require(raster)
 require(foreign)
 require(labgeo)
 require(dplyr)
 require(tidyverse)
 require(RQGIS)

#set QGIS directory
qgis_env <-set_env(root ='C:/Program Files/QGIS 2.18')
set_env()
open_app()

-Function and parametrs.

#entrada = folder with all rasters in .tif
#saida = folder witch zonal polygon will be dropped
#bacia = polygons

zonalTop = function(entrada, saida, bacia){

  nomesRasters = list.files(entrada, pattern="*.tif$")
  lerRasterCompl = list.files(entrada, pattern="*.tif$", full.names = TRUE)
  rasters = lapply(lerRasterCompl, raster)


  for (i in 1:length(rasters)){

    run_qgis(alg = "qgis:zonalstatistics",
             INPUT_RASTER = rasters[[i]],
             RASTER_BAND = 1,
             INPUT_VECTOR = bacia,
             GLOBAL_EXTENT = 1,
             OUTPUT_LAYER = paste(saida, tools::file_path_sans_ext(nomesRasters[[i]]),".shp", sep = ""))
  }

  nomesDbf = list.files(saida, pattern="*.dbf$")
  lerDbfCompl = list.files(saida, pattern="*.dbf$", full.names = TRUE)
  Dbfs = lapply(lerDbfCompl, read.dbf)

  for (i in 1:length(Dbfs)){

    names(Dbfs[[i]]) = paste(tools::file_path_sans_ext(nomesDbf[i]), names(Dbfs[[i]]),  sep="_")

  }


  Dbfs = clean_names(do.call("cbind", Dbfs))

  drop.cols <- grep("gridcode", colnames(Dbfs))

  Dbfs = Dbfs[,-drop.cols]

  Dbfs$gridcode = bacia@data$gridcode

  Dbfs = dplyr::select(Dbfs, gridcode, everything())

  return(Dbfs)

}


- Runnin Function Example

anch10k = zonalTop("E:/artigo_declividade/morfomometriatif/anchi/",
                   "E:/artigo_declividade/morfomometriatif/anchi/shapes10k",
                   bacia)