Create a snapshot of the data linked to entities. Including metadata, dates, samples, age models 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 = "SPECIAL-EPD",
password = rstudioapi::askForPassword())
# Using the entity name
snp1 <- special.epd::snapshot(conn, entity_name = "MBA3")
snp1
# Using the site name
snp2 <- special.epd::snapshot(conn, site_name = "Aammiq")
snp2
# Using the ID_ENTITY
snp3 <- special.epd::snapshot(conn, ID_ENTITY = 1)
snp3
# Using the ID_SITE
snp4 <- special.epd::snapshot(conn, ID_SITE = 2)
snp4
}
# Using the entity name
snp1 <- special.epd::snapshot("MBA3")
snp1
#> # A tibble: 1 × 8
#> ID_SITE ID_ENTITY site_name entity_name dates samples age_model
#> <int> <int> <chr> <chr> <int> <int> <int>
#> 1 1 1 Aalkistensee MBA3 7 57 57
#> # … with 1 more variable: pollen_counts <tibble[,3]>
# Using the site name
snp2 <- special.epd::snapshot("Aammiq", use_site_name = TRUE)
snp2
#> # A tibble: 1 × 8
#> ID_SITE ID_ENTITY site_name entity_name dates samples age_model
#> <int> <int> <chr> <chr> <int> <int> <int>
#> 1 2 2 Aammiq AMMIQ 4 96 96
#> # … with 1 more variable: pollen_counts <tibble[,3]>
# Using the ID_ENTITY
snp1 <- special.epd::snapshot(1)
snp1
#> # A tibble: 1 × 8
#> ID_SITE ID_ENTITY site_name entity_name dates samples age_model
#> <int> <int> <chr> <chr> <int> <int> <int>
#> 1 1 1 Aalkistensee MBA3 7 57 57
#> # … with 1 more variable: pollen_counts <tibble[,3]>
# Using the ID_SITE
snp2 <- special.epd::snapshot(2, use_id_site = TRUE)
snp2
#> # A tibble: 1 × 8
#> ID_SITE ID_ENTITY site_name entity_name dates samples age_model
#> <int> <int> <chr> <chr> <int> <int> <int>
#> 1 2 2 Aammiq AMMIQ 4 96 96
#> # … with 1 more variable: pollen_counts <tibble[,3]>
# Using the entity table
`%>%` <- magrittr::`%>%`
snp1 <- special.epd::entity %>%
dplyr::slice(1) %>%
special.epd::snapshot("MBA3")
snp1
#> # A tibble: 1 × 8
#> ID_SITE ID_ENTITY site_name entity_name dates samples age_model
#> <int> <int> <chr> <chr> <int> <int> <int>
#> 1 1 1 Aalkistensee MBA3 7 57 57
#> # … with 1 more variable: pollen_counts <tibble[,3]>
# Using a custom data frame (`tibble` object) with site names
snp2 <- tibble::tibble(
site_name = c("Lingreville", "Machova")
) %>%
special.epd::snapshot()
snp2
#> # A tibble: 5 × 8
#> ID_SITE ID_ENTITY site_name entity_name dates samples age_model
#> <int> <int> <chr> <chr> <int> <int> <int>
#> 1 810 916 Lingreville BRICQRUE 2 22 22
#> 2 810 917 Lingreville LINGR2C1 1 59 0
#> 3 810 918 Lingreville LINGR2C2 1 12 0
#> 4 810 919 Lingreville LINGREV4 1 29 0
#> 5 876 986 Machova MACHOVA 1 21 21
#> # … with 1 more variable: pollen_counts <tibble[,3]>