1_nuseds_collation
Bruno S. Carturan, Eric Hertz, Stephanie J. Peacock
2025-01-24
The goal of the script is to merge the two constituent datasets
all_areas_nuseds (referred to as
NUSEDS) and
conservation_unit_system_sites (referred to as
CUSS) so each time series in NUSEDS
(i.e., fish counts associated to a unique populations, characterized by
a unique IndexId/POP_ID &
GFE_ID association) can be attributed to a unique
conservation unit (CU) in CUSS (characterized by
CU_NAME and FULL_CU_IN). But there are
multiple inconsistencies between the two datasets that lead to discard a
significant amount of data points in NUSEDS, unless
fixes are implemented. This script is a attempt to implement such
fixes.
The dataset version corresponding to this script is:
Fisheries and Oceans Canada. 2024. NuSEDS - New Salmon Escapement Database System. Pacific Biological Station. Retrieved January 22, 2024, from https://open.canada.ca/data/en/dataset/c48669a3-045b-400d-b730-48aafe8c5ee6.
1 Import datasets
The NUSEDS (all_areas_nuseds) and CUSS (conservation_unit_system_sites) datasets are imported and duplicated rows are removed. The columns considered for NuSEDS are related to the population, location, fish counts and year of assessment:
## [1] "File imported: all_areas_nuseds_2025-02-21.csv ; Date modified: 2025-02-21 09:28:25.445271"## [1] "File imported: conservation_unit_system_sites_2025-02-20.csv ; Date modified: 2025-02-20 15:55:05.475634"The list of conservation units (CUs) as shown in the Pacific Salmon
Explorer (PSE) is imported.
The columns cu_name_pse and cu_name_dfo
correspond to CU_NAME in CUSS,
cu_index corresponds to FULL_CU_INDEX.
## region species_name species_qualified cuid cu_name_pse
## 1 Skeena Lake sockeye SEL 171 Alastair
## 2 Skeena Lake sockeye SEL 174 Ecstall/Lower
## 3 Skeena Lake sockeye SEL 175 Johnston
## 4 Skeena Lake sockeye SEL 176 Kitsumkalum
## 5 Skeena Lake sockeye SEL 177 Lakelse
## 6 Skeena Lake sockeye SEL 172 Mcdonell/Dennis/Aldrich
## cu_name_dfo cu_index
## 1 Alastair SEL-20-01
## 2 Ecstall/Lower SEL-20-04
## 3 Johnston SEL-20-05
## 4 Kitsumkalum SEL-20-06
## 5 Lakelse SEL-20-07
## 6 Aldrich SEL-20-02The DFO file of the stream locations and coordinates (emailed from Wu
Zhipeng, DFO, 09/04/2024) is imported. The columns NME and
ID correspond to SYSTEM_SITE and
GFE_ID in CUSS, respectively.
## # A tibble: 6 × 4
## NME ID X_LONGT Y_LAT
## <chr> <dbl> <chr> <chr>
## 1 STANLEY CREEK 1557 -132.691420767338 53.9746116925906
## 2 DAVIDSON CREEK 1558 -132.682181062338 53.9544135568635
## 3 NADEN RIVER 1559 -132.672499482506 53.9448571061959
## 4 LIGNITE CREEK 1560 -132.601901312242 53.97114945092
## 5 OTUN RIVER 1561 -132.260106013 54.07328672
## 6 BILL CREEK 1562 -132.395009112518 53.7494926521361The DFO hatchery data file (emailed from Brock Ramshaw, DFO,
03/07/2023) is imported because it contains GFE_ID (i.e.,
STOCK_GFE_ID and REL_GFE_ID) and coordinates
that are missing in the above DFO stream location file:
## # A tibble: 6 × 8
## STOCK_GFE_ID STOCK_WATERBODY_NAME STOCK_LATITUDE STOCK_LONGITUDE REL_GFE_ID
## <dbl> <chr> <dbl> <dbl> <dbl>
## 1 1001 TANKEEAH RIVER 52.3 -128. 1001
## 2 1001 TANKEEAH RIVER 52.3 -128. 1001
## 3 1001 TANKEEAH RIVER 52.3 -128. 11611
## 4 1001 TANKEEAH RIVER 52.3 -128. 11611
## 5 1001 TANKEEAH RIVER 52.3 -128. 1001
## 6 1001 TANKEEAH RIVER 52.3 -128. 1001
## # ℹ 3 more variables: REL_WATERBODY_NAME <chr>, REL_LATITUDE <dbl>,
## # REL_LONGITUDE <dbl>2 Initial modifications
We remove from NUSEDS and CUSS data
related to steelhead, Atlantic salmon and Kokanee salmon, corresponding
to 967 rows and 133 populations (POP_ID) in
NUSEDS and 0 in CUSS.
We create the column IndexId, which the the combination
of the species acronym (i.e., CO, CM, CN, PKO, PKE, SX) and
POP_ID:
## [1] "CN_48442" "CO_590" "CO_1794" "CO_1844" "CO_2172" "PKE_51264"We create the column MAX_ESTIMATE which is the maximum
value of the fish count columns:
## [1] "NATURAL_ADULT_SPAWNERS" "NATURAL_JACK_SPAWNERS"
## [3] "NATURAL_SPAWNERS_TOTAL" "ADULT_BROODSTOCK_REMOVALS"
## [5] "JACK_BROODSTOCK_REMOVALS" "TOTAL_BROODSTOCK_REMOVALS"
## [7] "OTHER_REMOVALS" "TOTAL_RETURN_TO_RIVER"3 Fixes on NUSEDS and CUSS
The major issue in NuSEDS is the discrepancy between the two
datasets. Normally, there should be the same population references
(i.e., unique IndexId/POP_ID &
GFE_ID combinations). But there are 11568 unique population
references in NUSEDS and only 7145 in
CUSS. Additionally, there are 4428 references in
NUSEDS that are not in CUSS and 5 that
are in CUSS but not in NUSEDS. This
section consists in solving these discrepancies so that the same
population references are present in both datasets.
3.1 Duplicated rows
There are 60 duplicated rows in NUSEDS when considering the following fields:
## [1] "SPECIES" "POP_ID"
## [3] "GFE_ID" "Year"
## [5] "NATURAL_ADULT_SPAWNERS" "NATURAL_JACK_SPAWNERS"
## [7] "NATURAL_SPAWNERS_TOTAL" "ADULT_BROODSTOCK_REMOVALS"
## [9] "JACK_BROODSTOCK_REMOVALS" "TOTAL_BROODSTOCK_REMOVALS"
## [11] "OTHER_REMOVALS" "TOTAL_RETURN_TO_RIVER"## SPECIES POP_ID GFE_ID Year MAX_ESTIMATE
## 1 Sockeye 44565 2489 1997 NA
## 2 Sockeye 44565 2489 1998 NA
## 3 Sockeye 44565 2489 2001 NA
## 4 Sockeye 44565 2489 2002 NA
## 5 Coho 44567 2489 1995 NA
## 6 Coho 44567 2489 1996 NA
## 7 Coho 44567 2489 1997 1
## 8 Coho 44567 2489 1998 12
## 9 Coho 44567 2489 1999 NA
## 10 Coho 44567 2489 2000 NA
## 11 Coho 44567 2489 2001 NA
## 12 Coho 44567 2489 2002 NA
## 13 Coho 44567 2489 2003 NA
## 14 Coho 44567 2489 2004 NA
## 15 Coho 44567 2489 2005 NA
## 16 Coho 44567 2489 2007 NA
## 17 Coho 44567 2489 2008 NA
## 18 Coho 44567 2489 2009 NA
## 19 Coho 44567 2489 2010 NA
## 20 Coho 44567 2489 2011 NA
## 21 Coho 44567 2489 2012 NA
## 22 Coho 44567 2489 2013 NA
## 23 Coho 44567 2489 2014 NA
## 24 Coho 44567 2489 2015 NA
## 25 Coho 44567 2489 2016 NA
## 26 Coho 44567 2489 2017 NA
## 27 Coho 44567 2489 2018 NA
## 28 Coho 44567 2489 2019 NA
## 29 Pink 44569 2489 1997 NA
## 30 Pink 44569 2489 1998 NA
## 31 Pink 44569 2489 2001 NA
## 32 Pink 44569 2489 2002 NA
## 33 Chum 44571 2489 1995 NA
## 34 Chum 44571 2489 1996 NA
## 35 Chum 44571 2489 1997 126
## 36 Chum 44571 2489 1998 93
## 37 Chum 44571 2489 1999 NA
## 38 Chum 44571 2489 2000 NA
## 39 Chum 44571 2489 2001 NA
## 40 Chum 44571 2489 2002 NA
## 41 Chum 44571 2489 2003 NA
## 42 Chum 44571 2489 2004 NA
## 43 Chum 44571 2489 2005 NA
## 44 Chum 44571 2489 2008 NA
## 45 Chum 44571 2489 2009 NA
## 46 Chum 44571 2489 2010 NA
## 47 Chum 44571 2489 2011 NA
## 48 Chum 44571 2489 2012 NA
## 49 Chum 44571 2489 2013 NA
## 50 Chum 44571 2489 2014 NA
## 51 Chum 44571 2489 2015 NA
## 52 Chum 44571 2489 2016 NA
## 53 Chum 44571 2489 2017 NA
## 54 Chum 44571 2489 2018 NA
## 55 Chum 44571 2489 2019 NA
## 56 Chinook 44573 2489 1997 NA
## 57 Chinook 44573 2489 1998 NA
## 58 Chinook 44573 2489 2001 NA
## 59 Chinook 44573 2489 2002 NA
## 60 Chum 51316 1174 2011 NAThese duplicated rows in NUSEDS are removed.
For CUSS, 0 duplicated rows are found:
## [1] MAP_LABEL GFE_ID SYSTEM_SITE
## [4] GFE_TYPE SPECIES_QUALIFIED Y_LAT
## [7] X_LONGT FAZ_ACRO MAZ_ACRO
## [10] JAZ_ACRO CU_NAME CU_ACRO
## [13] CU_LAT CU_LONGT CU_TYPE
## [16] CU_INDEX FULL_CU_IN SBJ_ID
## [19] POP_ID IS_INDICATOR CMNTS
## [22] EFFECTIVE_DT WATERSHED_CDE FWA_WATERSHED_CDE
## [25] coordinates_changed SPECIES species_acronym_ncc
## [28] IndexId
## <0 rows> (or 0-length row.names)These rows (if any) are removed as well.
3.2 Conflictual counts in NUSEDS
There are 1 instances where multiple MAX_ESTIMATE values
are available in a same Year for a given population:
## IndexId GFE_ID Year MAX_ESTIMATE
## 1 CN_46447 241 2016 494.000000
## 2 CN_46447 241 2016 475.414455For each of these cases, we keep the observation with the maximum
MAX_ESTIMATE value and remove the other(s) from
NUSEDS:
## IndexId GFE_ID Year MAX_ESTIMATE ESTIMATE_CLASSIFICATION
## 1 CN_46447 241 2016 475.414455 RELATIVE ABUNDANCE (TYPE-4)
## 2 CN_46447 241 2016 494.000000 RELATIVE ABUNDANCE (TYPE-4)
## ESTIMATE_METHOD remove
## 1 Calibrated Time Series TRUE
## 2 Calibrated Time Series FALSE3.3 Remove the IndexId & GFE_ID time series in NUSEDS with only NAs and/or 0s
We remove these time series to reduce the amount of cleaning to do after. There is the option to remove series with (1) only NAs and 0s or (2) only NAs.
Decision made:
## [1] "Time series uniqually made of NAs are removed (those also containing 0s are kept)."This procedure removes 101944 rows in NUSEDS, corresponding to 24.6% of the original dataset.
The data removed concerns 4424 time series, which are referenced in
removed_all:
## IndexId GFE_ID dataset comment
## 1 PKO_53054 1155 NUSEDS Only NAs for MAX_ESTIMATE
## 2 PKE_45947 413 NUSEDS Only NAs for MAX_ESTIMATE
## 3 CN_50404 1058 NUSEDS Only NAs for MAX_ESTIMATE
## 4 CM_43463 1745 NUSEDS Only NAs for MAX_ESTIMATE
## 5 CM_50368 1051 NUSEDS Only NAs for MAX_ESTIMATE
## 6 CN_44159 1907 NUSEDS Only NAs for MAX_ESTIMATENote that we do not remove these series in CUSS at this stage because they could be alternative series for the series in NUSEDS that do not appear in CUSS. It is only once series in NUSEDS absent in CUSS were found alternative series for, that we remove series in CUSS that have only NAs and/or 0s in NUSEDS.
3.4 Fix time series in CUSS that are not in NUSEDS
Look for each time series in CUSS (i.e., unique
IndexId & GFE_ID association) and:
check if there are
IndexIdassociated to multiple locations (i.e.,GFE_ID); if yes: trouble shoot manually because this should not happen:IndexIdshould be associated to one unique location.else look if there is a time series with the same
IndexId&GFE_IDin NUSEDS; if yes: all good :-)else: that could be due to the wrong attribution of either (i) the
IndexIdor (ii) theGFE_ID. The rest of the code looks for potential alternative series in NUSEDS with either a differentIndexId(but with the same species) or a differentGFE_ID. Alternative series identified NOT present in CUSS are kept, the ones present are not considered.
