View source: R/predImportMakeData.r
predImportMakeData | R Documentation |
This function is used to create multiple simulated data sets for further analysis. The simulated data represents data that one would typically need for modeling species distributions (i.e., training and test presences, test absences and background sites). Typical implementation is to use predImportMakeData
to create simulated data sets, then predImportTrainModels
to train SDMs on those data sets, then predImportEval
to evaluate the models.
predImportMakeData( geography, response, simDir, numTrainPres = 200, numTrainAbs = 200, numTestPres = 200, numTestAbs = 200, numBg = 10000, iters = 1:100, circle = FALSE, sizeNative = 1024, sizeResampled = NULL, fileFlag = NULL, userdata = NULL, b0 = NA, b1 = NA, b2 = NA, b11 = NA, b12 = NA, mu1 = NA, mu2 = mu2, sigma1 = NA, sigma2 = NA, rho = NA, overwrite = FALSE, verbose = 1, ... )
geography |
A list of lists describing the simulated environmental layers. Each sublist pertains to one later. See |
response |
A function describing the response of the species to the environment. This must be one of: |
simDir |
Character, path name of directory in which scenario data files are saved. |
numTrainPres |
Positive integer, number of training presences to locate. |
numTrainAbs |
Positive integer, number of training absences to locate. |
numTestPres |
Positive integer, number of test presences to locate. |
numTestAbs |
Positive integer, number of test absences to locate. |
numBg |
Positive integer, number of training and number of test background sites to locate. |
iters |
Vector of positive integers, data iterations to generate. |
circle |
Logical, if |
sizeNative |
Positive integer, size of landscape in number of cells on a side. This specifies the spatial resolution at which the species perceives the landscape. See Details. |
sizeResampled |
Positive integer, size of landscape in number of cells on a side. This specifies the spatial resolution at which environmental data for model calibration and evaluation is available to the "modeler". Note that resampling will thus change the environmental values of the training and test data. See Details. |
fileFlag |
Either |
userdata |
Either |
b0 |
Numeric, parameters for |
b1 |
Numeric, parameters for |
b2 |
Numeric, parameters for |
b11 |
Numeric, parameters for |
b12 |
Numeric, parameters for |
mu1 |
Numeric, parameters for |
mu2 |
Numeric, parameters for |
sigma1 |
Numeric, parameters for |
sigma2 |
Numeric, parameters for |
rho |
Numeric, parameters for |
overwrite |
Logical, if |
verbose |
Numeric, if 0 then show minimal output, 1 more output, 2 even more, >2 all of it. |
... |
Other arguments (unused). |
In addition to its many capabilities, this function can be used to examine the effects of differences in spatial resolution of the scale at which a species responds to the environment and the scale at which environmental data is available to the modeler. When sizeResampled
is NULL
then the response scale is the same as the scale of environmental data. But when sizeResampled
is not NULL
and different from sizeNative
then the landscape will be resampled to the stated resolution before environmental calibration and evaluation data is extracted. However, presences and absences and background sites will be drawn from the distribution of the true probability of presence generated using the native resolution landscape. Thus resampling to a different resolution maybe (intentionally) "confusing" to model because it wil be presented with data that is not necessarily indicative of the observed state (presence/background).
Nothing (saves data files to disc).
predImportTrainModels
, predImportEval
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