unfit/cleanPacFIN_notes.R
In iantaylor-NOAA/Lingcod_2021: Estimate the Status of Lingcod off the US West Coast in 2021
Gear groupings reflect those in the table at
https://pacfin.psmfc.org/pacfin_pub/data_rpts_pub/code_lists/gr.txt
GRID was assigned to geargroup with the following names:
HKL MSC NET POT TLS TWL TWS
26236 5 769 1457 636 101559 106
There are 0 records for which the state (i.e., 'CA', 'OR', 'WA')
could not be assigned and were labeled as 'UNK'.
CA OR WA
21941 40810 68299
SEX recoded from input (rows) to output (columns):
output
input F M U <NA>
F 68609 0 0 0
M 0 32076 0 0
U 0 0 30186 0
<NA> 0 0 179 0
The following length types were kept in the data:
output
F T U
84659 664 44915
Lengths range from 198 to 1550 (mm).
Ages ranged from 1 to 35 (years).
The table below includes the number of samples (n) per ageing method.
Each age sequence number, the PacFIN delineation for age read, has its own column.
The number of columns depends on the maximum number of age reads available.
If ANY method for a given fish matches those in keep, then that age will be kept
even if PacFIN did not use the age to create the final fish age.
AGE_METHOD1 AGE_METHOD2 AGE_METHOD3 n
1 3 <NA> <NA> 1
2 9 <NA> <NA> 148
3 B <NA> <NA> 8
4 L <NA> <NA> 1
5 T B <NA> 657
6 T T <NA> 642
7 T <NA> <NA> 40435
8 <NA> T <NA> 16
9 <NA> <NA> <NA> 89142
FISH_AGE_YEARS_FINAL matches value(s) for agers 1, 2, ...; NA means no exact match.
agematch
1 2 3 <NA>
41207 336 5 44
Investigate the following SAMPLES for errors because
FISH_AGE_YEARS_FINAL doesn't match the mean of all reads:
FISH_AGE_CODE_FINAL FISH_AGE_YEARS_FINAL age1 age2 age3
49240 NA 5 1 NA NA
63453 NA 6 5 5 NA
63855 NA 5 6 6 NA
63983 NA 4 6 5 NA
66102 NA 11 9 10 NA
66548 NA 8 9 10 NA
66744 NA 3 5 4 NA
66960 NA 12 13 14 NA
67899 NA 6 8 7 NA
68320 NA 8 7 6 NA
69681 NA 8 7 6 NA
69833 NA 6 9 NA NA
70731 NA 6 9 NA NA
75499 NA 8 7 6 NA
75547 NA 13 10 9 NA
75551 NA 13 12 11 NA
75571 NA 8 7 6 NA
76400 NA 10 9 8 NA
77010 NA 7 5 6 NA
77098 NA 7 5 5 NA
113494 NA 11 1 NA NA
The table below summarizes the number of records that are outside of
the area that should be included for US West Coast stock assessments
by PSMFC area, or some derivative thereof.
description
PSMFC CAN CAN (VNCVR) Sound and Straits
3D 0 2531 0
4A 0 0 2696
5A 4328 0 0
5B 9896 0 0
5C 118 0 0
N SAMPLE_TYPEs changed from M to S for special samples from OR: 0
N not in keep_sample_type (SAMPLE_TYPE): 3901
N with SAMPLE_TYPE of NA: 25
N not in keep_sample_method (SAMPLE_METHOD): 311
N with SAMPLE_NO of NA: 0
N without length: 812
N without Age: 89423
N without length and Age: 89687
N sample weights not available for OR: 231
N records: 131050
N remaining if CLEAN: 108131
N removed if CLEAN: 22919
> sink("cleanPacFIN.txt", split=TRUE)
> test <- PacFIN.Utilities::cleanPacFIN(bds.pacfin,
+ CLEAN = TRUE,
+ verbose = TRUE)
Gear groupings reflect those in the table at
https://pacfin.psmfc.org/pacfin_pub/data_rpts_pub/code_lists/gr.txt
GRID was assigned to geargroup with the following names:
HKL MSC NET POT TLS TWL TWS
26236 5 769 1457 636 101559 106
There are 0 records for which the state (i.e., 'CA', 'OR', 'WA')
could not be assigned and were labeled as 'UNK'.
CA OR WA
21941 40810 68299
SEX recoded from input (rows) to output (columns):
output
input F M U <NA>
F 68609 0 0 0
M 0 32076 0 0
U 0 0 30186 0
<NA> 0 0 179 0
The following length types were kept in the data:
output
F T U
84659 664 44915
Lengths range from 198 to 1550 (mm).
Ages ranged from 1 to 35 (years).
The table below includes the number of samples (n) per ageing method.
Each age sequence number, the PacFIN delineation for age read, has its own column.
The number of columns depends on the maximum number of age reads available.
