R/db_fill.R
In tpilz/LUMP: Landscape Unit Mapping Program for R
Defines functions
db_fill
Documented in
db_fill
# lumpR/db_fill.R
# Copyright (C) 2015, 2017 Tobias Pilz
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#' Fill parameter database
#'
#' Function to write parameter values relevant for modelling application with the
#' WASA hydrological model into an existing database, preferably created with
#' \code{\link[lumpR]{db_create}}.
#'
#' @param dbname Name of the data source (DSN) registered at ODBC. See \code{Details} of
#' \code{\link[lumpR]{db_create}}.
#'
#' @param tables \code{vector} with name(s) of the table(s) in the database that should
#' be filled with data. Order must correspond to the order of \code{dat_files}. By
#' default all tables are specified (see \code{Usage} for order of \code{dat_files}).
#' See \code{Details} for more information.
#'
#' @param dat_files \code{vector} with name(s) of the file(s) containing the data
#' that should be written into the database. Order must correspond to the order of
#' \code{tables}. See \code{Details} for information on file strcuture.
#'
#' @param dat_dir \code{string} giving the path to the directory containing \code{dat_files}.
#'
#' @param overwrite \code{logical}. Should Existing data be overwritten? If \code{FALSE}
#' existing values will be kept und the table expanded. Default: \code{FALSE}.
#'
#' @param verbose \code{logical}. Should detailed information during execution be
#' printed? Default: \code{TRUE}.
#'
#' @details
#' For each table a single file has to be prepared manually and/or using functions of
#' \code{lumpR}. All files have to be tabulator-separated textfiles, the top-line
#' being the header. Column names have to be identical to column names of the
#' respective tables in the database. All columns of a table have to exist in the
#' respective data file. If a certain column is not needed for your purpose or
#' contains missing values set values to \code{NA}. However, additional columns may exist
#' and will be omitted during database import and the order of the columns may be
#' freely chosen. Commentary lines are allowed and will be omitted during data import;
#' these have to begin with \code{#}. Duplicate entries or entries in the input file
#' which are already in the database table (unless you set \code{overwrite=T})
#' are not allowed and produce an error.
#'
#' \bold{r_subbas_contains_lu}\cr
#' Table referncing subbasins and corresponding landscape units inclunding their
#' areal fraction. \code{lu_ofile} produced by \code{\link[lumpR]{lump_grass_post}}
#' can be used. Columns:
#'
#' \emph{subbas_id}\cr
#' \code{integer}. Subbasin ID.
#'
#' \emph{lu_id}\cr
#' \code{integer}. Landscape Unit ID.
#'
#' \emph{fraction}\cr
#' \code{double}. Areal fraction of landscape unit within subbasin \emph{[-]}.
#'
#'
#' \bold{subbasins}\cr
#' Subbasin parameters. \code{sub_ofile} produced by \code{\link[lumpR]{lump_grass_post}}
#' can be used. Columns:
#'
#' \emph{pid}\cr
#' \code{integer}. Subbasin identifier.
#'
#' \emph{description}\cr
#' \code{character}. Short subbasin name or description.
#'
#' \emph{lat}\cr
#' \code{double}. Latitude of subbasin centroid in \emph{decimal degrees} (negative values for southern hemisphere).
#'
#' \emph{lon}\cr
#' \code{double}. Longitude of subbasin centroid in \emph{decimal degrees west of Greenwhich}, e.g.
#' Greenwich: 0°, New York: 75°, Berlin: 345°.
#'
#' \emph{elev}\cr
#' \code{double}. Average elevation above sea level of subbasin \emph{m}.
#'
#' \emph{drains_to}\cr
#' \code{integer}. Pid of subbasin the current subbasin drains to. The outlet
#' subbasin has to be labelled by one of c(9999,-9999,999,-999).
#'
#' \emph{area}\cr
#' \code{double}. Subbasin area in \emph{km^2}.
#'
#' \emph{a_stream_order}\cr
#' \code{integer}. Stream order. Set to \code{NA}. Calculated during WASA
#' input file creation.
#'
#' \emph{lag_time}\cr
#' \code{double}. Time in \emph{days} a runoff signal in the current
#' subbasin needs to be directed from the subbasin input to the outlet.
#'
#' \emph{retention}\cr
#' \code{double}. Maximum time period in \emph{days} over which a runoff signal
#' is distributed by the routing process.
#'
#' \emph{chan_len}\cr
#' \code{double}. Subbasin's main channel length in \emph{m}.
#'
#'
#' \bold{landscape_units}\cr
#' Landscape Unit parameters. Information can be obtained from \code{luoutfile}
#' created by \code{\link[lumpR]{prof_class}} (column 'x_length' which is identical
#' to 'slopelength') and \code{lupar_ofile} created by \code{\link[lumpR]{lump_grass_post}}
#' (all other information). Merge information by hand. Columns:
#'
#' \emph{pid}\cr
#' \code{integer}. Landscape Unit ID.
#'
#' \emph{description}\cr
#' \code{character}. Short name or description.
#'
#' \emph{kf_bedrock}\cr
#' \code{double}. Hydraulic conductivity of bedrock in \emph{mm/d}.
#'
#' \emph{slopelength}\cr
#' \code{double}. Mean slope length in landscape unit in \emph{m}. Meant is
#' the length in x-direction, not the hypotenuse of the hillslope profile triangle.
#'
#' \emph{soil_depth}\cr
#' \code{double}. Mean maximum depth of soil zone in \emph{mm}.
#'
#' \emph{allu_depth}\cr
#' \code{double}. Mean maximum depth of alluvial soil zone in \emph{mm}.
#'
#' \emph{riverbed_depth}\cr
#' \code{double}. Depth of river bed below terrain component in \emph{mm}.
#'
#' \emph{gw_flag}\cr
#' \code{integer}. Groundwater flag; 0: no groundwater, 1: with groundwater.
#'
#' \emph{gw_dist}\cr
#' \code{double}. Initial depth of groundwater below surface in \emph{mm}.
#'
#' \emph{frgw_delay}\cr
#' \code{double}. Storage coefficient for groundwater outflow in \emph{days}.
#'
#' \emph{sdr_lu}\cr
#' \code{double}. Sediment delivery ratio on LU-scale. For erosion modelling, only.
#'
#'
#' \bold{r_lu_contains_tc}\cr
#' Table referncing landscape units and corresponding terrain components inclunding their
#' areal fraction and hillslope position. \code{lucontainstcoutfile} created by
#' \code{\link[lumpR]{prof_class}} can be used directly. Columns:
#'
#' \emph{lu_id}\cr
#' \code{integer}. Landscape unit ID.
#'
#' \emph{tc_id}\cr
#' \code{integer}. Terrain component ID.
#'
#' \emph{fraction}\cr
#' \code{double}. Areal fraction of TC within LU \emph{[-]}.
#'
#' \emph{position}\cr
#' \code{integer}. Hillslope position of TC in LU (counting from hillslope bottom).
#'
#'
#' \bold{terrain_components}\cr
#' Terrain component specific parameters. Information from \code{terraincomponentsoutfile}
#' created by \code{\link[lumpR]{prof_class}} can be used. Columns:
#'
#' \emph{pid}\cr
#' \code{integer}. Terrain component ID.
#'
#' \emph{description}\cr
#' \code{character}. Short name or description.
#'
#' \emph{slope}\cr
#' \code{double}. Slope of terrain component in \emph{\%}.
#'
#' \emph{frac_rocky}\cr
#' \code{double}. Fraction of impermeable (rock) area \emph{[-]}.
#'
#' \emph{beta_fac}\cr
#' \code{double}. Ratio of rill/interrill erosion (for computation of the
#' L-factor see Renard et al., 1997, pp.101). For erosion modelling, only.
