R/read_opendata_csv.R
In Centre-for-Marine-Applied-Research/strings: Compile, Format, and Visualize Sensor String Data
Defines functions
read_mooring_csv
read_opendata_csv
Documented in
read_mooring_csv
read_opendata_csv
#' Read in csv file of county data assembled for Open Data Portal
#'
#' @description Reads in the file using data.table::fread and assigns the
#' appropriate class to each column.
#'
#' @param path Path to the csv file, including file name and extension.
#'
#' @return Returns a dataframe of the assembled data.
#'
#' @importFrom data.table fread
#' @importFrom dplyr mutate if_else
#' @importFrom lubridate force_tz
#' @export
read_opendata_csv <- function(path){
fread(
path,
colClasses = list(
character = c("STATION", "LEASE", "DEPLOYMENT_PERIOD",
"SENSOR", "DEPTH", "VARIABLE", "UNITS", "MOORING"),
POSIXct = "TIMESTAMP"),
data.table = FALSE
) %>%
mutate(
LEASE = if_else(LEASE == "NA", NA_character_, LEASE),
TIMESTAMP = force_tz(TIMESTAMP, tzone = "UTC")
)
}
#' Read mooring table
#'
#' @param path_mooring Path to mooring type table (including file name and
#' extension).
#'
#' @return Mooring table with standardized WATERBODY and STATION columns.
#'
#' @importFrom data.table fread
#' @importFrom dplyr distinct case_when if_else mutate select
#' @importFrom lubridate dmy
#'
#' @export
read_mooring_csv <- function(path_mooring){
#path <- file.path("Y:/Coastal Monitoring Program/Open Data/Deployment Data/MOORING_table.csv")
dat_raw <- fread(path_mooring, data.table = FALSE, header = TRUE)
dat <- dat_raw %>%
# fix spelling discrepancies
mutate(
Depl_Date = dmy(Depl_Date),
Recv_Date = dmy(Recv_Date),
WATERBODY = case_when(
Waterbody == "Black Harbour" &
Station_Name == "Burnt Island" ~ "Merigomish Harbour",
Waterbody == "Merigomish Harbour" &
Station_Name == "Robinson Cove" ~ "French Channel",
Waterbody == "Pipers lake" ~ "Piper Lake",
Waterbody == "St Marys Bay" ~ "St. Mary's Bay",
Waterbody == "St Margarets Bay" ~ "St. Margarets Bay",
Waterbody == "St Anns Bay" ~ "St. Ann's Bay",
Waterbody == "St Peters Inlet" ~ "St. Peters Inlet",
# Waterbody == "Owls Head Bay" ~ "Owl's Head Bay",
TRUE ~ Waterbody
),
STATION = case_when(
Station_Name == "1" ~ "0001",
Station_Name == "28" ~ "0028",
Station_Name == "75" ~ "Wine Harbour",
Station_Name == "622" ~ "0622",
Station_Name == "623" ~ "West Ferry Ramp",
Station_Name == "745" ~ "0745",
Station_Name == "778" ~ "0778",
Station_Name == "994" ~ "0994",
Station_Name == "1006" ~ "Saddle Island",
# Station_Name == "0191 / 1113" ~ "0191/1113",
Station_Name == "0191 / 1113" | Station_Name == "0191/1113" ~ "Burnt Island",
Station_Name == "1198" ~ "Northwest Branch",
Station_Name == "1114" ~ "The Channel",
Station_Name == "613" ~ "White Island",
Station_Name == "1091" ~ "Yankee Cove",
Station_Name == "839" ~ "The Basin",
Station_Name == "716" |Station_Name == "0716" ~ "0716 Center",
Station_Name == "1308" ~ "Jewers Bay",
Station_Name == "Beaver point" ~ "Beaver Point",
Station_Name == "Bear Island" & Depl_Date == as_date("2021-05-14") ~ "5005",