The procedure returns a simple data frame with the
IndexId & GFE_ID series concerned and
associated comment and eventual potential alternative series that have
to be checked manually after:
## i IndexId GFE_ID in_cuss in_nused
## 1 23 PKE_40049 1211 yes no
## 2 32 PKE_52934 1143 yes no
## 3 60 PKE_40149 1221 yes no
## 4 62 PKE_50494 812 yes no
## 5 112 PKO_46644 262 yes no
## 6 176 CN_46842 285 yes no
## comment
## 1 There is no alternative series in NUSEDS
## 2 There is no alternative series in NUSEDS
## 3 There is no alternative series in NUSEDS
## 4 There is no alternative series in NUSEDS
## 5 There is no alternative series in NUSEDS
## 6 Alternative series: CN_46842 & 2463, CN_46841 & 285There are 247 out of 7145 time series in CUSS that are not present in NUSEDS (i.e., 3.5%), and the vast majority of them do not have an alternative series in NUSEDS:
table(trackRecord$comment[cond])##
## Alternative series: CN_46842 & 2463, CN_46841 & 285
## 1
## Alternative series: PKE_54793433 & 1490
## 1
## Alternative series: SX_47954 & 21
## 1
## In CUSS: there are multiple GFE_IDs for CN_7479 : 133, 2373
## 1
## There is no alternative series in NUSEDS
## 2433.4.1 Alternative series present
The goal here is to go over all the cases where alternative series are available. The title of the figures below shows the focal series that is in CUSS but not in NUSEDS. The series on the top left corner are potential alternative series (i.e., they are present in NUSEDS but not in CUSS).
comment <- "Alternative series:"
trackRecord_cuss_alternative <- trackRecord[grepl(comment,trackRecord$comment),]## [1] 3## i IndexId GFE_ID in_cuss in_nused
## 1 176 CN_46842 285 yes no
## 2 3489 PKE_42409 1490 yes no
## 3 6685 SX_7763 21 yes no
## comment
## 1 Alternative series: CN_46842 & 2463, CN_46841 & 285
## 2 Alternative series: PKE_54793433 & 1490
## 3 Alternative series: SX_47954 & 21
The focal CUSS time series CN_46842 & GFE_ID =
285 corresponds to the CU_NAME:
## [1] "MIDDLE FRASER RIVER_SP_1.3"The two alternative time series are noted as two different runs,
according to NUSEDS’s POPULATION:
## [1] "Chilcotin River (Williams Lake Area) Chinook Run 2"
## [2] "Chilcotin River (Williams Lake Area) Chinook Run 1"Below are the focal and alternative location, and the distance
between the two GFE_ID is 0 km:
## SYSTEM_SITE GFE_ID X_LONGT Y_LAT
## 1 CHILCOTIN RIVER - LOWER 2463 -122.401309 51.7399528
## 2 CHILCOTIN RIVER 285 -122.401309 51.7399528Decision: It was decided to merge the two time series CN_46842 & GFE_ID = 2463 and CN_46841 & GFE_ID = 285 to the series CN_46842 & GFE_ID = 285 in NUSEDS because there is only one timing for this Middle Fraser River (Spring 5-2) Chinook CU and the two series are complementary.
Decision: we replace PKE_54793433 & GFE_ID = 1490 by PKE_42409 & GFE_ID = 1490 in NUSEDS.
The two time series have the same CU_NAME in
CUSS:
## SX_7763 SX_47954
## "WIDGEON" "WIDGEON"## [1] "75 rows were edited in all_areas_nuseds at the following fields: SPECIES, POP_ID, species_acronym_ncc, IndexId"Decision: Replace SX_47954 & GFE_ID = 21 by SX_7763 & GFE_ID = 21 in NUSEDS.
3.4.2 Alternative series not present in NUSEDS
The goal is to remove these IndexId &
GFE_ID references from CUSS and to specify
if they were simply not present in the original NUSEDS
or only contained NAs and/or 0s.
comment <- "There is no alternative series in NUSEDS"
trackRecord_cuss_noAlernative <- trackRecord[grepl(comment,trackRecord$comment),]## [1] 243## IndexId GFE_ID in_cuss in_nused comment
## 1 PKE_40049 1211 yes no There is no alternative series in NUSEDS
## 2 PKE_52934 1143 yes no There is no alternative series in NUSEDS
## 3 PKE_40149 1221 yes no There is no alternative series in NUSEDS
## 4 PKE_50494 812 yes no There is no alternative series in NUSEDS
## 5 PKO_46644 262 yes no There is no alternative series in NUSEDS
## 6 CM_3261 2637 yes no There is no alternative series in NUSEDS242 of the 243 IndexId & GFE_ID
references were removed previously from NUSEDS because
they contained only NAs and/or 0s. Only the following reference was not
in NUSEDS initially:
## GFE_ID SYSTEM_SITE SPECIES_QUALIFIED CU_NAME FULL_CU_IN
## 1 150 SEEBACH CREEK SER UPPER FRASER SER-063.4.3 Multiple GFE_IDs for a same IndexId (POP_ID) in CUSS
There should not be any IndexId associated to multiple
GFE_ID (it is a MANY TO ONE relationship).
comment <- "In CUSS: there are multiple GFE_IDs for"
trackRecord_cuss_multi_fgeid <- trackRecord[grepl(comment,trackRecord$comment),]This happens for 2 populations:
## i IndexId GFE_ID in_cuss in_nused
## 1 1169 CN_7479 133 yes no
## 2 1169 CN_7479 2373 yes yes
## 3 6288 SX_45525 2444 yes yes
## 4 6288 SX_45525 303 yes yes
## comment
## 1 In CUSS: there are multiple GFE_IDs for CN_7479 : 133, 2373
## 2 In CUSS: there are multiple GFE_IDs for CN_7479 : 133, 2373
## 3 In CUSS: there are multiple GFE_IDs for SX_45525 : 2444, 303
## 4 In CUSS: there are multiple GFE_IDs for SX_45525 : 2444, 303
The figure above only show the time series present in NUSEDS. The other time series is removed from CUSS.
These two time series of this CU (CU_NAME =
NADINA/FRANCOIS-EARLY SUMMER TIMING, NADINA/FRANCOIS-EARLY SUMMER
TIMING) should have a different IndexId
(i.e. POP_ID). We keep them as is and do not make any
change to NUSEDS and CUSS.
3.5 Fix populations in NUSEDS that are not in CUSS
The goal is to look for each IndexId &
GFE_ID series in NUSEDS that are not in
CUSS and to:
- Look if there are alternative series in NUSEDS that are also present in CUSS
if not, add the
IndexId&GFE_IDreference in CUSSif yes, see if the alternative series can be merged; if not, add the
IndexId&GFE_IDreference to CUSS
- Use the PSE’s CUs’ shape files for those without alternative series.
There are 242 IndexId & GFE_ID
references in NUSEDS that are not present in
CUSS, for instance:
## IndexId GFE_ID nb_dataPt alternative_IndexId alternative_GFE_ID
## 1 CM_1622 11 2 none none
## 2 CM_2434 4 11 none none
## 3 CM_297 14 1 CM_47925 none
## 4 CM_3212 2487 4 none none
## 5 CM_3305 11486 15 none 11485
## 6 CM_3305 11487 2 none 114853.5.1 Alternative IndexId (POP_ID) AND no alternative GFE_ID
The section concerns focal IndexId &
GFE_ID time series in NUSEDS that are not
in CUSS and for which there are alternative series in
CUSS with the same IndexId but a different
GFE_ID. The goal is to compare the focal vs. the
alternative time series and take the following actions:
if the time series are 100% complementary: merge them (i.e., edit
IndexIdin NUSEDS)if the time series are 100% duplicated: remove the focal series in NUSEDS
if the series are partially conflictual or if there are multiple potential alternative series: trubble shoot manually
There are 12 time series concerned:
## IndexId GFE_ID nb_dataPt alternative_IndexId
## 1 CM_297 14 1 CM_47925
## 2 CN_3331 1156 13 CN_53068 ; CN_53069
## 3 CN_3334 1194 36 CN_51519 ; CN_51518
## 4 CN_39983 1204 7 CN_39984
## 5 CN_7751 1208 1 CN_40023 ; CN_40024
## 6 CN_7809 442 18 CN_48442
## 7 CO_7776 2243 5 CO_3136
## 8 SX_3438 2434 6 SX_45085
## 9 SX_46279 224 5 SX_46278
## 10 SX_46308 227 14 SX_46309
## 11 SX_7639 26771 2 SX_7636
## 12 SX_7823 298 47 SX_46023The figures below show for each of these cases the decision made. The
figures also show the POPULATION of focal and alternative
IndexId. The i at the bottom left of each plot
is used after to reference the figures when fixing time series manually.
Several cases are set aside to be manually fixed after.
## IndexId GFE_ID complementary duplicate conflict decision nb_dataPt
## 1 CM_47925 14 100 0 0 NA 1
## [1] "***"
## IndexId GFE_ID complementary duplicate conflict decision nb_dataPt
## 1 CN_53068 1156 100 0 0 NA 13
## 2 CN_53069 1156 100 0 0 NA 13
## [1] "***"
## IndexId GFE_ID complementary duplicate conflict decision nb_dataPt
## 1 CN_51519 1194 90 0 10 NA 36
## 2 CN_51518 1194 100 0 0 NA 36
## [1] "***"
## IndexId GFE_ID complementary duplicate conflict decision nb_dataPt
## 1 CN_39984 1204 70 0 30 NA 7
## [1] "***"
## IndexId GFE_ID complementary duplicate conflict decision nb_dataPt
## 1 CN_40023 1208 100 0 0 NA 1
## 2 CN_40024 1208 0 0 100 NA 1
## [1] "***"
## IndexId GFE_ID complementary duplicate conflict decision nb_dataPt
## 1 CN_48442 442 100 0 0 NA 18
## [1] "***"
## [1] "Number of rows removed from dataframe = 5"
## IndexId GFE_ID complementary duplicate conflict decision nb_dataPt
## 1 CO_3136 2243 0 100 0 NA 5
## [1] "***"
## IndexId GFE_ID complementary duplicate conflict decision nb_dataPt
## 1 SX_45085 2434 0 30 70 NA 6
## [1] "***"
## IndexId GFE_ID complementary duplicate conflict decision nb_dataPt
## 1 SX_46278 224 0 0 100 NA 5
## [1] "***"
## IndexId GFE_ID complementary duplicate conflict decision nb_dataPt
## 1 SX_46309 227 40 40 20 NA 14
## [1] "***"
## IndexId GFE_ID complementary duplicate conflict decision nb_dataPt
## 1 SX_7636 26771 0 50 50 NA 2
## [1] "***"
## IndexId GFE_ID complementary duplicate conflict decision nb_dataPt
## 1 SX_46023 298 100 0 0 NA 47
## [1] "***"We now assess the cases set aside.
In the case i = 1 above, series CM_297 - 14 is merged to
the alternative series despite the potential mismatch in “Run” because
there is only one Chum CU in the Fraser. Its IndexId is change from
CM_297 to CM_47925 in NUSEDS.
In the case i = 2 above, series CN_3331 - 1156 was not
merged to any of the alternative series because of its unknown run
timing (see below). It is consequently removed from
NUSEDS.
## IndexId type POPULATION
## 1 CN_3331 focal Puntledge River Chinook (unknown timing)
## 2 CN_53068 alternative Puntledge River Spring Chinook
## 3 CN_53069 alternative Puntledge River Fall ChinookIn the case i = 3 above, series CN_3334 - 1194 was
initially going to be merged to the alternative series with which is was
100% compatible. But is was decided to remove it from
NUSEDS because its run timing is unknown:
## IndexId type POPULATION
## 1 CN_3334 focal Nanaimo River Chinook (unknown timing)
## 2 CN_51519 alternative Nanaimo River Fall Chinook
## 3 CN_51518 alternative Nanaimo River Summer ChinookIn the case i = 4 above, series CN_39983 - 1204 was not
merged to the alternative series because of different run timings:
## IndexId type POPULATION
## 1 CN_39983 focal Chemainus River Summer Chinook
## 2 CN_39984 alternative Chemainus River Fall ChinookIt was decided instead to associate the population CN_39983 to the CU
East Vancouver Island-Georgia Strait (Summer 4-1) in the PSE
because of the same run timing and the fact that the Chemainus river is
connected to this CU. The corresponding CU_NAME in
CUSS is:
## [1] "EAST VANCOUVER ISLAND-GEORGIA STRAIT_SU_0.3"The reference of the CN_39983 - 1204 time series is added to
CUSS. The CU-related fields in CUSS
are filled with the values corresponding to the above
CU_NAME. Here below is the row added to
CUSS:
## MAP_LABEL GFE_ID SYSTEM_SITE GFE_TYPE SPECIES_QUALIFIED Y_LAT
## 1 NA 1204 CHEMAINUS RIVER Stream CK 48.8979258
## X_LONGT FAZ_ACRO MAZ_ACRO JAZ_ACRO
## 1 -123.673181 EVI GStr EVI+GStr
## CU_NAME CU_ACRO CU_LAT
## 1 EAST VANCOUVER ISLAND-GEORGIA STRAIT_SU_0.3 EVIGStr-sum 49.5622666
## CU_LONGT CU_TYPE CU_INDEX FULL_CU_IN SBJ_ID POP_ID IS_INDICATOR CMNTS
## 1 -125.201122 Current 83 CK-83 NA 39983 <NA> <NA>
## EFFECTIVE_DT WATERSHED_CDE
## 1 <NA> 920-303500-00000-00000-0000-0000-000-000-000-000-000-000
## FWA_WATERSHED_CDE
## 1 920-302830-000000-000000-000000-000000-000000-000000-000000-000000-000000-000000-000000-000000-000000-000000-000000-000000-000000-000000-000000
## coordinates_changed SPECIES species_acronym_ncc IndexId
## 1 FALSE Chinook CN CN_39983In the case i = 5 above with the focal series CN_7751 -
1208, both alternative series belong to the same fall Chinook CU
(CU_NAME = EAST VANCOUVER ISLAND-COWICHAN AND
KOKSILAH_FA_0.x). The focal series is consequently deleted from
NUSEDS because its POPULATION indicates it
is a summer population, for which there is no CU in the PSE at this
location.
In the case i = 6 above, series CN_7809 - 442 can be
merged to the alternative series CN_48442 - 442 with which it is 100%
compatible. The run timing indicated in POPULATION in
NUSEDS are not incompatible:
## CN_7809
## "Okanagan River (Salmon Arm) Summer Chinook"
## CN_48442
## "Okanagan River (Salmon Arm) Chinook Run 1"However, we decide to merge the alternative time series to the focal one (i.e., change CN_48442 - 442 to CN_7809 - 442) instead of the contrary because the latter is longer and more recent. Consequently both NUSEDS and CUSS are edited.
## [1] "1 rows were edited in conservation_unit_system_sites at the following fields: POP_ID, SPECIES, species_acronym_ncc, IndexId"## [1] "4 rows were edited in all_areas_nuseds at the following fields: SPECIES, POPULATION, RUN_TYPE, POP_ID, species_acronym_ncc, IndexId"In the case i = 7 above, the focal series CO_7776 - 2243
is removed from NUSEDS because it is 100% duplicated
with the alternative series CO_3136 - 2243.
In the case i = 8 above, the focal series SX_3438 - 2434
has the POPULATION = Loftus Creek Late Sockeye, which
corresponds to the CU_NAME = “SHUSWAP COMPLEX-LATE TIMING”
in CUSS. We consequently do not merge the two series
but add the reference of the focal series in CUSS to
the SHUSWAP COMPLEX-LATE TIMING CU.
