docs/nuseds-adult-salmon-escapement-data.md

In jimtyhurst/salmonstats: Functions to Explore, Analyze, and Visualize Open Data about Salmon

NuSEDS Adult Salmon Escapement Data: Exploratory Data Analysis

Jim Tyhurst 2019-03-07

• Configuration
• New Salmon Escapement Database System (NuSEDS)
• MAX_ESTIMATE
• References

🔻 Work in Process … 🔺

Source code at: nuseds-adult-salmon-escapement-data.Rmd

Configuration

library(salmonstats)
library(descriptr)
library(tidyverse)

New Salmon Escapement Database System (NuSEDS)

NuSEDS is the Pacific Region’s centralized Oracle database that holds adult salmon escapement data. About 10,000 salmon spawning sites in DFO Pacific Region have been observed 0 to 10 times per year for 6 species for nearly 100 years (poorly before 1948). Data is aggregated within year; the raw data is largely on paper.

• zip file containing NUSEDS_20180416.csv http://www.pac.dfo-mpo.gc.ca/od-ds/science/sed-des/NUSEDS_20180416.zip
• meta data https://open.canada.ca/data/en/dataset/c48669a3-045b-400d-b730-48aafe8c5ee6

ns18 <- get_nused_data()
#> Parsed with column specification:
#> cols(
#>   .default = col_character(),
#>   ANALYSIS_YR = col_double(),
#>   ESCAPEMENT_ANALYST = col_logical(),
#>   INDEX_YN = col_logical(),
#>   RELIABILITY = col_logical(),
#>   NO_INSPECTIONS_USED = col_double(),
#>   START_SPAWN_DT_TO = col_logical(),
#>   END_SPAWN_DT_TO = col_logical(),
#>   MAX_ESTIMATE = col_double(),
#>   NATURAL_ADULT_SPAWNERS = col_logical(),
#>   NATURAL_JACK_SPAWNERS = col_logical(),
#>   NATURAL_SPAWNERS_TOTAL = col_logical(),
#>   ADULT_BROODSTOCK_REMOVALS = col_logical(),
#>   JACK_BROODSTOCK_REMOVALS = col_logical(),
#>   TOTAL_BROODSTOCK_REMOVALS = col_logical(),
#>   OTHER_REMOVALS = col_logical(),
#>   TOTAL_RETURN_TO_RIVER = col_logical(),
#>   UNSPECIFIED_RETURNS = col_double(),
#>   ENUMERATION_METHOD4 = col_logical(),
#>   ENUMERATION_METHOD5 = col_logical(),
#>   ENUMERATION_METHOD6 = col_logical()
#>   # ... with 14 more columns
#> )
#> See spec(...) for full column specifications.
#> Warning: 195129 parsing failures.
#>  row                 col           expected      actual                                            file
#> 1176 UPDATED_DTT         1/0/T/F/TRUE/FALSE 26/04/2006  '~/data/salmon/NuSEDS-2018/NUSEDS_20180416.csv'
#> 1764 ENUMERATION_METHOD4 1/0/T/F/TRUE/FALSE Helicopter  '~/data/salmon/NuSEDS-2018/NUSEDS_20180416.csv'
#> 2342 ENUMERATION_METHOD4 1/0/T/F/TRUE/FALSE Spot Checks '~/data/salmon/NuSEDS-2018/NUSEDS_20180416.csv'
#> 2489 ENUMERATION_METHOD4 1/0/T/F/TRUE/FALSE Spot Checks '~/data/salmon/NuSEDS-2018/NUSEDS_20180416.csv'
#> 3776 ENUMERATION_METHOD4 1/0/T/F/TRUE/FALSE Helicopter  '~/data/salmon/NuSEDS-2018/NUSEDS_20180416.csv'
#> .... ................... .................. ........... ...............................................
#> See problems(...) for more details.
dim(ns18)
#> [1] 392790     64

