PRE_FATE.params_PFGsoil: Create _SOIL_ parameter files for a 'FATE' simulation
In MayaGueguen/RFate: Vegetation modelling with the FATE model

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/PRE_FATE.params_PFGsoil.R

This script is designed to create parameter files containing soil contribution and tolerance for each PFG (one file for each of them) used in the soil module of FATE.

PRE_FATE.params_PFGsoil(
  name.simulation,
  mat.PFG.soil,
  mat.PFG.tol = NULL,
  opt.folder.name = NULL
)

`name.simulation`	a `string` corresponding to the main directory or simulation name of the `FATE` simulation
`mat.PFG.soil`	a `data.frame` with 3 to 7 columns : `PFG`, `type`, (or `active_germ_low`, `active_germ_medium`, `active_germ_high`) (or `strategy_ag`) `soil_contrib`, `soil_tol_min`, `soil_tol_max` (or `strategy_contrib`) (see `Details`)
`mat.PFG.tol`	(optional) a `data.frame` with 2 to 4 columns : `PFG`, `lifeStage`, `resources`, `tolerance` (or `strategy_tol`) (see `Details`)
`opt.folder.name`	(optional) a `string` corresponding to the name of the folder that will be created into the `name.simulation/DATA/PFGS/SOIL/` directory to store the results

The soil module allows the user to add the effect of soil competition within a primary vegetation succession.

Several parameters, given within mat.PFG.soil or mat.PFG.tol, are required for each PFG in order to set up the soil competition :

PFG: the concerned plant functional group
type: or life-form, based on Raunkier.
It should be either H (herbaceous), C (chamaephyte) or P (phanerophyte) for now
(active_germ_low): an integer between 0 and 10 corresponding to the proportion of seeds that will germinate for Low soil condition
(active_germ_medium): an integer between 0 and 10 corresponding to the proportion of seeds that will germinate for Medium soil condition
(active_germ_high): an integer between 0 and 10 corresponding to the proportion of seeds that will germinate for High soil condition
(strategy_ag): a string to choose the germination strategy :
poor_lover, indifferent, rich_lover
soil_contrib: a value corresponding to the PFG preference for soil fertility
(e.g. nitrogen value from Ellenberg or Flora Indicativa)
soil_tol_min: the minimum soil value tolerated by the PFG (on the same scale than soil_contrib)
soil_tol_max: the maximum soil value tolerated by the PFG (on the same scale than soil_contrib)
(strategy_contrib): a string to choose the contribution strategy :
ubiquist, tobedefined
lifeStage: the concerned life stage (Germinant, Immature, Mature)
resources: the concerned soil condition (Low, Medium, High)
tolerance: an integer between 0 and 10 corresponding to the proportion of surviving individuals
(strategy_tol): a string to choose the tolerance strategy :
ubiquist, tobedefined

These values will allow to calculate or define a set of characteristics for each PFG :

ACTIVE_GERM

proportion of seeds that will germinate for each soil condition (Low, Medium, High)

Three methods to define these proportions are available :

from predefined scenarios (using strategy_ag) :

| _L_ _M_ _H_ |

_______________

poor_lover
| 80% 90% 50% |

indifferent
| 90% 90% 90% |

rich_lover
| 50% 90% 80% |
from predefined rules (using type) :
- for H (herbaceous) : 80%, 100%, 50%
- for C (chamaephyte) or P (phanerophyte) : 90%, 100%, 90%
from user data :
with the values contained within the active_germ_low, active_germ_medium and active_germ_high columns, if provided

SOIL_CONTRIB SOIL_LOW SOIL_HIGH

Two methods to define these values are available :

from predefined scenarios (using strategy_contrib) :
- the values give the soil_tol_min, soil_contrib and soil_tol_max
- with L: low soil, M: medium soil, H: high soil
| ___ L ___ | ___ M ___ | ___ H ___ |

_____________________________________

ubiquist
__________ 1.5 _ 2.5 _ 4.5 __________

to be filled
from user data :
with the values contained within the soil_contrib, soil_tol_min and soil_tol_max columns, if provided

SOIL_TOL

defined for each life stage (Germinant, Immature, Mature)
and each soil condition (Low, Medium, High)

Three methods to define these tolerances are available :

from predefined scenarios (using strategy_tol) :
- the values give the percentage of surviving individuals to the concerned conditions
- with g: Germinant, i: Immature, m: Mature
- with L: low soil, M: medium soil, H: high soil
| ___ g ___ | ___ i ___ | ___ m ___ |

| _L _M_ H_ | _L _M_ H_ | _L _M_ H_ |

_____________________________________

ubiquist
| 90 100 90 | 90 100 90 | 90 100 90 |

to be filled
from predefined rules :

(A)
germinants are severely impacted by wrong soil conditions

(B)
immatures are half impacted by wrong soil conditions

(C)
matures are little impacted by wrong soil conditions
- the values give the percentage of surviving individuals to the concerned conditions
- with g: Germinant, i: Immature, m: Mature
- with L: low soil, M: medium soil, H: high soil
| ___ g ___ | ___ i ___ | ___ m ___ |

| _L _M_ H_ | _L _M_ H_ | _L _M_ H_ |

_____________________________________

| 10 100 30 | 40 100 60 | 70 100 90 |
from user data :
with the values contained within the lifeStage, resources and tolerance columns, if provided

A .txt file per PFG into the name.simulation/DATA/PFGS/SOIL/ directory with the following parameters :

NAME

name of the PFG

ACTIVE_GERM

germination rates depending on soil conditions
(from 0 to 10, corresponding to 0 to 100%)

SOIL_CONTRIB

contribution to the soil value of the pixel

SOIL_LOW

lower value of soil supported by the PFG,
defining the limit between Low and Medium soil resources for this PFG

SOIL_HIGH

upper value of soil supported by the PFG,
defining the limit between Medium and High soil resources for this PFG

SOIL_TOL

soil tolerance table (in a single row).
This is a vector of 9 numbers corresponding to the ability of the PFG to survive or not :

at different life stages (Germinant (Ge), Immature (Im), Mature (Ma))
under different soil conditions (Low (L), Medium (M) or High (H)).

These parameters should be given in this order : GeL, GeM, GeH, ImL, ImM, ImH, MaL, MaM, MaH
(from 0 to 10, corresponding to 0 to 100%).

A SOIL_COMPLETE_TABLE.csv file summarizing information for all groups into the name.simulation/DATA/PFGS/ directory.

If the opt.folder.name has been used, the files will be into the folder name.simulation/DATA/PFGS/SOIL/opt.folder.name/.

Maya Guéguen

PRE_FATE.skeletonDirectory, PRE_FATE.params_PFGsuccession

## Create a skeleton folder with the default name ('FATE_simulation')
PRE_FATE.skeletonDirectory()

## Create PFG soil parameter files
PRE_FATE.params_PFGsoil(name.simulation = "FATE_simulation"
                        , mat.PFG.soil = data.frame(PFG = c("PFG1", "PFG2", "PFG3")
                                                    , type = c("H", "H", "C")
                                                    , soil_contrib = c(2.5, 3, 4.8)
                                                    , soil_tol_min = c(2, 3, 3)
                                                    , soil_tol_max = c(3, 3, 6)))