In ices-tools-prod/fisheryO: Fisheries Overviews for ICES Advice

library(fisheryO)

active_year = 2017
ecoregion = "Baltic Sea Ecoregion"


stockPlot <- frmt_summary_tbl(active_year)$summary_table_frmt %>%
  filter(grepl(pattern = ecoregion, EcoRegion)) %>%
  select(-EcoRegion) %>%
  distinct(.keep_all = TRUE) %>%
  arrange(StockCode)

grey.path <- "~/git/ices-dk/fisheryO/inst/symbols/grey_q.png"
red.path <- "~/git/ices-dk/fisheryO/inst/symbols/red_cross.png"
green.path <- "~/git/ices-dk/fisheryO/inst/symbols/green_check.png"
orange.path <- "~/git/ices-dk/fisheryO/inst/symbols/orange_oh.png"

if(!all(unlist(lapply(c(grey.path, red.path, green.path, orange.path), file.exists)))) {
  stop("Check path for stock status icons")
}

FT <- stockPlot %>%
  mutate(Description = gsub("<em>|</em>", "", stockPlot$Description)) %>% 
  flextable::flextable() %>%

  flextable::display(i = ~ SBL == "RED", col_key = "SBL", pattern = "{{add_icon}}",
                     formatters = list(add_icon ~ flextable::as_image(SBL, src = red.path, width = .15, height = .15))) %>%
  flextable::display(i = ~ SBL == "GREY", col_key = "SBL", pattern = "{{add_icon}}",
                     formatters = list(add_icon ~ flextable::as_image(SBL, src = grey.path, width = .15, height = .15))) %>%
  flextable::display(i = ~ SBL == "GREEN", col_key = "SBL", pattern = "{{add_icon}}",
                     formatters = list(add_icon ~ flextable::as_image(SBL, src = green.path, width = .15, height = .15))) %>%
  flextable::display(i = ~ SBL == "ORANGE", col_key = "SBL", pattern = "{{add_icon}}",
                     formatters = list(add_icon ~ flextable::as_image(SBL, src = orange.path, width = .15, height = .15))) %>%
# F_2013
flextable::display(i = ~ F_2013 == "RED", col_key = "F_2013", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(F_2013, src = red.path, width = .15, height = .15))) %>%
flextable::display(i = ~ F_2013 == "GREY", col_key = "F_2013", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(F_2013, src = grey.path, width = .15, height = .15))) %>%
flextable::display(i = ~ F_2013 == "GREEN", col_key = "F_2013", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(F_2013, src = green.path, width = .15, height = .15))) %>%
flextable::display(i = ~ F_2013 == "ORANGE", col_key = "F_2013", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(F_2013, src = orange.path, width = .15, height = .15))) %>%
# F_2015
flextable::display(i = ~ F_2014 == "RED", col_key = "F_2014", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(F_2014, src = red.path, width = .15, height = .15))) %>%
flextable::display(i = ~ F_2014 == "GREY", col_key = "F_2014", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(F_2014, src = grey.path, width = .15, height = .15))) %>%
flextable::display(i = ~ F_2014 == "GREEN", col_key = "F_2014", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(F_2014, src = green.path, width = .15, height = .15))) %>%
flextable::display(i = ~ F_2014 == "ORANGE", col_key = "F_2014", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(F_2014, src = orange.path, width = .15, height = .15)))%>%
# F_2015
flextable::display(i = ~ F_2015 == "RED", col_key = "F_2015", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(F_2015, src = red.path, width = .15, height = .15))) %>%
flextable::display(i = ~ F_2015 == "GREY", col_key = "F_2015", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(F_2015, src = grey.path, width = .15, height = .15))) %>%
flextable::display(i = ~ F_2015 == "GREEN", col_key = "F_2015", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(F_2015, src = green.path, width = .15, height = .15))) %>%
flextable::display(i = ~ F_2015 == "ORANGE", col_key = "F_2015", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(F_2015, src = orange.path, width = .15, height = .15)))%>%
# F_2016
flextable::display(i = ~ F_2016 == "RED", col_key = "F_2016", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(F_2016, src = red.path, width = .15, height = .15))) %>%
flextable::display(i = ~ F_2016 == "GREY", col_key = "F_2016", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(F_2016, src = grey.path, width = .15, height = .15))) %>%
flextable::display(i = ~ F_2016 == "GREEN", col_key = "F_2016", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(F_2016, src = green.path, width = .15, height = .15))) %>%
flextable::display(i = ~ F_2016 == "ORANGE", col_key = "F_2016", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(F_2016, src = orange.path, width = .15, height = .15)))%>%
# SSB_2014
flextable::display(i = ~ SSB_2014 == "RED", col_key = "SSB_2014", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(SSB_2014, src = red.path, width = .15, height = .15))) %>%
flextable::display(i = ~ SSB_2014 == "GREY", col_key = "SSB_2014", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(SSB_2014, src = grey.path, width = .15, height = .15))) %>%
flextable::display(i = ~ SSB_2014 == "GREEN", col_key = "SSB_2014", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(SSB_2014, src = green.path, width = .15, height = .15))) %>%
flextable::display(i = ~ SSB_2014 == "ORANGE", col_key = "SSB_2014", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(SSB_2014, src = orange.path, width = .15, height = .15)))%>%
# SSB_2015
flextable::display(i = ~ SSB_2015 == "RED", col_key = "SSB_2015", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(SSB_2015, src = red.path, width = .15, height = .15))) %>%
flextable::display(i = ~ SSB_2015 == "GREY", col_key = "SSB_2015", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(SSB_2015, src = grey.path, width = .15, height = .15))) %>%
flextable::display(i = ~ SSB_2015 == "GREEN", col_key = "SSB_2015", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(SSB_2015, src = green.path, width = .15, height = .15))) %>%