If ANY method for a given fish matches those in keep, then that age will be kept
even if PacFIN did not use the age to create the final fish age.
AGE_METHOD1 AGE_METHOD2 AGE_METHOD3 n
1 3 <NA> <NA> 1
2 9 <NA> <NA> 148
3 B <NA> <NA> 8
4 L <NA> <NA> 1
5 T B <NA> 657
6 T T <NA> 642
7 T <NA> <NA> 40435
8 <NA> T <NA> 16
9 <NA> <NA> <NA> 89142
FISH_AGE_YEARS_FINAL matches value(s) for agers 1, 2, ...; NA means no exact match.
agematch
1 2 3 <NA>
41207 336 5 44
Investigate the following SAMPLES for errors because
FISH_AGE_YEARS_FINAL doesn't match the mean of all reads:
FISH_AGE_CODE_FINAL FISH_AGE_YEARS_FINAL age1 age2 age3
49240 NA 5 1 NA NA
63453 NA 6 5 5 NA
63855 NA 5 6 6 NA
63983 NA 4 6 5 NA
66102 NA 11 9 10 NA
66548 NA 8 9 10 NA
66744 NA 3 5 4 NA
66960 NA 12 13 14 NA
67899 NA 6 8 7 NA
68320 NA 8 7 6 NA
69681 NA 8 7 6 NA
69833 NA 6 9 NA NA
70731 NA 6 9 NA NA
75499 NA 8 7 6 NA
75547 NA 13 10 9 NA
75551 NA 13 12 11 NA
75571 NA 8 7 6 NA
76400 NA 10 9 8 NA
77010 NA 7 5 6 NA
77098 NA 7 5 5 NA
113494 NA 11 1 NA NA
The table below summarizes the number of records that are outside of
the area that should be included for US West Coast stock assessments
by PSMFC area, or some derivative thereof.
description
PSMFC CAN CAN (VNCVR) Sound and Straits
3D 0 2531 0
4A 0 0 2696
5A 4328 0 0
5B 9896 0 0
5C 118 0 0
N SAMPLE_TYPEs changed from M to S for special samples from OR: 0
N not in keep_sample_type (SAMPLE_TYPE): 3901
N with SAMPLE_TYPE of NA: 25
N not in keep_sample_method (SAMPLE_METHOD): 311
N with SAMPLE_NO of NA: 0
N without length: 812
N without Age: 89423
N without length and Age: 89687
N sample weights not available for OR: 231
N records: 131050
N remaining if CLEAN: 108131
N removed if CLEAN: 22919
iantaylor-NOAA/Lingcod_2021 documentation built on Oct. 30, 2024, 6:42 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Gear groupings reflect those in the table at
https://pacfin.psmfc.org/pacfin_pub/data_rpts_pub/code_lists/gr.txt
GRID was assigned to geargroup with the following names:
HKL MSC NET POT TLS TWL TWS
26236 5 769 1457 636 101559 106
There are 0 records for which the state (i.e., 'CA', 'OR', 'WA')
could not be assigned and were labeled as 'UNK'.
CA OR WA
21941 40810 68299
SEX recoded from input (rows) to output (columns):
output
input F M U <NA>
F 68609 0 0 0
M 0 32076 0 0
U 0 0 30186 0
<NA> 0 0 179 0
The following length types were kept in the data:
output
F T U
84659 664 44915
Lengths range from 198 to 1550 (mm).
Ages ranged from 1 to 35 (years).
The table below includes the number of samples (n) per ageing method.
Each age sequence number, the PacFIN delineation for age read, has its own column.
The number of columns depends on the maximum number of age reads available.
If ANY method for a given fish matches those in keep, then that age will be kept
even if PacFIN did not use the age to create the final fish age.
AGE_METHOD1 AGE_METHOD2 AGE_METHOD3 n
1 3 <NA> <NA> 1
2 9 <NA> <NA> 148
3 B <NA> <NA> 8
4 L <NA> <NA> 1
5 T B <NA> 657
6 T T <NA> 642
7 T <NA> <NA> 40435
8 <NA> T <NA> 16
9 <NA> <NA> <NA> 89142
FISH_AGE_YEARS_FINAL matches value(s) for agers 1, 2, ...; NA means no exact match.
agematch
1 2 3 <NA>
41207 336 5 44
Investigate the following SAMPLES for errors because
FISH_AGE_YEARS_FINAL doesn't match the mean of all reads:
FISH_AGE_CODE_FINAL FISH_AGE_YEARS_FINAL age1 age2 age3
49240 NA 5 1 NA NA
63453 NA 6 5 5 NA
63855 NA 5 6 6 NA
63983 NA 4 6 5 NA
66102 NA 11 9 10 NA
66548 NA 8 9 10 NA
66744 NA 3 5 4 NA
66960 NA 12 13 14 NA
67899 NA 6 8 7 NA
68320 NA 8 7 6 NA
69681 NA 8 7 6 NA
69833 NA 6 9 NA NA
70731 NA 6 9 NA NA
75499 NA 8 7 6 NA
75547 NA 13 10 9 NA
75551 NA 13 12 11 NA
75571 NA 8 7 6 NA
76400 NA 10 9 8 NA
77010 NA 7 5 6 NA
77098 NA 7 5 5 NA
113494 NA 11 1 NA NA
The table below summarizes the number of records that are outside of
the area that should be included for US West Coast stock assessments
by PSMFC area, or some derivative thereof.
