Authors:
Felipe Sodré Mendes Barros
Renato Crouzeilles
Julia Niemeyer
Function in development in R to simulate restoration in different properties maximizing or minimizing different themes (e.g.: opportunity cost).
Function developed to estimate amout of forest debt/credit in each property analysed, according to Brazilian Native Vegetation Law 12.651/12.
> source("restoration.function.R")
> args(preAnalysis)
function (forest_t = forest_t,
appt = appt,
car = carList[[4]],
restYears = 10)
- forest_t = Actual forest remnants (raster layer: 1 = forest; 0 = non forest; NA = non forest and non restorable sites [e.g.: Urban Areas] & areas outside the site of study);
- appt = Area of Riparian Protection (Área de Proteção Permanente, in portuguese) (raster layer: 1 = Riparian areas; 0 = non riparian areas; NA = areas outside the site of study);
- car = Rural Environmental Registry (Cadastro Ambiental Rural - CAR, in portuguese) (vector layer with property limits, with "ID" and "Car_modulo_fiscal" fields)
- restYears = Number of years to be simulated in the analysis. This will change the amount to be restored yearly
Data frame:
- car.area: Area of property
- f.total: Area of forest remnant
- app.area: Area of APP
- debt.app: Debit of APP (i.e.: Amount of pixels to be restored)
- rl.area: Area of Legal Reserve inside the property (discounting APP)
- debt.rl: Debit of Legal Reserve (in case of)
- credit.rl: Credit of Legal Reserve (in case of)
- TotalToRestore: Total amount to be restored (in pixels)
- ToRest2years: Total to be restored (in pixels) considering 20 years of restoration and that the restoration will be done according to parameter
restYears. - Car.ID: Property ID
- Modu_Fisc: Property modulo fiscal
- obs: Observation about property: wether it is all forested, unforested, not_analized, ...
head(debito)
---------------------------------------------------------------------------
X Car_ID Car_modulo_fiscal car.area f.total app.area debt.app
--- -------- ------------------- ---------- --------- ---------- ----------
1 34 50 683 240 25 16
2 42 89 1212 546 49 15
3 43 75 1020 177 144 113
4 49 68 931 269 27 26
5 76 9 122 58 0 0
6 79 27 374 224 0 0
---------------------------------------------------------------------------
Table: Table continues below
------------------------------------------------------------------------
obs rl.area debt.rl credit.rl TotalToRestore
----------------------- --------- --------- ----------- ----------------
Property with RL credit 111.6 0 119.4 16
Property with RL credit 193.4 0 318.6 15
Property with RL credit 60 0 86 113
Property with RL credit 159.2 0 108.8 26
Property with RL credit 24.4 0 33.6 0
Property with RL credit 74.8 0 149.2 0
------------------------------------------------------------------------
Table: Table continues below
-----------------
ToRestore2years
-----------------
1
1
11
2
0
0
-----------------
Function developed to run the conefor analysis after each year of restoration;
> args(run.conefor)
function (dispersal.dist = c(100, 1000, 5000),
nodes = "nodes_,
dists = "dists_",
landArea = 1e+05,
outFolder = ".",
windows = FALSE,
conefor.exe = "/home/felipe/Projetos/CONEFOR/conefor2.7.3Linux",
mean.dispersal = 0.5, metric = c("-IIC", "-PC")[2],
AddNodes = FALSE)
- dispersal.dist = Dispersan ditances to be used in the connectivity simulation;
- nodes = List of files with nodes ID and patch parameter (area) (tow columns data: ID, Parameter);
- dists = List of files with distances between nodes (tree columns data: ID origin, ID destiny, Distance);
- landArea = Landscape area;
- outFolder = Folder name where the result will be saved in;
- windows = TRUE/FALSE indicating if using windows O.S. (Not working now);
- conefor.exe = Path to conefor executable;
- mean.dispersal = Mean dispersal capacity;
- AddNodes = TRUE/FALSE indicates when conefor should estimates its index based on nodes added (see coneforPrep function for more infos);
----------------------
V1 V2
------------ ---------
IICnum 6.562e+16
EC(IIC) 256156000
IIC 0.5605
IICintra(%) 96.88
IICdirect(%) 2.198
IICstep(%) 0.9259
----------------------
-----------------------------------
Prefix Distance EC.IIC.
