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rsp2ebv               package:ecochange                R Documentation

_R_e_m_o_t_e _S_e_n_s_i_n_g _P_r_o_d_u_c_t _t_o _E_B_V

_D_e_s_c_r_i_p_t_i_o_n:

     This function processes regions of interest (polygon geometry or
     'GADM' unit) to integrate dissimilar remote sensing products (RSP)
     into Essential biodiversity variables.

_U_s_a_g_e:

     rsp2ebv(roi = NULL, ..., 
         lyrs = NULL, path, 
         sr, ofr = c(30, 30), 
         mc.cores = round(detectCores() * 
             0.6, 0))
     
_A_r_g_u_m_e_n_t_s:

     roi: 'SpatialPolygonsDataFrame'; or 'character'; or 'NULL'. Region
          of interest. This can be whether 1) a polygon geometry; or 2)
          the name of a 'GADM' unit (see 'getGADM'); or 3) a 'NULL'
          value. Default 'NULL' makes the function to print a list of
          'GADM' units.

     ...: If 'roi' is a 'GADM' unit then additional arguments in
          'getGADM' can be specified here.

    lyrs: 'character'. Remote sensing products, If 'NULL' then a list
          of products is printed, see 'listGP'.  Default 'NULL'.

    path: 'character'. Path name indicating where the variables are
          stored. If it is missing then a folder named as ''ecochange''
          located in a current temporary directory is used.

      sr: 'character'. 'PROJ.4' description of the target coordinate
          reference system. If missing then the target layers are
          projected to metric system 'UTM'.

     ofr: 'numeric'. 'c(xres,yres)'.  Output file resolution (in target
          georeferenced units). Default 'c(30,30)' m2.

mc.cores: 'numeric'. The number of cores. Default uses around 60
          percent of the cores.

_D_e_t_a_i_l_s:

     This function implements ''gdalUtils'' so it assumes the user has
     a working GDAL on their system. From the documentation: "If the
     ''gdalUtils_gdalPath'' option has been set (usually by
     ''gdal_setInstallation''), the GDAL found in that 'path' will be
     used. If nothing is found, ''gdal_setInstallation'' will be
     executed to attempt to find a working GDAL that has the right
     drivers as specified with the ''of'' (output format) parameter",
     see example below.

_V_a_l_u_e:

     'RasterStack' of essential biodiversity variables (UTM crs), or
     character lists suggesting GADM units/Global Products that can be
     used to download 'rsp' (see 'NULL' defaults in arguments ''roi''
     and ''lyrs'').

_A_u_t_h_o_r(_s):

     Wilson Lara Henao <wilarhen@temple.edu> [aut, cre], Victor
     Gutierrez-Velez [aut], Ivan Gonzales [aut]

_R_e_f_e_r_e_n_c_e_s:

     Jetz, W., McGeoch, M. A., Guralnick, R., Ferrier, S., Beck, J.,
     Costello, M. J., ... & Meyer, C. (2019). Essential biodiversity
     variables for mapping and monitoring species populations. Nature
     Ecology & Evolution, 3(4), 539-551.

     O'Connor, B., Secades, C., Penner, J., Sonnenschein, R., Skidmore,
     A., Burgess, N. D., & Hutton, J. M. (2015). Earth observation as a
     tool for tracking progress towards the Aichi Biodiversity Targets.
     Remote sensing in ecology and conservation, 1(1), 19-28.

     Skidmore, A. K., & Pettorelli, N. (2015). Agree on biodiversity
     metrics to track from space: Ecologists and space agencies must
     forge a global monitoring strategy. Nature, 523(7561), 403-406.

_E_x_a_m_p_l_e_s:

     ## First, we'll check to make sure there is a valid GDAL
     ## installation (from 'gdalUtils):
     
     
     gdalUtils::gdal_setInstallation()
     valid_install <- !is.null(getOption("gdalUtils_gdalPath"))
     
     
     ## Warnings from GDAL/PROJ are suppressed.
     
     ## A Global Surface Water layer ('seasonality') covering the extent of a
     ## Colombian municipality Cartagena del ChairÃ¡ is formated into an
     ## spatial \code{EBV}:
             load(system.file('cchaira_roi.RData',package = 'ecochange'))
     
     
     suppressWarnings(
     rsp_cchaira <- getrsp(roi = cchaira_roi,
       lyrs = 'seasonality', mc.cores = 2, path = tempdir())
     )
     
     file.exists(rsp_cchaira) ##TRUE
     
     suppressWarnings(
     season_cchaira <- rsp2ebv(roi = cchaira_roi,
                                   lyrs = 'seasonality', path = tempdir())
     )
     
     suppressWarnings(
     plotebv(season_cchaira)
     )
     

sh: gdal_calc.py: command not found
sh: gdal_calc.py: command not found
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