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Merge pull request #8 from Burke-Lauenroth-Lab/Enrich_dbW_with_Climat…
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…eNormals

Blobs of weather database: faster and with user-defined compression type
    branch 'Enrich_dbW_with_ClimateNormals' is incorrectly named
    dbW gained a 'Meta' table with information about version and compression type
    dbW version updated to 3.1
    BLOBs are now much faster retrieved (because the entire weather object is serialized instead of first being converted to a text string)
    compression type of the BLOBs is user-specified (or can be 'none'); default is 'gzip' which offers the best balance of speed and size; 'none' is the fastest (slightly) and the largest (by much)
    there are functions to upgrade older dbW to the current version
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@dschlaep
dschlaep authored Jul 11, 2016
2 parents 3b8c6cf + 6529fc4 commit c5d338f
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16 changes: 13 additions & 3 deletions DESCRIPTION
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Package: Rsoilwat31
Version: 1.0.1
Date: 06-22-2016
Date: 07-01-2016
Title: SoilWat v31
Authors@R: c(person("Ryan", "Murphy", role = "aut", email = "not@available.com"),
person("Daniel", "Schlaepfer", role = c("aut", "cre"), email = "daniel.schlaepfer@unibas.ch"),
person("John", "Bradford", role = "ctb", email = "not@available.com"),
person("William", "Lauenroth", role = "ctb", email = "not@available.com"))
Depends: R (>= 2.12.0), RSQLite
Description: SoilWat package is a R wrapper for the SOILWAT C code. It allows data to be accessed directly via memory. This package currently uses SOILWAT v3.2.0.
Depends:
R (>= 2.15.0)
Imports:
methods
Suggests:
RSQLite (>= 1.0.0),
DBI (>= 0.4.1),
testthat
Description: SoilWat package is a R wrapper for the SOILWAT C code. It allows
data to be accessed directly via memory. This package currently uses SOILWAT
v3.2.0.
LazyData: true
ByteCompile: true
License: GPL (>= 3)
URL: https://github.com/Burke-Lauenroth-Lab/Rsoilwat/tree/Rsoilwat_v31
BugReports: https://github.com/Burke-Lauenroth-Lab/Rsoilwat/issues
RoxygenNote: 5.0.1
6 changes: 5 additions & 1 deletion NAMESPACE
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Expand Up @@ -24,7 +24,11 @@ dbW_dataframe_to_weatherData,
dbW_weather_to_SOILWATfiles,

dbW_weatherData_to_monthly,
dbW_dataframe_to_monthly)
dbW_dataframe_to_monthly,

dbW_upgrade_v3to31,
dbW_upgrade_v2to3,
dbW_upgrade_v1to2)

exportClasses(
swFiles,
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199 changes: 199 additions & 0 deletions R/Rsoilwat31.R
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#' Package `Rsoilwat31': summary information
#'
#' The package `Rsoilwat' / 'Rsoilwat31' is a R implementation of SoilWat
#' Modeling Software. The C code was converted into a library with
#' input/output functions to R. SoilWat is a simulator of the dynamics of soil
#' water. Originally written in the 1900's by a highly trained team of Botany's
#' finest. It is now maintained by Dr. William Lauenroth's Lab and Dr. Daniel
#' Schlaepfer. The input data structure is S4. Generic functions that
#' apply to the input container or individual object control setting/getting
#' input data. Output data is in the form of lists.
#'
#'
#' @aliases Rsoilwat31 Rsoilwat31-package
#' @section Version: The version level of the package is given by the command
#' \code{packageDescription("Rsoilwat31")}. The most recent version of the
#' package can be obtained from github at
#' \url{https://github.com/Burke-Lauenroth-Lab/Rsoilwat}
#' @seealso \itemize{ \item \code{\link{sw_exec}} for running a simulation
#' \item \code{\link{sw_inputData}} and \code{\link{sw_inputDataFromFiles}} for
#' data input \item \code{\link{dbW_getWeatherData}} and
#' \code{\link{getWeatherData_folders}} for weather data input }
#' @references Bradford, J. B., D. R. Schlaepfer, and W. K. Lauenroth (2014)
#' Ecohydrology of adjacent sagebrush and lodgepole pine ecosystems: The
#' consequences of climate change and disturbance. \emph{Ecosystems}
#' \bold{17}:590--605.
#'
#' Schlaepfer, D. R., W. K. Lauenroth, and J. B. Bradford (2012)
#' Ecohydrological niche of sagebrush ecosystems. \emph{Ecohydrology}
#' \bold{5}:453--466.
#'
#' Parton, W.J. (1978). \emph{Abiotic section of ELM}. In: Grassland
#' simulation model (ed. Innis, G.S.). Springer New York, NY, pp. 31--53.
#'
#' Sala, O.E., Lauenroth, W.K. & Parton, W.J. (1992) Long-term soil-water
#' dynamics in the shortgrass steppe. \emph{Ecology} \bold{73}:1175--1181.
#'
#' @docType package
#' @name Rsoilwat31
#' @aliases Rsoilwat, SoilWat, SOILWAT, Rsoilwat-package
NULL