Station_Name == "Big point pond" ~ "Big Pond Point",
Station_Name == "Burnt island" ~ "Burnt Island",
Station_Name == "Larry's River" ~ "Larrys River",
Station_Name == "Long beach" ~ "Long Beach",
Station_Name == "Long Island two" ~ "Long Island 2",
Station_Name == "McNutt's Island" ~ "McNutts Island",
Station_Name == "Nyanza Bay West" ~ "Nyanza Bay - W",
Station_Name == "Nyanza Bay East" ~ "Nyanza Bay - E",
Station_Name == "Monks head" ~ "Monks Head",
Station_Name == "Owls head" | Station_Name == "Owl's Head" ~ "Owls Head",
Station_Name == "Pipers lake" ~ "Piper Lake",
Station_Name == "Shut-in Island" ~ "Shut-In Island",
Station_Name == "South side" | Station_Name == "South Side" ~ "Southside",
Station_Name == "St. Andrew's Channel - E"|
Station_Name == "St Andrews Channel - E" ~ "St. Andrews Channel - E",
Station_Name == "St Peters Canal - S" ~ "St. Peters Canal - S",
Station_Name == "St Peters Canal - N" |
Station_Name == "St Peters Canal North" |
Station_Name == "St. Peters Canal North"~ "St. Peters Canal - N",
Station_Name == "Tor Bay Center" ~ "Center Bay",
Station_Name == "Deny's Basin East" ~ "Denys Basin East",
Station_Name == "Deny's Basin West" ~ "Denys Basin West",
Station_Name == "193" ~ "0193",
WATERBODY == "Merigomish Harbour" &
Station_Name == "Burnt Island" ~ "Back Harbour",
Station_Name == "Little Narrows - S (Whyc.Bay)" ~ "Little Narrows - S",
Station_Name == "The Basin South" &
Depl_Date == as_date("2021-09-08") ~ "The Basin",
# Station_Name == "St. Peters Canal - N" ~ "St. Peters Canal North",
# Station_Name == "St. Peters Canal - S" ~ "St. Peters Canal South",
TRUE ~ Station_Name
)
) %>%
select(-Waterbody, -Station_Name) %>%
# CMAR corrected some Waterbodies and re-named some stations
mutate(
WATERBODY = case_when(
WATERBODY == "Tor Bay" & STATION == "Bald Rock" ~ "Whitehead Harbour",
WATERBODY == "Whycocomagh Bay" &
(STATION == "Deep Basin" |
STATION == "0814x East" |
STATION == "0814x West") ~ "Whycocomagh Basin",
WATERBODY == "Antigonish Harbour" & STATION == "Captains Pond" ~ "Grahams Cove",
WATERBODY == "Antigonish Harbour" & STATION == "Monks Head" ~ "Monks Head Harbour",
WATERBODY == "Pictou Harbour" & STATION == "Melmerby Beach" ~ "Little Harbour",
TRUE ~ WATERBODY
),
STATION = case_when(
WATERBODY == "Salt Bay" & STATION == "Salt Bay" ~ "Big Sluice",
WATERBODY == "Hourglass Lake" & STATION == "Deep Point" ~ "Hourglass Lake",
WATERBODY == "Arichat Harbour" & STATION == "667" ~ "0667",
WATERBODY == "Strait of Canso" & STATION == "Pulp Mill 2" ~ "Pulp Mill Site 2",
WATERBODY == "St. Mary's Bay" &
(STATION == "Sandy Cove" | STATION == "Sandy cove")
~ "Sandy Cove St. Mary's",
WATERBODY == "Chedabucto Bay" & STATION == "Sandy Cove" ~ "Sandy Cove Chedabucto",
WATERBODY == "Strait of Canso" & STATION == "Loch" ~ "Canso Lock",
TRUE ~ STATION
)
) %>%
mutate(
MOORING = if_else(Surface.Float. == "Y", "float", "fixed"),
# fix deployment/recovery dates
Depl_Date = case_when(
WATERBODY == "Country Harbour" & STATION == "0001" &
Depl_Date == as_date("2015-07-28") ~ as_date("2015-09-08"),
