.Rhistory

get_species_list <- function(country) {
country <- tolower(country)
readr::read_csv(
glue::glue(
"http://api.adu.org.za/sabap2/v2/monthly/species/country/{country}?format=csv"
),
col_types = readr::cols_only(
Spp = readr::col_integer(),
Common_group = readr::col_character(),
Common_species = readr::col_character(),
Genus = readr::col_character(),
Species = readr::col_character()
)
)
}
kenya_list <- get_species_list("kenya")
View(kenya_list)
find_species <- function(species_list, species_names) {
df_to_search <- species_list %>%
dplyr::mutate(SearchColumn = as.character(tolower(
glue::glue(
"{Common_group} {Common_species} {Genus} {Species} {Common_species} {Common_group} {Species} {Genus}"
)
)))
species_names %>%
purrr::map_df( ~ dplyr::filter(
df_to_search,
stringr::str_detect(df_to_search$SearchColumn, tolower(.x))
))
}
interesting_species <- c("boubou")
find_species(species_list = kenya_list, species_name = interesting_species)
library(magrittr)
find_species(species_list = kenya_list, species_name = interesting_species)
interesting_species <- c("drongo")
find_species(species_list = kenya_list, species_name = interesting_species)
library(rabm)
library(rabm)
#' region_type = 'country',
#' region_id = 'kenya',
#' return_type = 'data',
#' return_format = 'CSV'
#' )
#'
#'
#' }
#'
#'
extract_all <- function(start_date = '2019-01-01',
end_date = '2019-02-01',
region_type = 'country',
region_id = 'kenya',
return_type = 'data',
return_format = 'CSV') {
# requirements on inputs
if (is.na(as.Date(start_date, format = "%Y-%m-%d"))) {
stop(message = "start_date is incorrectly specified. Please use the YYYY-MM-DD format")
}
if (is.na(as.Date(end_date, format = "%Y-%m-%d"))) {
stop(message = "end_date is incorrectly specified. Please use the YYYY-MM-DD format")
}
region_type = tolower(region_type)
region_id = tolower(region_id)
return_type = tolower(return_type)
return_data <- readr::read_csv(
glue::glue(
"http://api.adu.org.za/sabap2/v2/R/{start_date}/{end_date}/{region_type}/{region_id}/{return_type}/all?format={return_format}"
),
col_types = readr::cols()
)
return_data
}
View(extract_all())
?get_species_list
start_date = '2019-01-01'
start_date = '2019-01-01'
start_date = '2019-01-01'
start_date = '2019-01-01'
end_date = '2019-02-01'
region_type = 'country'
region_id = 'kenya'
return_type = 'data'
return_format = 'CSV'
return_data <- readr::read_csv(
glue::glue(
"http://api.adu.org.za/sabap2/v2/R/{start_date}/{end_date}/{region_type}/{region_id}/count/all?format={return_format}"
),
col_types = readr::cols()
)
return_data
start_date = '2019-01-01'
end_date = '2019-02-01'
region_type = 'country'
region_id = 'kenya'
return_type = 'count'
return_format = 'CSV'
return_data <- readr::read_csv(
glue::glue(
"http://api.adu.org.za/sabap2/v2/R/{start_date}/{end_date}/{region_type}/{region_id}/count/all?format={return_format}"
),
col_types = readr::cols()
)
return_data
glue::glue(
"http://api.adu.org.za/sabap2/v2/R/{start_date}/{end_date}/{region_type}/{region_id}/count/all?format={return_format}"
)
start_date = '2019-01-01'
end_date = '2019-02-01'
region_type = 'country'
region_id = 'kenya'
return_type = 'count'
return_format = 'CSV'
return_data <- readr::read_csv(
glue::glue(
"http://api.adu.org.za/sabap2/v2/R/{start_date}/{end_date}/{region_type}/{region_id}/count?format={return_format}"
),
col_types = readr::cols()
)
return_data
return_data$records[1]
start_date = '2019-01-01'
end_date = '2019-02-01'
region_type = 'country'
region_id = 'kenya'
return_type = 'count'
return_format = 'JSON'
return_data_count <- readr::read_csv(
glue::glue(
"http://api.adu.org.za/sabap2/v2/R/{start_date}/{end_date}/{region_type}/{region_id}/count?format={return_format}"
),
col_types = readr::cols()
)
return_data_count
return_format = 'CSV'
return_data_count <- readr::read_csv(
glue::glue(
"http://api.adu.org.za/sabap2/v2/R/{start_date}/{end_date}/{region_type}/{region_id}/count?format={return_format}"
),
col_types = readr::cols()
)
#' start_date = '2019-01-01',
#' end_date = '2019-02-01',
#' region_type = 'country',
