README.md

In BigelowLab/azmpcfin: azmpdata - manage local data of DFO-MPO calanus database

azmpcfin

Requirements

• R v4.1+
• rlang
• dplyr
• readr
• sf

Installation

remotes::install_github("BigelowLab/azmpcfin")

Initial Use

The premise of this package is that data may be stored in a single location but accessed by many users. To achieve this resource-friendly goal and still simplified access for each user, we need to inform the package where the data resides. We do this by storing the path to the data location in each user’s home directory in a hidden text file, “\~/.azmpcfin”. That text file has just one line in it which contains the full path to the shared dataset. For example, the author’s contains mnt/ecocast/coredata/dfompo/AZMP_data which points to a shared network drive mounted on our linux platform.

When the package is first loaded (ala library(azmpcfin)) the existence of the file is check, and if missing a warning is issued.

You can create and populate that ~/.azmpcfin using a text editors, or you can create using the provided function set_data_path(). Here is how the author created his own…

library(azmpcfin)
azmpcfin::set_data_path("/mnt/ecocast/coredata/dfompo/AZMP_data")

That’s it. If you ever move the data you’ll have to modify the contents of this hidden text file.

Read the calanus data

suppressPackageStartupMessages({
  library(dplyr)
  library(azmpcfin)
})

x <- read_calanus()
glimpse(x)

## Rows: 7,802
## Columns: 30
## $ region                   <chr> "QC", "QC", "QC", "QC", "QC", "QC", "QC", "QC…
## $ transect                 <chr> "TSI", "TSI", "TSI", "TESL", "TESL", "TESL", …
## $ station                  <chr> "TSI3", "TSI5", "TSI6", "TESL1", "TESL2", "TE…
## $ year                     <dbl> 2000, 2000, 2000, 2000, 2000, 2000, 2000, 200…
## $ month                    <dbl> 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1…
## $ day                      <dbl> 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 6, …
## $ time                     <time> 22:55:00, 19:17:00, 17:28:00, 14:21:00, 15:4…
## $ timezone                 <chr> "UTC", "UTC", "UTC", "UTC", "UTC", "UTC", "UT…
## $ longitude                <dbl> -66.22983, -66.27050, -66.27500, -68.48500, -…
## $ latitude                 <dbl> 49.55117, 49.88333, 50.05333, 48.57583, 48.62…
## $ depth                    <dbl> 340, 276, 121, 38, 225, 331, 339, 341, 149, 3…
## $ mesh_size                <dbl> 202, 202, 202, 202, 202, 202, 202, 202, 202, …
## $ calanus_finmarchicus_i   <dbl> 223.02556, 178.40076, 711.74097, 387.92602, 9…
## $ calanus_finmarchicus_ii  <dbl> 223.02556, 356.80153, 1245.54670, 77.58520, 0…
## $ calanus_finmarchicus_iii <dbl> 1115.127790, 1427.206117, 711.740970, 232.755…
## $ calanus_finmarchicus_iv  <dbl> 4460.511161, 1962.408410, 1067.611456, 439.64…
## $ calanus_finmarchicus_v   <dbl> 35015.01262, 14093.66040, 1067.61146, 51.7234…
## $ calanus_finmarchicus_vi  <dbl> 1784.20446, 178.40076, 355.87049, 51.72347, 3…
## $ calanus_glacialis_i      <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ calanus_glacialis_ii     <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ calanus_glacialis_iii    <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ calanus_glacialis_iv     <dbl> 0.00000, 0.00000, 177.93524, 0.00000, 0.00000…
## $ calanus_glacialis_v      <dbl> 446.05112, 178.40076, 0.00000, 0.00000, 452.7…
## $ calanus_glacialis_vi     <dbl> 1115.12779, 535.20229, 0.00000, 0.00000, 1448…
## $ calanus_hyperboreus_i    <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ calanus_hyperboreus_ii   <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
## $ calanus_hyperboreus_iii  <dbl> 0.000000, 0.000000, 0.000000, 0.000000, 0.000…
## $ calanus_hyperboreus_iv   <dbl> 8697.996764, 1962.408410, 177.935243, 0.00000…
## $ calanus_hyperboreus_v    <dbl> 10482.20123, 3389.61453, 177.93524, 25.86173,…
## $ calanus_hyperboreus_vi   <dbl> 3122.35781, 1070.40459, 0.00000, 0.00000, 181…

BigelowLab/azmpcfin documentation built on March 19, 2022, 2:23 a.m.