flextable::display(i = ~ SSB_2015 == "ORANGE", col_key = "SSB_2015", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(SSB_2015, src = orange.path, width = .15, height = .15)))%>%
# SSB_2016
flextable::display(i = ~ SSB_2016 == "RED", col_key = "SSB_2016", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(SSB_2016, src = red.path, width = .15, height = .15))) %>%
flextable::display(i = ~ SSB_2016 == "GREY", col_key = "SSB_2016", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(SSB_2016, src = grey.path, width = .15, height = .15))) %>%
flextable::display(i = ~ SSB_2016 == "GREEN", col_key = "SSB_2016", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(SSB_2016, src = green.path, width = .15, height = .15))) %>%
flextable::display(i = ~ SSB_2016 == "ORANGE", col_key = "SSB_2016", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(SSB_2016, src = orange.path, width = .15, height = .15)))%>%
# SSB_2017
flextable::display(i = ~ SSB_2017 == "RED", col_key = "SSB_2017", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(SSB_2017, src = red.path, width = .15, height = .15))) %>%
flextable::display(i = ~ SSB_2017 == "GREY", col_key = "SSB_2017", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(SSB_2017, src = grey.path, width = .15, height = .15))) %>%
flextable::display(i = ~ SSB_2017 == "GREEN", col_key = "SSB_2017", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(SSB_2017, src = green.path, width = .15, height = .15))) %>%
flextable::display(i = ~ SSB_2017 == "ORANGE", col_key = "SSB_2017", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(SSB_2017, src = orange.path, width = .15, height = .15)))%>%
# D3C1
flextable::display(i = ~ D3C1 == "RED", col_key = "D3C1", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(D3C1, src = red.path, width = .15, height = .15))) %>%
flextable::display(i = ~ D3C1 == "GREY", col_key = "D3C1", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(D3C1, src = grey.path, width = .15, height = .15))) %>%
flextable::display(i = ~ D3C1 == "GREEN", col_key = "D3C1", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(D3C1, src = green.path, width = .15, height = .15))) %>%
flextable::display(i = ~ D3C1 == "ORANGE", col_key = "D3C1", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(D3C1, src = orange.path, width = .15, height = .15)))%>%
# D3C2
flextable::display(i = ~ D3C2 == "RED", col_key = "D3C2", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(D3C2, src = red.path, width = .15, height = .15))) %>%
flextable::display(i = ~ D3C2 == "GREY", col_key = "D3C2", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(D3C2, src = grey.path, width = .15, height = .15))) %>%
flextable::display(i = ~ D3C2 == "GREEN", col_key = "D3C2", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(D3C2, src = green.path, width = .15, height = .15))) %>%
flextable::display(i = ~ D3C2 == "ORANGE", col_key = "D3C2", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(D3C2, src = orange.path, width = .15, height = .15)))%>%
# GES
flextable::display(i = ~ GES == "RED", col_key = "GES", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(GES, src = red.path, width = .15, height = .15))) %>%
flextable::display(i = ~ GES == "GREY", col_key = "GES", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(GES, src = grey.path, width = .15, height = .15))) %>%
flextable::display(i = ~ GES == "GREEN", col_key = "GES", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(GES, src = green.path, width = .15, height = .15))) %>%
flextable::display(i = ~ GES == "ORANGE", col_key = "GES", pattern = "{{add_icon}}",
                   formatters = list(add_icon ~ flextable::as_image(GES, src = orange.path, width = .15, height = .15)))%>%
  flextable::fontsize(size = 9, part = "all") %>% 
  flextable::add_header(StockCode = "",
             Description = "",
             FisheriesGuild = "",
             AdviceCategory = "",
             DataCategory = "",
             SBL = "",
             F_2013 = "F reference point",
             F_2014 = "F reference point",
             F_2015 = "F reference point",
             F_2016 = "F reference point",
             SSB_2014 = "SSB reference point",
             SSB_2015 = "SSB reference point",
             SSB_2016 = "SSB reference point",
             SSB_2017 = "SSB reference point",
             D3C1 = "MSFD descriptor",
             D3C2 = "MSFD descriptor",
             GES = "MSFD descriptor", top = TRUE) %>%
  flextable::merge_h(part = "header") %>% 
  flextable::set_header_labels(StockCode = "Stock code",
                    Description = "Stock name",
                    FisheriesGuild = "Fish category",
                    AdviceCategory = "Advice type",
                    DataCategory = "Data category",
                    SBL = "Safe biological limits",
                    F_2013 = "2013",
                    F_2014 = "2014",
                    F_2015 = "2015",
                    F_2016 = "2016",
                    SSB_2014 = "2014",
                    SSB_2015 = "2015",
                    SSB_2016 = "2016",
                    SSB_2017 = "2017",
                    D3C1 = "D3C1",
                    D3C2 = "D3C2",
                    GES = "GES") %>%
    flextable::align(j = c("StockCode", 
                         "Description",
                         "FisheriesGuild",
                         "AdviceCategory",
                         "DataCategory"), align = "left", part = "all") %>% 
  flextable::align(j = c("SBL",
                         "F_2013", 
                         "F_2014",
                         "F_2015",
                         "F_2016",
                         "SSB_2014",
                         "SSB_2015",
                         "SSB_2016",
                         "SSB_2017",
                         "D3C1",
                         "D3C2", 
                         "GES"), align = "center", part = "all") %>% 
  flextable::autofit() 


