Package 'deltafish'

Clear cached deltafish files

Description

This function removes all cached files associated with the package

Usage

clear_cache()

Value

(NULL)

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Close connection to database

Description

Close connection to SQLite database. Recommended at the end of every session.

Usage

close_database(con = NULL)

Arguments

con	A DBI connection object from open_database()

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Collect data into R

Description

Collect data into R and convert dates/datetimes into the correct data types with the correct time zone. It is recommended to use this function instead of collect because the database RSQLite does not support date and time data types, so they are stored as character vectors. Although some date and time operations are still possible, when you collect the dataset, the Date and Datetime columns will be character vectors. This function will convert those columns (if they exist in your collected dataset) into the correct date and datetime format. RSQLite also does not have a logical data type and logical values are stored as integers. Thus, the Secchi_estimated column is converted to logical by this function as well.

Usage

collect_data(data)

Arguments

data	A DBI table that can be treated like a data.frame. See open_fish() and open_survey()

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Convert fish length

Description

Converts fish length data using the length conversion table. Returns an arrow dataset. This function is only needed to convert Suisun survey data.

Usage

convert_lengths(data)

Arguments

data	A DBI table that can be treated like a data.frame, with fish data. See open_fish()

Value

data_conv A DBI table with converted lengths

Examples

## Not run: 
library(dplyr)
con <- open_database()
fish <- open_fish(con) %>%
  filter(Taxa %in% c("Dorosoma petenense", "Morone saxatilis", "Spirinchus thaleichthys"))

fish_conv <- convert_lengths(fish) %>%
  collect()
close_database(con)

## End(Not run)

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Create fish database

Description

Function to create the fish database. Reads in raw data from the published EDI dataset.

Usage

create_fish_db(edi_pid = NULL, update = FALSE, download_method = "curl")

Arguments

edi_pid	(char) Optionally, a way to specify a specific revision of the dataset, in the format "edi.1075.1" Leave parameter unset to get the latest revision.
update	(logical) If set to TRUE, will update to latest version from EDI if a newer version is available
download_method	value for the method parameter of the download.file function.

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Is cached data up to date with latest EDI data

Description

Returns TRUE for up to date, FALSE if a newer version exists

Usage

is_cache_updated(cache_dir = "deltafish")

Arguments

cache_dir

(char) The cache directory, by default set to deltafish for most use cases.

Value

(logical) Whether cache is up to date

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Connect to database

Description

Connect to the fish database stored in local cache directory.

Usage

open_database()

Value

con A DBI connection object

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Connect fish data

Description

Connect to the fish table stored in the database

Usage

open_fish(con, quiet = FALSE)

Arguments

con	A DBI connection object from open_database()
quiet	silence message about fish length units.

Value

A DBI table that can be treated like a data.frame, with fish data

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Connect length conversion data

Description

Connect to the length conversion table stored in the database

Usage

open_length_conv(con)

Arguments

con	A DBI connection object from open_database()

Value

A DBI table that can be treated like a data.frame, with length conversion data

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Connect survey data

Description

Connect to the survey table stored in the database

Usage

open_survey(con)

Arguments

con	A DBI connection object from open_database()

Value

A DBI table that can be treated like a data.frame, with survey data

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Remove unknown fish lengths

Description

Removes unknown fish lengths. Returns a DBI table.

Usage

remove_unknown_lengths(data, univariate)

Arguments

data

A DBI table that can be treated like a data.frame, with fish data. See open_fish()

univariate

(logical) Will these data be used for univariate analyses (univariate=TRUE)? Or multi-species analyses (univariate=FALSE)? If univariate, when a Length_NA_flag=="Unknown length" record is found, all records of that taxa from that sample are removed. In effect, this is transforming those records into missing data. If univariate=FALSE, when a Length_NA_flag=="Unknown length" record is found, the entire sample is removed and no 0s are filled in, since accurate community data cannot be confirmed for that sample.

Value

data_known A DBI table with only known lengths

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Show list of cached deltafish files

Description

This function returns a list of files cached for the package.

Usage

show_cache()

Value

(list) A list of files

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Show revision number of cached files

Description

This function returns the EDI revision number of the cached data.

Usage

show_cached_revision(cache_dir = "deltafish")

Arguments

cache_dir

(char) The cache directory, by default set to deltafish for most use cases.

Value

(char) The revision number in the cache

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