Merge pull request #87 from PredictiveEcology/suz-dep

SpaDES.core removed from dependencies

Author: suz-estella

DESCRIPTION

@@ -5,7 +5,7 @@ Description: Implementation of several components of the Carbon Budget Model of
     Canadian Forest Service (v3).
 URL:
     https://github.com/PredictiveEcology/CBMutils
-Version: 2.5.4.9001
+Version: 2.5.4.9002
 Authors@R: c(
     person("Céline",    "Boisvenue", email = "celine.boisvenue@nrcan-rncan.gc.ca", role = c("aut", "cre")),
     person("Alex M",    "Chubaty",   email = "achubaty@for-cast.ca",               role = c("aut"), comment = c(ORCID = "0000-0001-7146-8135")),
@@ -44,12 +44,10 @@ Suggests:
     FNN,
     qs2,
     reproducible,
-    SpaDES.core,
     rmarkdown,
     testthat
 Remotes:
     PredictiveEcology/reproducible@development,
-    PredictiveEcology/SpaDES.core@development,
     PredictiveEcology/CBM4r@main
 VignetteBuilder: knitr, rmarkdown
 Encoding: UTF-8

R/CBM-plots_mapNPP.R

@@ -83,16 +83,14 @@ cbm4MapNPP <- function(cbm4_results, years = NULL, yearStart = 1){
 #' @export
 simMapNPP <- function(simCBM, year = NULL, useCache = TRUE){
 
-  if (is.null(year)){
-    year <- SpaDES.core::convertTimeunit(SpaDES.core::times(simCBM)$current, "year")
-  }
+  if (is.null(year)) year <- simYears(simCBM)$current
 
   if (!is.null(simCBM$CBM4data)){
 
     cbm4MapNPP(
       simCBM$CBM4data,
       years     = year,
-      yearStart = SpaDES.core::start(simCBM)
+      yearStart = simYears(simCBM)$start
     )[[1]]
 
   }else{

R/CBM-plots_mapTotalCarbon.R

@@ -81,16 +81,14 @@ cbm4MapTotalCarbon <- function(cbm4_results, years = NULL, yearStart = 1){
 #' @export
 simMapTotalCarbon <- function(simCBM, year = NULL, useCache = TRUE){
 
-  if (is.null(year)){
-    year <- SpaDES.core::convertTimeunit(SpaDES.core::times(simCBM)$current, "year")
-  }
+  if (is.null(year)) year <- simYears(simCBM)$current
 
   if (!is.null(simCBM$CBM4data)){
 
     cbm4MapTotalCarbon(
       simCBM$CBM4data,
       years     = year,
-      yearStart = SpaDES.core::start(simCBM)
+      yearStart = simYears(simCBM)$start
     )[[1]]
 
   }else{

R/CBM-plots_plotEmissionsProducts.R

@@ -105,12 +105,12 @@ simPlotEmissionsProducts <- function(simCBM, years = NULL, useCache = TRUE){
     cbm4PlotEmissionsProducts(
       simCBM$CBM4data,
       years     = years,
-      yearStart = SpaDES.core::start(simCBM)
+      yearStart = simYears(simCBM)$start
     )
 
   }else{
 
-    if (is.null(years)) years <- SpaDES.core::start(simCBM):SpaDES.core::end(simCBM)
+    if (is.null(years)) years <- with(simYears(simCBM), start:end)
 
     spadesCBMdbPlotEmissionsProducts(
       simCBM$spadesCBMdb,

R/CBM-plots_plotPoolProportions.R

@@ -119,13 +119,13 @@ simPlotPoolProportions <- function(simCBM, years = NULL, useCache = TRUE){
 
     cbm4PlotPoolProportions(
       simCBM$CBM4data,
-      years      = years,
-      yearStart = SpaDES.core::start(simCBM)
+      years     = years,
+      yearStart = simYears(simCBM)$start
     )
 
   }else{
 
-    if (is.null(years)) years <- c(0, SpaDES.core::start(simCBM):SpaDES.core::end(simCBM))
+    if (is.null(years)) years <- c(0, with(simYears(simCBM), start:end))
 
     spadesCBMdbPlotPoolProportions(
       simCBM$spadesCBMdb,

R/spadesCBMdb_dbReadRaw.R

@@ -11,9 +11,7 @@
 #' @export
 simCBMdbReadRaw <- function(simCBM, year, table, ...){
 
-  if (missing(year)){
-    year <- SpaDES.core::convertTimeunit(SpaDES.core::times(simCBM)$current, "year")
-  }
+  if (missing(year)) year <- simYears(simCBM)$current
 
   spadesCBMdbReadRaw(simCBM$spadesCBMdb, year = year, table = table, ...)
 }

R/spadesCBMdb_dbReadSummary.R

@@ -16,13 +16,9 @@
 simCBMdbReadSummary <- function(simCBM, summary, by = "cohortID", units = "t/ha",
                                 year = NULL, years = NULL, useCache = TRUE){
 
-  if (is.null(year) & by != "year"){
-    year <- SpaDES.core::convertTimeunit(SpaDES.core::times(simCBM)$current, "year")
-  }
-  if (is.null(years) & by == "year"){
-    simTimes <- lapply(SpaDES.core::times(simCBM)[c("start", "end")], SpaDES.core::convertTimeunit, "year")
-    years <- simTimes$start:simTimes$end
-  }
+  if (is.null(year)  & by != "year") year  <- simYears(simCBM)$current
+  if (is.null(years) & by == "year") years <- with(simYears(simCBM), start:end)
+
   spadesCBMdbReadSummary(
     simCBM$spadesCBMdb,
     summary  = summary,

R/spadesCBMdb_dbReadTable.R

@@ -11,9 +11,7 @@
 #' @export
 simCBMdbReadTable <- function(simCBM, year, table, useCache = TRUE){
 
-  if (missing(year)){
-    year <- SpaDES.core::convertTimeunit(SpaDES.core::times(simCBM)$current, "year")
-  }
+  if (missing(year)) year <- simYears(simCBM)$current
 
   spadesCBMdbReadTable(simCBM$spadesCBMdb, year = year, table = table, useCache = useCache)
 }

R/spadesCBMdb_dbWrite.R

@@ -10,9 +10,7 @@
 #' @export
 simCBMdbWrite <- function(simCBM, year, parameters = TRUE, state = TRUE, flux = TRUE, pools = TRUE){
 
-  if (missing(year)){
-    year <- SpaDES.core::convertTimeunit(SpaDES.core::times(simCBM)$current, "year")
-  }
+  if (missing(year)) year <- simYears(simCBM)$current
 
   spadesCBMdbWrite(
     simCBM$spadesCBMdb,

R/utils-simList.R

@@ -0,0 +1,21 @@
+
+# Get simList times in years without using SpaDES.core functions
+simYears <- function(sim){
+
+  simTimes <- sim@simtimes[c("current", "start", "end")]
+  simTimes <- lapply(simTimes, function(st){
+    if (attr(st, "unit") == "second"){
+      st <- st / (60 * 60 * 24 * 365.25)
+      attr(st, "unit") <- "year"
+    }
+    return(st)
+  })
+
+  if (!all(sapply(simTimes, attr, "unit") == "year") |
+      any(simTimes$start > c(sim$simTimes$current, sim$simTimes$end)) |
+      any(simTimes$end   < c(sim$simTimes$current, sim$simTimes$start))) stop(
+        "Converting sim@simtimes to unit 'year' failed")
+
+  return(simTimes)
+}
+