@@ -4832,7 +4827,7 @@ List of parameters
character
-LandR
+0
|
NA
@@ -5323,6 +5318,9 @@ List of outputs
integer
|
+internal use. Keeps track of which pixels are active
+ |
+
Internal use. Keeps track of which pixels are active.
|
@@ -5334,6 +5332,9 @@ List of outputs
integer
+internal use. Keeps track of which pixels are active in the reporting study area
+ |
+
Internal use. Keeps track of which pixels are active in the reporting study area.
|
@@ -5342,7 +5343,7 @@ List of outputs
ANPPMap
-SpatRaster
+RasterLayer
|
ANPP map at each succession time step (in g /m^2)
@@ -5367,6 +5368,9 @@ List of outputs
data.table
|
+data.table with cohort-level information on age, biomass, aboveground primary productivity (year’s biomass gain) and mortality (year’s biomass loss), by pixelGroup and ecolocation (i.e., ecoregionGroup ). Contains at least the following columns: pixelGroup (integer), ecoregionGroup (factor), speciesCode (factor), B (integer in g/m^2), age (integer in years), mortality (integer in g/m^2), aNPPAct (integer in g/m^2). May have other columns depending on additional simulated processes (i.e., cliamte sensitivity; see, e.g., P(sim)$keepClimateCols ).
+ |
+
data.table with cohort-level information on age, biomass, aboveground primary productivity (year’s biomass gain) and mortality (year’s biomass loss), by pixelGroup and ecolocation (i.e., ecoregionGroup ). Contains at least the following columns: pixelGroup (integer), ecoregionGroup (factor), speciesCode (factor), B (integer in latex2b27a1ad385d16c73646cd918252c6d2), age (integer in years), mortality (integer in latex2b27a1ad385d16c73646cd918252c6d2), aNPPAct (integer in latex2b27a1ad385d16c73646cd918252c6d2). May have other columns depending on additional simulated processes (i.e., climate sensitivity; see, e.g., P(sim)$keepClimateCols ).
|
@@ -5386,7 +5390,10 @@ List of outputs
ecoregionMap
-SpatRaster
+RasterLayer
+ |
+
+map with mapcodes match ecoregion table and speciesEcoregion table. Defaults to a dummy map matching rasterToMatch with two regions
|
Map with mapcodes match ecoregion table and speciesEcoregion table. Defaults to a dummy map matching rasterToMatch with two regions.
@@ -5400,6 +5407,9 @@ List of outputs
logical
|
+internal use. Keeps track of which pixels are inactive
+ |
+
Internal use. Keeps track of which pixels are inactive.
|
@@ -5411,6 +5421,9 @@ List of outputs
integer
+internal use. Keeps track of which pixels are inactive in the reporting study area
+ |
+
Internal use. Keeps track of which pixels are inactive in the reporting study area.
|
@@ -5422,6 +5435,9 @@ List of outputs
numeric
+Year of the most recent fire year
+ |
+
Year of the most recent fire.
|
@@ -5433,6 +5449,9 @@ List of outputs
numeric
+an internal counter keeping track of when the last regeneration event occurred
+ |
+
An internal counter keeping track of when the last regeneration event occurred.
|
@@ -5444,6 +5463,9 @@ List of outputs
data.frame
+define the relative biomass cut points to classify stand shade
+ |
+
Define the relative biomass cut points to classify stand shade.
|
@@ -5452,7 +5474,10 @@ List of outputs
mortalityMap
-SpatRaster
+RasterLayer
+ |
+
+map of biomass lost (in g/m^2) at each succession time step
|
Map of biomass lost (in \(g/m^2\)) at each succession time step.
@@ -5463,7 +5488,10 @@ List of outputs
pixelGroupMap
|
-SpatRaster
+RasterLayer
+ |
+
+updated community map at each succession time step
|
Updated community map at each succession time step.
