I need to select points randomly (without replacement) from a SpatialPointsDataFrame (input object) in R with a minimum distance of 3,000 meters between them. I want to get random 50% of all points. I know that "Create Random Points" tool from ArcGIS, as mentioned before Randomly sampling points in R with minimum distance constraint, can do this processing, but I really need to do this inside R. I tried to use sample() function but I still did not realised how to set the geographical constraint. I tried to run QGIS inside R, but it seems that QGIS does not have a tool for that.

> input
class       : SpatialPointsDataFrame 
features    : 205 
extent      : 203294.5, 259880.6, 7600123, 7668676  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=utm +zone=23 +south +ellps=GRS80 +units=m +no_defs 
variables   : 3
names       :     Sites, Long_X,   Lat_Y 
min values  : CPF - 050, 203295, 7600120 
max values  : JES - S94, 259881, 7668680 


> head(input)
Sites Long_X   Lat_Y
1 CPF - 050 235441 7617150
2 CPF - 052 234106 7615740
3 CPF - 054 232683 7614280
4 CPF - 056 233863 7614420
5 CPF - 058 234012 7612890
6 CPF - 062 236929 7612850

rdm_input <- sample(x= nrow(input), size=(0.5*205), replace= FALSE)
[1] 167 189 79 80 126 129 144 100 4 109 170 72 123 73 132 93 169 5 134 176 196 
158 152 183 23 136 180
[28] 130 12 142 179 11 13 66 22 2 96 29 54 137 120 171 184 36 113 3 81 115  30 
85 61 162 98 102
[55] 103 181 90 133 56 174 76 201 150 197 14 86 118 121 28 97 160 178 1 186 
141 163 172 32 65 168 74
[82] 114 182 128 131 67 70 165 187 185 69 17 194 16 154 119 192 156 106  25 
101 198 105 108 151 125 190 10
[109] 84 38 51 161 40 94 45 19 145 75 42 122 117 49 87