Searching data by location

[casaultb]

A question that came up in presenting the package to a group of potential users today:

Is it possible to search through data by location?
Eg. Show all data which was collected at HL-2

This is something @casaultb and @clayton33 have talked about before and we have not yet had time to implement this into variable_lookup(). Would be a great development if someone has the time. I do not think it would be too difficult to implement if we can connect the spatial lookup tables in multivaR.

How it might be possible:

connect to spatial lookup tables in multivaR
get the lat/lons for the area which user is searching (eg. if they input HL2, return the coordinates for HL2)
search through azmpdata metadata columns for those coordinates (or potentially a padded box around the area)
merge dataframes which match the coordinates
return a mega-dataframe which includes all data from a specific location

[jeff-jackson-dfo]

Hey Benoit, below is a script I wrote to retrieve all data from the azmpdata package for a specified station. I think your idea to search the package using a location is a great idea.

AZMP Data Station Lookup

Jeff Jackson
1/24/2021

Station Lookup function for azmpdata package

# Script to query the azmpdata package to find all data for a user specified station.
#
# Jeff Jackson 
# Created On: 22-JAN-2021
# Last Updated: 24-JAN-2021

# Example: 
#
# > hl2 <- station_lookup("HL2")
# [1] "The following dataset contains data about the specified station HL2: Derived_Annual_Stations"           
# [2] "The following dataset contains data about the specified station HL2: Derived_Monthly_Stations"          
# [3] "The following dataset contains data about the specified station HL2: Derived_Occupations_Sections"      
# [4] "The following dataset contains data about the specified station HL2: Derived_Occupations_Stations"      
# [5] "The following dataset contains data about the specified station HL2: Discrete_Occupations_Sections"     
# [6] "The following dataset contains data about the specified station HL2: Discrete_Occupations_Stations"     
# [7] "The following dataset contains data about the specified station HL2: Phytoplankton_Annual_Stations"     
# [8] "The following dataset contains data about the specified station HL2: Phytoplankton_Occupations_Stations"
# [9] "The following dataset contains data about the specified station HL2: Zooplankton_Annual_Stations"       
# [10] "The following dataset contains data about the specified station HL2: Zooplankton_Occupations_Sections"  
# [11] "The following dataset contains data about the specified station HL2: Zooplankton_Occupations_Stations"  
# >

station_lookup <- function(Station) {
  
  library(azmpdata)
  library(dplyr)
  
  # Get a list of all data sets in the azmpdata package
  dataSet <- data(package = "azmpdata")
  
  # Extract just the names of the data sets
  dataSetName <- dataSet$results[,3]
  
  # Identify the data frames that contain a "station" column
  ix <- unlist(lapply(dataSetName, function(x) "station" %in% colnames(eval(parse(text=x)))))
  subSet <- dataSetName[ix]
  
  # Filter the data frames to extract the data for the specified station
  subSetData <- lapply(subSet, function(x) eval(parse(text=x)) %>% filter(station == Station))

  # Remove any data frames that are empty
  iy <- which(lapply(subSetData, function(x) nrow(x) > 0) == TRUE)
  subSet <- subSet[iy]
  subSetData <- subSetData[iy]

  # Return the list of the data frames in the azmpdata package that contain data for
  # the user specified station; along with a list of the subsetted data frames 
  # for that station.
  return(list(subSet, subSetData))

}

hl2 <- station_lookup("HL2")

## 
##  casaultb/azmpdata status:
##  (Package ver: 0.2019.0.9100) Up to date
##  (Data ver:2021-01-14 ) is up to date

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

# To create the data frames with the same names only subset for the specified
#  station, run the following code on the R command line:
  
ssn <- hl2[[1]]
ssd <- hl2[[2]]
for (i in 1:length(ssn)) {
  assign(ssn[i], ssd[[i]])
}

ls(pattern = "Dis|Der|Phy|Zoo")

##  [1] "Derived_Annual_Stations"            "Derived_Occupations_Sections"       "Derived_Occupations_Stations"      
##  [4] "Discrete_Occupations_Sections"      "Discrete_Occupations_Stations"      "Phytoplankton_Annual_Stations"     
##  [7] "Phytoplankton_Occupations_Stations" "Zooplankton_Annual_Stations"        "Zooplankton_Occupations_Sections"  
## [10] "Zooplankton_Occupations_Stations"

head(Discrete_Occupations_Stations)

station	latitude	longitude	year	month	day	event_id	sample_id	depth	nominal_depth	chlorophyll	nitrate	phosphate	silicate	cruiseNumber	sea_temperature	salinity	sigmaTheta	descriptor
HL2	44.265	-63.3175	1999	1	13	18VA99666_99666001	99666001_201201	1	1	0.50703	4.7615	0.6015	5.4685	NA	NA	NA	NA	NA
HL2	44.265	-63.3175	1999	1	13	18VA99666_99666001	99666001_201202	5	5	0.54292	4.6810	0.6270	5.4350	NA	NA	NA	NA	NA
HL2	44.265	-63.3175	1999	1	13	18VA99666_99666001	99666001_201203	10	10	0.48010	4.7320	0.5595	5.5280	NA	NA	NA	NA	NA
HL2	44.265	-63.3175	1999	1	13	18VA99666_99666001	99666001_201204	20	20	0.41280	4.6800	0.5710	5.4635	NA	NA	NA	NA	NA
HL2	44.265	-63.3175	1999	1	13	18VA99666_99666001	99666001_201205	30	30	0.37242	4.9635	0.6310	5.8545	NA	NA	NA	NA	NA
HL2	44.265	-63.3175	1999	1	13	18VA99666_99666001	99666001_201206	40	40	0.37690	4.9945	0.6025	5.8175	NA	NA	NA	NA	NA

head of the Discrete_Occupations_Stations for only HL2 station data.

[EOGrady21]

This is great Jeff! Thanks for sharing!