In the case i = 9 above, the focal series SX_46279 - 224
has the POPULATION = Cayenne Creek (Clearwater) Late
Sockeye, which does not correspond to any CU_NAME in
CUSS. The data cannot be merged to the alternative
series SX_46278 - 224 because of different run timing. It is
consequently deleted from NUSEDS.
In the case i = 10 above, the focal series SX_46308 -
227 has the POPULATION = Ross Creek (Salmon Arm) Early
Summer Sockeye, which corresponds to the CU_NAME = “SHUSWAP
COMPLEX-EARLY SUMMER TIMING” in CUSS. We consequently
do not merge the two series but add the reference of the focal series in
CUSS to the SHUSWAP COMPLEX-LATE TIMING CU.
In the case i = 11 above, the focal series SX_7639 -
26771 has the POPULATION = Four Mile Creek (Salmon Arm)
Late Sockeye, which corresponds to the CU_NAME = “SHUSWAP
COMPLEX-LATE TIMING” in CUSS. We consequently do not
merge the two series but add the reference of the focal series in
CUSS to the SHUSWAP COMPLEX-LATE TIMING CU.
In the case i = 12 above, the focal series SX_7823 - 298
is merged to the alternative series (indexId is changed
from SX_7823 to SX_46023 in NUSEDS) because the focal
POPULATION (= Ormond Creek (Prince George) Early Summer
Sockeye) is compatible with the alternative CU_NAME (=
FRASER-EARLY SUMMER TIMING).
## [1] "47 rows were edited in all_areas_nuseds at the following fields: SPECIES, POPULATION, RUN_TYPE, POP_ID, species_acronym_ncc, IndexId"Note that could be a mismatch between the alternative
POPULATION (= Ormond Creek (Prince George) Summer Sockeye)
and its its own CU_NAME (= FRASER-EARLY SUMMER TIMING)
(FULL_CU_IN = SEL-06-06), and could instead be better
associated with the CU with CU_NAME =
FRANCOIS/FRASER-SUMMER TIMING (FULL_CU_IN = SEL-06-07). We
are not making any change in that regard.
3.5.2 Alternative GFE_ID
The focal time series (i.e., a unique IndexId -
GFE_ID not in CUSS) are compared to
alternative series with a different GFE_ID and potentially
a different IndexId (but of the same species).
There are 64 time series concerned:
## IndexId GFE_ID nb_dataPt alternative_IndexId alternative_GFE_ID
## 1 CM_3305 11486 15 none 11485
## 2 CM_3305 11487 2 none 11485
## 3 CM_3305 11488 3 none 11485
## 4 CM_46984 2529 2 none 62
## 5 CM_47906 441 2 none 3
## 6 CM_47907 5 1 none 7
## 7 CM_47925 15 8 CM_47928 14
## 8 CM_47925 17 3 CM_47939 14
## 9 CM_47925 31516 8 none 14
## 10 CM_47925 31740 8 none 14
## 11 CM_50616 2618 8 none 824
## 12 CM_50616 446068199 1 none 824
## 13 CN_2178 129 5 CN_47189 2476
## 14 CN_3306 11486 38 none 11485
## 15 CN_3306 11487 3 none 11485
## 16 CN_3306 11488 4 none 11485
## 17 CN_3333 1194 3 CN_51519 ; CN_51518 23735
## 18 CN_44577 2518 1 CN_44599 2492
## 19 CN_46801 33103 1 none 281
## 20 CN_46891 2466 2 none 290
## 21 CN_46891 2467 5 none 290
## 22 CN_46892 2466 23 none 290
## 23 CN_47277 2464 46 none 142
## 24 CN_48448 19723 1 none 443
## 25 CN_50618 2618 8 none 824
## 26 CN_50618 446068199 1 none 824
## 27 CO_3303 11487 3 none 11485
## 28 CO_3303 11488 3 none 11485
## 29 CO_44539 129 5 CO_47183 2476
## 30 CO_44539 2451 14 none 2476
## 31 CO_46170 2453 2 CO_44736 213
## 32 CO_46170 2461 7 none 213
## 33 CO_46170 54282 5 none 213
## 34 CO_46170 54283 2 none 213
## 35 CO_46240 221 2 CO_46250 220
## 36 CO_46240 3477 2 none 220
## 37 CO_46582 1754239945 14 none 256
## 38 CO_46582 2049268617 21 none 256
## 39 CO_46582 33045 21 none 256
## 40 CO_46582 57041 6 none 256
## 41 CO_46582 63379 4 none 256
## 42 CO_46582 719256264 23 none 256
## 43 CO_46602 212716981 22 none 258
## 44 CO_46602 2746 6 CO_46632 258
## 45 CO_46632 261 9 none 2746
## 46 CO_46795 1921661712 15 none 281
## 47 CO_46795 33103 16 none 281
## 48 CO_46835 2463 2 none 285
## 49 CO_47183 2451 2 none 129
## 50 CO_50612 2618 6 none 824
## 51 CO_50612 446068199 1 none 824
## 52 PKE_3304 11486 3 none 11485
## 53 PKE_50614 2618 6 none 824
## 54 PKO_3304 11486 4 none 11485
## 55 PKO_50614 2618 7 none 824
## 56 PKO_50614 446068199 2 none 824
## 57 PKO_51094 489440637 1 none 872
## 58 SX_3302 3416 23 SX_3310 11485
## 59 SX_3302 3444 23 SX_3325 11485
## 60 SX_3416 2746 41 none 261
## 61 SX_45141 2119 1 none 2193
## 62 SX_45182 1327 1 SX_52310 7990630
## 63 SX_50610 2618 13 none 824
## 64 SX_50610 446068199 3 none 824Notice in the table above that several time series have the same
IndexId. Again this is problematic because normally only
one GFE_ID can be associated to a given
IndexId (i.e., POP_ID). We show here after the
focal time series grouped with their alternative series. On top of each
figure is shown the POPULATION and WATERBODY
associated with each IndexId (i.e., POP_ID)
and GFE_ID, respectively. Belong each figure is shown a
summary table providing the number of data points
(nb_dataPt) and the % of them that are
complementary, duplicate and in
conflict compared with the alternative series. The decision
made in each case are provided after the figures, using the index
i shown at the bottom left of the plots for reference.
## [1] "*** i = 1 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 CM_3305 11486 NA 11485 15 100 0
## 2 CM_3305 11487 NA 11485 2 100 0
## 3 CM_3305 11488 NA 11485 3 100 0
## conflict
## 1 0
## 2 0
## 3 0
## [1] "*** i = 2 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 CN_3306 11486 NA 11485 38 100 0
## 2 CN_3306 11487 NA 11485 3 100 0
## 3 CN_3306 11488 NA 11485 4 100 0
## conflict
## 1 0
## 2 0
## 3 0
## [1] "*** i = 3 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 CO_3303 11487 NA 11485 3 100 0
## 2 CO_3303 11488 NA 11485 3 100 0
## conflict
## 1 0
## 2 0
## [1] "*** i = 4 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 PKE_3304 11486 NA 11485 3 100 0
## conflict
## 1 0
## [1] "*** i = 5 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 PKO_3304 11486 NA 11485 4 100 0
## conflict
## 1 0
## [1] "*** i = 6 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 SX_3302 3416 <NA> 11485 23 100 0
## 2 SX_3302 3444 <NA> 11485 23 100 0
## 3 SX_3302 3416 SX_3310 <NA> 23 100 0
## 4 SX_3302 3444 SX_3325 <NA> 23 100 0
## conflict
## 1 0
## 2 0
## 3 0
## 4 0
## [1] "*** i = 7 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 CO_47183 2451 NA 129 2 100 0
## conflict
## 1 0
## [1] "*** i = 8 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 CM_47925 15 <NA> 14 8 90 0
## 2 CM_47925 17 <NA> 14 3 100 0
## 3 CM_47925 31516 <NA> 14 8 90 10
## 4 CM_47925 31740 <NA> 14 8 90 0
## 5 CM_47925 15 CM_47928 <NA> 8 100 0
## 6 CM_47925 17 CM_47939 <NA> 3 100 0
## conflict
## 1 10
## 2 0
## 3 0
## 4 10
## 5 0
## 6 0
## [1] "*** i = 9 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 CN_47277 2464 NA 142 46 100 0
## conflict
## 1 0
## [1] "*** i = 10 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 CO_46170 2453 <NA> 213 2 100 0
## 2 CO_46170 2461 <NA> 213 7 100 0
## 3 CO_46170 54282 <NA> 213 5 100 0
## 4 CO_46170 54283 <NA> 213 2 100 0
## 5 CO_46170 2453 CO_44736 <NA> 2 100 0
## conflict
## 1 0
## 2 0
## 3 0
## 4 0
## 5 0
## [1] "*** i = 11 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 SX_45141 2119 NA 2193 1 100 0
## conflict
## 1 0
## [1] "*** i = 12 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 CO_46240 221 <NA> 220 2 100 0
## 2 CO_46240 3477 <NA> 220 2 100 0
## 3 CO_46240 221 CO_46250 <NA> 2 100 0
## conflict
## 1 0
## 2 0
## 3 0
## [1] "*** i = 13 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary
## 1 CN_3333 1194 <NA> 23735 3 100
## 2 CN_3333 1194 CN_51519 ; CN_51518 <NA> 3 100
## duplicate conflict
## 1 0 0
## 2 0 0
## [1] "*** i = 14 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 CN_2178 129 <NA> 2476 5 80 0
## 2 CN_2178 129 CN_47189 <NA> 5 100 0
## conflict
## 1 20
## 2 0
## [1] "*** i = 15 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 CO_44539 129 <NA> 2476 5 100 0
## 2 CO_44539 2451 <NA> 2476 14 90 0
## 3 CO_44539 129 CO_47183 <NA> 5 100 0
## conflict
## 1 0
## 2 10
## 3 0
## [1] "*** i = 16 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 CN_44577 2518 <NA> 2492 1 100 0
## 2 CN_44577 2518 CN_44599 <NA> 1 100 0
## conflict
## 1 0
## 2 0
## [1] "*** i = 17 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary
## 1 CO_46582 1754239945 NA 256 14 100
## 2 CO_46582 2049268617 NA 256 21 100
## 3 CO_46582 33045 NA 256 21 100
## 4 CO_46582 57041 NA 256 6 100
## 5 CO_46582 63379 NA 256 4 100
## 6 CO_46582 719256264 NA 256 23 100
## duplicate conflict
## 1 0 0
## 2 0 0
## 3 0 0
## 4 0 0
## 5 0 0
## 6 0 0
## [1] "*** i = 18 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary
## 1 CO_46602 212716981 <NA> 258 22 60
## 2 CO_46602 2746 <NA> 258 6 80
## 3 CO_46602 2746 CO_46632 <NA> 6 100
## duplicate conflict
## 1 0 40
## 2 0 20
## 3 0 0
## [1] "*** i = 19 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 SX_3416 2746 NA 261 41 100 0
## conflict
## 1 0
## [1] "*** i = 20 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 CO_46632 261 NA 2746 9 100 0
## conflict
## 1 0
## [1] "*** i = 21 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 CN_46801 33103 NA 281 1 0 0
## conflict
## 1 100
## [1] "*** i = 22 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary
## 1 CO_46795 1921661712 NA 281 15 100
## 2 CO_46795 33103 NA 281 16 100
## duplicate conflict
## 1 0 0
## 2 0 0
## [1] "*** i = 23 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 CO_46835 2463 NA 285 2 100 0
## conflict
## 1 0
## [1] "*** i = 24 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 CN_46891 2466 NA 290 2 0 0
## 2 CN_46891 2467 NA 290 5 0 100
## conflict
## 1 100
## 2 0
## [1] "*** i = 25 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 CN_46892 2466 NA 290 23 80 10
## conflict
## 1 0
## [1] "*** i = 26 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 CM_47906 441 NA 3 2 50 0
## conflict
## 1 50
## [1] "*** i = 27 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 CN_48448 19723 NA 443 1 100 0
## conflict
## 1 0
## [1] "*** i = 28 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 CM_46984 2529 NA 62 2 0 0
## conflict
## 1 100
## [1] "*** i = 29 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 CM_47907 5 NA 7 1 0 0
## conflict
## 1 100
## [1] "*** i = 30 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 SX_45182 1327 <NA> 7990630 1 100 0
## 2 SX_45182 1327 SX_52310 <NA> 1 100 0
## conflict
## 1 0
## 2 0
## [1] "*** i = 31 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary
## 1 CM_50616 2618 NA 824 8 40
## 2 CM_50616 446068199 NA 824 1 0
## duplicate conflict
## 1 0 60
## 2 0 100
## [1] "*** i = 32 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary
## 1 CN_50618 2618 NA 824 8 0
## 2 CN_50618 446068199 NA 824 1 0
## duplicate conflict
## 1 0 100
## 2 0 100
## [1] "*** i = 33 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary
## 1 CO_50612 2618 NA 824 6 0
## 2 CO_50612 446068199 NA 824 1 0
## duplicate conflict
## 1 0 100
## 2 0 100
## [1] "*** i = 34 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary duplicate
## 1 PKE_50614 2618 NA 824 6 0 0
## conflict
## 1 100
## [1] "*** i = 35 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary
## 1 PKO_50614 2618 NA 824 7 10
## 2 PKO_50614 446068199 NA 824 2 50
## duplicate conflict
## 1 0 90
## 2 0 50
## [1] "*** i = 36 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary
## 1 SX_50610 2618 NA 824 13 20
## 2 SX_50610 446068199 NA 824 3 70
## duplicate conflict
## 1 0 80
## 2 0 30
## [1] "*** i = 37 ***"
## IndexId GFE_ID IndexId_alter GFE_ID_alter nb_dataPt complementary
## 1 PKO_51094 489440637 NA 872 1 100
## duplicate conflict
## 1 0 0
In case i = 1: series CM_3305 - 11486 is not merged to alternative series CM_3305 - 11485 because these are different streams. Consequently, the reference of the focal series is added to CUSS. There other focal two time series CM_3305 - 11487 and CM_3305 - 11488 are removed from NUSEDS because they only have < 4 data points and are anterior to 2020.