descriptr::ds_screener(ns18)
#> --------------------------------------------------------------------------------
#> |       Column Name       |  Data Type  |  Levels  |  Missing  |  Missing (%)  |
#> --------------------------------------------------------------------------------
#> |          AREA           |  character  |    NA    |     4     |       0       |
#> |        WATERBODY        |  character  |    NA    |     0     |       0       |
#> |      GAZETTED_NAME      |  character  |    NA    |  157284   |     40.04     |
#> |      LOCAL_NAME_1       |  character  |    NA    |   46126   |     11.74     |
#> |      LOCAL_NAME_2       |  character  |    NA    |  266280   |     67.79     |
#> |      WATERSHED_CDE      |  character  |    NA    |   15815   |     4.03      |
#> |      WATERBODY_ID       |  character  |    NA    |   16643   |     4.24      |
#> |         RAB_CDE         |  character  |    NA    |   5452    |     1.39      |
#> |       POPULATION        |  character  |    NA    |     0     |       0       |
#> |        RUN_TYPE         |  character  |    NA    |  253842   |     64.63     |
#> |         SPECIES         |  character  |    NA    |     0     |       0       |
#> |       ANALYSIS_YR       |   numeric   |    NA    |     0     |       0       |
#> |        START_DTT        |  character  |    NA    |  267449   |     68.09     |
#> |         END_DTT         |  character  |    NA    |  278914   |     71.01     |
#> |   ESCAPEMENT_ANALYST    |   logical   |    NA    |  392790   |      100      |
#> |        ACCURACY         |  character  |    NA    |     0     |       0       |
#> |        PRECISION        |  character  |    NA    |     0     |       0       |
#> |        INDEX_YN         |   logical   |    NA    |  392790   |      100      |
#> |       RELIABILITY       |   logical   |    NA    |  392790   |      100      |
#> |     ESTIMATE_STAGE      |  character  |    NA    |     0     |       0       |
#> | ESTIMATE_CLASSIFICATION |  character  |    NA    |     4     |       0       |
#> |   NO_INSPECTIONS_USED   |   numeric   |    NA    |  344519   |     87.71     |
#> |     ESTIMATE_METHOD     |  character  |    NA    |     0     |       0       |
#> | STREAM_ARRIVAL_DT_FROM  |  character  |    NA    |  320267   |     81.54     |
#> |  STREAM_ARRIVAL_DT_TO   |  character  |    NA    |  377118   |     96.01     |
#> |   START_SPAWN_DT_FROM   |  character  |    NA    |  296839   |     75.57     |
#> |    START_SPAWN_DT_TO    |   logical   |    NA    |  392790   |      100      |
#> |   PEAK_SPAWN_DT_FROM    |  character  |    NA    |  294247   |     74.91     |
#> |    PEAK_SPAWN_DT_TO     |  character  |    NA    |  374421   |     95.32     |
#> |    END_SPAWN_DT_FROM    |  character  |    NA    |  300479   |     76.5      |
#> |     END_SPAWN_DT_TO     |   logical   |    NA    |  392790   |      100      |
#> |     ADULT_PRESENCE      |  character  |    NA    |    30     |     0.01      |
#> |      JACK_PRESENCE      |  character  |    NA    |   39515   |     10.06     |
#> |      MAX_ESTIMATE       |   numeric   |    NA    |  246758   |     62.82     |
#> | NATURAL_ADULT_SPAWNERS  |   logical   |    NA    |  390568   |     99.43     |
#> |  NATURAL_JACK_SPAWNERS  |   logical   |    NA    |  386904   |     98.5      |
#> | NATURAL_SPAWNERS_TOTAL  |   logical   |    NA    |  390972   |     99.54     |
#> |ADULT_BROODSTOCK_REMOVALS|   logical   |    NA    |  389432   |     99.15     |
#> |JACK_BROODSTOCK_REMOVALS |   logical   |    NA    |  389679   |     99.21     |
#> |TOTAL_BROODSTOCK_REMOVALS|   logical   |    NA    |  389120   |     99.07     |
#> |     OTHER_REMOVALS      |   logical   |    NA    |  391016   |     99.55     |
#> |  TOTAL_RETURN_TO_RIVER  |   logical   |    NA    |  392373   |     99.89     |
#> |   UNSPECIFIED_RETURNS   |   numeric   |    NA    |  280786   |     71.49     |
#> |   ENUMERATION_METHOD1   |  character  |    NA    |  356438   |     90.75     |
#> |   ENUMERATION_METHOD2   |  character  |    NA    |  383828   |     97.72     |
#> |   ENUMERATION_METHOD3   |  character  |    NA    |  390376   |     99.39     |
#> |   ENUMERATION_METHOD4   |   logical   |    NA    |  392790   |      100      |
#> |   ENUMERATION_METHOD5   |   logical   |    NA    |  392790   |      100      |
#> |   ENUMERATION_METHOD6   |   logical   |    NA    |  392790   |      100      |
#> |  NATURAL_ADULT_FEMALES  |   logical   |    NA    |  391369   |     99.64     |
#> |   NATURAL_ADULT_MALES   |   logical   |    NA    |  391359   |     99.64     |
#> |    EFFECTIVE_FEMALES    |   logical   |    NA    |  391343   |     99.63     |
#> |   WEIGHTED_PCT_SPAWN    |   logical   |    NA    |  391409   |     99.65     |
#> |  OTHER_ADULT_REMOVALS   |   logical   |    NA    |  391867   |     99.77     |
#> |   OTHER_JACK_REMOVALS   |   logical   |    NA    |  391858   |     99.76     |
#> |   TOT_ADULT_RET_RIVER   |   logical   |    NA    |  392685   |     99.97     |
#> |   TOT_JACK_RET_RIVER    |   logical   |    NA    |  392306   |     99.88     |
#> |      JUV_PRES_TYP       |   logical   |    NA    |  392466   |     99.92     |
#> |         ACT_ID          |   numeric   |    NA    |     0     |       0       |
#> |         POP_ID          |   numeric   |    NA    |     0     |       0       |
#> |         SPC_ID          |   numeric   |    NA    |     0     |       0       |
#> |         GFE_ID          |   numeric   |    NA    |     0     |       0       |
#> |       CREATED_DTT       |  character  |    NA    |     0     |       0       |
#> |       UPDATED_DTT       |   logical   |    NA    |  392790   |      100      |
#> --------------------------------------------------------------------------------
#> 
#>  Overall Missing Values           15495270 
#>  Percentage of Missing Values     61.64 %
#>  Rows with Missing Values         392790 
#>  Columns With Missing Values      51

MAX_ESTIMATE

The maximum estimated number taken from: NATURAL_ADULT_SPAWNERS, NATURAL_JACK_SPAWNERS, NATURAL_SPAWNERS_TOTAL, ADULT_BROODSTOCK_REMOVALS, JACK_BROODSTOCK_REMOVALS, TOTAL_BROODSTOCK_REMOVALS, OTHER_REMOVALS, TOTAL_RETURN_TO_RIVER, UNSPECIFIED_RETURNS.

References

Source code: nuseds-adult-salmon-escapement-data.Rmd

NUSEDS_20180416.csv http://www.pac.dfo-mpo.gc.ca/od-ds/science/sed-des/NUSEDS_20180416.zip

NuSEDS meta data https://open.canada.ca/data/en/dataset/c48669a3-045b-400d-b730-48aafe8c5ee6

jimtyhurst/salmonstats documentation built on May 23, 2019, 2:47 p.m.