# default argument values are as expected $spec_dat species_01 species_02 species_03 species_04 species_05 species_06 site1 0 1 0 0 0 0 site2 0 1 0 0 0 0 site3 0 1 0 0 0 0 site4 0 0 0 0 0 0 site5 0 0 0 0 0 0 site6 0 0 0 0 0 0 site7 1 0 0 1 2 0 site8 0 0 0 0 0 0 site9 0 0 0 0 0 0 site10 0 0 0 0 0 0 site11 0 0 0 0 0 0 site12 0 0 0 1 0 0 site13 1 0 0 0 0 0 site14 0 1 0 0 0 0 site15 1 0 1 0 0 0 site16 2 0 0 0 0 0 site17 0 0 0 0 0 1 site18 0 0 0 1 0 0 site19 0 0 0 0 0 0 site20 1 1 0 0 0 0 species_07 species_08 species_09 species_10 site1 0 0 0 1 site2 0 0 0 0 site3 0 0 0 0 site4 0 1 0 0 site5 0 0 0 0 site6 0 0 0 0 site7 0 0 0 0 site8 0 0 0 0 site9 0 0 0 0 site10 0 1 0 0 site11 0 0 0 0 site12 0 0 1 0 site13 0 0 0 0 site14 0 0 0 0 site15 0 0 0 0 site16 0 0 0 0 site17 0 0 0 0 site18 0 0 0 0 site19 0 0 0 0 site20 0 0 0 0 $xy_dat x y site1 4.199076e-01 0.05353719 site2 8.755603e-01 0.88598044 site3 7.863321e-01 0.68874505 site4 2.236330e-01 0.85575094 site5 1.651110e-01 0.69825998 site6 7.432384e-01 0.07190945 site7 1.749440e-01 0.40115741 site8 4.205051e-01 0.24936413 site9 2.501253e-01 0.57786277 site10 1.432311e-02 0.76434213 site11 8.893515e-01 0.40459095 site12 1.165417e-01 0.11927928 site13 5.818198e-01 0.45776408 site14 9.245616e-05 0.40997953 site15 8.813802e-01 0.20196394 site16 4.423126e-01 0.51167199 site17 4.452661e-01 0.74043186 site18 2.595009e-01 0.11219372 site19 3.153386e-01 0.34675683 site20 6.807509e-01 0.81490014 # plotting works $spec_dat species_1 species_2 species_3 species_4 species_5 site1 0 0 0 0 0 site2 1 0 0 0 0 site3 0 0 0 0 0 site4 0 0 0 0 0 site5 0 0 0 0 0 site6 0 0 0 0 0 site7 0 0 0 0 0 site8 0 0 0 0 0 site9 0 0 0 0 0 site10 0 0 0 0 1 site11 0 0 0 0 0 site12 0 0 0 0 0 site13 0 0 0 0 0 site14 0 0 0 0 0 site15 0 0 0 0 0 $xy_dat x y site1 0.797016193 0.7631862 site2 0.224128471 0.8214925 site3 0.542192869 0.1837661 site4 0.232075260 0.1864025 site5 0.697458069 0.5102983 site6 0.125395904 0.1283415 site7 0.506160301 0.6688033 site8 0.131537586 0.2452081 site9 0.425999100 0.4535324 site10 0.954605504 0.7716613 site11 0.695311394 0.8026411 site12 0.709190814 0.6094588 site13 0.499303610 0.4639678 site14 0.908076117 0.4367863 site15 0.005290534 0.7581264 --- $spec_dat species_1 species_2 species_3 species_4 species_5 site1 0 0 0 0 0 site2 0 0 0 0 0 site3 0 0 0 0 0 site4 0 0 0 0 0 site5 0 0 0 0 0 site6 0 0 0 0 0 site7 0 0 0 0 0 site8 0 0 0 0 0 site9 0 0 0 0 0 site10 0 0 0 0 0 site11 0 0 0 0 0 site12 0 0 0 0 0 site13 0 0 0 0 0 site14 0 0 0 0 0 site15 0 0 0 0 0 site16 0 0 0 0 0 site17 0 0 0 0 0 site18 0 0 0 0 1 site19 0 0 0 0 0 site20 0 0 0 0 0 site21 0 0 0 0 0 site22 0 0 0 0 0 site23 0 0 0 0 0 site24 0 0 0 0 0 site25 0 0 0 0 0 $xy_dat x y site1 0.0 0.0 site2 0.1 0.0 site3 0.2 0.0 site4 0.3 0.0 site5 0.4 0.0 site6 0.0 0.1 site7 0.1 0.1 site8 0.2 0.1 site9 0.3 0.1 site10 0.4 0.1 site11 0.0 0.2 site12 0.1 0.2 site13 0.2 0.2 site14 0.3 0.2 site15 0.4 0.2 site16 0.0 0.3 site17 0.1 0.3 site18 0.2 0.3 site19 0.3 0.3 site20 0.4 0.3 site21 0.0 0.4 site22 0.1 0.4 site23 0.2 0.4 site24 0.3 0.4 site25 0.4 0.4