WATERBODY == "Country Harbour" & STATION == "0622" &
Depl_Date == as_date("2015-07-28") ~ as_date("2015-09-08"),
WATERBODY == "Country Harbour" & STATION == "West Ferry Ramp" &
Depl_Date == as_date("2015-07-28") ~ as_date("2015-09-08"),
WATERBODY == "Marie Joseph Harbour" & STATION == "0028" &
Depl_Date == as_date("2015-07-28") ~ as_date("2015-09-08"),
WATERBODY == "Marie Joseph Harbour" & STATION == "Jewers Bay" &
Depl_Date == as_date("2015-07-28") ~ as_date("2015-09-08"),
WATERBODY == "Wine Harbour" & STATION == "Wine Harbour" &
Depl_Date == as_date("2015-07-28") ~ as_date("2015-09-08"),
WATERBODY == "Whitehead Harbour" &
Depl_Date == as_date("2015-07-29") ~ as_date("2015-09-08"),
WATERBODY == "Chedabucto Bay" & STATION == "Rook Island" &
Depl_Date == as_date("2020-05-20") ~ as_date("2020-05-21"),
WATERBODY == "Dover Bay" & STATION == "Seal Cove" &
Depl_Date == as_date("2021-09-14") ~ as_date("2021-09-15"),
WATERBODY == "St. Mary's Bay" & STATION == "Church Point 1" &
Depl_Date == as_date("2020-02-24") ~ as_date("2020-02-23"),
WATERBODY == "St. Mary's Bay" & STATION == "Church Point 2" &
Depl_Date == as_date("2020-02-24") ~ as_date("2020-02-23"),
TRUE ~ Depl_Date
),
Recv_Date = case_when(
WATERBODY == "Chedabucto Bay" & STATION == "Rook Island" &
Recv_Date == as_date("2020-05-20") ~ as_date("2020-05-21"),
STATION == "Barren Island" & Recv_Date == as_date("2022-08-16") ~
as_date("2022-08-17"),
TRUE ~ Recv_Date
)
) %>%
select(WATERBODY, STATION, Depl_Date, Recv_Date, MOORING) %>%
# remove 7 duplicate rows
distinct() %>%
mutate(
MOORING = case_when(
STATION == "Wine Harbour" & Depl_Date == as_date("2015-09-08") ~ "float",
TRUE ~ MOORING
)
)
}
# x <- dat_raw %>%
# filter(!is.na(Recv_Date), Recv_Date != "") %>%
# mutate(Recv_Date = dmy(Recv_Date))
#
# filter(x, is.na(Recv_Date))
Centre-for-Marine-Applied-Research/strings documentation built on Aug. 21, 2023, 8 a.m.
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Defines functions read_mooring_csv read_opendata_csv
Documented in read_mooring_csv read_opendata_csv
#' Read in csv file of county data assembled for Open Data Portal
#'
#' @description Reads in the file using data.table::fread and assigns the
#' appropriate class to each column.
#'
#' @param path Path to the csv file, including file name and extension.
#'
#' @return Returns a dataframe of the assembled data.
#'
#' @importFrom data.table fread
#' @importFrom dplyr mutate if_else
#' @importFrom lubridate force_tz
#' @export
read_opendata_csv <- function(path){
fread(
path,
colClasses = list(
character = c("STATION", "LEASE", "DEPLOYMENT_PERIOD",
"SENSOR", "DEPTH", "VARIABLE", "UNITS", "MOORING"),
POSIXct = "TIMESTAMP"),
data.table = FALSE
) %>%
mutate(
LEASE = if_else(LEASE == "NA", NA_character_, LEASE),
TIMESTAMP = force_tz(TIMESTAMP, tzone = "UTC")
)
}
#' Read mooring table
#'
#' @param path_mooring Path to mooring type table (including file name and
#' extension).
#'
#' @return Mooring table with standardized WATERBODY and STATION columns.
