Merge branch 'release/1.0.0'

Update description file with date and version

.gitignore

@@ -21,3 +21,7 @@ vignettes/*.pdf
 # vim backup
 
 *~
+
+man/*Rd
+inst/extdata/Rplots.pdf
+inst/extdata/plot_test.R

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: osmose
 Type: Package
 Title: Object Oriented Simulator of Marine Ecosystems
-Version: 0.1.3
-Date: 2018-12-12
+Version: 1.0.0
+Date: 2019-09-19
 Authors@R: c(
   person("Yunne-Jai", "Shin", role="aut"),
   person("Travers", "Morgane", role="aut"),
@@ -37,8 +37,8 @@ Imports:
   utils,
   knitr,
   rmarkdown,
-  ggplot2, 
-  ncdf4
+  ncdf4,
+  mgcv
 URL: http://www.osmose-model.org/ 
 LazyData: FALSE
 BugReports: https://github.com/osmose-model/osmose/issues

NAMESPACE

@@ -4,10 +4,34 @@ S3method(getVar,osmose)
 S3method(getVar,osmose.config)
 S3method(plot,osmose)
 S3method(plot,osmose.abundance)
+S3method(plot,osmose.abundanceDistribByAge)
+S3method(plot,osmose.abundanceDistribBySize)
+S3method(plot,osmose.abundanceDistribByTL)
 S3method(plot,osmose.biomass)
+S3method(plot,osmose.biomassDistribByAge)
+S3method(plot,osmose.biomassDistribBySize)
+S3method(plot,osmose.biomassDistribByTL)
+S3method(plot,osmose.biomassPredPreyIni)
 S3method(plot,osmose.config)
+S3method(plot,osmose.dietMatrix)
+S3method(plot,osmose.dietMatrixbyAge)
+S3method(plot,osmose.dietMatrixbySize)
+S3method(plot,osmose.meanSize)
+S3method(plot,osmose.meanSizeCatch)
+S3method(plot,osmose.meanTLByAge)
+S3method(plot,osmose.meanTLBySize)
+S3method(plot,osmose.mortalityRate)
+S3method(plot,osmose.mortalityRateDistribByAge)
+S3method(plot,osmose.mortalityRateDistribBySize)
+S3method(plot,osmose.predatorPressure)
+S3method(plot,osmose.predatorPressureDistribByAge)
+S3method(plot,osmose.predatorPressureDistribBySize)
 S3method(plot,osmose.yield)
+S3method(plot,osmose.yieldByAge)
+S3method(plot,osmose.yieldBySize)
 S3method(plot,osmose.yieldN)
+S3method(plot,osmose.yieldNByAge)
+S3method(plot,osmose.yieldNBySize)
 S3method(print,osmose)
 S3method(print,summary.osmose)
 S3method(report,osmose)
@@ -17,6 +41,7 @@ S3method(summary,osmose.dietMatrix)
 S3method(summary,osmose.meanTL)
 S3method(summary,osmose.meanTLCatch)
 S3method(summary,osmose.mortalityRate)
+export(F_msy)
 export(correct_ltl_file)
 export(existOsmoseParameter)
 export(extract_grid_mask)
@@ -25,13 +50,18 @@ export(find_species_index)
 export(getAverageMortality)
 export(getFishingBaseRate)
 export(getFishingMortality)
+export(getGrowthParameters)
 export(getMortality)
 export(getMortalityDeviation)
 export(getOsmoseParameter)
 export(getSizeSpectrum)
 export(getVar)
+export(list_osmose_versions)
 export(make_movement_netcdf)
 export(osmose2R)
+export(osmoseGrowth)
+export(osmose_calib_demo)
+export(osmose_demo)
 export(readOsmoseConfiguration)
 export(read_osmose)
 export(report)
@@ -42,24 +72,23 @@ export(writeFishingFiles)
 export(write_osmose)
 import(grDevices)
 import(graphics)
-importFrom(ggplot2,geom_area)
-importFrom(ggplot2,ggplot)
-importFrom(ggplot2,ggtitle)
-importFrom(ggplot2,scale_fill_brewer)
-importFrom(ggplot2,scale_fill_manual)
-importFrom(ggplot2,theme)
 importFrom(knitr,knit)
+importFrom(mgcv,gam)
 importFrom(ncdf4,nc_close)
 importFrom(ncdf4,nc_create)
 importFrom(ncdf4,nc_open)
+importFrom(ncdf4,ncatt_get)
+importFrom(ncdf4,ncatt_put)
 importFrom(ncdf4,ncdim_def)
+importFrom(ncdf4,ncvar_def)
 importFrom(ncdf4,ncvar_get)
 importFrom(ncdf4,ncvar_put)
 importFrom(rlist,list.merge)
 importFrom(rmarkdown,render)
 importFrom(stats,dlnorm)
 importFrom(stats,dnorm)
 importFrom(stats,median)
+importFrom(stats,predict)
 importFrom(stats,qnorm)
 importFrom(stats,quantile)
 importFrom(stats,sd)
@@ -69,4 +98,6 @@ importFrom(stringr,str_sub)
 importFrom(stringr,str_trim)
 importFrom(utils,read.csv)
 importFrom(utils,read.table)
+importFrom(utils,tail)
+importFrom(utils,write.csv)
 importFrom(utils,write.table)