officer::read_docx() %>% 
  flextable::body_add_flextable(FT) %>% 
  print(target = "~/tester.docx") %>% 
  invisible()



  #   SBL = fpar(SBL),
  #                    F_2013 = fpar(F_2013),
  #                    F_2014 = fpar(F_2014),
  #                    F_2015 = fpar(F_2015),
  #                    SSB_2014 = fpar(SSB_2014),
  #                    SSB_2015 = fpar(SSB_2015),
  #                    SSB_2016 = fpar(SSB_2016),
  #                    D3C1 = fpar(D3C1),
  #                    D3C2 = fpar(D3C2),
  #                    GES = fpar(GES)) %>% 
  # add_header(StockCode = "",
  #            Description = "",
  #            FisheriesGuild = "",
  #            AdviceCategory = "",
  #            DataCategory = "",
  #            SBL = "",
  #            F_2013 = "F reference points",
  #            F_2014 = "F reference points",
  #            F_2015 = "F reference points",
  #            SSB_2014 = "SSB reference points",
  #            SSB_2015 = "SSB reference points",
  #            SSB_2016 = "SSB reference points",
  #            D3C1 = "MSFD descriptors",
  #            D3C2 = "MSFD descriptors",
  #            GES = "MSFD descriptors", 
  #            top = TRUE ) %>% 
  # set_header_labels(StockCode = "Stock code",
  #                   FisheriesGuild = "Fish category",
  #                   AdviceCategory = "Data category",
  #                   F_2013 = "2013",
  #                   F_2014 = "2014",
  #                   F_2015 = "2015",
  #                   SSB_2014 = "2014",
  #                   SSB_2015 = "2015",
  #                   SSB_2016 = "2016") %>% 
  # align(align = "center", part = "all") %>% 
  # align(j = c(1:5), align = "left", part = "body") %>% 
  # theme_zebra(odd_header = "transparent", even_header = "transparent") %>% 
  # autofit()

# 
# base_text_prop <- textProperties(font.size = 10, color = "black", font.family = "Calibri")
# base_par_prop = parProperties( text.align = "left")
# icon_par_prop = parProperties( text.align = "center" )
# base_cell_prop = cellProperties( padding = 6 )
# 
# FT <- stockPlot %>%
#   FlexTable(header.columns = FALSE,
#             header.cell.props = base_cell_prop, 
#             header.par.props = base_par_prop, 
#             header.text.props = chprop(base_text_prop, font.weight = "bold"), 
#             body.cell.props = base_cell_prop, 
#             body.par.props = base_par_prop, 
#             body.text.props = base_text_prop) %>%
#   addHeaderRow(value = c("", "F reference points", "SSB reference points", "MSFD GES"), colspan = c(6, 3, 3, 3)) %>%
#   addHeaderRow(value = c("Stock code", "Stock name", "Fishery guild", 
#                          "Advice type", "Data category", "Safe biological limits",
#                          "2013", "2014", "2015", "2014", "2015", "2016",
#                          "D3C1", "D3C2", "GES<sub>Stock</sub>")) %>%
#   setZebraStyle(odd = "#F9F9F9", even = "#FFFFFF" ) %>%
#   setFlexTableBorders(inner.vertical = borderProperties(width = 0), 
#                       inner.horizontal = borderProperties( width = 1 , color = "#DDDDDD"),
#                       outer.vertical = borderProperties( width = 0 ),
#                       outer.horizontal = borderProperties( width = 1, color = "grey30")) %>%
#   setFlexTableWidths(widths = c(0.5, 3, 1, 0.7, rep(0.5, 11)))
# 
# FT[, 5:15] <- chprop(base_par_prop, text.align = "center")