#'
#' \emph{sdr}\cr
#' \code{double}. Sediment delivery ratio on TC-scale. For erosion modelling, only.
#'
#'
#' \bold{r_tc_contains_svc}\cr
#' Table referncing terrain components and corresponding soil-vegetation components
#' inclunding their areal fraction. \code{tccontainssvcoutfile} created by
#' \code{\link[lumpR]{prof_class}} can be used directly. Columns:
#'
#' \emph{tc_id}\cr
#' \code{integer}. Terrain component ID.
#'
#' \emph{svc_id}\cr
#' \code{integer}. Soil-vegetation component ID.
#'
#' \emph{fraction}\cr
#' \code{double}. Areal fraction of SVC within TC \emph{[-]}.
#'
#'
#' \bold{vegetation}\cr
#' Vegetation parameters. Columns:
#'
#' \emph{pid}\cr
#' \code{integer}. Vegetation type ID.
#'
#' \emph{description}\cr
#' \code{character}. Short name or description.
#'
#' \emph{stomat_r}\cr
#' \code{double}. Stomata resistance without water stress in \emph{s/m}.
#'
#' \emph{min_suction}\cr
#' \code{double}. Suction threshold for water stress effect on resistance:
#' Begin of stomata closure. In \emph{hPa}.
#'
#' \emph{max_suction}\cr
#' \code{double}. Suction threshold for water stress effect on resistance:
#' Total closure of stomata, wilting point. In \emph{hPa}.
#'
#' \emph{height1}\cr
#' \code{double}. Average height of vegetation canopy \emph{before} rainy season in \emph{m}.
#'
#' \emph{height2}\cr
#' \code{double}. Average height of vegetation canopy \emph{at the beginning of} rainy season in \emph{m}.
#'
#' \emph{height3}\cr
#' \code{double}. Average height of vegetation canopy \emph{at the end of} rainy season in \emph{m}.
#'
#' \emph{height4}\cr
#' \code{double}. Average height of vegetation canopy \emph{after} rainy season in \emph{m}.
#'
#' \emph{root_depth1}\cr
#' \code{double}. Rooting depth of vegetation \emph{before} rainy season in \emph{m}.
#'
#' \emph{root_depth2}\cr
#' \code{double}. Rooting depth of vegetation \emph{at the beginning of} rainy season in \emph{m}.
#'
#' \emph{root_depth3}\cr
#' \code{double}. Rooting depth of vegetation \emph{at the end of} rainy season in \emph{m}.
#'
#' \emph{root_depth4}\cr
#' \code{double}. Rooting depth of vegetation \emph{after} rainy season in \emph{m}.
#'
#' \emph{lai1}\cr
#' \code{double}. Leaf area index of vegetation cover \emph{before} rainy season \emph{[-]}.
#'
#' \emph{lai2}\cr
#' \code{double}. Leaf area index of vegetation cover \emph{at the beginning of} rainy season \emph{[-]}.
#'
#' \emph{lai3}\cr
#' \code{double}. Leaf area index of vegetation cover \emph{at the end of} rainy season \emph{[-]}.
#'
#' \emph{lai4}\cr
#' \code{double}. Leaf area index of vegetation cover \emph{after} rainy season \emph{[-]}.
#'
#' \emph{alb1}\cr
#' \code{double}. Surface albedo \emph{before} rainy season \emph{[-]}.
#'
#' \emph{alb2}\cr
#' \code{double}. Surface albedo \emph{at the beginning of} rainy season \emph{[-]}.
#'
#' \emph{alb3}\cr
#' \code{double}. Surface albedo \emph{at the end of} rainy season \emph{[-]}.
#'
#' \emph{alb4}\cr
#' \code{double}. Surface albedo \emph{after} rainy season \emph{[-]}.
#'
#' \emph{c_manning_n}\cr
#' \code{double}. \emph{Optional for Erosion modelling}.
#'
#' \emph{c_musle_c1}\cr
#' \code{double}. \emph{Optional for Erosion modelling}.
#'
#' \emph{c_musle_c2}\cr
#' \code{double}. \emph{Optional for Erosion modelling}.
#'
#' \emph{c_musle_c3}\cr
#' \code{double}. \emph{Optional for Erosion modelling}.
#'
#' \emph{c_musle_c4}\cr
#' \code{double}. \emph{Optional for Erosion modelling}.
#'
#' \emph{intfc}\cr
#' \code{double}. Interception capacity per unit LAI in \emph{m}. For ECHSE's WASA engine only.
#'
#' \emph{crop_makk}\cr
#' \code{double}. Crop-factor for calculation of pot. evapotransp. after Makkink
#' (optional) \emph{[-]}.
#'
#' \emph{crop_faoref}\cr
#' \code{double}. Crop-factor for calculation of pot. evapotransp. after FAO reference method
#' (optional) \emph{[-]}.
#'
#' \emph{par_stressHum}\cr
#' \code{double}. Parameter to calculate water vapour deficit stomatal conductance
#' stress factor. In WASA it was a hard-coded parameter of value 0.03 \emph{[1/hPa]}.
#'
#' \emph{glo_half}\cr
#' \code{double}. Solar radiation at which stomatal conductance is half of its maximum
#' \emph{[W/m2]}.
#'
#'
#' \bold{soils}\cr
#' General soil parameters (horizon-specific parameters see below). Columns:
#'
#' \emph{pid}\cr
#' \code{integer}. Soil type ID.
#'
#' \emph{description}\cr
#' \code{character}. Short name or description.
#'
#' \emph{bedrock_flag}\cr
#' \code{integer}. Bedrock below deepest horizon: 0: not considered, 1: considered.
#'
#' \emph{alluvial_flag}\cr
#' \code{integer}. Soil type is alluvial soil: 0: no, 1: yes.
#'
#' \emph{b_om}\cr
#' \code{double}. Topsoil organic matter content (mass fraction) \emph{[-]}.
#'
#' \emph{a_musle_k}\cr
#' \code{double}. Used for internal calculations, set \code{NA}.
#'
#' \emph{a_clay}\cr
#' \code{double}. Used for internal calculations, set \code{NA}.
#'
#' \emph{a_silt}\cr
#' \code{double}. Used for internal calculations, set \code{NA}.
#'
#' \emph{a_sand}\cr
#' \code{double}. Used for internal calculations, set \code{NA}.
#'
#' \emph{a_f_csand}\cr
#' \code{double}. Used for internal calculations, set \code{NA}.
#'
#' \emph{a_f_cl_si}\cr
#' \code{double}. Used for internal calculations, set \code{NA}.
#'
#' \emph{a_f_orgc}\cr
#' \code{double}. Used for internal calculations, set \code{NA}.
#'
#' \emph{a_f_hisand}\cr
#' \code{double}. Used for internal calculations, set \code{NA}.
#'
#' \emph{Phil_s}\cr
#' \code{double}. Infiltration: Philip parameter: Sorptivity;
#' calculated internally in ECHSE if set to NA value \code{ms^(-1/2)}.
#'
#' \emph{Phil_a}\cr
#' \code{double}. Infiltration: Philip parameter: second term
#' parameter; calculated internally if set to NA value \code{m/s}.
#'
#' \emph{Hort_ini}\cr
#' \code{double}. Infiltration: Horton parameter: initial
#' infiltration rate \code{m/s}.
#'
#' \emph{Hort_end}\cr
#' \code{double}. Infiltration: Horton parameter: final
#' infiltration rate \code{m/s}.
#'
#' \emph{Hort_k}\cr
#' \code{double}. Infiltration: Horton parameter: decay constant \code{1/s}.
#'
#'
#' \bold{horizons}\cr
#' Horizon specific soil parameters. Columns:
#'
#' \emph{pid}\cr
#' \code{integer}. Horizon ID.