#' region_id = 'kenya',
#' return_type = 'data',
#' return_format = 'CSV')
#'
#'
#'
#'
extract_all <- function(start_date = '2019-01-01',
end_date = '2019-02-01',
region_type = 'country',
region_id = 'kenya',
return_type = 'data',
return_format = 'CSV') {
# requirements on inputs
if (is.na(as.Date(start_date, format = "%Y-%m-%d"))) {
stop(message = "start_date is incorrectly specified. Please use the YYYY-MM-DD format")
}
if (is.na(as.Date(end_date, format = "%Y-%m-%d"))) {
stop(message = "end_date is incorrectly specified. Please use the YYYY-MM-DD format")
}
region_type = tolower(region_type)
region_id = tolower(region_id)
return_type = tolower(return_type)
# get number of records to be returned
return_data_count <- readr::read_csv(
glue::glue(
"http://api.adu.org.za/sabap2/v2/R/{start_date}/{end_date}/{region_type}/{region_id}/count?format={return_format}"
),
col_types = readr::cols()
)
if (return_data_count$records[1] > 250000) {
stop(message = "Your query returns more than 250,000 records. The API does not allow more than 250,000 records to be drawn at one. Please split your query.")
}
# get data
return_data <- readr::read_csv(
glue::glue(
"http://api.adu.org.za/sabap2/v2/R/{start_date}/{end_date}/{region_type}/{region_id}/{return_type}/all?format={return_format}"
),
col_types = readr::cols()
)
return_data
}
View(extract_all())
#' Extract raw data from the Africa Bird Atlas
#'
#' @param start_date A character representing the start date from which you want to query the database. It must be in the YYYY-MM-DD format. Defaults to 1 Jan,2019. Example: '2019-01-26'.
#' @param end_date A character representing the end date to which you want to query the database. It must be in the YYYY-MM-DD format. Defaults to 1 Feb, 2019. Example: '2019-02-26'.
#' @param region_type Can take one of the following types: country, pentad, group, qdgc. Default is 'country'
#' @param region_id Has to be co-defined with `region_type`. That is, it is an instantiation of the `region_type`. For instance if the `region_type` = 'country', then the `region_id` = 'kenya'. Or if `region_type` = 'pentad', then  `region_id` = '3355_1825'. Default is 'kenya'.
#' @param return_type There are two options, 'data' and 'count'. 'data' is the actual records submitted to the africa bird map. 'count' return a count of the rows. Default is 'data'.
#' @param return_format Default s 'CSV', though the API default is 'JSON'
#'
#' @return Depending on the return_format, the function will return a dataframe with the following:
#' 1. `return_type = data` A tidy dataframe is returned with the records that fall within the specification defined.
#' 2. `return_type = count` A tidy dataframe is returns with the number of rows that will be produced if the return_type was to be specified as 'data'.
#'
#' @examples
#'
#' # extract data for all of Kenya for Jan 2019
#'
#' extract_all(
#' start_date = '2019-01-01',
#' end_date = '2019-02-01',
#' region_type = 'country',
#' region_id = 'kenya',
#' return_type = 'data',
#' return_format = 'CSV')
#'
#'
#'
#'
extract_all <- function(start_date = '2019-01-01',
end_date = '2019-02-01',
region_type = 'country',
region_id = 'kenya',
return_type = 'data',
return_format = 'CSV') {
# requirements on inputs
if (is.na(as.Date(start_date, format = "%Y-%m-%d"))) {
stop(message = "start_date is incorrectly specified. Please use the YYYY-MM-DD format")
}
if (is.na(as.Date(end_date, format = "%Y-%m-%d"))) {
stop(message = "end_date is incorrectly specified. Please use the YYYY-MM-DD format")
}
region_type = tolower(region_type)
region_id = tolower(region_id)
return_type = tolower(return_type)
# get number of records to be returned
return_data_count <- readr::read_csv(
glue::glue(
"http://api.adu.org.za/sabap2/v2/R/{start_date}/{end_date}/{region_type}/{region_id}/count?format={return_format}"
),
col_types = readr::cols()
)
if (return_data_count$records[1] > 4000) {
stop(message = "Your query returns more than 250,000 records. The API does not allow more than 250,000 records to be drawn at one. Please split your query.")
