New field in 2020 data call

[hgerritsen]

Hello, The 2020 data call asks for a new field: Anonymized vessel id. From the 2019 WGFSD report i understand that this means that for rows with 2 vessels or less should be disaggregated by vessel (if there are 2) and a vessel id should be provided. I have put together some code, that i think could do the trick and could be added to the workflow script (around line 512). I am not 100% sure that it is ok and there may be a better way but here is my attempt:

VE_lut <- data.frame(VE_REF=unique(c(table1$VE_REF,table2$VE_REF)))
VE_lut$VE_ID <- paste0('IRL',sprintf("%03d", 1:nrow(VE_lut))) # use relevant country code!
## check that there are fewer than 999 unique vessels!
nrow(VE_lut)

table1 <- left_join(table1,VE_lut)
table2 <- left_join(table2,VE_lut)

table1 <- table1 %>%
    group_by(RT, VE_COU,
             Year, Month,
             Csquare, LENGTHCAT,
             LE_GEAR, LE_MET) %>% 
    mutate(n_vessels = n_distinct(VE_REF, na.rm = TRUE))
table1$VE_ID[table1$n_vessels>2] <- NA #only provide vessel id for cells with 1 or 2 vessels

## Aggregation of VMS data:
table1Save <- table1 %>%
    group_by(RT, VE_COU,
             Year, Month,
             Csquare, LENGTHCAT,
             LE_GEAR, LE_MET, VE_ID) %>%
    summarise(sum_intv = sum(INTV, na.rm = TRUE),
              sum_kwHour = sum(kwHour, na.rm = TRUE),
              sum_le_kg_tot = sum(LE_KG_TOT, na.rm = TRUE),
              sum_le_euro_tot = sum(LE_EURO_TOT, na.rm = TRUE),
              mean_si_sp = mean(SI_SP, na.rm = TRUE),
              mean_ve_len = mean(VE_LEN, na.rm = TRUE),
              mean_ve_kf = mean(VE_KW, na.rm = TRUE),
              n_vessels = n_distinct(VE_REF, na.rm = TRUE)) %>%
    as.data.frame()

table2 <- table2 %>%
    group_by(RT, VE_COU,
             Year, Month,
             LE_RECT, LE_GEAR,
             LE_MET, LENGTHCAT,
             tripInTacsat) %>%
    mutate(n_vessels = n_distinct(VE_REF, na.rm = TRUE))
table2$VE_ID[table2$n_vessels>2] <- NA #only provide vessel id for cells with 1 or 2 vessels

## Aggregation of LogBook data:
table2Save <- table2 %>%
    group_by(RT, VE_COU,
             Year, Month,
             LE_RECT, LE_GEAR,
             LE_MET, VE_ID, LENGTHCAT,
             tripInTacsat) %>%
    summarise(sum_intv = sum(INTV, na.rm = TRUE),
              sum_kwDays = sum(kwDays, na.rm = TRUE),
              sum_le_kg_tot = sum(LE_KG_TOT, na.rm = TRUE),
              sum_le_euro_tot = sum( LE_EURO_TOT, na.rm = TRUE),
              n_vessels = n_distinct(VE_REF, na.rm = TRUE)) %>%
    as.data.frame()

[colinpmillar]

Thanks Hans - will review and add in tonight - can I add you as author of the commit?

[hgerritsen]

Yes, that would be good. I didn’t want to go messing with the code, so I raised it as an issue, rather than requesting write access to the github but if you think it makes sense I would be happy to add it to the script. I also informed the WGSFD chairs by email. Hans

From: Colin Millar [mailto:notifications@github.com] Sent: Wednesday 26 February 2020 15:43 To: ices-eg/wg_WGSFD wg_WGSFD@noreply.github.com Cc: Hans Gerritsen hans.Gerritsen@Marine.ie; Author author@noreply.github.com Subject: Re: [ices-eg/wg_WGSFD] New field in 2020 data call (#23)

Thanks Hans - will review and add in tonight - can I add you as author of the commit?

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[colinpmillar]

Actually you are in the WGSFD sharepoint group - so I can give you write access. That might be easier, as you have actual data to work with - I just have mocked up data.

If are up for that - would you mind looking at adding it to the https://github.com/ices-eg/wg_WGSFD/tree/test-workflow branch?

[hgerritsen]

OK

[hgerritsen]

Done.

[colinpmillar]

thanks so much!!