Note that GFE_ID = 11485 is present in the DFO
streams file (under ID) but coordinates are
not:
## # A tibble: 1 × 4
## NME ID X_LONGT Y_LAT
## <chr> <dbl> <chr> <chr>
## 1 WATERSHED ABOVE STAMP FALLS 11486 <NA> <NA>However, the GFE_ID and coordinates are in the DFO
hatchery file so we use these values:
## STOCK_GFE_ID STOCK_WATERBODY_NAME STOCK_LATITUDE STOCK_LONGITUDE
## 1 11486 STAMP RIVER 49.329344 -124.912868In case i = 2: series CN_3306 - 11486 in green is not merged to alternative series CN_3306 - 11485 in red for the same reason as above; its reference are instead added to CUSS. The other focal series CN_3306 - 11487 and CN_3306 - 11488 are deleted because they have <= 4 data points and are anterior to 2020.
In case i = 3: focal series CO_3303 - 11487 and CO_3303 - 11488 are
removed from NUSEDS because their GFE_ID
correspond to different locations, they have < 4 data points and they
are anterior to 2020.
In case i = 4: series PKE_3304 - 11486 in blue is not merged to alternative series PKE_3304 - 11485 in red for the same reason as above; its reference are instead added to CUSS.
In case i = 5: series PKO_3304 - 11486 in blue is not merged to alternative series PKO_3304 - 11485 in red for the same reason as above; its reference are instead added to CUSS.
In case i = 6: series PKO_3302 - 3416 in black (bottom plot) is merged to alternative series SX_3310 - 3416 in red and series PKO_3302 - 3444 in blue (bottom plot) is merged to alternative series SX_3325 - 3444 in green.
In case i = 7: series CO_47183 - 2451 in blue is merged to alternative series CO_47183 - 129 in red because the location of the focal series leads to the location of the alternative series.
In case i = 8: the focal series CM_47925 - 15 in red (bottom plot) is merged to the alternative series CM_47928 - 15 in back (bottom plot).
Similarly, the focal series CM_47925 - 17 in green (bottom plot) is merged to the alternative series CM_47939 - 17 in blue (bottom plot).
The other two focal series CM_47925 - 31516 in black (top plot) and
CM_47925 - 31740 in blue (top plot) are added to CUSS.
Their GFE_IDs are not in CUSS and their
are in the DFO streams file.
In case i = 9: it is a special situation deserving more attention.
There are two different issues related to CN_47277: (1) it
is associated to two locations (GFE_IDs) and (2) in one
location (GFE_ID = 142), there is another time series with
IndexId = CN_2483, which belong to the same CU:
The SYSTEM_SITE for GFE_ID = 142 is:
## SYSTEM_SITE GFE_ID X_LONGT Y_LAT
## 1 SWIFT RIVER 142 -122.115545 53.015621The GFE_ID = 2464 is not in CUSS but it
is in the DFO streams file but does not have
coordinates:
## # A tibble: 1 × 4
## NME ID X_LONGT Y_LAT
## <chr> <dbl> <chr> <chr>
## 1 COTTONWOOD RIVER - LOWER 2464 <NA> <NA>Notice above that the NME (= SYSTEM_SITE)
for ID (= GFE_ID) = 2464 matches
the POPULATION of CN_47277, which is not the
case for GFE_ID = 142:
## IndexId POPULATION
## 1 CN_47277 Cottonwood River (Quesnel) Chinook Run 1
## 2 CN_2483 Swift River (Quesnel) Chinook Run 1DECISION: we decide to merge the alternative series
CN_47277 - 142 to the focal series
CN_47277 - 2464 in NUSEDS and to add
CN_47277 - 2464 to CUSS (and to then
remove CN_47277 - 142 from CUSS):
As show above, there is no coordinates for the location with
GFE_ID = 2464. We consequently defined them manually using
Google Maps; they corresponds to the mouth of Cottonwood river:
## SYSTEM_SITE GFE_ID X_LONGT Y_LAT
## 1 COTTONWOOD RIVER - LOWER 2464 -122.610584 53.119965In case i = 10: the focal series CO_46170 - 2461 in dark green (top plot) is merged to the alternative series CO_46170 - 213 in red.
## [1] "7 rows were edited in all_areas_nuseds at the following fields: AREA, WATERBODY, GAZETTED_NAME, LOCAL_NAME_1, LOCAL_NAME_2, WATERSHED_CDE, WATERBODY_ID, GFE_ID"The other focal series CO_46170 - 54282 in black (“DAM”; top plot) is
instead added to CUSS. Its GFE_ID is not
in CUSS: but it is in DFO streams file
but without coordinates:
## [1] SYSTEM_SITE GFE_ID Y_LAT X_LONGT
## <0 rows> (or 0-length row.names)It is also not in the DFO hatchery file”
## # A tibble: 0 × 3
## # ℹ 3 variables: REL_GFE_ID <dbl>, REL_LATITUDE <dbl>, REL_LONGITUDE <dbl>## # A tibble: 0 × 3
## # ℹ 3 variables: STOCK_GFE_ID <dbl>, STOCK_LATITUDE <dbl>,
## # STOCK_LONGITUDE <dbl>It is in the DFO streams file but without coordinates:
## # A tibble: 1 × 4
## NME ID Y_LAT X_LONGT
## <chr> <dbl> <chr> <chr>
## 1 NICOLA RIVER (DAM) 54282 <NA> <NA>We consequently define the coordinates manually using Google Maps:
## SYSTEM_SITE GFE_ID Y_LAT X_LONGT
## NA NICOLA RIVER (DAM) 54282 50.163045 -120.665873The focal series CO_46170 - 54283 is removed because it does not have coordinates, it is unclear what “(DOT)” stands for and there is only two data points.
Finally, the focal series CO_46170 - 2453 in red (bottom plot) is merged to the alternative series CO_44736 - 2453 in blue.
## [1] "2 rows were edited in all_areas_nuseds at the following fields: SPECIES, POPULATION, RUN_TYPE, POP_ID, species_acronym_ncc, IndexId"In case i = 11: the focal series SX_45141 - 2119 in blue is not merged to SX_45141 - 2119 because the two location are far apart; it is instead added to CUSS.
In case i = 12: the focal series CO_46240 - 221 is merged to the
alternative series CO_46250 - 221 (bottom plot) because the two
POPULATIONs belong to the same CU_NAME = SOUTH
THOMPSON and the time series are compatible:
## nb_dataPt complementary duplicate conflict
## 1 2 2 0 0The GFE_ID of the other focal series CO_46240 - 3477 is
not in CUSS but it is in the DFO streams
file and we can see that its coordinates are very similar to
the coordinates of the alternative time series:
## # A tibble: 2 × 4
## NME ID Y_LAT X_LONGT
## <chr> <dbl> <chr> <chr>
## 1 ADAMS RIVER 220 50.8943855175699 -119.554135949561
## 2 ADAMS RIVER - LOWER 3477 50.893862861 -119.550567544The second focal series CO_46240 - 3477 is consequently merged to the alternative series CO_46240 - 220 in NUSEDS.
In case i = 13: the focal series CN_3333 - 1194 is not merged to the alternative series CN_3333 - 23735 (top plot) because the two locations are two far apart; it is added to CUSS instead.
In case i = 14: the focal series CN_2178 - 129 in blue is a duplicate of the atlernative series CN_47189 - 129 in red (bottom plot); it is consequently removed from NUSEDS.
In case i = 15: the focal series CO_44539 - 2451 in blue (top plot)
is not merged to the alternative series CO_44539 - 2476 in red because
of a conflicting point; its reference is instead added to
CUSS. The second focal series CO_44539 - 129 in blue
(bottom plot) is not merged to the alternative series CO_47183 - 129 in
red, notably because this would create a conflict with the merge done
with series CO_47183 - 2451 at step i = 7.
In case i = 16: there is a clear discrepancy between focal series
CN_44577 - 2518’s POPULATION = Chandindu River
(Yukon/Arctic) Chinook and its SYSTEM_SITE =
rS SYSTEM_SITE: these two locations are very far apart. We
decide to merge it to the alternative series CN_44599 - 2518 (bottom
plot) by changing its IndexId/POP_ID.
In case i = 17: all 6 focal series are added to
CUSS. Their GFE_ID are present in the DFO
streams but the coordinates are missing for most of them:
## # A tibble: 6 × 4
## NME ID X_LONGT Y_LAT
## <chr> <dbl> <chr> <chr>
## 1 BIRCH ISLAND CHANNEL 33045 <NA> <NA>
## 2 UPPER NORTH THOMPSON RIVER MAINSTEM 2049268617 <NA> <NA>
## 3 MIDDLE NORTH THOMPSON RIVER MAINSTEM 1754239945 <NA> <NA>
## 4 PIG CHANNEL COMBINED 719256264 <NA> <NA>
## 5 UPPER NORTH THOMPSON RIVER-MILEDGE CONFLUENCE 57041 <NA> <NA>
## 6 ENGINEERED CHANNEL 63379 -119.860244 51.58644The coordinates are consequently defined manually using Google Maps and the map in page 31 of Arbeider et al. 2020. Interior Fraser Coho Salmon Recovery Potential Assessment:
## SYSTEM_SITE GFE_ID X_LONGT
## 1 BIRCH ISLAND CHANNEL 33045 -119.889197
## 2 UPPER NORTH THOMPSON RIVER MAINSTEM 2049268617 -119.177796
## 3 MIDDLE NORTH THOMPSON RIVER MAINSTEM 1754239945 -119.701668
## 4 PIG CHANNEL COMBINED 719256264 -119.810014
## 5 UPPER NORTH THOMPSON RIVER-MILEDGE CONFLUENCE 57041 -119.173514
## 6 ENGINEERED CHANNEL 63379 -119.860244
## Y_LAT
## 1 51.598602
## 2 52.345236
## 3 51.593091
## 4 51.579465
## 5 52.281312
## 6 51.58644In case i = 18: the focal series CO_46602 - 2746 in blue (bottom plot) is merged to the alternative series CO_46632 - 2476 in red. The other focal series CO_46602 - 212716981 in green (top plot) is added to CUSS.
In case i = 19: the focal series SX_3416 - 2746 in blue (bottom plot) is merged to the alternative series SX_3416 - 261 in red.
In case i = 20: the focal series CO_46632 - 261 in blue (bottom plot) is merged to the alternative series CO_46632 - 2746 in red.
In case i = 21: the focal series CN_46801 - 33103 is removed from NUSEDS because its value is almost a duplicate of the value in the alternative series for this one year.
In case i = 22: the focal series CO_46795 - 33103 in blue is merged
to the alternative series CO_46795 - 281 in red. The other focal series
CO_46795 - 1921661712 in green is added to CUSS. Its
GFE_ID is in the DFO streams file but
coordinates are not:
## # A tibble: 2 × 4
## NME ID X_LONGT Y_LAT
## <chr> <dbl> <chr> <chr>
## 1 BLUE RIVER - LOWER 33103 -119.27964147 52.104610605
## 2 BLUE RIVER - UPPER 1921661712 <NA> <NA>The coordinates are consequently defined manually using Google Maps:
## SYSTEM_SITE GFE_ID Y_LAT X_LONGT
## 1 BLUE RIVER - UPPER 1921661712 52.112252 -119.289006In case i = 23: the two locations are the same:
## SYSTEM_SITE GFE_ID Y_LAT X_LONGT
## 1 CHILCOTIN RIVER - LOWER 2463 51.7399528 -122.401309
## 2 CHILCOTIN RIVER 285 51.7399528 -122.401309Because the focal series CO_46835 - 2463 is much more recent that the
alternative series CO_46835 - 285, it the latter that is modified in
CUSS (i.e., the GFE_ID of the alternative
series is changed to the one of the focal series) and in
NUSEDS.
In case i = 24: the focal series CN_46891 - 2467 in blue is a duplicate of the alternative series CN_46891 - 290 in red; it is consequently removed from NUSEDS. The other focal series CN_46891 - 2466 is not merge to the alternative series because the two locations are far apart (also we could be counting fish twice here); it is added to CUSS instead.
In case i = 25: the focal series CN_46892 - 2466 in blue has three duplicated points with the alternative time series CN_46892 - 290 in red, and a conflicting point. However, this conflicting point in the alternative time series is a duplicated point in the third time series CN_46891 - 290 in purple in the bottom plot below. We consequently (1) remove the duplicated point in the alternative series (in red) and (2) merge the focal series to the latter.
In case i = 26: the focal series CM_47906 - 441 in blue is not merged
to the alternative series because the points are conflictual; it is
added to CUSS instead. Its GFE_ID (- 441)
is not in CUSS but the coordinates were found in the
DFO streams file:
## # A tibble: 1 × 4
## NME ID X_LONGT Y_LAT
## <chr> <dbl> <chr> <chr>
## 1 EAGLE CREEK 441 -122.935076432 49.243360825In case i = 27: the focal series CN_48448 - 443 in blue is merged to the alternative series.
In case i = 28: the focal series CM_46984 - 2529 is added to CUSS instead of being merged to the alternative series because the two series are not compatible and in two different locations.
In case i = 29: the focal series CM_47907 - 5 is removed from NUSEDS because it only has one data point, it is conflictual with the alternative series and it is anterior to 2020.
In case i = 30: the focal series SX_45182 - 1327 is merged to the alternative series SX_45182 - 7990630 (top plot) because locations are very close and the one data point is compatible.