@@ -5485,7 +5513,10 @@ List of outputs
reproductionMap
|
-SpatRaster
+RasterLayer
+ |
+
+Regeneration map (biomass gains in g/m^2) at each succession time step
|
Regeneration map (biomass gains in latex2b27a1ad385d16c73646cd918252c6d2) at each succession time step
@@ -5496,7 +5527,10 @@ List of outputs
simulatedBiomassMap
|
-SpatRaster
+RasterLayer
+ |
+
+Biomass map at each succession time step (in g/m^2)
|
Biomass map at each succession time step (in latex2b27a1ad385d16c73646cd918252c6d2)
@@ -5510,6 +5544,9 @@ List of outputs
data.table
|
+contains simulation results by ecoregionGroup (main output)
+ |
+
Contains simulation results by ecoregionGroup (main output)
|
@@ -5543,6 +5580,9 @@ List of outputs
data.table
+define the maxANPP, maxB and SEP change with both ecoregion and simulation time
+ |
+
Define the maxANPP , maxB and SEP change with both ecoregion and simulation time.
|
@@ -5551,7 +5591,10 @@ List of outputs
speciesLayers
-SpatRaster
+RasterStack
+ |
+
+species percent cover raster layers, based on input speciesLayers object. Not changed by this module.
|
Species percent cover raster layers, based on input speciesLayers object. Not changed by this module.
@@ -5587,6 +5630,9 @@ List of outputs
data.table
|
+The total species biomass (in g/m^2 as in cohortData ), average age and aNPP (in g/m^2 as in cohortData ), across the landscape (used for plotting and reporting).
+ |
+
The total species biomass (in latex2b27a1ad385d16c73646cd918252c6d2 as in cohortData ), average age and aNPP (in latex2b27a1ad385d16c73646cd918252c6d2 as in cohortData ), across the landscape (used for plotting and reporting).
|
@@ -5598,6 +5644,9 @@ List of outputs
data.table
+No. pixels of each leading vegetation type (used for plotting and reporting).
+ |
+
Number of pixels of each leading vegetation type (used for plotting and reporting).
|
@@ -5609,6 +5658,9 @@ List of outputs
data.table
+The averages of total biomass (in tonnes/ha , not g/m^2 like in cohortData ), age and aNPP (also in tonnes/ha) across the landscape (used for plotting and reporting).
+ |
+
The averages of total biomass (in tonnes/ha , not latex2b27a1ad385d16c73646cd918252c6d2 like in cohortData ), age and aNPP (also in tonnes/ha) across the landscape (used for plotting and reporting).
|
@@ -5628,7 +5680,7 @@ List of outputs
vegTypeMap
-SpatRaster
+RasterLayer
|
Map of leading species in each pixel, colored according to sim$sppColorVect . Species mixtures calculated according to P(sim)$vegLeadingProportion and P(sim)$mixedType .
@@ -5657,8 +5709,7 @@ Simulation flow and module events
LandMine);
Post-disturbance mortality/regeneration (OPTIONAL) – simulated by a
regeneration module (e.g., Biomass_regeneration);
-Seed dispersal (every successionTimestep ; Dispersal event):
-
+Seed dispersal (every successionTimestep ; Dispersal event):
- seed dispersal can be a slow process and has been adapted to occur every
10 years (default
successionTimestep ). The user can set it to occur
@@ -5666,25 +5717,20 @@ Simulation flow and module events
to estimate species establishment probabilities, these values are
integrated over 10 years.
- see Scheller & Domingo (2012) for details on dispersal algorithms.
-
-
-- Growth and mortality (
mortalityAndGrowth event):
-
+
+Growth and mortality (mortalityAndGrowth event):
- unlike dispersal, growth and mortality always occur time step (year).
- see Scheller & Mladenoff (2004) for further detail.
-
-
-- Cohort age binning (every
successionTimestep ; cohortAgeReclassification
-event):
-
+
+Cohort age binning (every successionTimestep ; cohortAgeReclassification
+event):
- follows the same frequency as dispersal, collapsing cohorts (i.e.,
summing their biomass/mortality/aNPP) to ages classes with resolution
equal to
successionTimestep .
- see Scheller & Miranda (2015) for further detail.