#'
#' \emph{description}\cr
#' \code{character}. Short name or description.
#'
#' \emph{soil_id}\cr
#' \code{integer}. Soil type ID.
#'
#' \emph{position}\cr
#' \code{integer}. Position of soil type specific horizon counting from surface.
#'
#' \emph{theta_r}\cr
#' \code{double}. Residual volumetric soil water content \emph{[-]}.
#'
#' \emph{theta_pwp}\cr
#' \code{double}. Volumetric soil water content at permanent wilting point \emph{[-]}.
#'
#' \emph{fk}\cr
#' \code{double}. Volumetric soil water content at field capacity (316 hPa / pF=2.6) \emph{[-]}.
#'
#' \emph{fk63}\cr
#' \code{double}. Volumetric soil water content at field capacity (63 hPa / pF=1.8) \emph{[-]}.
#'
#' \emph{nfk}\cr
#' \code{double}. Usable field capacity in terms of volumetric soil water content \emph{[-]}.
#'
#' \emph{theta_s}\cr
#' \code{double}. Saturated volumetric soil water content \emph{[-]}.
#'
#' \emph{thickness}\cr
#' \code{double}. Thickness of soil horizon in \emph{mm}.
#'
#' \emph{ks}\cr
#' \code{double}. Saturated hydraulic conductivity in \emph{mm/day}.
#'
#' \emph{suction}\cr
#' \code{double}. Suction at the wetting front in \emph{mm}.
#'
#' \emph{pore_size_i}\cr
#' \code{double}. Pore size index.
#'
#' \emph{bubb_pres}\cr
#' \code{double}. Bubble pressure in \emph{cm}.
#'
#' \emph{coarse_frag}\cr
#' \code{double}. Volumetric fraction of coarse fragments \emph{[-]}.
#'
#' \emph{shrinks}\cr
#' \code{integer}. Flag for soil structure, currently not used, set to \code{0} (not \code{NA}!).
#'
#' \emph{soil_dens}\cr
#' \code{double}. Bulk density in \emph{kg/m3}.
#'
#'
#' \bold{soil_veg_components}\cr
#' Parameters specific for soil-vegetation components. \code{svc_ofile} created by
#' \code{\link[lumpR]{lump_grass_prep}} can be used directly. Columns:
#'
#' \emph{pid}\cr
#' \code{integer}. Soil-vegetation component ID.
#'
#' \emph{description}\cr
#' \code{character}. Short name or description.
#'
#' \emph{soil_id}\cr
#' \code{integer}. Soil type ID.
#'
#' \emph{veg_id}\cr
#' \code{integer}. Vegetation type ID.
#'
#' \emph{musle_k}\cr
#' \code{double}. MUSLE K-factor [(ton acre hr)/(acre ft-ton inch)].
#'
#' \emph{musle_p}\cr
#' \code{double}. MUSLE P-factor.
#'
#' \emph{coarse_frac}\cr
#' \code{double}. Fraction of coarse fragments in \emph{\%}.
#'
#' \emph{special_area}\cr
#' \code{integer}. Flag for special areas: 1: water, 2: impervious, 0: ordinary SVC.
#'
#' \emph{manning_n}\cr
#' \code{double}. Mannings n roughness coefficient for overland flow.
#'
#' \emph{musle_c1}\cr
#' \code{double}. \emph{Optional for Erosion modelling}.
#'
#' \emph{musle_c2}\cr
#' \code{double}. \emph{Optional for Erosion modelling}.
#'
#' \emph{musle_c3}\cr
#' \code{double}. \emph{Optional for Erosion modelling}.
#'
#' \emph{musle_c4}\cr
#' \code{double}. \emph{Optional for Erosion modelling}.
#'
#'
#' \bold{particle_classes}\cr
#' Definition of particle size classes. Columns:
#'
#' \emph{class_id}\cr
#' \code{integer}. Particle class ID.
#'
#' \emph{description}\cr
#' \code{character}. Short name or description.
#'
#' \emph{upper_limit}\cr
#' \code{double}. Upper size limit of particles in \emph{mm}.
#'
#'
#' \bold{r_soil_contains_particles}\cr
#' Table referncing soil types and corresponding particle size classes including
#' their specific shares. Columns:
#'
#' \emph{soil_id}\cr
#' \code{integer}. Soil type ID.
#'
#' \emph{class_id}\cr
#' \code{integer}. Particle class ID.
#'
#' \emph{fraction}\cr
#' \code{double}. Mass-fraction that falls into the respective particle size class \emph{[-]}.
#'
#'
#' \bold{rainy_season}\cr
#' Fill in output of \code{\link[lumpR]{rainy_season}}. You can define separate
#' seasonalities for different vegetation types if you want (i.e. 'growing season'
#' instead of 'rainy season'). In this case the rainy/growing season starts and ends
#' differently for the respective vegetation types. This, however, is not
#' respected by function \code{\link[lumpR]{rainy_season}} which determines seasonalities
#' based on precipitation only. You can use the wildcard value '-1' for all
#' (remaining) vegetation types.
#' Columns:
#'
#' \emph{pid}\cr
#' \code{integer}. Dataset ID.
#'
#' \emph{subbas_id}\cr
#' \code{integer}. Id of subbasin or '-1' as wildcard for all (remaining) subbasins.
#'
#' \emph{veg_id}\cr
#' \code{integer}. Id of vegetation type or '-1' as wildcard for all (remaining)
#' vegetation types.
#'
#' \emph{yearm}\cr
#' \code{integer}. Current year or '-1' as wildcard for all (remaining) years.
#'
#' \emph{node1}\cr
#' \code{integer}. Start day of year (DOY) of rainy/growing season.
#'
#' \emph{node2}\cr
#' \code{integer}. DOY when climax of vegetation is reached.
#'
#' \emph{node3}\cr
#' \code{integer}. DOY of end of rainy/growing season (begin of vegetation degradation).
#'
#' \emph{node4}\cr
#' \code{integer}. DOY of end of main phase of vegetation degradation.
#'
#'
#' \bold{reservoirs_strategic}\cr
#' Strategic reservoir parameters. Fill in output of \code{\link[lumpR]{reservoir_strategic}}.
#'
#' \emph{pid}\cr
#' ID of the corresponding subbasin.
#'
#' \emph{res_id}\cr
#' Unique numeric reservoir identifier (if \code{res_file} is given, it also needs to be
#' defined in the vector file's attribute table!).
#'
#' \emph{name}\cr
#' OPTIONAL: name of the reservoir. Will be filled with \code{<NA>} if not given.
#'
#' \emph{minlevel}\cr
#' Initial minimum level in the reservoir [m]. Value varies because of sediment
#' accumulation.
#'
#' \emph{maxlevel}\cr
#' Maximum water level in the reservoir [m].
#'
#' \emph{vol0}\cr
#' Initial volume of the reservoir [10^3 m^3]. Value varies because of sediment
#' accumulation. Set to '-999' if information is not available.
#'
#' \emph{storecap}\cr
#' Initial storage capacity of the reservoir [10^3 m^3]. Value varies because of
#' sediment accumulation.
#'
#' \emph{damflow}\cr
#' Target outflow discharge of the reservoir (90 \% reliability) [m^3/s].
#'
#' \emph{damq_frac}\cr
#' Fraction of Q90 released from the reservoir in regular years [-].
#'
#' \emph{withdrawal}\cr
#' Water withdrawal discharge from the reservoir to supply the water use sectors
#' [m^3/s]. Outflow discharge through the dam is not considered.
#'
#' \emph{damyear}\cr
#' Year of construction of the dam (YYYY).
#'
#' \emph{maxdamarea}\cr
#' Initial maximum area of the reservoir [ha]. Value varies because of sediment
#' accumulation.
