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.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

DESCRIPTION

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+Package: NFRRPhilippines
+Type: Package
+Title: NFRRPhilippines
+Version: 0.3.0
+Author: Ryan T. Sharp
+Maintainer: Ryan T. Sharp <[email protected]>
+Description: A set of tools for fitting an epidemiological model to the Newton Fund Rice Research experimental data.
+License: file LICENCE
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.1.2
+Imports:
+    reshape2
+    ,plyr
+    ,dplyr
+    ,minpack.lm
+    ,deSolve
+    ,grid
+    ,ggplot2
+    ,gtable
+    ,RColorBrewer
+    ,scales
+    ,utils
+    ,DEoptim
+    ,stats4

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(add_finalNSampleWeek)
+export(calc_sumPlotWeek)
+export(clean_experimentData)
+export(clean_plotWeekSum)
+export(fitOut_philippinesStandard)
+export(load_all_experimentData)
+export(load_experimentData)
+export(load_sampleDatesFile)
+export(modelOut_philippinesStandard)
+export(model_resExpJoint2)
+export(model_susExpJoint2)
+export(name_basePath)
+export(name_experimentDataFile)
+export(name_institute)
+export(opt_conjugateParams)
+export(opt_get_compModDatJoint)
+export(opt_get_control)
+export(opt_get_fitFuncParams)
+export(opt_is_converged)
+export(opt_paramsNLS)
+export(opt_residFunc_standard)
+export(opt_residuals)
+export(opt_run_fitFunc)
+export(opt_tryFit)
+export(setup_env)
+export(solve_opt1D)
+export(update_dead_experimentData)
+import(bindrcpp)
+import(dplyr)
+importFrom(deSolve,rk)
+importFrom(plyr,join)
+importFrom(reshape2,melt)
+importFrom(rlang,sym)
+importFrom(stats,nls)
+importFrom(utils,read.csv)

NFRR_Philippines.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

R/add_finalNSampleWeek.R

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+#' [Title]
+#'
+#' [Description]
+#' @param data data produced from \code{\link{calc_sumPlotWeek}}
+#' @param allDataTypes data frame giving a series of year/season/site combinations to load
+#' @param filepath location of folder containing sample dates data files
+#' @export
+add_finalNSampleWeek = function(
+    data, allDataTypes, filepath,
+    country, experiment
+){
+    oriFNSW = read.csv(
+        paste0(filepath, "\\", country, "\\", experiment, "\\", "Final_N_Week.csv")
+    )
+
+    oriDat = data
+    finDat = NULL
+    for(i in 1:nrow(allDataTypes)){ #i=1 i=2
+        year = allDataTypes$year[i]
+        season = allDataTypes$season[i]
+        site = allDataTypes$site[i]
+
+        finalNSampleWeek = oriFNSW[
+            as.character(oriFNSW$Season)==season
+            & oriFNSW$Year==year
+            & as.character(oriFNSW$Site)==site
+            ,
+        ]
+
+        data = oriDat[
+            as.character(oriDat$season)==season
+            & oriDat$year==year
+            & as.character(oriDat$site)==site
+            ,
+        ]
+        data$Final_N_Sample_Week = finalNSampleWeek$Final_N_Sample_Week[match(data$Plot_f, finalNSampleWeek$Plot)]
+
+        finDat = rbind(finDat,data)
+    }
+
+
+    return(finDat)
+}