In the cases (i = 31, 32, 33, 34, 35, 36): there are two recurrent
GFE_IDs of focal series that seem to be the same locations
because they have the same WATERBODY in
NUSEDS:
## WATERBODY GFE_ID
## 1 CLEARWATER CREEK 2618
## 2 Clearwater Creek 446068199These two GFE_IDs are not in CUSS, and
only one is in the DFO streams file:
## # A tibble: 1 × 4
## NME ID Y_LAT X_LONGT
## <chr> <dbl> <chr> <chr>
## 1 CLEARWATER CREEK 2618 50.6158337647 -125.276480824In addition, the two focal series with these GFE_IDs are
compatible in each cases, so we decide to merge them by changing the
GFE_ID from 446068199 to 2618 in
NUSEDS:
## [1] "In case i = 31, focal series SX_45182 - 446068199 merged to focal series SX_45182 - 2618"
## [1] "1 rows were edited in all_areas_nuseds at the following fields: AREA, WATERBODY, GAZETTED_NAME, LOCAL_NAME_1, LOCAL_NAME_2, WATERSHED_CDE, WATERBODY_ID, GFE_ID"
## [1] ""
## [1] "In case i = 32, focal series CM_50616 - 446068199 merged to focal series CM_50616 - 2618"
## [1] "1 rows were edited in all_areas_nuseds at the following fields: AREA, WATERBODY, GAZETTED_NAME, LOCAL_NAME_1, LOCAL_NAME_2, WATERSHED_CDE, WATERBODY_ID, GFE_ID"
## [1] ""
## [1] "In case i = 33, focal series CN_50618 - 446068199 merged to focal series CN_50618 - 2618"
## [1] "1 rows were edited in all_areas_nuseds at the following fields: AREA, WATERBODY, GAZETTED_NAME, LOCAL_NAME_1, LOCAL_NAME_2, WATERSHED_CDE, WATERBODY_ID, GFE_ID"
## [1] ""
## [1] "In case i = 35, focal series CO_50612 - 446068199 merged to focal series CO_50612 - 2618"
## [1] "2 rows were edited in all_areas_nuseds at the following fields: AREA, WATERBODY, GAZETTED_NAME, LOCAL_NAME_1, LOCAL_NAME_2, WATERSHED_CDE, WATERBODY_ID, GFE_ID"
## [1] ""
## [1] "In case i = 36, focal series PKO_50614 - 446068199 merged to focal series PKO_50614 - 2618"
## [1] "3 rows were edited in all_areas_nuseds at the following fields: AREA, WATERBODY, GAZETTED_NAME, LOCAL_NAME_1, LOCAL_NAME_2, WATERSHED_CDE, WATERBODY_ID, GFE_ID"
## [1] ""The resulting merged focal series are not merged to the alternative series but are added to CUSS instead
In case i = 37: the focal series PKO_51094 - 489440637’s
GFE_ID = 489440637 is not in CUSS, nor in
the other two DFO files. The Atltzi river is close to the Kingcome river
and the one data point is compatible with the alternative series
PKO_51094 - 872, to which it is consequently merged to.
3.5.3 No alternative series
There remain 166 series in NUSEDS with no
alternative series, i.e., both their IndexId
(POP_ID) and SPECIES & GFE_ID are absent
from CUSS. We rescue these time series by identifying
the CU they belong to using the CUs’ shape files of the PSE. Series with
X_LONGT and Y_LAT values that intersects one
unique CU layer of the same species are attributed the CU’s
FULL_CU_IN and CU_NAME and the reference is
added to CUSS.
## IndexId GFE_ID nb_dataPt alternative_IndexId alternative_GFE_ID
## 1 CM_1622 11 2 none none
## 2 CM_2434 4 11 none none
## 3 CM_3212 2487 4 none none
## 4 CM_41256 1349 1 none none
## 5 CM_41371 1362 6 none none
## 6 CM_42458 1497 3 none none
## 7 CM_43568 1766 1 none none
## 8 CM_44524 2473 1 none none
## 9 CM_44558 2486 1 none none
## 10 CM_45283 2024 1 none none
## 11 CM_45393 2076 7 none none
## 12 CM_45931 7990588 4 none none
## 13 CM_46787933 2488 3 none none
## 14 CM_47648 499 1 none none
## 15 CM_51026 865 1 none none
## 16 CM_51161 879 3 none none
## 17 CM_52086 1303 5 none none
## 18 CM_52096 7990617 2 none none
## 19 CM_52171 1312 3 none none
## 20 CM_52186 1314 1 none none
## 21 CM_562 2716 14 none none
## 22 CM_7009 2837 3 none none
## 23 CM_7734 182 4 none none
## 24 CM_7735 52747 7 none none
## 25 CM_7736 52748 7 none none
## 26 CM_7737 189 10 none none
## 27 CM_7739 52749 5 none none
## 28 CM_7765 55413 1 none none
## 29 CM_7768 2441 6 none none
## 30 CM_7769 55417 1 none none
## 31 CM_7774 55420 2 none none
## 32 CM_7775 2252 5 none none
## 33 CM_7784 57042 3 none none
## 34 CM_7796 2685 5 none none
## 35 CM_7812 2684 1 none none
## 36 CM_7816 3554 1 none none
## 37 CN_3213 2487 4 none none
## 38 CN_3320 11487 2 none none
## 39 CN_3324 11486 1 none none
## 40 CN_41103 1333 3 none none
## 41 CN_46841 2454 5 none none
## 42 CN_46841 2462 28 none none
## 43 CN_49102 802 1 none none
## 44 CN_50009 723 1 none none
## 45 CN_50319 1041 1 none none
## 46 CN_50638 826 2 none none
## 47 CN_50698 832 1 none none
## 48 CN_7808 64739 44 none none
## 49 CO_1624 11 1 none none
## 50 CO_1826 99 1 none none
## 51 CO_3027 2655 2 none none
## 52 CO_3211 2487 4 none none
## 53 CO_3321 11486 11 none none
## 54 CO_43196 1662 1 none none
## 55 CO_43616 1776 1 none none
## 56 CO_44441 2656 13 none none
## 57 CO_44840 2312 2 none none
## 58 CO_44988 2374 7 none none
## 59 CO_45303 2030 1 none none
## 60 CO_45879 403 1 none none
## 61 CO_46310 227 2 none none
## 62 CO_46855 287 1 none none
## 63 CO_46865 288 1 none none
## 64 CO_47232 134 1 none none
## 65 CO_48090 481 1 none none
## 66 CO_48205 640 2 none none
## 67 CO_49415 602 1 none none
## 68 CO_52082 1303 13 none none
## 69 CO_52242 1320 3 none none
## 70 CO_52262 1322 5 none none
## 71 CO_52272 1323 7 none none
## 72 CO_52376 1073 16 none none
## 73 CO_572 95 1 none none
## 74 CO_7420 23726 3 none none
## 75 CO_7729 2239 6 none none
## 76 CO_7747 32077 1 none none
## 77 CO_7764 55413 1 none none
## 78 CO_7771 2422 6 none none
## 79 CO_7772 11491 7 none none
## 80 CO_7773 55420 1 none none
## 81 CO_7776 2692 1 none none
## 82 CO_7779 57040 1 none none
## 83 CO_7780 2397 1 none none
## 84 CO_7793 2681 7 none none
## 85 CO_7814 2687 1 none none
## 86 CO_792 208 2 none none
## 87 CO_959 199 2 none none
## 88 PKE_3277 2236 1 none none
## 89 PKE_3432 11572 2 none none
## 90 PKE_3447 2708 2 none none
## 91 PKE_45304 2030 2 none none
## 92 PKE_45454 2107 1 none none
## 93 PKE_45930 7990588 1 none none
## 94 PKE_48638 757 1 none none
## 95 PKE_48658 759 1 none none
## 96 PKE_50012 724 2 none none
## 97 PKE_51064 869 4 none none
## 98 PKE_51882 990 4 none none
## 99 PKE_52377 1073 8 none none
## 100 PKE_52387 1075 1 none none
## 101 PKE_52392 1076 5 none none
## 102 PKE_52492 1096 1 none none
## 103 PKE_52754 1125 3 none none
## 104 PKE_7797 2685 2 none none
## 105 PKE_88092422 2601 3 none none
## 106 PKO_180 2616 1 none none
## 107 PKO_3195 2737 1 none none
## 108 PKO_3277 2236 1 none none
## 109 PKO_40049 1211 1 none none
## 110 PKO_41037 1574 1 none none
## 111 PKO_43007 1624 1 none none
## 112 PKO_44654 2574 1 none none
## 113 PKO_45930 7990588 1 none none
## 114 PKO_49088 801 1 none none
## 115 PKO_50007 723 1 none none
## 116 PKO_50012 724 1 none none
## 117 PKO_52377 1073 8 none none
## 118 PKO_52392 1076 6 none none
## 119 PKO_52492 1096 1 none none
## 120 PKO_52754 1125 4 none none
## 121 PKO_7792 2252 1 none none
## 122 PKO_7797 2685 3 none none
## 123 PKO_7811 2688 1 none none
## 124 PKO_7813 2684 1 none none
## 125 PKO_7817 3554 1 none none
## 126 PKO_88092422 2601 2 none none
## 127 SX_1874 3505 8 none none
## 128 SX_3077 2753 12 none none
## 129 SX_3085 2761 5 none none
## 130 SX_3092 426 9 none none
## 131 SX_3221 1991 9 none none
## 132 SX_39730 1433 1 none none
## 133 SX_40015 1208 1 none none
## 134 SX_42680 1671 1 none none
## 135 SX_42950 1613 1 none none
## 136 SX_43095 1642 1 none none
## 137 SX_43770 1807 1 none none
## 138 SX_44140 1904 1 none none
## 139 SX_44160 1908 1 none none
## 140 SX_44165 1909 1 none none
## 141 SX_45038 2396 1 none none
## 142 SX_45040 2398 1 none none
## 143 SX_45056 2405 2 none none
## 144 SX_48264 652 1 none none
## 145 SX_50005 723 1 none none
## 146 SX_50010 724 3 none none
## 147 SX_50340 1046 5 none none
## 148 SX_51000 863 1 none none
## 149 SX_51060 869 1 none none
## 150 SX_51145 878 5 none none
## 151 SX_51155 879 1 none none
## 152 SX_52080 1303 51 none none
## 153 SX_52120 1307 44 none none
## 154 SX_52390 1076 11 none none
## 155 SX_52750 1125 5 none none
## 156 SX_52890 1139 4 none none
## 157 SX_52960 1146 1 none none
## 158 SX_7640 26773 3 none none
## 159 SX_7689 3510 7 none none
## 160 SX_7694 3446 3 none none
## 161 SX_7805 2792 3 none none
## 162 SX_7807 185 6 none none
## 163 SX_7815 2687 1 none none
## 164 SX_7818 64745 1 none none
## 165 SX_7822 58219 1 none none
## 166 SX_80808204 2601 1 none noneThe are 14 time series without coordinates provided for their
GFE_ID. We use the SYSTEM_SITE (if available)
and WATERBODY and Google Maps to define
X_LONGT and Y_LAT manually when possible:
## GFE_ID WATERBODY X_LONGT Y_LAT coordinates_changed
## 1 7990588 RETURN CHANNEL CREEKS NA NA FALSE
## 2 1303 KENNEDY LAKE BEACHES -125.580441 49.049133 TRUE
## 3 52749 SILVERMERE LAKE -122.408753 49.174967 TRUE
## 4 55417 CAMILOS CREEK -121.393056 49.386667 TRUE
## 5 57042 HANSEN CREEK -128.346389 50.778889 TRUE
## 6 11487 STAMP RIVER BELOW FALLS NA NA FALSE
## 7 95 SEMMIHAULT CREEK -121.956111 49.153056 TRUE
## 8 2681 MCLELLAN CREEK -126.619731 52.387830 TRUE
## 9 208 COTTONWOOD CREEK -123.145631 49.762523 TRUE
## 10 199 FEE CREEK NA NA FALSE
## 11 3505 OLSEN CREEK -122.631537 49.597168 TRUE
## 12 1307 CLAYOQUOT ARM BEACHES -125.591878 49.099033 TRUE
## 13 2792 MOORE LAKE -129.501134 53.409530 TRUE
## 14 64745 ATNARKO LAKES -125.713941 52.163834 TRUETime series without coordinates or intersecting more that one CU boundary are removed from NUSEDS. Below we show a plot for each time series followed by the action made:
## [1] "*** r = 1 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_1622 Lower Fraser CM-2 Current
## [1] ""
## [1] "*** r = 2 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_2434 Lower Fraser CM-2 Current
## [1] ""
## [1] "*** r = 3 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_3212 Southwest & West Vancouver Island CM-10 Current
## [1] ""
## [1] "*** r = 4 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_41256 Southwest & West Vancouver Island CM-10 Current
## [1] ""
## [1] "*** r = 5 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_41371 Southwest & West Vancouver Island CM-10 Current
## [1] ""
## [1] "*** r = 6 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_42458 East HG CM-21 Current
## [1] ""
## [1] "*** r = 7 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_43568 Portland Canal-Observatory CM-32 Current
## [1] ""
## [1] "*** r = 8 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_44524 Southwest & West Vancouver Island CM-10 Current
## [1] ""
## [1] "*** r = 9 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_44558 Southwest & West Vancouver Island CM-10 Current
## [1] ""
## [1] "*** r = 10 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_45283 Southwest & West Vancouver Island CM-10 Current
## [1] ""
## [1] "*** r = 11 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_45393 Georgia Strait CM-4 Current
## [1] ""
## [1] "*** r = 12 ***"
## [1] "The series above is removed from NUSEDS because: No coordinates available"
## [1] "*** r = 13 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_46787933 Southwest & West Vancouver Island CM-10 Current
## [1] ""
## [1] "*** r = 14 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_47648 Upper Skeena No FULL_CU_in but cuid = 242 <NA>
## [1] ""
## [1] "*** r = 15 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_51026 Southern Coastal Streams CM-8 Current
## [1] ""
## [1] "*** r = 16 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_51161 Southern Coastal Streams CM-8 Current
## [1] ""
## [1] "*** r = 17 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_52086 Southwest & West Vancouver Island CM-10 Current
## [1] ""
## [1] "*** r = 18 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_52096 Southwest & West Vancouver Island CM-10 Current
## [1] ""
## [1] "*** r = 19 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_52171 Southwest & West Vancouver Island CM-10 Current
## [1] ""
## [1] "*** r = 20 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_52186 Southwest & West Vancouver Island CM-10 Current
## [1] ""
## [1] "*** r = 21 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_562 Lower Fraser CM-2 Current
## [1] ""
## [1] "*** r = 22 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_7009 Georgia Strait CM-4 Current
## [1] ""
## [1] "*** r = 23 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_7734 Lower Fraser CM-2 Current
## [1] ""
## [1] "*** r = 24 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_7735 Lower Fraser CM-2 Current
## [1] ""
## [1] "*** r = 25 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_7736 Lower Fraser CM-2 Current
## [1] ""
## [1] "*** r = 26 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_7737 Lower Fraser CM-2 Current
## [1] ""
## [1] "*** r = 27 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_7739 Lower Fraser CM-2 Current
## [1] ""
## [1] "*** r = 28 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_7765 Southwest & West Vancouver Island CM-10 Current
## [1] ""
## [1] "*** r = 29 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_7768 Lower Fraser CM-2 Current
## [1] ""
## [1] "*** r = 30 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_7769 Lower Fraser CM-2 Current
## [1] ""
## [1] "*** r = 31 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_7774 Southwest & West Vancouver Island CM-10 Current
## [1] ""
## [1] "*** r = 32 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_7775 Bella Coola-Dean Rivers (Chum) CM-16 Current
## [1] ""
## [1] "*** r = 33 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_7784 Northwest Vancouver Island CM-11 Current
## [1] ""
## [1] "*** r = 34 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_7796 Spiller-Fitz-Hugh-Burke (Chum) CM-15 Current
## [1] ""
## [1] "*** r = 35 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_7812 Spiller-Fitz-Hugh-Burke (Chum) CM-15 Current
## [1] ""
## [1] "*** r = 36 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CM_7816 Spiller-Fitz-Hugh-Burke (Chum) CM-15 Current
## [1] ""
## [1] "*** r = 37 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CN_3213 CK031-West Vancouver Island-South_FA_0.x CK-31 Current
## [1] ""
## [1] "*** r = 38 ***"
## [1] "The series above is removed from NUSEDS because: No coordinates available"
## [1] "*** r = 39 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CN_3324 CK031-West Vancouver Island-South_FA_0.x CK-31 Current
## [1] ""
## [1] "*** r = 40 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CN_41103 CK031-West Vancouver Island-South_FA_0.x CK-31 Current
## [1] ""
## [1] "*** r = 41 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CN_46841 CK010-Middle Fraser River_SP_1.3 CK-10 Current
## [1] ""
## [1] "*** r = 42 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CN_46841 CK010-Middle Fraser River_SP_1.3 CK-10 Current
## [1] ""
## [1] "*** r = 43 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CN_49102 CK020-Southern Mainland-Georgia Strait_FA_0.x CK-20 Current
## [1] ""
## [1] "*** r = 44 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CN_50009 CK020-Southern Mainland-Georgia Strait_FA_0.x CK-20 Current
## [1] ""
## [1] "*** r = 45 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CN_50319 North & Central Coast-early timing (Chinook) CK-42 Current
## [1] ""
## [1] "*** r = 46 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CN_50638 CK028-Southern Mainland-Southern Fjords_FA_0.x CK-28 Current
## [1] ""
## [1] "*** r = 47 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CN_50698 CK028-Southern Mainland-Southern Fjords_FA_0.x CK-28 Current
## [1] ""
## [1] "*** r = 48 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CN_7808 CK002-Boundary Bay_FA_0.3 CK-2 VREQ[Current]
## [1] ""
## [1] "*** r = 49 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_1624 Lower Fraser CO-47 Current
## [1] ""
## [1] "*** r = 50 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_1826 Lower Fraser CO-47 Current
## [1] ""
## [1] "*** r = 51 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_3027 Douglas Channel-Kitimat Arm (Coho) CO-29 Current
## [1] ""
## [1] "*** r = 52 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_3211 Clayoquot CO-18 Current
## [1] ""
## [1] "*** r = 53 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_3321 West Vancouver Island CO-17 Current
## [1] ""
## [1] "*** r = 54 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_43196 Haida Gwaii-West CO-24 Current
## [1] ""
## [1] "*** r = 55 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_43616 Portland Sound-Observatory Inlet-Portland Canal CO-37 Current
## [1] ""
## [1] "*** r = 56 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_44441 Middle Skeena-CO CO-33 Current
## [1] ""
## [1] "*** r = 57 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_44840 Portland Sound-Observatory Inlet-Portland Canal CO-37 Current
## [1] ""
## [1] "*** r = 58 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_44988 South Thompson CO-8 Current
## [1] ""
## [1] "*** r = 59 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_45303 Hecate Strait Mainland (Coho) CO-27 Current
## [1] ""
## [1] "*** r = 60 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_45879 Georgia Strait Mainland CO-11 Current
## [1] ""
## [1] "*** r = 61 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_46310 South Thompson CO-8 Current
## [1] ""
## [1] "*** r = 62 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_46855 Interior Fraser CO-48 Current
## [1] ""
## [1] "*** r = 63 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_46865 Interior Fraser CO-48 Current
## [1] ""
## [1] "*** r = 64 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_47232 Interior Fraser CO-48 Current
## [1] ""
## [1] "*** r = 65 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_48090 Lower Skeena-CO CO-32 Current
## [1] ""
## [1] "*** r = 66 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_48205 Lower Nass CO-35 Current
## [1] ""
## [1] "*** r = 67 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_49415 Middle Skeena-CO CO-33 Current
## [1] ""
## [1] "*** r = 68 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_52082 Clayoquot CO-18 Current
## [1] ""
## [1] "*** r = 69 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_52242 Clayoquot CO-18 Current
## [1] ""
## [1] "*** r = 70 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_52262 Clayoquot CO-18 Current
## [1] ""
## [1] "*** r = 71 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_52272 Clayoquot CO-18 Current
## [1] ""
## [1] "*** r = 72 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_52376 Douglas Channel-Kitimat Arm (Coho) CO-29 Current
## [1] ""
## [1] "*** r = 73 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_572 Lower Fraser CO-47 Current
## [1] ""
## [1] "*** r = 74 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_7420 South Thompson CO-8 Current
## [1] ""
## [1] "*** r = 75 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_7729 Bella Coola-Dean Rivers (Coho) CO-22 Current
## [1] ""
## [1] "*** r = 76 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_7747 East Vancouver Island-Georgia Strait CO-13 Current
## [1] ""
## [1] "*** r = 77 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_7764 Clayoquot CO-18 Current
## [1] ""
## [1] "*** r = 78 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_7771 Interior Fraser CO-48 Current
## [1] ""
## [1] "*** r = 79 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_7772 Interior Fraser CO-48 Current
## [1] ""
## [1] "*** r = 80 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_7773 Clayoquot CO-18 Current
## [1] ""
## [1] "*** r = 81 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_7776 Northern Coastal Streams (Coho) CO-30 Current
## [1] ""
## [1] "*** r = 82 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_7779 Lower Thompson CO-7 Current
## [1] ""
## [1] "*** r = 83 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_7780 Interior Fraser CO-48 Current
## [1] ""
## [1] "*** r = 84 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_7793 Bella Coola-Dean Rivers (Coho) CO-22 Current
## [1] ""
## [1] "*** r = 85 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_7814 Hecate Strait Mainland (Coho) CO-27 Current
## [1] ""
## [1] "*** r = 86 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 CO_792 Howe Sound-Burrard Inlet CO-10 Current
## [1] ""
## [1] "*** r = 87 ***"
## [1] "The series above is removed from NUSEDS because: No coordinates available"
## [1] "*** r = 88 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKE_3277 Nass-Skeena Estuary (even) PKE-7 Current
## [1] ""
## [1] "*** r = 89 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKE_3432 Hecate Strait-Fjords (Pink-Even Year) PKE-6 Current
## [1] ""
## [1] "*** r = 90 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKE_3447 Hecate Lowlands (Pink-Even Year) PKE-5 Current
## [1] ""
## [1] "*** r = 91 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKE_45304 Hecate Lowlands (Pink-Even Year) PKE-5 Current
## [1] ""
## [1] "*** r = 92 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKE_45454 Middle-Upper Skeena (even) PKE-8 Current
## [1] ""
## [1] "*** r = 93 ***"
## [1] "The series above is removed from NUSEDS because: No coordinates available"
## [1] "*** r = 94 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKE_48638 Georgia Strait PKE-1 Current
## [1] ""
## [1] "*** r = 95 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKE_48658 Georgia Strait PKE-1 Current
## [1] ""
## [1] "*** r = 96 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKE_50012 Georgia Strait PKE-1 Current
## [1] ""
## [1] "*** r = 97 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKE_51064 Southern Fjords PKE-4 Current
## [1] ""
## [1] "*** r = 98 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKE_51882 Hecate Strait-Fjords (Pink-Even Year) PKE-6 Current
## [1] ""
## [1] "*** r = 99 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKE_52377 Hecate Strait-Fjords (Pink-Even Year) PKE-6 Current
## [1] ""
## [1] "*** r = 100 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKE_52387 Hecate Strait-Fjords (Pink-Even Year) PKE-6 Current
## [1] ""
## [1] "*** r = 101 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKE_52392 Hecate Strait-Fjords (Pink-Even Year) PKE-6 Current
## [1] ""
## [1] "*** r = 102 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKE_52492 Hecate Lowlands (Pink-Even Year) PKE-5 Current
## [1] ""
## [1] "*** r = 103 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKE_52754 Southern Fjords PKE-4 Current
## [1] ""
## [1] "*** r = 104 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKE_7797 Hecate Lowlands (Pink-Even Year) PKE-5 Current
## [1] ""
## [1] "*** r = 105 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKE_88092422 Nass-Skeena Estuary (even) PKE-7 Current
## [1] ""
## [1] "*** r = 106 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKO_180 Georgia Strait PKO-3 Current
## [1] ""
## [1] "*** r = 107 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKO_3195 Lower Skeena (odd) PKO-15 Current
## [1] ""
## [1] "*** r = 108 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKO_3277 Nass-Portland-Observatory PKO-17 Current
## [1] ""
## [1] "*** r = 109 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKO_40049 Georgia Strait PKO-3 Current
## [1] ""
## [1] "*** r = 110 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKO_41037 North Haida Gwaii PKO-10 Current
## [1] ""
## [1] "*** r = 111 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKO_43007 East Haida Gwaii PKO-9 Current
## [1] ""
## [1] "*** r = 112 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKO_44654 Fraser River PKO-1 Current
## [1] ""
## [1] "*** r = 113 ***"
## [1] "The series above is removed from NUSEDS because: No coordinates available"
## [1] "*** r = 114 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKO_49088 Georgia Strait PKO-3 Current
## [1] ""
## [1] "*** r = 115 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKO_50007 East Howe Sound-Burrard Inlet PKO-2 Current
## [1] ""
## [1] "*** r = 116 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKO_50012 East Howe Sound-Burrard Inlet PKO-2 Current
## [1] ""
## [1] "*** r = 117 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKO_52377 Hecate Strait-Fjords (Pink-Odd Year) PKO-13 Current
## [1] ""
## [1] "*** r = 118 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKO_52392 Hecate Strait-Fjords (Pink-Odd Year) PKO-13 Current
## [1] ""
## [1] "*** r = 119 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKO_52492 Hecate Strait-Lowlands (Pink-Odd Year) PKO-12 Current
## [1] ""
## [1] "*** r = 120 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKO_52754 Southern Fjords PKO-7 Current
## [1] ""
## [1] "*** r = 121 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME
## 1 PKO_7792 Homathko-Klinaklini-Smith-Rivers-Bella Coola-Dean (Pink-Odd Year)
## FULL_CU_IN CU_TYPE
## 1 PKO-8 Current
## [1] ""
## [1] "*** r = 122 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKO_7797 Hecate Strait-Lowlands (Pink-Odd Year) PKO-12 Current
## [1] ""
## [1] "*** r = 123 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKO_7811 Hecate Strait-Lowlands (Pink-Odd Year) PKO-12 Current
## [1] ""
## [1] "*** r = 124 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKO_7813 Hecate Strait-Lowlands (Pink-Odd Year) PKO-12 Current
## [1] ""
## [1] "*** r = 125 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKO_7817 Hecate Strait-Lowlands (Pink-Odd Year) PKO-12 Current
## [1] ""
## [1] "*** r = 126 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 PKO_88092422 Lower Skeena (odd) PKO-15 Current
## [1] ""
## [1] "*** r = 127 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_1874 Pitt_Early Summer SEL-03-05 Current
## [1] ""
## [1] "*** r = 128 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_3077 Takla/Trembleur_Early Stuart SEL-06-14 Current
## [1] ""
## [1] "*** r = 129 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_3085 Takla/Trembleur_Early Stuart SEL-06-14 Current
## [1] ""
## [1] "*** r = 130 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_3092 Takla/Trembleur/Stuart_Summer SEL-06-13 Current
## [1] ""
## [1] "*** r = 131 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_3221 Bowron_Early Summer SEL-07-01 Current
## [1] ""
## [1] "*** r = 132 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_39730 NW Vancouver Island SER-11 Current
## [1] ""
## [1] "*** r = 133 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_40015 East Vancouver Island and Georgia Strait SER-08 Current
## [1] ""
## [1] "*** r = 134 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_42680 West Haida Gwaii SER-14 Current
## [1] ""
## [1] "*** r = 135 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_42950 East Haida Gwaii SER-13 Current
## [1] ""
## [1] "*** r = 136 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_43095 West Haida Gwaii SER-14 Current
## [1] ""
## [1] "*** r = 137 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_43770 Northn Coastal Streams (Sockeye-River) SER-17 Current
## [1] ""
## [1] "*** r = 138 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_44140 Northern Coastal Fjords (Sockeye-River) SER-16 Current
## [1] ""
## [1] "*** r = 139 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_44160 Northern Coastal Fjords (Sockeye-River) SER-16 Current
## [1] ""
## [1] "*** r = 140 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_44165 Northern Coastal Fjords (Sockeye-River) SER-16 Current
## [1] ""
## [1] "*** r = 141 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_45038 Quesnel_Summer SEL-06-10 Current
## [1] ""
## [1] "*** r = 142 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_45040 Quesnel_Summer SEL-06-10 Current
## [1] ""
## [1] "*** r = 143 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_45056 Quesnel_Summer SEL-06-10 Current
## [1] ""
## [1] "*** r = 144 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_48264 Lower Nass-Portland SER-20 Current
## [1] ""
## [1] "*** r = 145 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_50005 East Vancouver Island and Georgia Strait SER-08 Current
## [1] ""
## [1] "*** r = 146 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_50010 East Vancouver Island and Georgia Strait SER-08 Current
## [1] ""
## [1] "*** r = 147 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_50340 Northern Coastal Fjords (Sockeye-River) SER-16 Current
## [1] ""
## [1] "*** r = 148 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_51000 Southern Fjords SER-09 Current
## [1] ""
## [1] "*** r = 149 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_51060 Southern Fjords SER-09 Current
## [1] ""
## [1] "*** r = 150 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_51145 Southern Fjords SER-09 Current
## [1] ""
## [1] "*** r = 151 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_51155 Southern Fjords SER-09 Current
## [1] ""
## [1] "*** r = 152 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_52080 Kennedy SEL-13-14 Current
## [1] ""
## [1] "*** r = 153 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_52120 West Vancouver Island SER-10 Current
## [1] ""
## [1] "*** r = 154 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_52390 Northern Coastal Fjords (Sockeye-River) SER-16 Current
## [1] ""
## [1] "*** r = 155 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_52750 Southern Fjords SER-09 Current
## [1] ""
## [1] "*** r = 156 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_52890 East Vancouver Island and Georgia Strait SER-08 Current
## [1] ""
## [1] "*** r = 157 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_52960 East Vancouver Island and Georgia Strait SER-08 Current
## [1] ""
## [1] "*** r = 158 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_7640 Shuswap_Late SEL-09-03 Current
## [1] ""
## [1] "*** r = 159 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_7689 Pitt_Early Summer SEL-03-05 Current
## [1] ""
## [1] "*** r = 160 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_7694 East Vancouver Island and Georgia Strait SER-08 Current
## [1] ""
## [1] "*** r = 161 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_7805 Tsimtack/Moore/Roger (Sockeye-Lake) SEL-19-62 Current
## [1] ""
## [1] "*** r = 162 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_7807 Harrison-upstream migrating_Late SEL-03-04 Current
## [1] ""
## [1] "*** r = 163 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_7815 Northn Coastal Streams (Sockeye-River) SER-17 Current
## [1] ""
## [1] "*** r = 164 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_7818 South Atnarko Lakes (Sockeye-Lake) SEL-16-01 Current
## [1] ""
## [1] "*** r = 165 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_7822 Lillooet/Harrison_Late SEL-04-01 Current
## [1] ""
## [1] "*** r = 166 ***"
## [1] "The time series above is added to CUSS in association with the CU:"
## IndexId CU_NAME FULL_CU_IN CU_TYPE
## 1 SX_80808204 Skeena River SER-18 Current
## [1] ""3.6 Fix: coordinates of certain locations in CUSS (optional)
There are multiple locations in CUSS that have
different SYSTEM_SITE and GFE_ID but exactly
the same geographic coordinates. This is because the coordinates are not
defined as the survey location but the “Location of the mouth of the
waterbody if flowing, or the centroid if not.”. There can be large
distances between the coordinates in CUSS and the real
survey locations for large water bodies. We offer the option to update
the coordinates of certain locations to avoid overlap.
