Package 'n2khelper'

Title: Auxiliary Functions for the Analysis and Reporting of the Natura 2000 Monitoring
Description: Auxiliary functions for analysing Natura 2000 monitoring data.
Authors: Thierry Onkelinx [aut, cre] , Research Institute for Nature and Forest [cph, fnd]
Maintainer: Thierry Onkelinx <[email protected]>
License: GPL-3
Version: 0.5.0
Built: 2024-11-11 03:13:58 UTC
Source: https://github.com/inbo/n2khelper

Help Index


Check if the object is a character

Description

Factors are converted to character.

Usage

check_character(x, name = "x", na_action = na.fail)

Arguments

x

the object to check

name

the name of the object to use in the error message

na_action

stats::na.fail() throws an error in case of NA (default). stats::na.omit() will return x without the NA values. stats::na.pass() will return x with the NA values.

Value

The function gives the character back. It throws an error when the input is not a character.

Examples

check_character(c("20", "b"))

Check if the covariates are available in a dataframe

Description

Check if the covariates are available in a dataframe

Usage

check_dataframe_covariate(df, covariate, response = "Count", error = TRUE)

Arguments

df

the data.frame to check

covariate

The right hand side of the model as a character

response

The left hand side of the model as a character

error

When TRUE (default), the function returns an error when a variable is missing. Otherwise it returns a warning.


Check if a data.frame contains variables

Description

Check if a data.frame contains variables

Usage

check_dataframe_variable(
  df,
  variable,
  name = "df",
  force_na = FALSE,
  error = TRUE
)

Arguments

df

the data.frame to check

variable

either a character vector with the names of the variable to check or a named list. The names of the list must match the names of the required variables in the data.frame. The elements of the list contain the accepted classes for each varaible.

name

the name of the data.frame to use in the error message

force_na

check the class of variables with all NA

error

When TRUE (default), the function returns an error when a variable is missing. Otherwise it returns a warning.

Value

The function returns TRUE when all variables are present. If returns FALSE when a variable is missing and error = FALSE.

Examples

check_dataframe_variable(
 df = data.frame(a = integer(0)),
 variable = "a"
)
check_dataframe_variable(
 df = data.frame(a = integer(0)),
 variable = list(a = c("integer", "numeric"))
)

Check if a table is available in a given ODBC connection

Description

Check if a table is available in a given ODBC connection

Usage

check_dbtable(table, schema = "public", channel, error = TRUE)

Arguments

table

The name of the table

schema

The schema. Defaults to 'public'

channel

the open dplyr connection to the database.

error

Indicates the behaviour when a table is missing. Gives an error when error = TRUE (default). Return FALSE otherwise.

Value

TRUE when all tables are present in the ODBC connection.


Check if a variable is available in a given table

Description

Check if a variable is available in a given table

Usage

check_dbtable_variable(
  table,
  variable,
  schema = "public",
  channel,
  error = TRUE
)

Arguments

table

The name of the table

variable

A vector with the names of the columns

schema

The schema of the table. Defaults to public

channel

the open dplyr connection to the database.

error

Indicates the behaviour when a variable is missing. Gives an error when error = TRUE (default). Return FALSE otherwise.

Value

TRUE when all variables are present in the table.


Test if an id exists in a given field of the table

Description

Test if an id exists in a given field of the table

Usage

check_id(value, variable, table, channel)

Arguments

value

the id value

variable

A vector with the names of the columns

table

The name of the table

channel

the open dplyr connection to the database.


check if a path is an exisiting file or directory

Description

check if a path is an exisiting file or directory

Usage

check_path(path, type = c("file", "directory"), error = TRUE)

Arguments

path

the path of the directory or file name

type

either "file" or "directory"

error

When TRUE (default), the function returns an error when a variable is missing. Otherwise it returns a warning.


Check if the object is a single POSIX

Description

Check if the object is a single POSIX

Usage

check_single_posix(x, name = "x", past = FALSE)

Arguments

x

the object to check

name

the name of the object to use in the error message

past

Should the function throw an error when x is in the future? Default is FALSE.

Value

The function gives the single POSIX back. It throws an error when the input is not a single character.

Examples

check_single_posix(Sys.time())

Check if the object is a single probability

Description

Check if the object is a single probability

Usage

check_single_probability(x, name = "x")

Arguments

x

the object to check

name

the name of the object to use in the error message

Value

The function gives the single probability back. It throws an error when the input is not a single probability.

Examples

check_single_probability(0.5)

Open a trusted connection to the NBN database

Description

Open a trusted connection to the NBN database

Usage

connect_nbn()

Opens an ODBC connection to the 'results' database

Description

Opens an ODBC connection to the 'results' database

Usage

connect_result(username, password, develop = TRUE)

Arguments

username

the username to connect to the database.

password

the password for the username.

develop

Logical value. Indicates the location of the results database


connect to the unit test database

Description

connect to the unit test database

Usage

connect_ut_db(
  host = "localhost",
  dbname = "n2kunittest",
  user = "unittest_analysis",
  password = "unittest",
  port = 5432,
  ...
)

Arguments

host

Host name and port number of PostgreSQL database.

dbname

Database name.

user

User name and password.

password

User name and password.

port

Port number of database. Defaults to 5432

...

arguments past to DBI::dbConnect().


Split dates into periods within each year

Description

The periods are defined by a day and month. The same day from different years with be in the same period.