description
PSMFC CAN CAN (VNCVR) Sound and Straits
3D 0 2531 0
4A 0 0 2696
5A 4328 0 0
5B 9896 0 0
5C 118 0 0
N SAMPLE_TYPEs changed from M to S for special samples from OR: 0
N not in keep_sample_type (SAMPLE_TYPE): 3901
N with SAMPLE_TYPE of NA: 25
N not in keep_sample_method (SAMPLE_METHOD): 311
N with SAMPLE_NO of NA: 0
N without length: 812
N without Age: 89423
N without length and Age: 89687
N sample weights not available for OR: 231
N records: 131050
N remaining if CLEAN: 108131
N removed if CLEAN: 22919
> sink("cleanPacFIN.txt", split=TRUE)
> test <- PacFIN.Utilities::cleanPacFIN(bds.pacfin,
+ CLEAN = TRUE,
+ verbose = TRUE)
Gear groupings reflect those in the table at
https://pacfin.psmfc.org/pacfin_pub/data_rpts_pub/code_lists/gr.txt
GRID was assigned to geargroup with the following names:
HKL MSC NET POT TLS TWL TWS
26236 5 769 1457 636 101559 106
There are 0 records for which the state (i.e., 'CA', 'OR', 'WA')
could not be assigned and were labeled as 'UNK'.
CA OR WA
21941 40810 68299
SEX recoded from input (rows) to output (columns):
output
input F M U <NA>
F 68609 0 0 0
M 0 32076 0 0
U 0 0 30186 0
<NA> 0 0 179 0
The following length types were kept in the data:
output
F T U
84659 664 44915
Lengths range from 198 to 1550 (mm).
Ages ranged from 1 to 35 (years).
The table below includes the number of samples (n) per ageing method.
Each age sequence number, the PacFIN delineation for age read, has its own column.
The number of columns depends on the maximum number of age reads available.
If ANY method for a given fish matches those in keep, then that age will be kept
even if PacFIN did not use the age to create the final fish age.
AGE_METHOD1 AGE_METHOD2 AGE_METHOD3 n
1 3 <NA> <NA> 1
2 9 <NA> <NA> 148
3 B <NA> <NA> 8
4 L <NA> <NA> 1
5 T B <NA> 657
6 T T <NA> 642
7 T <NA> <NA> 40435
8 <NA> T <NA> 16
9 <NA> <NA> <NA> 89142
FISH_AGE_YEARS_FINAL matches value(s) for agers 1, 2, ...; NA means no exact match.
agematch
1 2 3 <NA>
41207 336 5 44
Investigate the following SAMPLES for errors because
FISH_AGE_YEARS_FINAL doesn't match the mean of all reads:
FISH_AGE_CODE_FINAL FISH_AGE_YEARS_FINAL age1 age2 age3
49240 NA 5 1 NA NA
63453 NA 6 5 5 NA
63855 NA 5 6 6 NA
63983 NA 4 6 5 NA
66102 NA 11 9 10 NA
66548 NA 8 9 10 NA
66744 NA 3 5 4 NA
66960 NA 12 13 14 NA
67899 NA 6 8 7 NA
68320 NA 8 7 6 NA
69681 NA 8 7 6 NA
69833 NA 6 9 NA NA
70731 NA 6 9 NA NA
75499 NA 8 7 6 NA
75547 NA 13 10 9 NA
75551 NA 13 12 11 NA
75571 NA 8 7 6 NA
76400 NA 10 9 8 NA
77010 NA 7 5 6 NA
77098 NA 7 5 5 NA
113494 NA 11 1 NA NA
The table below summarizes the number of records that are outside of
the area that should be included for US West Coast stock assessments
by PSMFC area, or some derivative thereof.
description
PSMFC CAN CAN (VNCVR) Sound and Straits
3D 0 2531 0
4A 0 0 2696
5A 4328 0 0
5B 9896 0 0
5C 118 0 0
N SAMPLE_TYPEs changed from M to S for special samples from OR: 0
N not in keep_sample_type (SAMPLE_TYPE): 3901
N with SAMPLE_TYPE of NA: 25
N not in keep_sample_method (SAMPLE_METHOD): 311
N with SAMPLE_NO of NA: 0
N without length: 812
N without Age: 89423
N without length and Age: 89687
N sample weights not available for OR: 231
N records: 131050
N remaining if CLEAN: 108131
N removed if CLEAN: 22919
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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