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Index Based Methods Working Group
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Error in summarize_results.R #37

Closed liz-brooks closed 4 years ago

liz-brooks commented 4 years ago

Error: Problem with mutate() input om_ssb. ✖ $ operator is invalid for atomic vectors ℹ Input om_ssb is map(wham, ~pluck(.x$result$sim_data_series$SSB)).

i ran this on results of progress table rows 1-111 and tried again on results from progress table rows 1-2775 (25 iterations of the first 111 entries).

1 run (111 rows) took 2.65 mins and 72,268 KB 25 runs (2775 rows) took 49.3 mins and 1.558 GB

i did not upload output .rds file but will if that would help.

timjmiller commented 4 years ago

Is "results" one of the elements of mse_output? If so, is "sim_data_series" an element of mse_output$results ? I'm just wondering if the structure of mse_output is different than expected on line 25 of summarize_results.R. If the needed elements are there, but in a different list structure, then it is just a matter of changing the code of summarize_results.R to get that structure right.

On Tue, Sep 22, 2020 at 1:11 PM Liz Brooks notifications@github.com wrote:

Error: Problem with mutate() input om_ssb. ✖ $ operator is invalid for atomic vectors ℹ Input om_ssb is map(wham, ~pluck(.x$result$sim_data_series$SSB)).

i ran this on results of progress table rows 1-111 and tried again on results from progress table rows 1-2775 (25 iterations of the first 111 entries).

1 run (111 rows) took 2.65 mins and 72,268 KB 25 runs (2775 rows) took 49.3 mins and 1.558 GB

i did not upload output .rds file but will if that would help.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/cmlegault/IBMWG/issues/37, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEIGN7BU735EUHG462JMA7TSHDLEFANCNFSM4RWA4WOQ .

-- Timothy J. Miller, PhD Research Fishery Biologist NOAA, Northeast Fisheries Science Center Woods Hole, MA 508-495-2365

liz-brooks commented 4 years ago

so, result exists in the object, as does result$sim_data_series, and result$sim_data_series$SSB, and that is a vector of length 90 (with reasonable looking values. i had previously noticed that there are two objects named "input" in $result (see below) and remembered that when i saw chris's email about that this morning. doesn't seem like that is related to this issue, but should be checked. i can replicate that error by looking at mse_output$wham[[x]]$result$sim_data_series$SSB and it first craps out where x=18 (below in blue). it looks like the 18th entry corresponds to 17001 true_Skate_CR in the progress table. and there are quite a few other rows with the same problem, not all the same method (pasted below). does that help diagnose the issue?

names(mse_output)[1] "rowid" "iscen" "specs" "isim" "seed" "wham" > names(mse_output$wham)NULL> names(mse_output$wham[[1]])[1] "result" "error" > names(mse_output$wham[[1]]$result) [1] "sim_data_series" "advice" "refpts" "input" "observed_om" "true_om" [7] "true_sim" "observed_sim" "seed" "input"

length(mse_output$wham[[1]]$result$sim_data_series$SSB)[1] 90 mse_output$wham[[1]]$result$sim_data_series$SSB [1] 20384.851 18165.979 16374.400 15052.922 14351.812 14025.941 13450.704 13435.277 14246.317 15620.853 [11] 15984.823 14937.875 13252.790 11952.825 11778.782 12302.305 12831.720 13666.296 14514.980 15030.191 [21] 15105.656 14273.684 13618.811 13388.837 12880.503 11704.984 13879.203 16273.852 18922.363 21923.020 [31] 25228.758 28331.766 30078.689 30096.904 29081.504 28323.725 29469.562 33131.271 37687.540 42857.309 [41] 49082.765 54807.006 59273.905 60496.384 58640.390 55513.216 52335.378 48652.186 43430.968 38042.780 [51] 32046.479 24559.291 17978.351 12942.435 8464.255 6143.918 5341.131 4744.618 4276.841 4030.150 [61] 3841.020 3487.597 3229.279 3130.768 3106.401 3403.807 4150.007 5417.217 9583.313 17555.059 [71] 25980.112 35507.397 45815.945 59625.049 81896.732 109794.507 134706.942 150932.453 161874.380 166927.767 [81] 169489.743 171300.746 166288.714 152488.656 136923.053 120241.721 104762.001 90183.585 76928.593 66077.340 length(mse_output$wham)[1] 2775