Usage

cut_date(x, dm, include_last = TRUE)

Arguments

x

the dates in POSIXt or Date format.

dm

the breakpoints of the periods in 'day-month' format.

include_last

Should the last period include the last day? Defaults to TRUE.

Examples

x <- as.POSIXct(
    c(
    "2015-01-01", "2014-01-02", "2013-01-03", "2012-01-31", "2011-02-01",
    "2012-12-31"
   )
)
cut_date(x, dm = c("1-1", "1-2", "1-3"))

Get the NBN key of a species

Description

Get the NBN key of a species

Usage

get_nbn_key(name, language = "la", channel, authority = FALSE)

Arguments

name

a vector of species names to check

language

The language to use. Defaults to "la" 'scientific name"

channel

An open RODBC channel to the NBN database

authority

Do the species names include authority?


Try multiple languages to get a matching NBN key

Description

Try multiple languages to get a matching NBN key

Usage

get_nbn_key_multi(species, orders = c("la", "nl", "en"), channel)

Arguments

species

A data.frame with the name of species in one or more languages

orders

the order in which the languages are tried to get a matching NBN key.

channel

An open RODBC channel to the NBN database


Get the name associated with an NBN key

Description

Get the name associated with an NBN key

Usage

get_nbn_name(nbn_key, channel)

Arguments

nbn_key

A vector with NBN keys

channel

An open RODBC channel to the NBN database


Returns the path of the datasource within the git repository

Description

The details are stored in the results database.

Usage

git_connect(
  data_source_name,
  channel,
  type = c("ssh", "https"),
  username = character(0),
  password = character(0),
  commit_user,
  commit_email
)

Arguments

data_source_name

The name of the data source

channel

the ODBC channel to the database with the connection strings

type

Use 'ssh' or 'https' for authentication

username

the username in case the ConnectMethod is "Credentials supplied by the user running the report". Ignored in all other cases.

password

the password to be used in combination with the username.

commit_user

the name of the user how will commit

commit_email

the email of the user how will commit


The gitConnection class

Description

The gitConnection class

Open a git connection

Usage

git_connection(repo_path, key, username, password, commit_user, commit_email)

Arguments

repo_path

The path of the root of the repository

key

Optional: the path to a private ssh key. The public key is assumed to have the same path with a '.pub' extension. Using in case of ssh authentication.

username

The optional username used in case of https authentication. Ignored when key is provided.

password

The password required for the ssh key or the username. Should be missing when the ssh-key doesn't require a password.

commit_user

the name of the user how will commit

commit_email

the email of the user how will commit

Slots

Repository

a git repository

Credentials

the credentials for the repository

CommitUser

the name of the user how will commit

CommitEmail

the email of the user how will commit


Test if the argument is either character or factor

Description

Test if the argument is either character or factor

Usage

is_chartor(x)

Arguments

x

the object to check


Merge NBN keys into a species dataframe

Description

Merge NBN keys into a species dataframe

Usage

match_nbn_key(species, nbn_key, variable)

Arguments

species

a data.frame with the species names

nbn_key

a data.frame with the NBN keys

variable

the name of the variable of species to match with InputName from nbn_key


connect to a data source through ODBC

Description

The connection string is stored in the results database.

Usage

odbc_connect(data_source_name, username, password, channel)

Arguments

data_source_name

The name of the data source

username

the username in case the ConnectMethod is "Credentials supplied by the user running the report". Ignored in all other cases.

password

the password to be used in combination with the username.

channel

the ODBC channel to the database with the connection strings


Get the id of the matching records

Description

Get the id of the matching records

Usage

odbc_get_id(table, ..., schema = "public", channel, id_variable = "id")

Arguments

table

The name of the table

...

arguments passed to filter().

schema

The schema of the table. Defaults to public

channel

the open dplyr connection to the database.

id_variable

name of the id variable


Get the corresponding id's

Description

Get the corresponding id's

Usage

odbc_get_multi_id(
  data,
  id_field,
  merge_field,
  table,
  channel,
  create = FALSE,
  select = TRUE,
  rows_at_time = 1000
)

Arguments

data

the data.frame

id_field

the id fields

merge_field

the merge fields

table

The name of the table

channel

the open dplyr connection to the database.

create

When TRUE, the function creates unmatching records AND updates attributes. Defaults to FALSE.

select

Return the matching ID's when TRUE. Returns invisible NULL when FALSE. select = FALSE is only relevant in combination with create = TRUE.

rows_at_time

Number of rows to insert in one SQL statement

Value

a data.frame with data and the id's


Append a data.frame to a table through an ODBC connection

Description

Append a data.frame to a table through an ODBC connection

Usage

odbc_insert(
  data,
  table,
  channel,
  schema = "dbo",
  append = TRUE,
  rows_at_time = 1000
)

Arguments

data

the data.frame

table

The name of the table

channel

the open dplyr connection to the database.

schema

The schema of the table. Defaults to public

append

Append the data or overwrite existing rows?

rows_at_time

Number of rows to insert in one SQL statement

Value

The status of the SQL INSERT for each row in returned but invisible.


Read an object from an environment

Description

Read an object from an environment

Usage

read_object_environment(object, env, warn = TRUE)

Arguments

object

the name of the object

env

the environment

warn

Issue a warning if the object is not found in the environment. Defaults to TRUE

Value

the object or NULL is the object doesn't exists in the environment

Examples

object <- "test"
  value <- TRUE
  env <- new.env()
  assign(x = object, value = value, envir = env)
  read_object_environment(object, env)