R/aaa-.R

@@ -4,18 +4,19 @@ NULL
 NULL
 #' @importFrom stats median sd quantile setNames dlnorm dnorm qnorm
 NULL
-#' @importFrom utils read.csv read.table write.table
+#' @importFrom utils read.csv read.table write.table tail write.csv
 NULL
 #' @importFrom rlist list.merge
 NULL
 #' @importFrom stringr str_split str_trim str_sub
 NULL
-# barrier.n: adding some functions for ggplot
-#' @importFrom ggplot2 ggplot geom_area scale_fill_brewer scale_fill_manual theme ggtitle
-NULL
 #' @importFrom rmarkdown render
 NULL
 #' @importFrom knitr knit
 NULL
-#' @importFrom ncdf4 nc_open nc_close ncvar_put ncvar_get ncvar_put nc_create ncdim_def
+#' @importFrom ncdf4 nc_open nc_close ncvar_put ncvar_get ncvar_put nc_create ncdim_def ncatt_get ncvar_def ncatt_put
+NULL
+#' @importFrom mgcv gam
+NULL
+#' @importFrom stats predict
 NULL

R/osmose-auxiliar.R

@@ -1,4 +1,16 @@
 
+#' Returns the list of Osmoee Java versions
+#'
+#' @return List of Osmose Java versions
+#' @export
+#'
+#' @examples list_osmose_versions()
+list_osmose_versions = function() {
+  dirin = system.file(package="osmose", "java")
+  output = list.files(path=dirin, pattern=".jar")
+  return(output)
+}
+
 # 
 # isfalse = function(x) {
 #   output = !isTRUE(x)  

R/osmose-class.R

@@ -28,10 +28,12 @@ plot.osmose = function(x, what = "biomass", ...) {
 #' Get variable
 #' @description Function to get a variable from an object of \code{osmose} 
 #' class. This function uses the getVar method (see the \code{\link{getVar.osmose}}).
+#'
 #' @param object Object of \code{osmose} class (see the \code{\link{read_osmose}} function).
-#' @param var Name of variable to extract. It could be: "biomass","abundance",
-#'  "yield", "yieldN".
+#' @param what Variable to extract
+#' @param how Output format
 #' @param ... Additional arguments of the function.
+#'
 #' @return An array or a list containing the extracted data.
 #' @export
 getVar = function(object, what, how, ...) {
@@ -67,8 +69,9 @@ getVar.osmose = function(object, what, how=c("matrix", "data.frame", "list"),
       stop(message) 
   }
 
-  if(inherits(out, "array") & isTRUE(expected))
+  if(inherits(out, "array") & isTRUE(expected)) {
     out = apply(out, c(1, 2), mean, na.rm=TRUE)
+  }
 
   if(how=="matrix") return(out)