#'
#' \emph{damdead}\cr
#' Initial dead volume of the reservoir [10^3 m^3]. Value varies because of
#' sediment accumulation.
#'
#' \emph{damalert}\cr
#' Initial alert volume of the reservoir [10^3 m^3]. Value varies because of
#' sediment accumulation.
#'
#' \emph{dama, damb}\cr
#' Parameters of the area-volume relationship in the reservoir:
#' area = dama * Vol^damb [-]. Values of reservoir area and volume are
#' expressed in m^2 and m^3, respectively.
#'
#' \emph{q_outlet}\cr
#' Maximum outflow discharge released through the bottom outlets of the
#' reservoir [m^3/s].
#'
#' \emph{fvol_botm}\cr
#' Fraction of storage capacity that indicates the minimum storage volume for
#' sediment release through the bottom outlets of the reservoir [-].
#'
#' \emph{fvol_over}\cr
#' Fraction of storage capacity that indicates the minimum storage volume for
#' water release through the spillway of the reservoir [-].
#'
#' \emph{damc, damd}\cr
#' Parameters of the spillway rating curve of the reservoir: Qout = damc * Hv^damd
#' [-]. Values of water height over the spillway and overflow discharges are
#' expressed in m and m^3/s, respectively.
#'
#' \emph{elevbottom}\cr
#' Bottom outlet elevation of the reservoir [m].
#'
#'
#' \bold{reservoirs_small_classes}\cr
#' Small reservoir parameters. Fill in output of \code{\link[lumpR]{reservoir_lumped}} (\code{reservoirs_small_classes.dat}).
#' \emph{pid}\cr
#' reservoir class ID
#' \emph{name}\cr
#' optional name tag. Leave empty if not used.
#' \emph{maxlake0}\cr
#' Upper limit of reservoir size class in terms of volume [m^3]
#' \emph{lake_vol0_factor}\cr
#' Fraction of storage capacity that indicates the initial water volume in the reservoir size classes [-]
#' \emph{lake_change}\cr
#' Factor that indicates yearly variation in the number of reservoirs of the size classes [-]
#' \emph{alpha_Molle}\cr
#' Parameters of the area-volume relationship in the reservoir size classes (Area=alpha.k.(Vol/k)alpha/(alpha-1)) [-]. Values of reservoir area and volume are expressed in m² and m³, respectively
#' \emph{k_Molle}\cr
#' Parameters of the area-volume relationship in the reservoir size classes (Area=alpha.k.(Vol/k)alpha/(alpha-1)) [-]. Values of reservoir area and volume are expressed in m² and m³, respectively
#' \emph{damc}\cr
#' Parameters of the spillway rating curve in the reservoir size classes (Qout=damc.Hv^damd) [-]. Values of water height over the spillway and overflow discharges are expressed in m and m³/s, respectively
#' \emph{damd}\cr
#' Parameters of the spillway rating curve in the reservoir size classes (Qout=damc.Hv^damd) [-]. Values of water height over the spillway and overflow discharges are expressed in m and m³/s, respectively
#'
#' \bold{r_subbas_contains_reservoirs_small}\cr
#' Small reservoir distribution in subbasins. Fill in output of \code{\link[lumpR]{reservoir_lumped}} (\code{r_subbas_contains_reservoirs_small.dat}).
#' \emph{subbas_id}\cr
#' foreign key to subbas',
#' \emph{res_class_id}\cr
#' foreign key to reservoirs_small_classes',
#' \emph{n_reservoirs}\cr
#' number of reservoirs [-]',
#' \emph{maxlake}\cr
#' Mean value of initial storage capacity of the hypothetical representative reservoirs of the size classes [m^3]',
#'
#'
#' @references
#' \bold{lumpR paper}\cr
#' Pilz, T.; Francke, T.; Bronstert, A. (2017): lumpR 2.0.0: an R package facilitating
#' landscape discretisation for hillslope-based hydrological models.
#' \emph{Geosci. Model Dev.}, 10, 3001-3023, doi: 10.5194/gmd-10-3001-2017
#'
#' \bold{Theory of lumpR}\cr
#' Francke, T.; Guentner, A.; Mamede, G.; Mueller, E. N. and Bronstert, A (2008):
#' Automated catena-based discretization of landscapes for the derivation of
#' hydrological modelling units. \emph{International Journal of Geographical
#' Information Science, Informa UK Limited}, 22(2), 111-132, DOI: 10.1080/13658810701300873
#'
#' \bold{Information on WASA and parameters}\cr
#' Guentner, A. (2002): Large-scale hydrological modelling in the semi-arid
#' North-East of Brazil. \emph{PIK Report 77}, Potsdam Institute for Climate
#' Impact Research, Potsdam, Germany.
#'
#' \bold{More information on subbasin parameters}\cr
#' Bronstert, A., Guentner, A., Jaeger, A., Krol, M. & Krywkow, J. (1999): Grossraeumige
#' hydrologische Parametrisierung und Modellierung als Teil der integrierten
#' Modellierung. In: Fohrer, N. & Doell, P. (Eds.): Modellierung des Wasser- und
#' Stofftransports in grossen Einzugsgebieten. \emph{Kassel University Press}, Kassel,
#' Germany, 31-40.
#'
#'
#' @author
#' Tobias Pilz \email{tpilz@@uni-potsdam.de}, Till Francke \email{francke@@uni-potsdam.de}
#'
db_fill <- function(
dbname,
tables=c("r_subbas_contains_lu", "subbasins", "landscape_units", "r_lu_contains_tc",
"terrain_components", "r_tc_contains_svc", "vegetation", "soils", "horizons",
"soil_veg_components", "particle_classes", "r_soil_contains_particles", "rainy_season","reservoirs_strategic",
"reservoirs_small", "r_subbas_contains_reservoirs_small" ),
dat_files,
dat_dir,
overwrite=FALSE,
verbose=TRUE
) {
if(verbose) message("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
if(verbose) message("% START db_fill()")
if(verbose) message("%")
if(verbose) message("% Connecting to and checking database ...")
# connect to ODBC registered database
con <- connect_db(dbname)
#modify error handler to gracefully close ODBC-connection before aborting (otherwise, ODBC-handles are left open)
org_error_handler = getOption("error") #original error handler
closeODBC_and_stop = function()
{
odbcCloseAll()
options(error=org_error_handler) #restore original handler
}
options(error=closeODBC_and_stop) #modify error handler
# ensure MySQL/MariaDB uses ANSI quotation (double quotes instead of back ticks)
if(grepl("MariaDB", odbcGetInfo(con)["DBMS_Name"], ignore.case=T))
sqlQuery(con, "SET sql_mode='ANSI';")
# check database (all 'tables' have to exist)
check_tbl <- tables %in% sqlTables(con)$TABLE_NAME
if (any(!check_tbl))
stop(paste0("Table(s) ", paste(tables[which(!check_tbl)], sep=", "), " could not be found in database '", dbname, "'."))
if(verbose) message("% OK")
# write data into database (use internal function defined in db_internals.R)
if(verbose) message("%")
if(verbose) message("% Write data into database ...")
for (t in 1:length(tables)) {
writedb(con = con, file = paste(dat_dir,dat_files[t], sep="/"), table = tables[t],
overwrite = overwrite, verbose = verbose)
}
# update table meta_info
write_metainfo(con,
"db_fill()",
paste(tables, collapse=", "), "all",
paste0("Automated filling of tables with R package lumpR using files from location ", dat_dir, "."),
FALSE)
if(verbose) message("% OK")
if(verbose) message("%")
if(verbose) message("% All data written successfully. Close ODBC connection.")
tryCatch(odbcClose(con), error=function(e){})
if(verbose) message("%")
if(verbose) message("% DONE!")
if(verbose) message("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
} # EOF
tpilz/LUMP documentation built on Aug. 5, 2023, 1:31 a.m.
