Fieldmap databaseR/load_data_herblayer.R
load_data_herblayer.RdThis function queries the given database to retrieve data on vegetation
(ready for use in calculate_vegetation() function).
year_main_survey refers to year of the main vegetation survey
(source is table vegetation),
while year refers to year of recording of that specific species
(possibly different for spring flora; source is table herblayer)
load_data_herblayer(
database,
plottype = NA,
forest_reserve = NA,
processed = TRUE
)name of Fieldmap/Access database (with specific Fieldmap
structure) including path
possibility to select only data for a certain plot type, e.g. 'CP' for Circular plot or 'CA' for Core area (the default NA means that data from all plots are retrieved)
possibility to select only data for 1 forest reserve by giving the name of the forest reserve (the default NA means that data from all plots are retrieved)
Should only processed and surveyed data be added? Defaults to TRUE (yes).
Dataframe with vegetation data on the species level ('herb layer'), containing columns as species, coverage_id, browse_index_id, date_vegetation (= date of survey of specific species, different for spring flora and other flora in the same plot), year (= year of survey of specific species, possibly different for spring flora and other flora), ....
library(forrescalc)
# (add path to your own fieldmap database here)
path_to_fieldmapdb <-
system.file("example/database/mdb_bosres.sqlite", package = "forrescalc")
load_data_herblayer(path_to_fieldmapdb)
#> forest_reserve plot_id plottype subplot_id period year date_vegetation
#> 1 Everzwijnbad 101 CP 1 1 2002 2002-05-30 00:00:00
#> 2 Everzwijnbad 101 CP 1 1 2002 2002-05-30 00:00:00
#> 3 Withoefse heide 204 CP 1 1 2003 2003-07-01 00:00:00
#> 4 Liedekerke 1005 CP 1 1 2006 2006-07-24 00:00:00
#> 5 Kersselaerspleyn 2006 CP 1 1 2001 2001-07-01 00:00:00
#> 6 Kersselaerspleyn 11000 CA 155511 1 2000 2000-08-01 00:00:00
#> 7 Kersselaerspleyn 11000 CA 155512 1 2000 2000-08-01 00:00:00
#> 8 Kersselaerspleyn 11000 CA 155513 1 2000 2000-08-01 00:00:00
#> 9 Harras 21000 CA 17 1 2009 2009-04-14 00:00:00
#> 10 Harras 21000 CA 18 1 2009 2009-04-14 00:00:00
#> 11 Harras 21000 CA 19 1 2009 2009-04-14 00:00:00
#> 12 Harras 21000 CA 20 1 2009 2009-04-14 00:00:00
#> 13 Harras 21000 CA 21 1 2009 2009-06-18 00:00:00
#> 14 Harras 21000 CA 21 1 2009 2009-04-14 00:00:00
#> 15 Harras 21000 CA 22 1 2009 2009-04-14 00:00:00
#> 16 Harras 21000 CA 23 1 2009 2009-04-14 00:00:00
#> 17 Harras 21000 CA 24 1 2009 2009-04-14 00:00:00
#> 18 Harras 21000 CA 25 1 2009 2009-04-14 00:00:00
#> 19 Harras 21000 CA 26 1 2009 2009-04-14 00:00:00
#> 20 Sevendonck A 141100 CA 1 1 2007 2007-06-18 00:00:00
#> 21 Sevendonck A 141100 CA 2 1 2007 2007-06-18 00:00:00
#> 22 Sevendonck A 141100 CA 3 1 2007 2007-06-18 00:00:00
#> 23 Everzwijnbad 101 CP 1 2 2013 2013-06-11 00:00:00
#> 24 Everzwijnbad 101 CP 1 2 2013 2013-05-17 00:00:00
#> 25 Liedekerke 1005 CP 1 2 2016 2016-06-17 00:00:00
#> 26 Kersselaerspleyn 2006 CP 1 2 2011 2011-05-27 00:00:00
#> 27 Kersselaerspleyn 11000 CA 155511 2 2011 2011-06-24 00:00:00
#> 28 Kersselaerspleyn 11000 CA 155521 2 2011 2011-05-12 00:00:00
#> 29 Kersselaerspleyn 11000 CA 155531 2 2011 2011-05-12 00:00:00
#> 30 Harras 21000 CA 17 2 2019 2019-04-10 10:26:12
#> 31 Harras 21000 CA 18 2 2019 2019-04-10 10:30:45
#> 32 Harras 21000 CA 19 2 2019 2019-04-10 10:30:45
#> 33 Harras 21000 CA 20 2 2019 2019-04-10 10:30:45
#> 34 Harras 21000 CA 21 2 2019 2019-04-10 10:30:45
#> 35 Harras 21000 CA 22 2 2019 2019-04-10 10:30:45
#> 36 Harras 21000 CA 23 2 2019 2019-04-10 10:30:45
#> 37 Harras 21000 CA 24 2 2019 2019-04-10 13:16:11