-------------- ---------- ---------
10__run_1.txt 10 252122000
10__run_10.txt 10 252123000
10__run_2.txt 10 252122000
10__run_3.txt 10 252122000
10__run_4.txt 10 252122000
10__run_5.txt 10 252123000
-----------------------------------
------------------------------------------
V1 V2 V3 V4
------------- ---- ------------ ----------
10__run_1.txt 10 IICnum 6.357e+16
10__run_1.txt 10 EC(IIC) 252122000
10__run_1.txt 10 IIC 0.543
10__run_1.txt 10 IICintra(%) 100
10__run_1.txt 10 IICdirect(%) 0
10__run_1.txt 10 IICstep(%) -2.853e-09
------------------------------------------
Function used to alocate the amout of area to be restored.
> args(restore)
function (sorted = sorted, carRestCost = carRestCost, totalcost = totalcost, s.value = ToRest2years[a, ])
- sorted = The pixels sorted in the function, according to the amount necesssary to be restored;
- carRestCost = raster created in the script with opportunity cost (or any other theme) in the area to be restored;
- totalCost = Raster datainput necessary to run the function. This layer must contain the opportunity cost (or any other theme) for each pixel;
- s.value = Amount to be restored (sampled) by function;
- restoration = Raster data with the forest remnant input plus pixels restored with the simulation;
- RestSampled = Raster data with only the pixels restored with the simulation;
- TotalRestCost = Sum of pixels values sampled in the simulation process (the information of this values can change according to the theme used in the simulation. e.g.: opportunity cost);
Small function to manage output files and directories. In from argument must be inserted path where the files will be change from whereas to should be the path to the folder where the files must be changed to.
> args(change.dir)
function (from, to)
NULL
Function to create the nodes and distances files before running conefor (run.conefor()). This function extract from a raster file the reamnants (nodes) ID and area saving them as nodes_*.txt, and estimates the distances between them, which will be saved as dists_*.txt;
> args(coneforPrep)
function (forest = forest_t, AddNodes = FALSE, onlyAdded = TRUE,
i = 1)
- forest = The spatial raster file with remants (values = 1);
- AddNodes = Logical - This function can be used to identify nodes to be added. If this is the case, set as TRUE (default = FALSE);
- onlyAdded = Logical - Indicates whther or not actual forest (with values 1) must have its importances calculated togheter with non forest (nodes added). If TRUE, forest pixels will have -1 values which won't be analysed on run.conefor(AddNodes = TRUE);
- i = Integer - As the function can be called inside restoration iteraction, the index i will be used to diferenciate the iteraction number in the file names;
- nodes_ = Files containing remants ID and Area. In case of AddNodes = TRUE, a third column will indicate 1 = existing remnants and 0 = potential remnants;
- dists_ = Files containing distances between all nodes. First column origin ID, second column destiny ID third column distance;
Function created to read all node importance created with run.conefor (Addnodes=TRUE) for one or several dispersal distances and produce spatial raster with node importance as pixel value.
> args(readImportance)
function (rasterTemplate = forest_t, nodes = readOGR("/home/felipe/Projetos/Funcao_Restauracao/",
layer = "forest_pol_AddNodes_run_1"), dispersal.dist = c(100,
1000, 5000), Indice = c("dIIC", "dPC")[1])
- rasterTemplate = Raster data to be used as a template in the creation of node importance raster (extent, resolution, CRS);
- nodes = Shape file created with run.conefor(Addnodes="TRUE") which will recieve the importance estimated and will be rasterized;
- dispersal.dist = Dispersal distances used to estimate the nodes importante in run.conefor function;
- Indice = Indice used to estimate nodes importances in run.conefor function;
- PC_importance_ = Raster with nodes importance for each pixel, indicating the dispersal distance in the name (sufix);