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Defines functions db_fill
Documented in db_fill
# lumpR/db_fill.R
# Copyright (C) 2015, 2017 Tobias Pilz
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#' Fill parameter database
#'
#' Function to write parameter values relevant for modelling application with the
#' WASA hydrological model into an existing database, preferably created with
#' \code{\link[lumpR]{db_create}}.
#'
#' @param dbname Name of the data source (DSN) registered at ODBC. See \code{Details} of
#' \code{\link[lumpR]{db_create}}.
#'
#' @param tables \code{vector} with name(s) of the table(s) in the database that should
#' be filled with data. Order must correspond to the order of \code{dat_files}. By
#' default all tables are specified (see \code{Usage} for order of \code{dat_files}).
#' See \code{Details} for more information.
#'
#' @param dat_files \code{vector} with name(s) of the file(s) containing the data
#' that should be written into the database. Order must correspond to the order of
#' \code{tables}. See \code{Details} for information on file strcuture.
#'
#' @param dat_dir \code{string} giving the path to the directory containing \code{dat_files}.
#'
#' @param overwrite \code{logical}. Should Existing data be overwritten? If \code{FALSE}
#' existing values will be kept und the table expanded. Default: \code{FALSE}.
#'
#' @param verbose \code{logical}. Should detailed information during execution be
#' printed? Default: \code{TRUE}.
#'
#' @details
#' For each table a single file has to be prepared manually and/or using functions of
#' \code{lumpR}. All files have to be tabulator-separated textfiles, the top-line
#' being the header. Column names have to be identical to column names of the
#' respective tables in the database. All columns of a table have to exist in the
#' respective data file. If a certain column is not needed for your purpose or
#' contains missing values set values to \code{NA}. However, additional columns may exist
#' and will be omitted during database import and the order of the columns may be
#' freely chosen. Commentary lines are allowed and will be omitted during data import;
#' these have to begin with \code{#}. Duplicate entries or entries in the input file
#' which are already in the database table (unless you set \code{overwrite=T})
#' are not allowed and produce an error.
#'
#' \bold{r_subbas_contains_lu}\cr
#' Table referncing subbasins and corresponding landscape units inclunding their
#' areal fraction. \code{lu_ofile} produced by \code{\link[lumpR]{lump_grass_post}}
#' can be used. Columns:
#'
#' \emph{subbas_id}\cr
#' \code{integer}. Subbasin ID.
#'
#' \emph{lu_id}\cr
#' \code{integer}. Landscape Unit ID.
#'
#' \emph{fraction}\cr
#' \code{double}. Areal fraction of landscape unit within subbasin \emph{[-]}.
#'
#'
#' \bold{subbasins}\cr
#' Subbasin parameters. \code{sub_ofile} produced by \code{\link[lumpR]{lump_grass_post}}
#' can be used. Columns:
#'
#' \emph{pid}\cr
#' \code{integer}. Subbasin identifier.
#'
#' \emph{description}\cr
#' \code{character}. Short subbasin name or description.
#'
#' \emph{lat}\cr
#' \code{double}. Latitude of subbasin centroid in \emph{decimal degrees} (negative values for southern hemisphere).
#'
#' \emph{lon}\cr
#' \code{double}. Longitude of subbasin centroid in \emph{decimal degrees west of Greenwhich}, e.g.
#' Greenwich: 0°, New York: 75°, Berlin: 345°.
#'
#' \emph{elev}\cr
#' \code{double}. Average elevation above sea level of subbasin \emph{m}.
#'
#' \emph{drains_to}\cr
#' \code{integer}. Pid of subbasin the current subbasin drains to. The outlet
#' subbasin has to be labelled by one of c(9999,-9999,999,-999).
#'
#' \emph{area}\cr
#' \code{double}. Subbasin area in \emph{km^2}.
#'
#' \emph{a_stream_order}\cr
#' \code{integer}. Stream order. Set to \code{NA}. Calculated during WASA
#' input file creation.
#'
#' \emph{lag_time}\cr
#' \code{double}. Time in \emph{days} a runoff signal in the current
#' subbasin needs to be directed from the subbasin input to the outlet.
#'
#' \emph{retention}\cr
#' \code{double}. Maximum time period in \emph{days} over which a runoff signal
#' is distributed by the routing process.
#'
#' \emph{chan_len}\cr
#' \code{double}. Subbasin's main channel length in \emph{m}.
#'
#'
#' \bold{landscape_units}\cr
#' Landscape Unit parameters. Information can be obtained from \code{luoutfile}
#' created by \code{\link[lumpR]{prof_class}} (column 'x_length' which is identical
#' to 'slopelength') and \code{lupar_ofile} created by \code{\link[lumpR]{lump_grass_post}}
#' (all other information). Merge information by hand. Columns:
#'
#' \emph{pid}\cr
#' \code{integer}. Landscape Unit ID.
#'
#' \emph{description}\cr
#' \code{character}. Short name or description.
#'
#' \emph{kf_bedrock}\cr
#' \code{double}. Hydraulic conductivity of bedrock in \emph{mm/d}.
#'
#' \emph{slopelength}\cr
#' \code{double}. Mean slope length in landscape unit in \emph{m}. Meant is
#' the length in x-direction, not the hypotenuse of the hillslope profile triangle.
#'
#' \emph{soil_depth}\cr
#' \code{double}. Mean maximum depth of soil zone in \emph{mm}.
#'
#' \emph{allu_depth}\cr
#' \code{double}. Mean maximum depth of alluvial soil zone in \emph{mm}.
#'
#' \emph{riverbed_depth}\cr
#' \code{double}. Depth of river bed below terrain component in \emph{mm}.
#'
#' \emph{gw_flag}\cr
#' \code{integer}. Groundwater flag; 0: no groundwater, 1: with groundwater.
#'
#' \emph{gw_dist}\cr
#' \code{double}. Initial depth of groundwater below surface in \emph{mm}.
#'
#' \emph{frgw_delay}\cr
#' \code{double}. Storage coefficient for groundwater outflow in \emph{days}.
#'
#' \emph{sdr_lu}\cr
#' \code{double}. Sediment delivery ratio on LU-scale. For erosion modelling, only.
#'
#'
#' \bold{r_lu_contains_tc}\cr
#' Table referncing landscape units and corresponding terrain components inclunding their
#' areal fraction and hillslope position. \code{lucontainstcoutfile} created by
#' \code{\link[lumpR]{prof_class}} can be used directly. Columns:
#'
#' \emph{lu_id}\cr
#' \code{integer}. Landscape unit ID.
#'
#' \emph{tc_id}\cr
#' \code{integer}. Terrain component ID.
#'
#' \emph{fraction}\cr
#' \code{double}. Areal fraction of TC within LU \emph{[-]}.
#'
#' \emph{position}\cr
#' \code{integer}. Hillslope position of TC in LU (counting from hillslope bottom).
#'
#'
#' \bold{terrain_components}\cr
#' Terrain component specific parameters. Information from \code{terraincomponentsoutfile}
#' created by \code{\link[lumpR]{prof_class}} can be used. Columns:
#'
#' \emph{pid}\cr
#' \code{integer}. Terrain component ID.
#'
#' \emph{description}\cr
#' \code{character}. Short name or description.
#'
#' \emph{slope}\cr
#' \code{double}. Slope of terrain component in \emph{\%}.
#'
#' \emph{frac_rocky}\cr
#' \code{double}. Fraction of impermeable (rock) area \emph{[-]}.
#'
#' \emph{beta_fac}\cr
#' \code{double}. Ratio of rill/interrill erosion (for computation of the
#' L-factor see Renard et al., 1997, pp.101). For erosion modelling, only.