#' Class \code{"swInputData"}
#'
#' %% ~~ A concise (1-5 lines) description of what the class is. ~~ This class
#' is a container class to the input file S4 objects. The generic functions
#' listed work on this and the proper sw Class in the container's slots.
#'
#'
#' @name swInputData-class
#' @aliases swInputData-class get_Markov,swInputData-method
#' get_swCloud,swInputData-method get_swFiles,swInputData-method
#' get_swOUT,swInputData-method get_swProd,swInputData-method
#' get_swSite,swInputData-method get_swSoils,swInputData-method
#' get_swSWC,swInputData-method get_swWeatherData,swInputData-method
#' get_swWeather,swInputData-method get_swYears,swInputData-method
#' get_WeatherHistory,swInputData-method set_Markov<-,swInputData-method
#' set_swCloud<-,swInputData-method set_swFiles<-,swInputData-method
#' set_swOUT<-,swInputData-method set_swProd<-,swInputData-method
#' set_swSite<-,swInputData-method set_swSoils<-,swInputData,swSoils-method
#' set_swSWC<-,swInputData,swSWC-method
#' set_swWeatherData<-,swInputData,swWeatherData-method
#' set_swWeather<-,swInputData-method set_swYears<-,swInputData-method
#' set_WeatherHistory<-,swInputData,list-method swClear,swInputData-method
#' swCloud_Humidity<-,swInputData-method swCloud_Humidity,swInputData-method
#' swCloud_SkyCover<-,swInputData-method swCloud_SkyCover,swInputData-method
#' swCloud_SnowDensity<-,swInputData-method
#' swCloud_SnowDensity,swInputData-method
#' swCloud_Transmissivity<-,swInputData-method
#' swCloud_Transmissivity,swInputData-method
#' swCloud_WindSpeed<-,swInputData-method swCloud_WindSpeed,swInputData-method
#' swFiles_Cloud<-,swInputData-method swFiles_Cloud,swInputData-method
#' swFiles_Estab<-,swInputData-method swFiles_Estab,swInputData-method
#' swFiles_filesIn<-,swInputData-method swFiles_filesIn,swInputData-method
#' swFiles_LogFile<-,swInputData-method swFiles_LogFile,swInputData-method
#' swFiles_MarkovCov<-,swInputData-method swFiles_MarkovCov,swInputData-method
#' swFiles_MarkovProbs<-,swInputData-method
#' swFiles_MarkovProbs,swInputData-method
#' swFiles_OutputPrefix<-,swInputData-method
#' swFiles_OutputPrefix,swInputData-method swFiles_Output<-,swInputData-method
#' swFiles_Output,swInputData-method swFiles_Prod<-,swInputData-method
#' swFiles_Prod,swInputData-method swFiles_ProjDir<-,swInputData-method
#' swFiles_ProjDir,swInputData-method swFiles_SiteParams<-,swInputData-method
#' swFiles_SiteParams,swInputData-method swFiles_Soils<-,swInputData-method
#' swFiles_Soils,swInputData-method swFiles_SWCsetup<-,swInputData-method
#' swFiles_SWCsetup,swInputData-method
#' swFiles_WeatherPrefix<-,swInputData-method
#' swFiles_WeatherPrefix,swInputData-method
#' swFiles_WeatherSetup<-,swInputData-method
#' swFiles_WeatherSetup,swInputData-method swFiles_Years<-,swInputData-method
#' swFiles_Years,swInputData-method swLog_setLine<-,swInputData-method
#' swMarkov_Conv<-,swInputData-method swMarkov_Conv,swInputData-method
#' swMarkov_Prob<-,swInputData-method swMarkov_Prob,swInputData-method
#' swOUT_OutputSeparator<-,swInputData-method
#' swOUT_OutputSeparator,swInputData-method swOUT_TimeStep<-,swInputData-method
#' swOUT_TimeStep,swInputData-method swProd_Albedo<-,swInputData-method
#' swProd_Albedo,swInputData-method swProd_CanopyHeight<-,swInputData-method
#' swProd_CanopyHeight,swInputData-method
#' swProd_Composition<-,swInputData-method
#' swProd_Composition,swInputData-method swProd_Cover_stcr<-,swInputData-method
#' swProd_Cover_stcr,swInputData-method
#' swProd_CritSoilWaterPotential<-,swInputData-method
#' swProd_CritSoilWaterPotential,swInputData-method
#' swProd_Es_param_limit<-,swInputData-method
#' swProd_Es_param_limit,swInputData-method
#' swProd_EsTpartitioning_param<-,swInputData-method
#' swProd_EsTpartitioning_param,swInputData-method
#' swProd_HydrRedstro<-,swInputData-method
#' swProd_HydrRedstro,swInputData-method
#' swProd_HydrRedstro_use<-,swInputData-method
#' swProd_HydrRedstro_use,swInputData-method
#' swProd_LitterInterParam<-,swInputData-method
#' swProd_LitterInterParam,swInputData-method
#' swProd_MonProd_grass<-,swInputData-method