-
-
+
Summary tables of regeneration (summaryRegen event), biomass, age, growth
and mortality (summaryBGM event);
Plots of maps (plotMaps event) and averages (plotAvgs and
@@ -5930,8 +5976,10 @@ Set up R libraries
.libPaths(pkgPath, include.site = FALSE)
if (!require(Require, lib.loc = pkgPath)) {
- remotes::install_github("PredictiveEcology/Require@5c44205bf407f613f53546be652a438ef1248147",
- upgrade = FALSE, force = TRUE)
+ remotes::install_github(
+ paste0("PredictiveEcology/",
+ "Require@5c44205bf407f613f53546be652a438ef1248147"),
+ upgrade = FALSE, force = TRUE)
library(Require, lib.loc = pkgPath)
}
@@ -5948,7 +5996,8 @@ Get the module and module dependencies
dependencies are installed in their correct version.
SpaDES.project::packagesInModules makes a list of necessary packages for all
modules in the paths$modulePath , and Require installs them.
-Require("PredictiveEcology/SpaDES.project@6d7de6ee12fc967c7c60de44f1aa3b04e6eeb5db",
+Require(paste0("PredictiveEcology/",
+ "SpaDES.project@6d7de6ee12fc967c7c60de44f1aa3b04e6eeb5db"),
require = FALSE, upgrade = FALSE, standAlone = TRUE)
paths <- list(inputPath = normPath(file.path(tempDir, "inputs")),
@@ -6038,7 +6087,7 @@ Run simulation
outputs = outputs,
debug = TRUE)
-
+
Figure 7: Biomass_core automatically generates simulation visuals of species dynamics across the landscape in terms of total biomass, number of presences and age and productivity (above), as well as yearly plots of total biomass, productivity, mortality, reproduction and leading species in each pixel (below).
diff --git a/Biomass_core.md b/Biomass_core.md
index bef10a7..0e7dbed 100644
--- a/Biomass_core.md
+++ b/Biomass_core.md
@@ -1,6 +1,6 @@
---
title: "LandR _Biomass_core_ Manual"
-date: "Last updated: 2022-11-03"
+date: "Last updated: 2022-10-24"
output:
bookdown::html_document2:
toc: true
@@ -44,7 +44,7 @@ always_allow_html: true
-[![module-version-Badge](D:/GitHub/LandR-Manual/modules/Biomass_core/figures/moduleVersionBadge.png)](https://github.com/PredictiveEcology/Biomass_core/commit/c081e5bf998e73eb35f64002af43c10c5e604a98)
+[![module-version-Badge](D:/GitHub/LandR-Manual/modules/Biomass_core/figures/moduleVersionBadge.png)](https://github.com/PredictiveEcology/Biomass_core/commit/b3dc7c6b8dc3e07fa07304c7008255e83d20abe7)
[![Issues-badge](D:/GitHub/LandR-Manual/modules/Biomass_core/figures/issuesBadge.png)](https://github.com/PredictiveEcology/Biomass_core/issues)
@@ -87,7 +87,7 @@ LANDIS-II counterpart, and we refer the reader to the corresponding LBSE manual
the model.
@@ -851,26 +851,26 @@ then *Biomass_core* attempts to use any species for which if finds available spe
simulation as cohort dynamics are simulated. It must contain the following
columns:
- - *pixelGroup* -- integer. *pixelGroup* ID. See
- [Hashing](#biomass-core-vs-lbse-enhan2).
-
- - *ecoregionGroup* -- character. Ecolocation names. See `ecoregionMap` and
- `ecoregion` objects above.
-
- - *speciesCode* -- character. Species ID.
-
- - *age* -- integer. Cohort age.
-
- - *B* -- integer. Cohort biomass of the current year in $g/m^2$.
-
- - *mortality* -- integer. Cohort dead biomass of the current year in
- $g/m^2$. Usually filled with 0s in initial conditions.