#'
#' @importFrom data.table fread
#' @importFrom dplyr distinct case_when if_else mutate select
#' @importFrom lubridate dmy
#'
#' @export
read_mooring_csv <- function(path_mooring){
#path <- file.path("Y:/Coastal Monitoring Program/Open Data/Deployment Data/MOORING_table.csv")
dat_raw <- fread(path_mooring, data.table = FALSE, header = TRUE)
dat <- dat_raw %>%
# fix spelling discrepancies
mutate(
Depl_Date = dmy(Depl_Date),
Recv_Date = dmy(Recv_Date),
WATERBODY = case_when(
Waterbody == "Black Harbour" &
Station_Name == "Burnt Island" ~ "Merigomish Harbour",
Waterbody == "Merigomish Harbour" &
Station_Name == "Robinson Cove" ~ "French Channel",
Waterbody == "Pipers lake" ~ "Piper Lake",
Waterbody == "St Marys Bay" ~ "St. Mary's Bay",
Waterbody == "St Margarets Bay" ~ "St. Margarets Bay",
Waterbody == "St Anns Bay" ~ "St. Ann's Bay",
Waterbody == "St Peters Inlet" ~ "St. Peters Inlet",
# Waterbody == "Owls Head Bay" ~ "Owl's Head Bay",
TRUE ~ Waterbody
),
STATION = case_when(
Station_Name == "1" ~ "0001",
Station_Name == "28" ~ "0028",
Station_Name == "75" ~ "Wine Harbour",
Station_Name == "622" ~ "0622",
Station_Name == "623" ~ "West Ferry Ramp",
Station_Name == "745" ~ "0745",
Station_Name == "778" ~ "0778",
Station_Name == "994" ~ "0994",
Station_Name == "1006" ~ "Saddle Island",
# Station_Name == "0191 / 1113" ~ "0191/1113",
Station_Name == "0191 / 1113" | Station_Name == "0191/1113" ~ "Burnt Island",
Station_Name == "1198" ~ "Northwest Branch",
Station_Name == "1114" ~ "The Channel",
Station_Name == "613" ~ "White Island",
Station_Name == "1091" ~ "Yankee Cove",
Station_Name == "839" ~ "The Basin",
Station_Name == "716" |Station_Name == "0716" ~ "0716 Center",
Station_Name == "1308" ~ "Jewers Bay",
Station_Name == "Beaver point" ~ "Beaver Point",
Station_Name == "Bear Island" & Depl_Date == as_date("2021-05-14") ~ "5005",
Station_Name == "Big point pond" ~ "Big Pond Point",
Station_Name == "Burnt island" ~ "Burnt Island",
Station_Name == "Larry's River" ~ "Larrys River",
Station_Name == "Long beach" ~ "Long Beach",
Station_Name == "Long Island two" ~ "Long Island 2",
Station_Name == "McNutt's Island" ~ "McNutts Island",
Station_Name == "Nyanza Bay West" ~ "Nyanza Bay - W",
Station_Name == "Nyanza Bay East" ~ "Nyanza Bay - E",
Station_Name == "Monks head" ~ "Monks Head",
Station_Name == "Owls head" | Station_Name == "Owl's Head" ~ "Owls Head",
Station_Name == "Pipers lake" ~ "Piper Lake",
Station_Name == "Shut-in Island" ~ "Shut-In Island",
Station_Name == "South side" | Station_Name == "South Side" ~ "Southside",
Station_Name == "St. Andrew's Channel - E"|
Station_Name == "St Andrews Channel - E" ~ "St. Andrews Channel - E",
Station_Name == "St Peters Canal - S" ~ "St. Peters Canal - S",
Station_Name == "St Peters Canal - N" |
Station_Name == "St Peters Canal North" |
Station_Name == "St. Peters Canal North"~ "St. Peters Canal - N",
Station_Name == "Tor Bay Center" ~ "Center Bay",
Station_Name == "Deny's Basin East" ~ "Denys Basin East",
Station_Name == "Deny's Basin West" ~ "Denys Basin West",
Station_Name == "193" ~ "0193",
WATERBODY == "Merigomish Harbour" &
Station_Name == "Burnt Island" ~ "Back Harbour",
Station_Name == "Little Narrows - S (Whyc.Bay)" ~ "Little Narrows - S",
Station_Name == "The Basin South" &
Depl_Date == as_date("2021-09-08") ~ "The Basin",