#'
#' \emph{sdr}\cr
#' \code{double}. Sediment delivery ratio on TC-scale. For erosion modelling, only.
#'
#'
#' \bold{r_tc_contains_svc}\cr
#' Table referncing terrain components and corresponding soil-vegetation components
#' inclunding their areal fraction. \code{tccontainssvcoutfile} created by
#' \code{\link[lumpR]{prof_class}} can be used directly. Columns:
#'
#' \emph{tc_id}\cr
#' \code{integer}. Terrain component ID.
#'
#' \emph{svc_id}\cr
#' \code{integer}. Soil-vegetation component ID.
#'
#' \emph{fraction}\cr
#' \code{double}. Areal fraction of SVC within TC \emph{[-]}.
#'
#'
#' \bold{vegetation}\cr
#' Vegetation parameters. Columns:
#'
#' \emph{pid}\cr
#' \code{integer}. Vegetation type ID.
#'
#' \emph{description}\cr
#' \code{character}. Short name or description.
#'
#' \emph{stomat_r}\cr
#' \code{double}. Stomata resistance without water stress in \emph{s/m}.
#'
#' \emph{min_suction}\cr
#' \code{double}. Suction threshold for water stress effect on resistance:
#' Begin of stomata closure. In \emph{hPa}.
#'
#' \emph{max_suction}\cr
#' \code{double}. Suction threshold for water stress effect on resistance:
#' Total closure of stomata, wilting point. In \emph{hPa}.
#'
#' \emph{height1}\cr
#' \code{double}. Average height of vegetation canopy \emph{before} rainy season in \emph{m}.
#'
#' \emph{height2}\cr
#' \code{double}. Average height of vegetation canopy \emph{at the beginning of} rainy season in \emph{m}.
#'
#' \emph{height3}\cr
#' \code{double}. Average height of vegetation canopy \emph{at the end of} rainy season in \emph{m}.
#'
#' \emph{height4}\cr
#' \code{double}. Average height of vegetation canopy \emph{after} rainy season in \emph{m}.
#'
#' \emph{root_depth1}\cr
#' \code{double}. Rooting depth of vegetation \emph{before} rainy season in \emph{m}.
#'
#' \emph{root_depth2}\cr
#' \code{double}. Rooting depth of vegetation \emph{at the beginning of} rainy season in \emph{m}.
#'
#' \emph{root_depth3}\cr
#' \code{double}. Rooting depth of vegetation \emph{at the end of} rainy season in \emph{m}.
#'
#' \emph{root_depth4}\cr
#' \code{double}. Rooting depth of vegetation \emph{after} rainy season in \emph{m}.
#'
#' \emph{lai1}\cr
#' \code{double}. Leaf area index of vegetation cover \emph{before} rainy season \emph{[-]}.
#'
#' \emph{lai2}\cr
#' \code{double}. Leaf area index of vegetation cover \emph{at the beginning of} rainy season \emph{[-]}.
#'
#' \emph{lai3}\cr
#' \code{double}. Leaf area index of vegetation cover \emph{at the end of} rainy season \emph{[-]}.
#'
#' \emph{lai4}\cr
#' \code{double}. Leaf area index of vegetation cover \emph{after} rainy season \emph{[-]}.
#'
#' \emph{alb1}\cr
#' \code{double}. Surface albedo \emph{before} rainy season \emph{[-]}.
#'
#' \emph{alb2}\cr
#' \code{double}. Surface albedo \emph{at the beginning of} rainy season \emph{[-]}.
#'
#' \emph{alb3}\cr
#' \code{double}. Surface albedo \emph{at the end of} rainy season \emph{[-]}.
#'
#' \emph{alb4}\cr
#' \code{double}. Surface albedo \emph{after} rainy season \emph{[-]}.
#'
#' \emph{c_manning_n}\cr
#' \code{double}. \emph{Optional for Erosion modelling}.
#'
#' \emph{c_musle_c1}\cr
#' \code{double}. \emph{Optional for Erosion modelling}.
#'
#' \emph{c_musle_c2}\cr
#' \code{double}. \emph{Optional for Erosion modelling}.
#'
#' \emph{c_musle_c3}\cr
#' \code{double}. \emph{Optional for Erosion modelling}.
#'
#' \emph{c_musle_c4}\cr
#' \code{double}. \emph{Optional for Erosion modelling}.
#'
#' \emph{intfc}\cr
#' \code{double}. Interception capacity per unit LAI in \emph{m}. For ECHSE's WASA engine only.
#'
#' \emph{crop_makk}\cr
#' \code{double}. Crop-factor for calculation of pot. evapotransp. after Makkink
#' (optional) \emph{[-]}.
#'
#' \emph{crop_faoref}\cr
#' \code{double}. Crop-factor for calculation of pot. evapotransp. after FAO reference method
#' (optional) \emph{[-]}.
#'
#' \emph{par_stressHum}\cr
#' \code{double}. Parameter to calculate water vapour deficit stomatal conductance
#' stress factor. In WASA it was a hard-coded parameter of value 0.03 \emph{[1/hPa]}.
#'
#' \emph{glo_half}\cr
#' \code{double}. Solar radiation at which stomatal conductance is half of its maximum
#' \emph{[W/m2]}.
#'
#'
#' \bold{soils}\cr
#' General soil parameters (horizon-specific parameters see below). Columns:
#'
#' \emph{pid}\cr
#' \code{integer}. Soil type ID.
#'
#' \emph{description}\cr
#' \code{character}. Short name or description.
#'
#' \emph{bedrock_flag}\cr
#' \code{integer}. Bedrock below deepest horizon: 0: not considered, 1: considered.
#'
#' \emph{alluvial_flag}\cr
#' \code{integer}. Soil type is alluvial soil: 0: no, 1: yes.
#'
#' \emph{b_om}\cr
#' \code{double}. Topsoil organic matter content (mass fraction) \emph{[-]}.
#'
#' \emph{a_musle_k}\cr
#' \code{double}. Used for internal calculations, set \code{NA}.
#'
#' \emph{a_clay}\cr
#' \code{double}. Used for internal calculations, set \code{NA}.
#'
#' \emph{a_silt}\cr
#' \code{double}. Used for internal calculations, set \code{NA}.
#'
#' \emph{a_sand}\cr
#' \code{double}. Used for internal calculations, set \code{NA}.
#'
#' \emph{a_f_csand}\cr
#' \code{double}. Used for internal calculations, set \code{NA}.
#'
#' \emph{a_f_cl_si}\cr
#' \code{double}. Used for internal calculations, set \code{NA}.
#'
#' \emph{a_f_orgc}\cr
#' \code{double}. Used for internal calculations, set \code{NA}.
#'
#' \emph{a_f_hisand}\cr
#' \code{double}. Used for internal calculations, set \code{NA}.
#'
#' \emph{Phil_s}\cr
#' \code{double}. Infiltration: Philip parameter: Sorptivity;
#' calculated internally in ECHSE if set to NA value \code{ms^(-1/2)}.
#'
#' \emph{Phil_a}\cr
#' \code{double}. Infiltration: Philip parameter: second term
#' parameter; calculated internally if set to NA value \code{m/s}.
#'
#' \emph{Hort_ini}\cr
#' \code{double}. Infiltration: Horton parameter: initial
#' infiltration rate \code{m/s}.
#'
#' \emph{Hort_end}\cr
#' \code{double}. Infiltration: Horton parameter: final
#' infiltration rate \code{m/s}.
#'
#' \emph{Hort_k}\cr
#' \code{double}. Infiltration: Horton parameter: decay constant \code{1/s}.
#'
#'
#' \bold{horizons}\cr
#' Horizon specific soil parameters. Columns:
#'
#' \emph{pid}\cr
#' \code{integer}. Horizon ID.