-
- - *aNPPAct* -- integer. Actual aboveground net primary productivity of the
- current year in $g/m^2$. `B` is the result of the previous year's `B`
- minus the current year's `mortality` plus `aNPPAct`. Usually filled with
- 0s in initial conditions. See "*1.1.3 Cohort growth and ageing*" section
- of @SchellerMiranda2015.
+- *pixelGroup* -- integer. *pixelGroup* ID. See
+[Hashing](#biomass-core-vs-lbse-enhan2).
+
+- *ecoregionGroup* -- character. Ecolocation names. See `ecoregionMap` and
+`ecoregion` objects above.
+
+- *speciesCode* -- character. Species ID.
+
+- *age* -- integer. Cohort age.
+
+- *B* -- integer. Cohort biomass of the current year in $g/m^2$.
+
+- *mortality* -- integer. Cohort dead biomass of the current year in
+$g/m^2$. Usually filled with 0s in initial conditions.
+
+- *aNPPAct* -- integer. Actual aboveground net primary productivity of the
+current year in $g/m^2$. `B` is the result of the previous year's `B`
+minus the current year's `mortality` plus `aNPPAct`. Usually filled with
+0s in initial conditions. See "*1.1.3 Cohort growth and ageing*" section
+of @SchellerMiranda2015.
- `pixelGroupMap` -- a raster layer with `pixelGroup` IDs per pixel. Pixels
are always grouped based on identical `ecoregionGroup`, `speciesCode`, `age`
@@ -1296,7 +1296,7 @@ event (growth and mortality are always yearly);
64 |
NA |
NA |
- Passed to `httr::config(ssl_verifypeer = P(sim)$.sslVerify)` when downloading KNN (NFI) datasets. Set to 0L if necessary to bypass checking the SSL certificate (this may be necessary when NFI's website SSL certificate is not correctly configured). |
+ Passed to `httr::config(ssl_verifypeer = P(sim)$.sslVerify)` when downloading KNN (NFI) datasets. Set to 0L if necessary to bypass checking the SSL certificate (this may be necessary when NFI's FTP website SSL certificate is down/out-of-date). |
.studyAreaName |
@@ -1448,7 +1448,7 @@ in `simInit`[^biomass_core-5].
speciesEcoregion |
data.table |
- define the `maxANPP`, `maxB` and `SEP` change with both ecoregion and simulation time. |
+ define the maxANPP, maxB and SEP change with both ecoregion and simulation time |
speciesLayers |
@@ -1468,7 +1468,7 @@ in `simInit`[^biomass_core-5].
summaryBySpecies1 |
data.table |
- Number of pixels of each leading vegetation type (used for plotting and reporting). |
+ No. pixels of each leading vegetation type (used for plotting and reporting). |
summaryLandscape |
@@ -1788,15 +1788,15 @@ from smaller to larger maps (Fig. \@ref(fig:figLBSEtest5)b).
```r
options(repos = c(CRAN = "https://cloud.r-project.org"))
-tempDir <- tempdir()
-
+# tempDir <- tempdir()
+tempDir <- "C:/Users/cbarros/AppData/Local/Temp/Biomass_core-example"
pkgPath <- file.path(tempDir, "packages", version$platform,
paste0(version$major, ".", strsplit(version$minor, "[.]")[[1]][1]))
dir.create(pkgPath, recursive = TRUE)
.libPaths(pkgPath, include.site = FALSE)
if (!require(Require, lib.loc = pkgPath)) {
- remotes::install_github("PredictiveEcology/Require@5c44205bf407f613f53546be652a438ef1248147",
+ remotes::install_github("PredictiveEcology/Require@f2c791eb05fb0ad99b278619198ef925f85cbb9d",
upgrade = FALSE, force = TRUE)
library(Require, lib.loc = pkgPath)
}
@@ -1908,8 +1908,7 @@ and where inputs should be downloaded to (`"reproducible.destinationPath"`).
```r
opts <- options(reproducible.useCache = TRUE,
- reproducible.destinationPath = paths$inputPath,
- spades.useRequire = FALSE)
+ reproducible.destinationPath = paths$inputPath)
graphics.off()
mySim <- simInitAndSpades(times = times,
params = parameters,
|