View source: R/BIOMOD_Report.R
BIOMOD_Report | R Documentation |
This function allows to produce summary report or ODMAP table from a biomod2 simulation folder.
BIOMOD_Report(
bm.out,
strategy = "report",
params.color = list(color1 = "#eb4034", color2 = "#e0918b", color3 = "#658f70"),
params.ODMAP = list(O.mod.objective = NULL, O.boundary = NULL, O.obs.type = NULL,
O.pred.type = NULL, D.eco.level = NULL, D.samp.design = NULL)
)
bm.out |
a |
strategy |
a |
params.color |
a |
params.ODMAP |
a |
This function gathers and formats all objects contained in one biomod2 modeling folder
to produce, based on Rmarkdown
templates, standardized reports to help the user :
summarize its modeling results
share them through standardized informations through ODMAP protocol
provide reproducible code
Different data types are available, and require different values :
biomod2 provides functions to summarize the information, such as
print
, plot
or summary
methods adapted to BIOMOD.[...].out
objects, as well as
get_[...]
and bm_Plot[...]
functions. All these are called here and applied to objects
contained in the provided modeling folder.
following Zurell et al. 2020, ODMAP (Overview, Data, Model, Assessment and Prediction) protocol aims to standardize documentation of modeling to help improve both transparency and reproducibility of results. ODMAP v1.0 website provides an application to fill this type of report. biomod2 tries here to help one user to pre-fill the fields of this protocol.
call
slot contained within BIOMOD.formated.data
,
BIOMOD.models.out
, BIOMOD.projection.out
and
BIOMOD.ensemble.models.out
objects keep in memory the R command used to obtain
them. All these calls are gathered here in one summary file.
A standardized .html
file obtained from an Rmarkdown
template, and a .csv
table in the case of ODMAP report.
Maya Guéguen
Zurell D, Franklin J, König C, Bouchet PJ, Serra-Diaz JM, Dormann CF, Elith J, Fandos Guzman G, Feng X, Guillera-Arroita G, Guisan A, Leitão PJ, Lahoz-Monfort JJ, Park DS, Peterson AT, Rapacciuolo G, Schmatz DR, Schröder B, Thuiller W, Yates KL, Zimmermann NE, Merow C (2020) A standard protocol for describing species distribution models. Ecography 43: 1261-1277. DOI: 10.1111/ecog.04960
ODMAP
, match.call
library(terra)
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