#'
#' \emph{description}\cr
#' \code{character}. Short name or description.
#'
#' \emph{soil_id}\cr
#' \code{integer}. Soil type ID.
#'
#' \emph{position}\cr
#' \code{integer}. Position of soil type specific horizon counting from surface.
#'
#' \emph{theta_r}\cr
#' \code{double}. Residual volumetric soil water content \emph{[-]}.
#'
#' \emph{theta_pwp}\cr
#' \code{double}. Volumetric soil water content at permanent wilting point \emph{[-]}.
#'
#' \emph{fk}\cr
#' \code{double}. Volumetric soil water content at field capacity (316 hPa / pF=2.6) \emph{[-]}.
#'
#' \emph{fk63}\cr
#' \code{double}. Volumetric soil water content at field capacity (63 hPa / pF=1.8) \emph{[-]}.
#'
#' \emph{nfk}\cr
#' \code{double}. Usable field capacity in terms of volumetric soil water content \emph{[-]}.
#'
#' \emph{theta_s}\cr
#' \code{double}. Saturated volumetric soil water content \emph{[-]}.
#'
#' \emph{thickness}\cr
#' \code{double}. Thickness of soil horizon in \emph{mm}.
#'
#' \emph{ks}\cr
#' \code{double}. Saturated hydraulic conductivity in \emph{mm/day}.
#'
#' \emph{suction}\cr
#' \code{double}. Suction at the wetting front in \emph{mm}.
#'
#' \emph{pore_size_i}\cr
#' \code{double}. Pore size index.
#'
#' \emph{bubb_pres}\cr
#' \code{double}. Bubble pressure in \emph{cm}.
#'
#' \emph{coarse_frag}\cr
#' \code{double}. Volumetric fraction of coarse fragments \emph{[-]}.
#'
#' \emph{shrinks}\cr
#' \code{integer}. Flag for soil structure, currently not used, set to \code{0} (not \code{NA}!).
#'
#' \emph{soil_dens}\cr
#' \code{double}. Bulk density in \emph{kg/m3}.
#'
#'
#' \bold{soil_veg_components}\cr
#' Parameters specific for soil-vegetation components. \code{svc_ofile} created by
#' \code{\link[lumpR]{lump_grass_prep}} can be used directly. Columns:
#'
#' \emph{pid}\cr
#' \code{integer}. Soil-vegetation component ID.
#'
#' \emph{description}\cr
#' \code{character}. Short name or description.
#'
#' \emph{soil_id}\cr
#' \code{integer}. Soil type ID.
#'
#' \emph{veg_id}\cr
#' \code{integer}. Vegetation type ID.
#'
#' \emph{musle_k}\cr
#' \code{double}. MUSLE K-factor [(ton acre hr)/(acre ft-ton inch)].
#'
#' \emph{musle_p}\cr
#' \code{double}. MUSLE P-factor.
#'
#' \emph{coarse_frac}\cr
#' \code{double}. Fraction of coarse fragments in \emph{\%}.
#'
#' \emph{special_area}\cr
#' \code{integer}. Flag for special areas: 1: water, 2: impervious, 0: ordinary SVC.
#'
#' \emph{manning_n}\cr
#' \code{double}. Mannings n roughness coefficient for overland flow.
#'
#' \emph{musle_c1}\cr
#' \code{double}. \emph{Optional for Erosion modelling}.
#'
#' \emph{musle_c2}\cr
#' \code{double}. \emph{Optional for Erosion modelling}.
#'
#' \emph{musle_c3}\cr
#' \code{double}. \emph{Optional for Erosion modelling}.
#'
#' \emph{musle_c4}\cr
#' \code{double}. \emph{Optional for Erosion modelling}.
#'
#'
#' \bold{particle_classes}\cr
#' Definition of particle size classes. Columns:
#'
#' \emph{class_id}\cr
#' \code{integer}. Particle class ID.
#'
#' \emph{description}\cr
#' \code{character}. Short name or description.
#'
#' \emph{upper_limit}\cr
#' \code{double}. Upper size limit of particles in \emph{mm}.
#'
#'
#' \bold{r_soil_contains_particles}\cr
#' Table referncing soil types and corresponding particle size classes including
#' their specific shares. Columns:
#'
#' \emph{soil_id}\cr
#' \code{integer}. Soil type ID.
#'
#' \emph{class_id}\cr
#' \code{integer}. Particle class ID.
#'
#' \emph{fraction}\cr
#' \code{double}. Mass-fraction that falls into the respective particle size class \emph{[-]}.
#'
#'
#' \bold{rainy_season}\cr
#' Fill in output of \code{\link[lumpR]{rainy_season}}. You can define separate
#' seasonalities for different vegetation types if you want (i.e. 'growing season'
#' instead of 'rainy season'). In this case the rainy/growing season starts and ends
#' differently for the respective vegetation types. This, however, is not
#' respected by function \code{\link[lumpR]{rainy_season}} which determines seasonalities
#' based on precipitation only. You can use the wildcard value '-1' for all
#' (remaining) vegetation types.
#' Columns:
#'
#' \emph{pid}\cr
#' \code{integer}. Dataset ID.
#'
#' \emph{subbas_id}\cr
#' \code{integer}. Id of subbasin or '-1' as wildcard for all (remaining) subbasins.
#'
#' \emph{veg_id}\cr
#' \code{integer}. Id of vegetation type or '-1' as wildcard for all (remaining)
#' vegetation types.
#'
#' \emph{yearm}\cr
#' \code{integer}. Current year or '-1' as wildcard for all (remaining) years.
#'
#' \emph{node1}\cr
#' \code{integer}. Start day of year (DOY) of rainy/growing season.
#'
#' \emph{node2}\cr
#' \code{integer}. DOY when climax of vegetation is reached.
#'
#' \emph{node3}\cr
#' \code{integer}. DOY of end of rainy/growing season (begin of vegetation degradation).
#'
#' \emph{node4}\cr
#' \code{integer}. DOY of end of main phase of vegetation degradation.
#'
#'
#' \bold{reservoirs_strategic}\cr
#' Strategic reservoir parameters. Fill in output of \code{\link[lumpR]{reservoir_strategic}}.
#'
#' \emph{pid}\cr
#' ID of the corresponding subbasin.
#'
#' \emph{res_id}\cr
#' Unique numeric reservoir identifier (if \code{res_file} is given, it also needs to be
#' defined in the vector file's attribute table!).
#'
#' \emph{name}\cr
#' OPTIONAL: name of the reservoir. Will be filled with \code{<NA>} if not given.
#'
#' \emph{minlevel}\cr
#' Initial minimum level in the reservoir [m]. Value varies because of sediment
#' accumulation.
#'
#' \emph{maxlevel}\cr
#' Maximum water level in the reservoir [m].
#'
#' \emph{vol0}\cr
#' Initial volume of the reservoir [10^3 m^3]. Value varies because of sediment
#' accumulation. Set to '-999' if information is not available.
#'
#' \emph{storecap}\cr
#' Initial storage capacity of the reservoir [10^3 m^3]. Value varies because of
#' sediment accumulation.
#'
#' \emph{damflow}\cr
#' Target outflow discharge of the reservoir (90 \% reliability) [m^3/s].
#'
#' \emph{damq_frac}\cr
#' Fraction of Q90 released from the reservoir in regular years [-].
#'
#' \emph{withdrawal}\cr
#' Water withdrawal discharge from the reservoir to supply the water use sectors
#' [m^3/s]. Outflow discharge through the dam is not considered.
#'
#' \emph{damyear}\cr
#' Year of construction of the dam (YYYY).
#'
#' \emph{maxdamarea}\cr
#' Initial maximum area of the reservoir [ha]. Value varies because of sediment
#' accumulation.
