id_site = TRUE)
snp2
#> # A tibble: 1 × 6
#> ID_SITE ID_ENTITY ID_SAMPLE site_name entity_name pollen_counts$clean
#> <int> <int> <int> <chr> <chr> <int>
#> 1 2 36 15870 10 [HFL10] HFL10 1
#> # … with 2 more variables: pollen_counts$intermediate <int>, $amalgamated <int>
# Using the entity table
`%>%` <- magrittr::`%>%`
snp1 <- smpds::entity %>%
dplyr::slice(1) %>%
smpds::snapshot()
snp1
#> # A tibble: 1 × 6
#> ID_SITE ID_ENTITY ID_SAMPLE site_name entity_name pollen_counts$clean
#> <int> <int> <int> <chr> <chr> <int>
#> 1 1 1 9709 05-Mo 05-Mo 1
#> # … with 2 more variables: pollen_counts$intermediate <int>, $amalgamated <int>
# Using a custom data frame (`tibble` object) with site names
snp2 <- tibble::tibble(
site_name = c("Aligol lake", "Big Sandy Creek")
) %>%
smpds::snapshot()
snp2
#> # A tibble: 7 × 6
#> ID_SITE ID_ENTITY ID_SAMPLE site_name entity_name pollen_counts$cle…
#> <int> <int> <int> <chr> <chr> <int>
#> 1 158 317 6066 Aligol lake Aligol core_0 7
#> 2 158 318 6067 Aligol lake Aligol core_4 7
#> 3 158 319 6068 Aligol lake Aligol core_8 7
#> 4 158 320 17764 Aligol lake Connor_a1 (AL1) 7
#> 5 158 321 17765 Aligol lake Connor_a2 (AL2) 7
#> 6 158 322 17766 Aligol lake Connor_a3 (AL3) 7
#> 7 772 1683 14037 Big Sandy Creek BIGSANDY 7
#> # … with 2 more variables: pollen_counts$intermediate <int>, $amalgamated <int>