Decision made:
## [1] "Coordinates for certain locations are updated manually to avoid overlaps."
## [1] "We do so using Google Maps and the field 'SYSTEM_SITE'"There are 21 unique coordinates with multiple
SYSTEM_SITE and GFE_ID (n = 41). We group
locations with identical coordinates and for each of the group
(identified with a letter in the table below):
## SYSTEM_SITE GFE_ID Y_LAT X_LONGT group
## 1 FENNELL CREEK AND SASKUM CREEK 2746 51.352577 -119.723268 A
## 2 FENNELL CREEK 261 51.352577 -119.723268 A
## 3 CENTRE CREEK 82 49.103185 -121.536585 B
## 4 CENTRE CHANNEL 2533 49.103185 -121.536585 B
## 5 FOLEY CREEK 78 49.106138 -121.635958 C
## 6 FOLEY CREEK SIDE CHANNEL 381 49.106138 -121.635958 C
## 7 NORRISH CREEK 51 49.173172 -122.135356 D
## 8 HAWKINS CREEK 54 49.173172 -122.135356 D
## 9 BAXTER BEACH 11513 52.722503 -120.860114 E
## 10 BEAR BEACH - SHORE 11514 52.722503 -120.860114 E
## 11 BETTY FRANK'S - SHORE 11515 52.722503 -120.860114 E
## 12 LILLOOET RIVER - LOWER 177 49.747468 -122.145828 F
## 13 LILLOOET RIVER 2475 49.747468 -122.145828 F
## 14 CAYOOSH CREEK 131 50.668727 -121.972610 G
## 15 SETON AND CAYOOSH CREEKS 7990579 50.668727 -121.972610 G
## 16 BOISE CREEK 24 49.624229 -122.659958 H
## 17 BOISE CREEK - NORTH 26776 49.624229 -122.659958 H
## 18 FRASER RIVER 1 49.118876 -123.191011 I
## 19 FRASER RIVER AND TRIBUTARIES 7990634 49.118876 -123.191011 I
## 20 CHILCOTIN RIVER - LOWER 2463 51.739953 -122.401309 J
## 21 CHILCOTIN RIVER 285 51.739953 -122.401309 J
## 22 SOMASS RIVER 1261 49.246397 -124.819840 K
## 23 SOMASS-SPROAT-GC SYSTEM 11485 49.246397 -124.819840 K
## 24 CLAYOQUOT RIVER - LOWER 1310 49.183381 -125.537647 L
## 25 CLAYOQUOT RIVER 2487 49.183381 -125.537647 L
## 26 PINKUT CREEK 501255 54.446302 -125.460072 M
## 27 PINKUT CREEK - BELOW WEIR 2115 54.446302 -125.460072 M
## 28 FORESTRY CREEK 2678 52.376885 -126.584031 N
## 29 MARTY'S CREEK 2680 52.376885 -126.584031 N
## 30 CAYEGHLE CREEK 1450 50.342470 -127.439898 O
## 31 CAYEGHLE SYSTEM 2302 50.342470 -127.439898 O
## 32 TAKLA LAKE 2439 55.075216 -125.538582 P
## 33 TAKLA - SHORE 19719 55.075216 -125.538582 P
## 34 FULTON RIVER 501254 54.814315 -126.146194 Q
## 35 FULTON RIVER - BELOW WEIR 2111 54.814315 -126.146194 Q
## 36 JENNY BAY CREEKS 1798 52.224030 -127.598389 R
## 37 JENNY BAY SOUTH CREEK 2693 52.224030 -127.598389 R
## 38 FANNIE COVE LEFT HAND CREEK 2687 52.043911 -128.068542 S
## 39 FANNIE COVE RIGHT HAND CREEK 2708 52.043911 -128.068542 S
## 40 SEWELL INLET CREEK L.H. #2 1594 52.876978 -131.949569 T
## 41 THORSEN CREEK 1595 52.876978 -131.949569 T## [1] "For group A:"## GFE_ID SYSTEM_SITE Y_LAT X_LONGT Y_LAT_new
## 1 2746 FENNELL CREEK AND SASKUM CREEK 51.352577 -119.723268 NA
## 2 261 FENNELL CREEK 51.352577 -119.723268 51.344756
## X_LONGT_new
## 1 NA
## 2 -119.797289## [1] "For group B:"## GFE_ID SYSTEM_SITE Y_LAT X_LONGT Y_LAT_new X_LONGT_new
## 1 82 CENTRE CREEK 49.103185 -121.536585 NA NA
## 2 2533 CENTRE CHANNEL 49.103185 -121.536585 49.090741 -121.531078## [1] "For group C:"## GFE_ID SYSTEM_SITE Y_LAT X_LONGT Y_LAT_new X_LONGT_new
## 1 78 FOLEY CREEK 49.106138 -121.635958 49.107077 -121.636804
## 2 381 FOLEY CREEK SIDE CHANNEL 49.106138 -121.635958 NA NA## [1] "For group D:"## GFE_ID SYSTEM_SITE Y_LAT X_LONGT Y_LAT_new X_LONGT_new
## 1 51 NORRISH CREEK 49.173172 -122.135356 NA NA
## 2 54 HAWKINS CREEK 49.173172 -122.135356 49.169178 -122.19174## [1] "For group E:"## GFE_ID SYSTEM_SITE Y_LAT X_LONGT Y_LAT_new X_LONGT_new
## 1 11513 BAXTER BEACH 52.722503 -120.860114 NA NA
## 2 11514 BEAR BEACH - SHORE 52.722503 -120.860114 52.720154 -120.867586
## 3 11515 BETTY FRANK'S - SHORE 52.722503 -120.860114 52.746393 -120.837075## [1] "For group F:"## GFE_ID SYSTEM_SITE Y_LAT X_LONGT Y_LAT_new X_LONGT_new
## 1 177 LILLOOET RIVER - LOWER 49.747468 -122.145828 NA NA
## 2 2475 LILLOOET RIVER 49.747468 -122.145828 49.740213 -122.14739## [1] "For group G:"## GFE_ID SYSTEM_SITE Y_LAT X_LONGT Y_LAT_new X_LONGT_new
## 1 131 CAYOOSH CREEK 50.668727 -121.97261 50.680016 -121.929476
## 2 7990579 SETON AND CAYOOSH CREEKS 50.668727 -121.97261 NA NA## [1] "For group H:"## GFE_ID SYSTEM_SITE Y_LAT X_LONGT Y_LAT_new X_LONGT_new
## 1 24 BOISE CREEK 49.624229 -122.659958 NA NA
## 2 26776 BOISE CREEK - NORTH 49.624229 -122.659958 49.626847 -122.671116## [1] "For group I:"## GFE_ID SYSTEM_SITE Y_LAT X_LONGT Y_LAT_new
## 1 1 FRASER RIVER 49.118876 -123.191011 NA
## 2 7990634 FRASER RIVER AND TRIBUTARIES 49.118876 -123.191011 49.111242
## X_LONGT_new
## 1 NA
## 2 -123.168505## [1] "For group J:"## GFE_ID SYSTEM_SITE Y_LAT X_LONGT Y_LAT_new X_LONGT_new
## 1 2463 CHILCOTIN RIVER - LOWER 51.739953 -122.401309 NA NA
## 2 285 CHILCOTIN RIVER 51.739953 -122.401309 51.745035 -122.413504## [1] "For group K:"## GFE_ID SYSTEM_SITE Y_LAT X_LONGT Y_LAT_new X_LONGT_new
## 1 1261 SOMASS RIVER 49.246397 -124.81984 NA NA
## 2 11485 SOMASS-SPROAT-GC SYSTEM 49.246397 -124.81984 49.294603 -124.879074## [1] "For group L:"## GFE_ID SYSTEM_SITE Y_LAT X_LONGT Y_LAT_new X_LONGT_new
## 1 1310 CLAYOQUOT RIVER - LOWER 49.183381 -125.537647 NA NA
## 2 2487 CLAYOQUOT RIVER 49.183381 -125.537647 49.201198 -125.51245## [1] "For group M:"## GFE_ID SYSTEM_SITE Y_LAT X_LONGT Y_LAT_new X_LONGT_new
## 1 501255 PINKUT CREEK 54.446302 -125.460072 54.445124 -125.458809
## 2 2115 PINKUT CREEK - BELOW WEIR 54.446302 -125.460072 NA NA## [1] "For group N:"## GFE_ID SYSTEM_SITE Y_LAT X_LONGT Y_LAT_new X_LONGT_new
## 1 2678 FORESTRY CREEK 52.376885 -126.584031 52.378979 -126.581766
## 2 2680 MARTY'S CREEK 52.376885 -126.584031 NA NA## [1] "For group O:"## GFE_ID SYSTEM_SITE Y_LAT X_LONGT Y_LAT_new X_LONGT_new
## 1 1450 CAYEGHLE CREEK 50.34247 -127.439898 NA NA
## 2 2302 CAYEGHLE SYSTEM 50.34247 -127.439898 50.342682 -127.437795## [1] "For group P:"## GFE_ID SYSTEM_SITE Y_LAT X_LONGT Y_LAT_new X_LONGT_new
## 1 2439 TAKLA LAKE 55.075216 -125.538582 NA NA
## 2 19719 TAKLA - SHORE 55.075216 -125.538582 55.08134 -125.560056## [1] "For group Q:"## GFE_ID SYSTEM_SITE Y_LAT X_LONGT Y_LAT_new X_LONGT_new
## 1 501254 FULTON RIVER 54.814315 -126.146194 NA NA
## 2 2111 FULTON RIVER - BELOW WEIR 54.814315 -126.146194 54.81601 -126.163338## [1] "For group R:"## GFE_ID SYSTEM_SITE Y_LAT X_LONGT Y_LAT_new X_LONGT_new
## 1 1798 JENNY BAY CREEKS 52.22403 -127.598389 52.225501 -127.598108
## 2 2693 JENNY BAY SOUTH CREEK 52.22403 -127.598389 NA NA## [1] "For group S:"## GFE_ID SYSTEM_SITE Y_LAT X_LONGT Y_LAT_new
## 1 2687 FANNIE COVE LEFT HAND CREEK 52.043911 -128.068542 52.044541
## 2 2708 FANNIE COVE RIGHT HAND CREEK 52.043911 -128.068542 NA
## X_LONGT_new
## 1 -128.068576
## 2 NA## [1] "For group T:"## GFE_ID SYSTEM_SITE Y_LAT X_LONGT Y_LAT_new X_LONGT_new
## 1 1594 SEWELL INLET CREEK L.H. #2 52.876978 -131.949569 52.877146 -132.0007
## 2 1595 THORSEN CREEK 52.876978 -131.949569 NA NAThe fields X_LONGT and Y_LAT are updated in
CUSS, and the new field
coordinates_changed is added to indicate which locations
are concerned.
## [1] "The fields 'X_LONGT' and 'Y_LAT' are updated in CUSS, and the new field 'coordinates_changed' is added to indicate which locations are concerned."# check is there still are different GFE_IDs with same coordinates:
coord_duplicated <- locations[,c("X_LONGT","Y_LAT")][duplicated(locations[,c("X_LONGT","Y_LAT")]),]
nrow(coord_duplicated) # 0## [1] 04 Merge NUSEDS and CUSS
At this stage NUSEDS and CUSS have
the same 7094 time series and can consequently be merged using the
common fields IndexId (i.e., POP_ID) and
GFE_ID.
col_common <- c("IndexId","POP_ID","GFE_ID")
col_nuseds <- c("SPECIES","POPULATION","WATERBODY","AREA","Year","MAX_ESTIMATE",
"ENUMERATION_METHODS", #
"ESTIMATE_CLASSIFICATION",
"ESTIMATE_METHOD",
"GAZETTED_NAME",
"LOCAL_NAME_1",
"LOCAL_NAME_2",
"ADULT_PRESENCE",
"JACK_PRESENCE")
col_cuss <- c("SPECIES_QUALIFIED","CU_NAME","CU_TYPE","FAZ_ACRO","JAZ_ACRO","MAZ_ACRO",
"FULL_CU_IN","SYSTEM_SITE","Y_LAT","X_LONGT","IS_INDICATOR",
"CU_LAT","CU_LONGT","coordinates_changed")
nuseds_final <- base::merge(x = all_areas_nuseds[,c(col_common,col_nuseds)],
y = conservation_unit_system_sites[,c(col_common,col_cuss)],
by = col_common,
all.x = T)5 Additional fixes
5.1 Replace zeros by NAs (optional)
So far we have not been able to determine which zeros are actual 0s and those which should be NAs. We consequently implemented the option to replace all 0s by NAs (n = 3453, or 1.1% of the data points).