#'
#' \emph{damdead}\cr
#' Initial dead volume of the reservoir [10^3 m^3]. Value varies because of
#' sediment accumulation.
#'
#' \emph{damalert}\cr
#' Initial alert volume of the reservoir [10^3 m^3]. Value varies because of
#' sediment accumulation.
#'
#' \emph{dama, damb}\cr
#' Parameters of the area-volume relationship in the reservoir:
#' area = dama * Vol^damb [-]. Values of reservoir area and volume are
#' expressed in m^2 and m^3, respectively.
#'
#' \emph{q_outlet}\cr
#' Maximum outflow discharge released through the bottom outlets of the
#' reservoir [m^3/s].
#'
#' \emph{fvol_botm}\cr
#' Fraction of storage capacity that indicates the minimum storage volume for
#' sediment release through the bottom outlets of the reservoir [-].
#'
#' \emph{fvol_over}\cr
#' Fraction of storage capacity that indicates the minimum storage volume for
#' water release through the spillway of the reservoir [-].
#'
#' \emph{damc, damd}\cr
#' Parameters of the spillway rating curve of the reservoir: Qout = damc * Hv^damd
#' [-]. Values of water height over the spillway and overflow discharges are
#' expressed in m and m^3/s, respectively.
#'
#' \emph{elevbottom}\cr
#' Bottom outlet elevation of the reservoir [m].
#'
#'
#' \bold{reservoirs_small_classes}\cr
#' Small reservoir parameters. Fill in output of \code{\link[lumpR]{reservoir_lumped}} (\code{reservoirs_small_classes.dat}).
#' \emph{pid}\cr
#' reservoir class ID
#' \emph{name}\cr
#' optional name tag. Leave empty if not used.
#' \emph{maxlake0}\cr
#' Upper limit of reservoir size class in terms of volume [m^3]
#' \emph{lake_vol0_factor}\cr
#' Fraction of storage capacity that indicates the initial water volume in the reservoir size classes [-]
#' \emph{lake_change}\cr
#' Factor that indicates yearly variation in the number of reservoirs of the size classes [-]
#' \emph{alpha_Molle}\cr
#' Parameters of the area-volume relationship in the reservoir size classes (Area=alpha.k.(Vol/k)alpha/(alpha-1)) [-]. Values of reservoir area and volume are expressed in m² and m³, respectively
#' \emph{k_Molle}\cr
#' Parameters of the area-volume relationship in the reservoir size classes (Area=alpha.k.(Vol/k)alpha/(alpha-1)) [-]. Values of reservoir area and volume are expressed in m² and m³, respectively
#' \emph{damc}\cr
#' Parameters of the spillway rating curve in the reservoir size classes (Qout=damc.Hv^damd) [-]. Values of water height over the spillway and overflow discharges are expressed in m and m³/s, respectively
#' \emph{damd}\cr
#' Parameters of the spillway rating curve in the reservoir size classes (Qout=damc.Hv^damd) [-]. Values of water height over the spillway and overflow discharges are expressed in m and m³/s, respectively
#'
#' \bold{r_subbas_contains_reservoirs_small}\cr
#' Small reservoir distribution in subbasins. Fill in output of \code{\link[lumpR]{reservoir_lumped}} (\code{r_subbas_contains_reservoirs_small.dat}).
#' \emph{subbas_id}\cr
#' foreign key to subbas',
#' \emph{res_class_id}\cr
#' foreign key to reservoirs_small_classes',
#' \emph{n_reservoirs}\cr
#' number of reservoirs [-]',
#' \emph{maxlake}\cr
#' Mean value of initial storage capacity of the hypothetical representative reservoirs of the size classes [m^3]',
#'
#'
#' @references
#' \bold{lumpR paper}\cr
#' Pilz, T.; Francke, T.; Bronstert, A. (2017): lumpR 2.0.0: an R package facilitating
#' landscape discretisation for hillslope-based hydrological models.
#' \emph{Geosci. Model Dev.}, 10, 3001-3023, doi: 10.5194/gmd-10-3001-2017
#'
#' \bold{Theory of lumpR}\cr
#' Francke, T.; Guentner, A.; Mamede, G.; Mueller, E. N. and Bronstert, A (2008):
#' Automated catena-based discretization of landscapes for the derivation of
#' hydrological modelling units. \emph{International Journal of Geographical
#' Information Science, Informa UK Limited}, 22(2), 111-132, DOI: 10.1080/13658810701300873
#'
#' \bold{Information on WASA and parameters}\cr
#' Guentner, A. (2002): Large-scale hydrological modelling in the semi-arid
#' North-East of Brazil. \emph{PIK Report 77}, Potsdam Institute for Climate
#' Impact Research, Potsdam, Germany.
#'
#' \bold{More information on subbasin parameters}\cr
#' Bronstert, A., Guentner, A., Jaeger, A., Krol, M. & Krywkow, J. (1999): Grossraeumige
#' hydrologische Parametrisierung und Modellierung als Teil der integrierten
#' Modellierung. In: Fohrer, N. & Doell, P. (Eds.): Modellierung des Wasser- und
#' Stofftransports in grossen Einzugsgebieten. \emph{Kassel University Press}, Kassel,
#' Germany, 31-40.
#'
#'
#' @author
#' Tobias Pilz \email{tpilz@@uni-potsdam.de}, Till Francke \email{francke@@uni-potsdam.de}
#'
db_fill <- function(
dbname,
tables=c("r_subbas_contains_lu", "subbasins", "landscape_units", "r_lu_contains_tc",
"terrain_components", "r_tc_contains_svc", "vegetation", "soils", "horizons",
"soil_veg_components", "particle_classes", "r_soil_contains_particles", "rainy_season","reservoirs_strategic",
"reservoirs_small", "r_subbas_contains_reservoirs_small" ),
dat_files,
dat_dir,
overwrite=FALSE,
verbose=TRUE
) {
if(verbose) message("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
if(verbose) message("% START db_fill()")
if(verbose) message("%")
if(verbose) message("% Connecting to and checking database ...")
# connect to ODBC registered database
con <- connect_db(dbname)
#modify error handler to gracefully close ODBC-connection before aborting (otherwise, ODBC-handles are left open)
org_error_handler = getOption("error") #original error handler
closeODBC_and_stop = function()
{
odbcCloseAll()
options(error=org_error_handler) #restore original handler
}
options(error=closeODBC_and_stop) #modify error handler
# ensure MySQL/MariaDB uses ANSI quotation (double quotes instead of back ticks)
if(grepl("MariaDB", odbcGetInfo(con)["DBMS_Name"], ignore.case=T))
sqlQuery(con, "SET sql_mode='ANSI';")
# check database (all 'tables' have to exist)
check_tbl <- tables %in% sqlTables(con)$TABLE_NAME
if (any(!check_tbl))
stop(paste0("Table(s) ", paste(tables[which(!check_tbl)], sep=", "), " could not be found in database '", dbname, "'."))
if(verbose) message("% OK")
# write data into database (use internal function defined in db_internals.R)
if(verbose) message("%")
if(verbose) message("% Write data into database ...")
for (t in 1:length(tables)) {
writedb(con = con, file = paste(dat_dir,dat_files[t], sep="/"), table = tables[t],
overwrite = overwrite, verbose = verbose)
}
# update table meta_info
write_metainfo(con,
"db_fill()",
paste(tables, collapse=", "), "all",
paste0("Automated filling of tables with R package lumpR using files from location ", dat_dir, "."),
FALSE)
if(verbose) message("% OK")
if(verbose) message("%")
if(verbose) message("% All data written successfully. Close ODBC connection.")
tryCatch(odbcClose(con), error=function(e){})
if(verbose) message("%")
if(verbose) message("% DONE!")
if(verbose) message("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
} # EOF
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