mfdb_import_data {mfdb} | R Documentation |
MareFrame Data Import functions
Description
Functions to import data into MareFrame DB
Usage
mfdb_import_temperature(mdb, data_in)
mfdb_import_survey(mdb, data_in, data_source = 'default_sample')
mfdb_import_survey_index(mdb, data_in, data_source = 'default_index')
mfdb_import_stomach(mdb, predator_data, prey_data, data_source = "default_stomach")
Arguments
mdb |
Database connection created by |
data_in , predator_data , prey_data |
A |
data_source |
A name for this data, e.g. the filename it came from. Used so you can replace it later without disturbing other data. |
Details
All functions will replace existing data in the case study with new data, unless you specify a data_source
,
in which case then only existing data with the same data_source
will be replaced.
If you want to remove the data, import empty data.frames with the same data_source
.
mfdb_import_temperature
imports temperature time-series data for
areacells. The data_in
should be a data.frame with the following columns:
- id
A numeric ID for this areacell (will be combined with the case study number internally)
- year
Required. Year each sample was taken, e.g.
c(2000,2001)
- month
Required. Month (1–12) each sample was taken, e.g.
c(1,12)
- areacell
Required. Areacell sample was taken within
- temperature
The temperature at given location/time
mfdb_import_survey
imports institution surveys and commercial sampling for your case study. The
data_in
should be a data.frame with the following columns:
- institute
Optional. An institute name, see mfdb::institute for possible values
- gear
Optional. Gear name, see mfdb::gear for possible values
- vessel
Optional. Vessel defined previously with
mfdb_import_vessel_taxonomy(...)
- tow
Optional. Tow defined previously with
mfdb_import_tow_taxonomy(...)
- sampling_type
Optional. A sampling_type, see mfdb::sampling_type for possible values
- year
Required. Year each sample was taken, e.g.
c(2000,2001)
- month
Required. Month (1–12) each sample was taken, e.g.
c(1,12)
- areacell
Required. Areacell sample was taken within
- species
Optional, default
c(NA)
. Species of sample, see mfdb::species for possible values- age
Optional, default
c(NA)
. Age of sample, or mean age- sex
Optional, default
c(NA)
. Sex of sample, see mfdb::sex for possible values- length
Optional, default
c(NA)
. Length of sample / mean length of all samples- length_var
Optional, default
c(NA)
. Sample variance, if data is already aggregated- length_min
Optional, default
c(NA)
. Minimum theoretical length, if data is already aggregated- weight
Optional, default
c(NA)
. Weight of sample / mean weight of all samples- weight_var
Optional, default
c(NA)
. Sample variance, if data is already aggregated- weight_total
Optional, default
c(NA)
. Total weight of all samples, can be used with count = NA to represent an unknown number of samples- liver_weight
Optional, default
c(NA)
. Weight of sample / mean liver weight of all samples- liver_weight_var
Optional, default
c(NA)
. Sample variance, if data is already aggregated- gonad_weight
Optional, default
c(NA)
. Weight of sample / mean gonad weight of all samples- gonad_weight_var
Optional, default
c(NA)
. Sample variance, if data is already aggregated- stomach_weight
Optional, default
c(NA)
. Weight of sample / mean stomach weight of all samples- stomach_weight_var
Optional, default
c(NA)
. Sample variance, if data is already aggregated- count
Optional, default
c(1)
. Number of samples this row represents (i.e. if the data is aggregated)
mfdb_import_survey_index
adds indicies that can be used as abundance information, for example.
Before using mfdb_import_survey_index
, make sure that the index_type
you intend to use
exists by using mfdb_import_cs_taxonomy. The data_in
should be a data.frame with the
following columns:
- index_type
Required. the name of the index data you are storing, e.g. 'acoustic'
- year
Required. Year each sample was taken, e.g.
c(2000,2001)
- month
Required. Month (1–12) each sample was taken, e.g.
c(1,12)
- areacell
Required. Areacell sample was taken within
- value
Value of the index at this point in space/time
mfdb_import_stomach
imports data on predators and prey. The predator and prey
data are stored separately, however they should be linked by the stomach_name
column.
If a prey has a stomach name that doesn't match a predator, then an error will be returned.
The predator_data
should be a data.frame with the following columns:
- stomach_name
Required. An arbitary name that provides a link between the predator and prey tables
- institute
Optional. An institute name, see mfdb::institute for possible values
- gear
Optional. Gear name, see mfdb::gear for possible values
- vessel
Optional. Vessel defined previously with
mfdb_import_vessel_taxonomy(mdb, ...)
- tow
Optional. Tow defined previously with
mfdb_import_tow_taxonomy(...)
- sampling_type
Optional. A sampling_type, see mfdb::sampling_type for possible values
- year
Required. Year each sample was taken, e.g.
c(2000,2001)
- month
Required. Month (1–12) each sample was taken, e.g.
c(1,12)
- areacell
Required. Areacell sample was taken within
- species
Optional, default
c(NA)
. Species of sample, see mfdb::species for possible values- age
Optional, default
c(NA)
. Age of sample, or mean age- sex
Optional, default
c(NA)
. Sex of sample, see mfdb::sex for possible values- maturity_stage
Optional, default
c(NA)
. Maturity stage of sample, see mfdb::maturity_stage for possible values- stomach_state
Optional, default
c(NA)
. Stomach state of sample, see mfdb::stomach_state for possible values- length
Optional, default
c(NA)
. Length of sample- weight
Optional, default
c(NA)
. Weight of sample
The prey_data
should be a data.frame with the following columns:
- stomach_name
Required. The stomach name of the predator this was found in
- species
Optional, default
c(NA)
. Species of sample, see mfdb::species for possible values- digestion_stage
Optional, default
c(NA)
. Stage of digestion of the sample, see mfdb::digestion_stage for possible values- length
Optional, default
c(NA)
. Length of sample / mean length of all samples- weight
Optional, default
c(NA)
. Weight of sample / mean weight of all samples- weight_total
Optional, default
c(NA)
. Total weight of all samples- count
Optional, default
c(NA)
. Number of samples this row represents (i.e. if the data is aggregated), count = NA represents an unknown number of samples
Value
NULL
Examples
mdb <- mfdb(tempfile(fileext = '.duckdb'))
# We need to set-up vocabularies first
mfdb_import_area(mdb, data.frame(
id = c(1,2,3),
name = c('35F1', '35F2', '35F3'),
size = c(5)))
mfdb_import_vessel_taxonomy(mdb, data.frame(
name = c('1.RSH', '2.COM'),
stringsAsFactors = FALSE))
mfdb_import_sampling_type(mdb, data.frame(
name = c("RES", "LND"),
description = c("Research", "Landings"),
stringsAsFactors = FALSE))
data_in <- read.csv(text = '
year,month,areacell,species,age,sex,length
1998,1,35F1,COD,3,M,140
1998,1,35F1,COD,3,M,150
1998,1,35F1,COD,3,F,150
')
data_in$institute <- 'MRI'
data_in$gear <- 'GIL'
data_in$vessel <- '1.RSH'
data_in$sampling_type <- 'RES'
mfdb_import_survey(mdb, data_in, data_source = 'cod-1998')
mfdb_disconnect(mdb)