R/calc_sumPlotWeek.R

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+#' @importFrom reshape2 melt
+#' @importFrom utils read.csv
+#' @importFrom rlang sym
+#' @import dplyr
+#' @import bindrcpp
+NULL
+
+#' Sum infected (I) and total tillers (N=H+I) from each plot-week
+#'
+#' Sums the number of infections and total number of tillers from each plot-week for a given site.
+#' @param site site name (one of "Pila","Victoria","Malayantoc","Maligaya").
+#' @param year the year the data was collected
+#' @param season the season the data was collected
+#' @return dataframe with the date/DAT/Week# sampled, number of tillers infected and total number of tillers.
+#' @export
+calc_sumPlotWeek = function(data=NULL, country=NULL, experiment=NULL, site=NULL, year=NULL, season=NULL, sumVar="numTillers", filepath){
+
+    if(is.null(data)){
+        datMelt = load_all_experimentData(allDataTypes = data.frame(country=country, experiment=experiment, site=site, year=year, season=season), filepath=filepath)
+    } else{
+        datMelt = data
+    }
+
+    datMelt[,sumVar][datMelt[,sumVar]<0] = 0 #set any negative values to 0. - any deduction of -ve counts to N must be done prior to this.
+
+    symVar=sym(sumVar)
+
+    plotWeekSum = datMelt %>%
+        group_by_(~Week, ~Line, ~Rep, ~type, ~site, ~year, ~season, ~country, ~DAT, ~WeekDate, ~Plot_f) %>%
+        summarise(test = sum(!!symVar)) %>%
+        as.data.frame()
+    names(plotWeekSum)[match("test",names(plotWeekSum))] = sumVar
+
+    country = unique(plotWeekSum$country)
+    if(length(country)!=1) stop("Multiple countries in plotWeekSum!")
+
+    #Add finalNSampleWeek
+    plotWeekSum = add_finalNSampleWeek(data=plotWeekSum, allDataTypes=data.frame(site=site,year=year,season=season), country=country, experiment=experiment, filepath=filepath)
+    plotWeekSum$isNRepeated = (plotWeekSum$Week > plotWeekSum$Final_N_Sample_Week) & plotWeekSum$type=="N"
+
+    #Add plot type
+    plotWeekSum$Plot_Type = c("sus", "res")[as.numeric(grepl("Res",plotWeekSum$Plot_f))+1]
+    plotWeekSum = clean_plotWeekSum(site=site, year=year, season=season, plotWeekSum=plotWeekSum)
+
+    return(plotWeekSum)
+}

R/clean_plotWeekSum.R

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+#' [Title]
+#'
+#' [Description]
+#' @param site site name (one of "Pila","Victoria","Malayantoc","Maligaya").
+#' @param year the year the data was collected
+#' @param season the season the data was collected
+#' @param type Either "I" or "N".
+#' @param plotWeekSum data produced from \code{\link{calc_sumPlotWeek}}
+#' @return plotWeekSum with compromised data removed.
+#' @export
+clean_plotWeekSum = function(site, year, season, type, plotWeekSum){
+    if(site=="Malayantoc" & year==2016 & season=="Wet"){
+        plotWeekSum = plotWeekSum[!(
+                grepl("Sus", plotWeekSum$Plot_f)
+                &plotWeekSum$Week==5
+                &plotWeekSum$type=="I"
+            )
+            ,
+        ]
+    }
+
+    return(plotWeekSum)
+}

R/fitOut_philippinesStandard.R

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+#' Philippines - Standard Residual; Published Fit
+#'
+#' Code to produce model for Philippines - Standard Redisual; Published Fit
+#' @param year year of experiment
+#' @param season season of experiment
+#' @param site site name of site where experiment was performed
+#' @return model values
+#' @export
+fitOut_philippinesStandard = function(year, season, site, compare=F, compareA=T, residFuncName = "standard", filepath, env=NULL){
+
+  #==============================================================================#
+  # Fit model to epidemiological data using nls.lm (Sharp, 2017)
+  #==============================================================================#
+
+  library(stats4)
+
+  if(is.null(env)){
+    env <- new.env()
+    setup_env(year, season, site, filepath=filepath, env=env)
+  }
+
+  fitFunc = env$fitFunc
+  initParams = env$initParams
+  lower = env$lower
+  upper = env$upper
+  tColStr = env$tColStr
+  plotSum = env$plotSum
+  N0 = env$N0
+  args = env$args
+  modelFunc = env$modelFunc
+  joint = env$joint
+  solved = env$solved
+  aOrder = env$aOrder
+  control = env$control
+  residFunc = env$residFunc
+
+  fitval = opt_tryFit(
+    fitFunc=fitFunc,initParams=initParams,lower=lower,upper=upper,tColStr=tColStr,plotSum=plotSum,N0=N0,args=args,
+    modelFunc=modelFunc, joint=joint, solved=solved,
+    aOrder=aOrder,
+    control=control,
+    residFunc=residFunc
+    ,maxRecs = 10
+  )
+
+  return(fitval)
+}