# Station_Name == "St. Peters Canal - N" ~ "St. Peters Canal North",
# Station_Name == "St. Peters Canal - S" ~ "St. Peters Canal South",
TRUE ~ Station_Name
)
) %>%
select(-Waterbody, -Station_Name) %>%
# CMAR corrected some Waterbodies and re-named some stations
mutate(
WATERBODY = case_when(
WATERBODY == "Tor Bay" & STATION == "Bald Rock" ~ "Whitehead Harbour",
WATERBODY == "Whycocomagh Bay" &
(STATION == "Deep Basin" |
STATION == "0814x East" |
STATION == "0814x West") ~ "Whycocomagh Basin",
WATERBODY == "Antigonish Harbour" & STATION == "Captains Pond" ~ "Grahams Cove",
WATERBODY == "Antigonish Harbour" & STATION == "Monks Head" ~ "Monks Head Harbour",
WATERBODY == "Pictou Harbour" & STATION == "Melmerby Beach" ~ "Little Harbour",
TRUE ~ WATERBODY
),
STATION = case_when(
WATERBODY == "Salt Bay" & STATION == "Salt Bay" ~ "Big Sluice",
WATERBODY == "Hourglass Lake" & STATION == "Deep Point" ~ "Hourglass Lake",
WATERBODY == "Arichat Harbour" & STATION == "667" ~ "0667",
WATERBODY == "Strait of Canso" & STATION == "Pulp Mill 2" ~ "Pulp Mill Site 2",
WATERBODY == "St. Mary's Bay" &
(STATION == "Sandy Cove" | STATION == "Sandy cove")
~ "Sandy Cove St. Mary's",
WATERBODY == "Chedabucto Bay" & STATION == "Sandy Cove" ~ "Sandy Cove Chedabucto",
WATERBODY == "Strait of Canso" & STATION == "Loch" ~ "Canso Lock",
TRUE ~ STATION
)
) %>%
mutate(
MOORING = if_else(Surface.Float. == "Y", "float", "fixed"),
# fix deployment/recovery dates
Depl_Date = case_when(
WATERBODY == "Country Harbour" & STATION == "0001" &
Depl_Date == as_date("2015-07-28") ~ as_date("2015-09-08"),
WATERBODY == "Country Harbour" & STATION == "0622" &
Depl_Date == as_date("2015-07-28") ~ as_date("2015-09-08"),
WATERBODY == "Country Harbour" & STATION == "West Ferry Ramp" &
Depl_Date == as_date("2015-07-28") ~ as_date("2015-09-08"),
WATERBODY == "Marie Joseph Harbour" & STATION == "0028" &
Depl_Date == as_date("2015-07-28") ~ as_date("2015-09-08"),
WATERBODY == "Marie Joseph Harbour" & STATION == "Jewers Bay" &
Depl_Date == as_date("2015-07-28") ~ as_date("2015-09-08"),
WATERBODY == "Wine Harbour" & STATION == "Wine Harbour" &
Depl_Date == as_date("2015-07-28") ~ as_date("2015-09-08"),
WATERBODY == "Whitehead Harbour" &
Depl_Date == as_date("2015-07-29") ~ as_date("2015-09-08"),
WATERBODY == "Chedabucto Bay" & STATION == "Rook Island" &
Depl_Date == as_date("2020-05-20") ~ as_date("2020-05-21"),
WATERBODY == "Dover Bay" & STATION == "Seal Cove" &
Depl_Date == as_date("2021-09-14") ~ as_date("2021-09-15"),
WATERBODY == "St. Mary's Bay" & STATION == "Church Point 1" &
Depl_Date == as_date("2020-02-24") ~ as_date("2020-02-23"),
WATERBODY == "St. Mary's Bay" & STATION == "Church Point 2" &
Depl_Date == as_date("2020-02-24") ~ as_date("2020-02-23"),
TRUE ~ Depl_Date
),
Recv_Date = case_when(
WATERBODY == "Chedabucto Bay" & STATION == "Rook Island" &
Recv_Date == as_date("2020-05-20") ~ as_date("2020-05-21"),
STATION == "Barren Island" & Recv_Date == as_date("2022-08-16") ~
as_date("2022-08-17"),
TRUE ~ Recv_Date
)
) %>%
select(WATERBODY, STATION, Depl_Date, Recv_Date, MOORING) %>%
# remove 7 duplicate rows
distinct() %>%
mutate(
MOORING = case_when(
STATION == "Wine Harbour" & Depl_Date == as_date("2015-09-08") ~ "float",
TRUE ~ MOORING
)
)
}
# x <- dat_raw %>%
# filter(!is.na(Recv_Date), Recv_Date != "") %>%
# mutate(Recv_Date = dmy(Recv_Date))
#
# filter(x, is.na(Recv_Date))
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