}
# get data
return_data <- readr::read_csv(
glue::glue(
"http://api.adu.org.za/sabap2/v2/R/{start_date}/{end_date}/{region_type}/{region_id}/{return_type}/all?format={return_format}"
),
col_types = readr::cols()
)
return_data
}
View(extract_all())
library(rabm)
species_ids = 123
start_date = '2019-01-01'
end_date = '2019-02-01'
region_type = 'country'
region_id = 'kenya'
return_type = 'data'
return_format = 'CSV'
return_data_count <- readr::read_csv(
glue::glue(
"http://api.adu.org.za/sabap2/v2/R/{start_date}/{end_date}/{region_type}/{region_id}/species/{species_id}/count?format={return_format}"
),
col_types = readr::cols()
)
species_id = 123
start_date = '2019-01-01'
end_date = '2019-02-01'
region_type = 'country'
region_id = 'kenya'
return_type = 'data'
return_format = 'CSV'
return_data_count <- readr::read_csv(
glue::glue(
"http://api.adu.org.za/sabap2/v2/R/{start_date}/{end_date}/{region_type}/{region_id}/species/{species_id}/count?format={return_format}"
),
col_types = readr::cols()
)
return_data_count
species_id = 123
start_date = '2019-01-01'
end_date = '2019-02-01'
region_type = 'country'
region_id = 'kenya'
return_type = 'data'
return_format = 'CSV'
return_data_count <- readr::read_csv(
glue::glue(
"http://api.adu.org.za/sabap2/v2/R/{start_date}/{end_date}/{region_type}/{region_id}/count/species/{species_id}?format={return_format}"
),
col_types = readr::cols()
)
return_data_count
species_id = 123
start_date = '2019-01-01'
end_date = '2019-02-01'
region_type = 'country'
region_id = 'kenya'
return_type = 'data'
return_format = 'CSV'
return_data_count <- readr::read_csv(
glue::glue(
"http://api.adu.org.za/sabap2/v2/R/{start_date}/{end_date}/{region_type}/{region_id}/count/species/{species_id}?format={return_format}"
),
col_types = readr::cols()
)
return_data_count
species_id = 762
start_date = '2019-01-01'
end_date = '2019-02-01'
region_type = 'country'
region_id = 'kenya'
return_type = 'data'
return_format = 'CSV'
return_data_count <- readr::read_csv(
glue::glue(
"http://api.adu.org.za/sabap2/v2/R/{start_date}/{end_date}/{region_type}/{region_id}/count/species/{species_id}?format={return_format}"
),
col_types = readr::cols()
)
return_data_count
extract_species(762)
test <- c("a", "b", "c")
test
paste(test, collapse = ",")
test <- "a"
paste(test, collapse = ",")
library(rabm)
devtools::load_all(".")
devtools::use_vignette("rabm-vignette")
install.packages("pkgdown")
library(rabm)
pkgdown::build_site()
library(rabm)
pkgdown::build_site()
library(rabm)
pkgdown::build_site()
library(rabm)
pkgdown::build_site()
library(rabm)
?find_species
library(rabm)
library(rabm)
library(rabm)
find_species(rabm::get_species_list("Kenya"), species_names = c("Bulbul"))
usethis::use_pipe()
devtools::document()
usethis::use_pipe()
devtools::document()
library(rabm)
find_species(rabm::get_species_list("Kenya"), species_names = c("Bulbul"))
usethis::use_pipe(export = TRUE)
?usethis::use_pipe(export = TRUE)
find_species(rabm::get_species_list("Kenya"), species_names = c("Bulbul"))
?usethis::use_pipe(export = TRUE)
usethis::use_pipe(export = TRUE)
devtools::document()
devtools::document()
devtools::load_all()
library(rabm)
rabm::get_species_list("Kenya")
library(rabm)
library(rabm)
library(rabm)
find_species(rabm::get_species_list("Kenya"), species_names = c("Bulbul"))
?pipe
pkgdown::build_home()
vignette("roxygen2")
usethis::use_pipe()
devtools::document()
find_species(rabm::get_species_list("Kenya"), species_names = c("Bulbul"))
find_species(rabm::get_species_list("Kenya"), species_names = c("Bulbul"))