Decision made:
## [1] "Zeros are NOT replaced by NAs."5.2 Multiple series of same CU in one location
There are many cases where a CU in a given location (i.e., a unique
GFE_ID) is associated to multiple series
(i.e. IndexId/POP_ID), which should not
happen. Observing these cases reveals clear duplicated data points or
single data point that are not worth keeping. To fix these issues we
proceed as follow:
Case 1: one of the duplicated series has only one data point:
if it is complementary: merge to the other (longer) series
if it is in conflict or a duplicate: remove the focal series
Case 2: the shorter series is 100% duplicated: removed the focal series
Case 3: for the rest of the duplicated series,
points that are conflictual or duplicated are summed up
points that are complementary are merged
By summing data points in a few cases, we assume that the different runs (e.g., “Chinook Run 1” and “Chinook Run 2”) can be considered a single population. For example, the Bridge River has Summer and Late run sockeye surveys, but these are both in the MIDDLE FRASER river-type sockeye CU and are summed to yield the Bridge River survey for that CU in the PSE.
The figures below show the time series before and after correction with the action made (i.e., “MERGED”, “DELETED”, “SUMMED”) indicated.
There are a few instances where a special fix is done, as indicated below in the corresponding figures.
In the few instances where data points are summed, we define the
ESTIMATE_CLASSIFICATION (e.g., “RELATIVE ABUNDANCE
(TYPE-3)”) as the value corresponding to the highest
MAX_ESTIMATE value between the two data points. In these
cases, a table follows the figure and show the data points that are
summed with their corresponding Year and
ESTIMATE_CLASSIFICATION.
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "Below is MAX_ESTIMATE and ESTIMATE_CLASSIFICATION for the data points summed:"
## GFE_ID Year IndexId_s1 MAX_ESTIMATE_s1 ESTIMATE_CLASSIFICATION_s1 IndexId_s2
## 1 800 2003 CM_49081 1877 RELATIVE ABUNDANCE (TYPE-4) CM_49080
## MAX_ESTIMATE_s2 ESTIMATE_CLASSIFICATION_s2
## 1 2603 RELATIVE ABUNDANCE (TYPE-5)
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "Special fix (above): the blue points before 1950 are deleted, the other ones are summed to the red series."
## [1] "Below is MAX_ESTIMATE and ESTIMATE_CLASSIFICATION for the data points summed:"
## GFE_ID Year IndexId_s1 MAX_ESTIMATE_s1 ESTIMATE_CLASSIFICATION_s1
## 10 816 1995 CM_50537 3000 RELATIVE ABUNDANCE (TYPE-5)
## 11 816 1996 CM_50537 2200 RELATIVE ABUNDANCE (TYPE-5)
## 12 816 1997 CM_50537 1000 RELATIVE ABUNDANCE (TYPE-5)
## 13 816 1998 CM_50537 1000 RELATIVE ABUNDANCE (TYPE-5)
## 14 816 2000 CM_50537 200 RELATIVE ABUNDANCE (TYPE-5)
## 15 816 2002 CM_50537 2012 PRESENCE-ABSENCE (TYPE-6)
## 16 816 2003 CM_50537 215 RELATIVE ABUNDANCE (TYPE-5)
## 17 816 2005 CM_50537 107 RELATIVE ABUNDANCE (TYPE-5)
## IndexId_s2 MAX_ESTIMATE_s2 ESTIMATE_CLASSIFICATION_s2
## 10 CM_50536 27000 RELATIVE ABUNDANCE (TYPE-5)
## 11 CM_50536 2300 RELATIVE ABUNDANCE (TYPE-5)
## 12 CM_50536 6000 RELATIVE ABUNDANCE (TYPE-5)
## 13 CM_50536 4000 RELATIVE ABUNDANCE (TYPE-5)
## 14 CM_50536 6800 RELATIVE ABUNDANCE (TYPE-5)
## 15 CM_50536 20567 PRESENCE-ABSENCE (TYPE-6)
## 16 CM_50536 71023 RELATIVE ABUNDANCE (TYPE-3)
## 17 CM_50536 2354 RELATIVE ABUNDANCE (TYPE-3)
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "Below is MAX_ESTIMATE and ESTIMATE_CLASSIFICATION for the data points summed:"
## GFE_ID Year IndexId_s1 MAX_ESTIMATE_s1 ESTIMATE_CLASSIFICATION_s1 IndexId_s2
## 1 861 1995 CM_50987 1000 UNKNOWN CM_50986
## 2 861 1996 CM_50987 350 UNKNOWN CM_50986
## MAX_ESTIMATE_s2 ESTIMATE_CLASSIFICATION_s2
## 1 800 UNKNOWN
## 2 450 UNKNOWN
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "Below is MAX_ESTIMATE and ESTIMATE_CLASSIFICATION for the data points summed:"
## GFE_ID Year IndexId_s1 MAX_ESTIMATE_s1 ESTIMATE_CLASSIFICATION_s1 IndexId_s2
## 1 968 1994 CM_51772 10000 UNKNOWN CM_51771
## 2 968 1997 CM_51772 10000 UNKNOWN CM_51771
## 3 968 1999 CM_51772 5000 UNKNOWN CM_51771
## MAX_ESTIMATE_s2 ESTIMATE_CLASSIFICATION_s2
## 1 110000 UNKNOWN
## 2 85000 UNKNOWN
## 3 70000 UNKNOWN
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "Special fix (above): the two red points are deleted; one is a duplicate, there other one has 'UNKNOWN' ESTIMATE_CLASSIFICATION:"
## [1] GFE_ID Year
## [3] IndexId_s1 MAX_ESTIMATE_s1
## [5] ESTIMATE_CLASSIFICATION_s1 IndexId_s2
## [7] MAX_ESTIMATE_s2 ESTIMATE_CLASSIFICATION_s2
## <0 rows> (or 0-length row.names)
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "Below is MAX_ESTIMATE and ESTIMATE_CLASSIFICATION for the data points summed:"
## GFE_ID Year IndexId_s1 MAX_ESTIMATE_s1 ESTIMATE_CLASSIFICATION_s1
## 1 214 1999 CN_46187 432 RELATIVE: VARYING MULTI-YEAR METHODS
## IndexId_s2 MAX_ESTIMATE_s2 ESTIMATE_CLASSIFICATION_s2
## 1 CN_46186 114 RELATIVE ABUNDANCE (TYPE-4)
## [1] "***"
## [1] "Below is MAX_ESTIMATE and ESTIMATE_CLASSIFICATION for the data points summed:"
## GFE_ID Year IndexId_s1 MAX_ESTIMATE_s1 ESTIMATE_CLASSIFICATION_s1
## 1 215 1999 CN_46197 237 RELATIVE: VARYING MULTI-YEAR METHODS
## IndexId_s2 MAX_ESTIMATE_s2 ESTIMATE_CLASSIFICATION_s2
## 1 CN_46196 208 RELATIVE ABUNDANCE (TYPE-4)
## [1] "***"
## [1] "Below is MAX_ESTIMATE and ESTIMATE_CLASSIFICATION for the data points summed:"
## GFE_ID Year IndexId_s1 MAX_ESTIMATE_s1 ESTIMATE_CLASSIFICATION_s1
## 1 176 1998 CN_46962 2141 RELATIVE: CONSTANT MULTI-YEAR METHODS
## 2 176 2008 CN_46962 421 RELATIVE ABUNDANCE (TYPE-4)
## IndexId_s2 MAX_ESTIMATE_s2 ESTIMATE_CLASSIFICATION_s2
## 1 CN_46961 1098 RELATIVE ABUNDANCE (TYPE-4)
## 2 CN_46961 422 RELATIVE ABUNDANCE (TYPE-4)
## [1] "***"
## [1] "Special fix (above): the two blue points are deleted; one is a duplicate, there other one is very close to be one."
## [1] "***"
## [1] "***"
## [1] "Below is MAX_ESTIMATE and ESTIMATE_CLASSIFICATION for the data points summed:"
## GFE_ID Year IndexId_s1 MAX_ESTIMATE_s1 ESTIMATE_CLASSIFICATION_s1 IndexId_s2
## 1 241 1998 CO_1720 309 UNKNOWN CO_46441
## MAX_ESTIMATE_s2 ESTIMATE_CLASSIFICATION_s2
## 1 206 UNKNOWN
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "Below is MAX_ESTIMATE and ESTIMATE_CLASSIFICATION for the data points summed:"
## GFE_ID Year IndexId_s1 MAX_ESTIMATE_s1 ESTIMATE_CLASSIFICATION_s1 IndexId_s2
## 2 129 2008 CO_44539 15 RELATIVE ABUNDANCE (TYPE-4) CO_47183
## 3 129 2009 CO_44539 101 RELATIVE ABUNDANCE (TYPE-3) CO_47183
## MAX_ESTIMATE_s2 ESTIMATE_CLASSIFICATION_s2
## 2 33 RELATIVE ABUNDANCE (TYPE-4)
## 3 46 RELATIVE ABUNDANCE (TYPE-3)
## [1] "***"
## [1] "***"
## [1] "Below is MAX_ESTIMATE and ESTIMATE_CLASSIFICATION for the data points summed:"
## GFE_ID Year IndexId_s1 MAX_ESTIMATE_s1 ESTIMATE_CLASSIFICATION_s1 IndexId_s2
## 1 896 1995 CO_49517 200 UNKNOWN CO_49516
## 2 896 1996 CO_49517 100 UNKNOWN CO_49516
## MAX_ESTIMATE_s2 ESTIMATE_CLASSIFICATION_s2
## 1 400 UNKNOWN
## 2 800 UNKNOWN
## [1] "***"
## [1] "***"
## [1] "Below is MAX_ESTIMATE and ESTIMATE_CLASSIFICATION for the data points summed:"
## GFE_ID Year IndexId_s1 MAX_ESTIMATE_s1 ESTIMATE_CLASSIFICATION_s1 IndexId_s2
## 1 899 1994 CO_49547 600 UNKNOWN CO_49546
## 2 899 1996 CO_49547 350 UNKNOWN CO_49546
## 3 899 1997 CO_49547 50 UNKNOWN CO_49546
## MAX_ESTIMATE_s2 ESTIMATE_CLASSIFICATION_s2
## 1 300 UNKNOWN
## 2 200 UNKNOWN
## 3 100 UNKNOWN
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "Below is MAX_ESTIMATE and ESTIMATE_CLASSIFICATION for the data points summed:"
## GFE_ID Year IndexId_s1 MAX_ESTIMATE_s1 ESTIMATE_CLASSIFICATION_s1 IndexId_s2
## 1 850 1992 CO_50873 100 UNKNOWN CO_50872
## 2 850 1993 CO_50873 60 UNKNOWN CO_50872
## MAX_ESTIMATE_s2 ESTIMATE_CLASSIFICATION_s2
## 1 250 UNKNOWN
## 2 211 UNKNOWN
## [1] "***"
## [1] "Below is MAX_ESTIMATE and ESTIMATE_CLASSIFICATION for the data points summed:"
## GFE_ID Year IndexId_s1 MAX_ESTIMATE_s1 ESTIMATE_CLASSIFICATION_s1 IndexId_s2
## 1 852 1993 CO_50893 1370 UNKNOWN CO_50892
## 2 852 1995 CO_50893 420 UNKNOWN CO_50892
## MAX_ESTIMATE_s2 ESTIMATE_CLASSIFICATION_s2
## 1 28 UNKNOWN
## 2 220 UNKNOWN
## [1] "***"
## [1] "***"
## [1] "Below is MAX_ESTIMATE and ESTIMATE_CLASSIFICATION for the data points summed:"
## GFE_ID Year IndexId_s1 MAX_ESTIMATE_s1 ESTIMATE_CLASSIFICATION_s1 IndexId_s2
## 2 860 1995 CO_50973 150 UNKNOWN CO_50972
## MAX_ESTIMATE_s2 ESTIMATE_CLASSIFICATION_s2
## 2 392 UNKNOWN
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "Below is MAX_ESTIMATE and ESTIMATE_CLASSIFICATION for the data points summed:"
## GFE_ID Year IndexId_s1 MAX_ESTIMATE_s1 ESTIMATE_CLASSIFICATION_s1 IndexId_s2
## 1 874 1997 CO_51113 100 UNKNOWN CO_51112
## 2 874 1998 CO_51113 9500 UNKNOWN CO_51112
## MAX_ESTIMATE_s2 ESTIMATE_CLASSIFICATION_s2
## 1 25 UNKNOWN
## 2 3700 UNKNOWN
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "Below is MAX_ESTIMATE and ESTIMATE_CLASSIFICATION for the data points summed:"
## GFE_ID Year IndexId_s1 MAX_ESTIMATE_s1 ESTIMATE_CLASSIFICATION_s1 IndexId_s2
## 1 133 2013 SX_7728 25 RELATIVE ABUNDANCE (TYPE-4) SX_47221
## 2 133 2014 SX_7728 68 RELATIVE ABUNDANCE (TYPE-3) SX_47221
## 3 133 2016 SX_7728 0 RELATIVE ABUNDANCE (TYPE-4) SX_47221
## 4 133 2017 SX_7728 0 RELATIVE ABUNDANCE (TYPE-3) SX_47221
## 5 133 2018 SX_7728 0 RELATIVE ABUNDANCE (TYPE-3) SX_47221
## 6 133 2019 SX_7728 4 RELATIVE ABUNDANCE (TYPE-4) SX_47221
## 7 133 2022 SX_7728 0 RELATIVE ABUNDANCE (TYPE-4) SX_47221
## MAX_ESTIMATE_s2 ESTIMATE_CLASSIFICATION_s2
## 1 2131 RELATIVE ABUNDANCE (TYPE-4)
## 2 502 RELATIVE ABUNDANCE (TYPE-3)
## 3 61 RELATIVE ABUNDANCE (TYPE-3)
## 4 158 RELATIVE ABUNDANCE (TYPE-3)
## 5 88 RELATIVE ABUNDANCE (TYPE-3)
## 6 121 RELATIVE ABUNDANCE (TYPE-4)
## 7 4844 RELATIVE ABUNDANCE (TYPE-4)
## [1] "***"
## [1] "***"
## [1] "***"
## [1] "***"6 Export datasets
The following files are exported:
1_NuSEDS_escapement_data_collated_DATE.csv: the cleaned combined NUSEDS and CUSS datasets
1_series_inNUSEDS_noInCUSS_DATE.csv: information about the series in NUSEDS and not in CUSS
1_series_removed_DATE.csv: the series removed from either NUSEDS or CUSS and why
1_series_added_DATE.csv: the series added to either NUSEDS or CUSS and why
log_file.csv: the log file reporting the name of the main file exported, the date of the export, the name of the present script, the name of the original NUSEDS or CUSS files and the choices related to removing zeros or not.