#> 38 Harras 21000 CA 25 2 2019 2019-04-10 13:22:26
#> 39 Harras 21000 CA 26 2 2019 2019-04-10 13:22:26
#> 40 Sevendonck A 141100 CA 1 2 2017 2017-06-22 12:26:59
#> 41 Sevendonck A 141100 CA 2 2 2017 2017-06-22 11:44:27
#> 42 Sevendonck A 141100 CA 3 2 2017 2017-06-22 11:16:31
#> 43 Kersselaerspleyn 2006 CP 2001 3 2021 2021-06-18 00:00:00
#> 44 Kersselaerspleyn 11000 CA 155511 3 2021 2021-07-20 00:00:00
#> 45 Kersselaerspleyn 11000 CA 155521 3 2021 2021-07-20 00:00:00
#> 46 Kersselaerspleyn 11000 CA 155521 3 2021 2021-04-21 00:00:00
#> 47 Kersselaerspleyn 11000 CA 155531 3 2021 2021-04-21 00:00:00
#> totalplotarea_ha plotarea_ha species coverage_id browse_index_id
#> 1 0.1017876 0.0256 131 1 NA
#> 2 0.1017876 0.0256 161 6 NA
#> 3 0.1257000 0.0256 NA NA NA
#> 4 0.0706858 0.0256 161 18 NA
#> 5 0.2827000 0.0256 161 6 NA
#> 6 10.7485378 10.7485 NA NA NA
#> 7 10.7485378 10.7485 NA NA NA
#> 8 10.7485378 10.7485 NA NA NA
#> 9 0.9800008 0.9800 131 1 NA
#> 10 0.9800008 0.9800 131 6 NA
#> 11 0.9800008 0.9800 131 8 NA
#> 12 0.9800008 0.9800 131 10 NA
#> 13 0.9800008 0.9800 161 2 NA
#> 14 0.9800008 0.9800 131 9 NA
#> 15 0.9800008 0.9800 131 13 NA
#> 16 0.9800008 0.9800 131 11 NA
#> 17 0.9800008 0.9800 131 8 NA
#> 18 0.9800008 0.9800 131 11 NA
#> 19 0.9800008 0.9800 131 8 NA
#> 20 0.4989261 0.5000 161 11 NA
#> 21 0.4989261 0.5000 161 8 NA
#> 22 0.4989261 0.5000 161 1 NA
#> 23 0.1017876 0.0256 161 7 NA
#> 24 0.1017876 0.0256 131 8 NA
#> 25 0.0706858 0.0256 161 17 100
#> 26 0.2827000 0.0256 161 1 NA
#> 27 10.7485378 10.7485 NA NA NA
#> 28 10.7485378 10.7485 131 3 NA
#> 29 10.7485378 10.7485 131 3 NA
#> 30 0.9800008 0.9800 131 6 100
#> 31 0.9800008 0.9800 131 7 100
#> 32 0.9800008 0.9800 131 11 100
#> 33 0.9800008 0.9800 131 11 100
#> 34 0.9800008 0.9800 131 13 100
#> 35 0.9800008 0.9800 131 14 100
#> 36 0.9800008 0.9800 131 14 100
#> 37 0.9800008 0.9800 131 11 100
#> 38 0.9800008 0.9800 131 15 100
#> 39 0.9800008 0.9800 131 11 100
#> 40 0.4989261 0.5000 161 14 100
#> 41 0.4989261 0.5000 161 6 100
#> 42 0.4989261 0.5000 161 6 100
#> 43 0.2827000 0.0256 161 4 120
#> 44 10.7485378 10.7485 NA NA 100
#> 45 10.7485378 10.7485 161 1 100
#> 46 10.7485378 10.7485 131 2 100
#> 47 10.7485378 10.7485 131 4 100
#> coverage_class_average_perc length_core_area_m width_core_area_m
#> 1 0.5 NA NA
#> 2 2.0 NA NA
#> 3 NA NA NA
#> 4 97.5 NA NA
#> 5 2.0 NA NA
#> 6 NA NA NA
#> 7 NA NA NA
#> 8 NA NA NA
#> 9 0.5 140 70
#> 10 2.0 140 70
#> 11 7.5 140 70
#> 12 20.0 140 70
#> 13 0.5 140 70
#> 14 12.5 140 70
#> 15 50.0 140 70
#> 16 30.0 140 70
#> 17 7.5 140 70
#> 18 30.0 140 70
#> 19 7.5 140 70
#> 20 30.0 100 50
#> 21 7.5 100 50
#> 22 0.5 100 50
#> 23 4.0 NA NA
#> 24 7.5 NA NA
#> 25 90.0 NA NA
#> 26 0.5 NA NA
#> 27 NA NA NA
#> 28 0.5 NA NA
#> 29 0.5 NA NA
#> 30 2.0 140 70
#> 31 4.0 140 70
#> 32 30.0 140 70
#> 33 30.0 140 70
#> 34 50.0 140 70
#> 35 60.0 140 70
#> 36 60.0 140 70
#> 37 30.0 140 70
#> 38 70.0 140 70
#> 39 30.0 140 70
#> 40 60.0 100 50
#> 41 2.0 100 50
#> 42 2.0 100 50
#> 43 0.5 NA NA
#> 44 NA NA NA
#> 45 0.5 NA NA
#> 46 0.5 NA NA
#> 47 0.5 NA NA
#> core_area_ha
#> 1 NA
#> 2 NA
#> 3 NA
#> 4 NA
#> 5 NA
#> 6 10.7485
#> 7 10.7485
#> 8 10.7485
#> 9 0.9800
#> 10 0.9800
#> 11 0.9800
#> 12 0.9800
#> 13 0.9800
#> 14 0.9800
#> 15 0.9800
#> 16 0.9800
#> 17 0.9800
#> 18 0.9800
#> 19 0.9800
#> 20 0.5000
#> 21 0.5000
#> 22 0.5000
#> 23 NA
#> 24 NA
#> 25 NA
#> 26 NA
#> 27 10.7485
#> 28 10.7485
#> 29 10.7485
#> 30 0.9800
#> 31 0.9800
#> 32 0.9800
#> 33 0.9800
#> 34 0.9800
#> 35 0.9800
#> 36 0.9800
#> 37 0.9800
#> 38 0.9800
#> 39 0.9800
#> 40 0.5000
#> 41 0.5000
#> 42 0.5000
#> 43 NA
#> 44 10.7485
#> 45 10.7485
#> 46 10.7485
#> 47 10.7485