mse_output$wham[[18]]$result$sim_data_series$SSBError in mse_output$wham[[18]]$result$sim_data_series : $ operator is invalid for atomic vectors cbind(bad, progress$IBM[bad]) bad [1,] "18" "true_Skate_CR" [2,] "19" "true_Skate_CR" [3,] "20" "true_Skate_CR" [4,] "21" "true_Skate_CR" [5,] "22" "true_Skate_CR" [6,] "23" "true_Skate_CR" [7,] "24" "true_Skate_CR" [8,] "25" "M_CC" [9,] "26" "M_CC" [10,] "27" "M_CC" [11,] "28" "M_CC" [12,] "29" "M_CC" [13,] "30" "M_CC" [14,] "31" "M_CC" [15,] "32" "M_CC" [16,] "33" "planBsmoothfxn" [17,] "58" "ExpandSurvey_modified" [18,] "59" "ExpandSurvey_modified" [19,] "60" "ExpandSurvey_modified" [20,] "61" "ExpandSurvey_modified" [21,] "62" "ExpandSurvey_modified" [22,] "63" "ExpandSurvey_modified" [23,] "64" "ExpandSurvey_modified" [24,] "65" "ExpandSurvey_modified" [25,] "74" "run.aim" [26,] "75" "run.aim" [27,] "76" "run.aim" [28,] "77" "run.aim" [29,] "78" "run.aim" [30,] "79" "run.aim" [31,] "80" "run.aim" [32,] "81" "M_CC" [33,] "82" "M_CC" [34,] "83" "M_CC" [35,] "84" "M_CC" [36,] "85" "M_CC" [37,] "86" "M_CC" [38,] "87" "M_CC" [39,] "88" "M_CC" [40,] "89" "M_CC" [41,] "90" "M_CC" [42,] "91" "M_CC" [43,] "92" "M_CC" [44,] "93" "M_CC" [45,] "94" "M_CC" [46,] "95" "M_CC" [47,] "96" "M_CC" [48,] "97" "JoeDLM"

On Tue, Sep 22, 2020 at 2:00 PM Tim Miller notifications@github.com wrote:

Is "results" one of the elements of mse_output? If so, is "sim_data_series" an element of mse_output$results ? I'm just wondering if the structure of mse_output is different than expected on line 25 of summarize_results.R. If the needed elements are there, but in a different list structure, then it is just a matter of changing the code of summarize_results.R to get that structure right.

On Tue, Sep 22, 2020 at 1:11 PM Liz Brooks notifications@github.com wrote:

Error: Problem with mutate() input om_ssb. ✖ $ operator is invalid for atomic vectors ℹ Input om_ssb is map(wham, ~pluck(.x$result$sim_data_series$SSB)).

i ran this on results of progress table rows 1-111 and tried again on results from progress table rows 1-2775 (25 iterations of the first 111 entries).

1 run (111 rows) took 2.65 mins and 72,268 KB 25 runs (2775 rows) took 49.3 mins and 1.558 GB

i did not upload output .rds file but will if that would help.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/cmlegault/IBMWG/issues/37, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AEIGN7BU735EUHG462JMA7TSHDLEFANCNFSM4RWA4WOQ

.

-- Timothy J. Miller, PhD Research Fishery Biologist NOAA, Northeast Fisheries Science Center Woods Hole, MA 508-495-2365

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/cmlegault/IBMWG/issues/37#issuecomment-696885102, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACFL5LNUQIYE4C7PTPTMH43SHDQ4XANCNFSM4RWA4WOQ .

-- 


Liz Brooks, PhD
Operations Research Analyst
Population Dynamics Branch
NOAA/NMFS
Northeast Fisheries Science Center
166 Water Street                       phone: 508.495.2238
Woods Hole, MA  02543             fax: 508.495.2393
cmlegault commented 4 years ago

All IBMs appear to be working. Thanks everyone!