#' swProd_MonProd_grass,swInputData-method
#' swProd_MonProd_shrub<-,swInputData-method
#' swProd_MonProd_shrub,swInputData-method
#' swProd_MonProd_tree<-,swInputData-method
#' swProd_MonProd_tree,swInputData-method swProd_Shade<-,swInputData-method
#' swProd_Shade,swInputData-method swProd_VegInterParam<-,swInputData-method
#' swProd_VegInterParam,swInputData-method
#' swReadLines,swInputData,character-method
#' swSite_DrainageCoefficient<-,swInputData-method
#' swSite_DrainageCoefficient,swInputData-method
#' swSite_EvapCoefficients<-,swInputData-method
#' swSite_EvapCoefficients,swInputData-method
#' swSite_IntrinsicSiteParams<-,swInputData-method
#' swSite_IntrinsicSiteParams,swInputData-method
#' swSite_ModelCoefficients<-,swInputData-method
#' swSite_ModelCoefficients,swInputData-method
#' swSite_ModelFlags<-,swInputData-method swSite_ModelFlags,swInputData-method
#' swSite_SnowSimulationParams<-,swInputData-method
#' swSite_SnowSimulationParams,swInputData-method
#' swSite_SoilTemperatureConsts<-,swInputData-method
#' swSite_SoilTemperatureConsts,swInputData-method
#' swSite_SoilTemperatureFlag<-,swInputData-method
#' swSite_SoilTemperatureFlag,swInputData-method
#' swSite_SWClimits<-,swInputData-method swSite_SWClimits,swInputData-method
#' swSite_TranspCoefficients<-,swInputData-method
#' swSite_TranspCoefficients,swInputData-method
#' swSite_TranspirationRegions<-,swInputData-method
#' swSite_TranspirationRegions,swInputData-method
#' swSoils_Layers<-,swInputData,matrix-method swSoils_Layers,swInputData-method
#' swSWC_FirstYear<-,swInputData,integer-method
#' swSWC_FirstYear,swInputData-method
#' swSWC_HistoricData<-,swInputData,swSWC_hist-method
#' swSWC_HistoricData,swInputData-method
#' swSWC_HistoricList<-,swInputData,list-method
#' swSWC_HistoricList,swInputData-method
#' swSWC_Method<-,swInputData,integer-method swSWC_Method,swInputData-method
#' swSWC_prefix<-,swInputData,character-method swSWC_prefix,swInputData-method
#' swSWC_use<-,swInputData,logical-method swSWC_use,swInputData-method
#' swWeather_DaysRunningAverage<-,swInputData-method
#' swWeather_DaysRunningAverage,swInputData-method
#' swWeather_FirstYearHistorical<-,swInputData-method
#' swWeather_FirstYearHistorical,swInputData-method
#' swWeather_MonScalingParams<-,swInputData-method
#' swWeather_MonScalingParams,swInputData-method
#' swWeather_pct_SnowDrift<-,swInputData-method
#' swWeather_pct_SnowDrift,swInputData-method
#' swWeather_pct_SnowRunoff<-,swInputData-method
#' swWeather_pct_SnowRunoff,swInputData-method
#' swWeather_UseMarkov<-,swInputData-method
#' swWeather_UseMarkov,swInputData-method
#' swWeather_UseSnow<-,swInputData-method swWeather_UseSnow,swInputData-method
#' swWriteLines,swInputData,character-method swYears_EDOEY<-,swInputData-method
#' swYears_EDOEY,swInputData-method swYears_EndYear<-,swInputData-method
#' swYears_EndYear,swInputData-method swYears_FDOFY<-,swInputData-method
#' swYears_FDOFY,swInputData-method swYears_isNorth<-,swInputData-method
#' swYears_isNorth,swInputData-method swYears_StartYear<-,swInputData-method
#' swYears_StartYear,swInputData-method
#' @docType class
#' @note %% ~~further notes~~
#' @section Objects from the Class: Objects can be created by calls of the form
#' \code{new("swInputData", ...)}. %% ~~ describe objects here ~~
#' @author %% ~~who you are~~ Ryan Murphy
#' @seealso %% ~~objects to See Also as \code{\link{~~fun~~}}, ~~~ %% ~~or
#' \code{\linkS4class{CLASSNAME}} for links to other classes ~~~
#' \code{\linkS4class{swFiles}} \code{\linkS4class{swYears}}
#' \code{\linkS4class{swWeather}} \code{\linkS4class{swCloud}}
#' \code{\linkS4class{swMarkov}} \code{\linkS4class{swProd}}
#' \code{\linkS4class{swSite}} \code{\linkS4class{swSoils}}
#' \code{\linkS4class{swEstab}} \code{\linkS4class{swOUT}}
#' \code{\linkS4class{swSWC}} \code{\linkS4class{swLog}}
#' @references %% ~~put references to the literature/web site here~~
#' https://github.com/Burke-Lauenroth-Lab/Rsoilwat
#' @keywords classes
#' @examples
#'
#' showClass("swInputData")
#'
NULL




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