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tests/testthat/_snaps/cpr_rand_test.md
In canaper: Categorical Analysis of Neo- And Paleo-Endemism
Output is formatted as expected
Code
cpr_rand_test(phylocom$comm, phylocom$phy, null_model = "swap", n_reps = 10,
quiet = TRUE)
Output
pd_obs pd_rand_mean pd_rand_sd pd_obs_z pd_obs_c_upper
clump1 0.3018868 0.4584906 0.03563325 -4.3948781 0
clump2a 0.3207547 0.4641509 0.04464966 -3.2115862 0
clump2b 0.3396226 0.4830189 0.02976644 -4.8173793 0
clump4 0.4150943 0.4509434 0.04398021 -0.8151179 0
even 0.5660377 0.4679245 0.02142061 4.5803177 10
random 0.5094340 0.4716981 0.03444796 1.0954451 8
pd_obs_c_lower pd_obs_q pd_obs_p_upper pd_obs_p_lower pd_alt_obs
clump1 10 10 0.0 1.0 0.3333333
clump2a 10 10 0.0 1.0 0.3541667
clump2b 10 10 0.0 1.0 0.3750000
clump4 7 10 0.0 0.7 0.4375000
even 0 10 1.0 0.0 0.5625000
random 2 10 0.8 0.2 0.5208333
pd_alt_rand_mean pd_alt_rand_sd pd_alt_obs_z pd_alt_obs_c_upper
clump1 0.4833333 0.03074437 -4.8789427 0
clump2a 0.4833333 0.03227486 -4.0020828 0
clump2b 0.5104167 0.02820847 -4.8005681 0
clump4 0.4729167 0.03113404 -1.1375543 0
even 0.5000000 0.02196026 2.8460499 10
random 0.4979167 0.02680592 0.8549108 8
pd_alt_obs_c_lower pd_alt_obs_q pd_alt_obs_p_upper pd_alt_obs_p_lower
clump1 10 10 0.0 1.0
clump2a 10 10 0.0 1.0
clump2b 10 10 0.0 1.0
clump4 8 10 0.0 0.8
even 0 10 1.0 0.0
random 1 10 0.8 0.1
rpd_obs rpd_rand_mean rpd_rand_sd rpd_obs_z rpd_obs_c_upper
clump1 0.9056604 0.9480594 0.02889592 -1.46730000 0
clump2a 0.9056604 0.9590221 0.03945354 -1.35252111 0
clump2b 0.9056604 0.9462078 0.02127311 -1.90604245 0
clump4 0.9487871 0.9523440 0.04174814 -0.08519907 5
even 1.0062893 0.9359165 0.01603741 4.38804158 10
random 0.9781132 0.9469540 0.03698009 0.84259495 7
rpd_obs_c_lower rpd_obs_q rpd_obs_p_upper rpd_obs_p_lower pe_obs
clump1 10 10 0.0 1.0 0.1333333
clump2a 8 10 0.0 0.8 0.1081761
clump2b 10 10 0.0 1.0 0.1286164
clump4 3 10 0.5 0.3 0.1411950
even 0 10 1.0 0.0 0.2506289
random 3 10 0.7 0.3 0.2380503
pe_rand_mean pe_rand_sd pe_obs_z pe_obs_c_upper pe_obs_c_lower
clump1 0.1677358 0.02224209 -1.5467304 1 9
clump2a 0.1696541 0.02480060 -2.4788908 0 10
clump2b 0.1716981 0.02340134 -1.8409958 0 10
clump4 0.1632704 0.03027039 -0.7292761 1 9
even 0.1693711 0.03068082 2.6484902 10 0
random 0.1582704 0.02963402 2.6921723 10 0
pe_obs_q pe_obs_p_upper pe_obs_p_lower pe_alt_obs pe_alt_rand_mean
clump1 10 0.1 0.9 0.1472222 0.1671528
clump2a 10 0.0 1.0 0.1194444 0.1651042
clump2b 10 0.0 1.0 0.1420139 0.1743056
clump4 10 0.1 0.9 0.1454861 0.1604861
even 10 1.0 0.0 0.2246528 0.1741667
random 10 1.0 0.0 0.2211806 0.1587847
pe_alt_rand_sd pe_alt_obs_z pe_alt_obs_c_upper pe_alt_obs_c_lower
clump1 0.01482223 -1.3446397 1 9
clump2a 0.02123409 -2.1503028 0 10
clump2b 0.01631082 -1.9797693 0 10
clump4 0.01795720 -0.8353193 1 9
even 0.02709530 1.8632792 10 0
random 0.02576632 2.4216047 10 0
pe_alt_obs_q pe_alt_obs_p_upper pe_alt_obs_p_lower rpe_obs
clump1 10 0.1 0.9 0.9056604
clump2a 10 0.0 1.0 0.9056604
clump2b 10 0.0 1.0 0.9056604
clump4 10 0.1 0.9 0.9705048
even 10 1.0 0.0 1.1156280
random 10 1.0 0.0 1.0762714
rpe_rand_mean rpe_rand_sd rpe_obs_z rpe_obs_c_upper rpe_obs_c_lower
clump1 1.0019661 0.08572047 -1.1234857 1 9
clump2a 1.0300549 0.10965468 -1.1344201 0 8
clump2b 0.9825458 0.05753612 -1.3362985 1 9
clump4 1.0156585 0.12320378 -0.3664962 6 4
even 0.9692653 0.04299290 3.4043453 10 0
random 0.9978245 0.10380152 0.7557401 8 2
rpe_obs_q rpe_obs_p_upper rpe_obs_p_lower
clump1 10 0.1 0.9
clump2a 10 0.0 0.8
clump2b 10 0.1 0.9
clump4 10 0.6 0.4
even 10 1.0 0.0
random 10 0.8 0.2
Custom randomization algorithms work
Code
cpr_rand_test(phylocom$comm, phylocom$phy, cs_object, n_reps = 10, quiet = TRUE)
Output
pd_obs pd_rand_mean pd_rand_sd pd_obs_z pd_obs_c_upper
clump1 0.3018868 0.5415094 0.07118319 -3.3662813 0
clump2a 0.3207547 0.4603774 0.08903315 -1.5682096 0
clump2b 0.3396226 0.4735849 0.08027188 -1.6688568 0
clump4 0.4150943 0.5037736 0.07957901 -1.1143547 1
even 0.5660377 0.4811321 0.09423474 0.9010017 9
random 0.5094340 0.4396226 0.12674165 0.5508159 7
pd_obs_c_lower pd_obs_q pd_obs_p_upper pd_obs_p_lower pd_alt_obs
clump1 10 10 0.0 1.0 0.3333333
clump2a 10 10 0.0 1.0 0.3541667
clump2b 10 10 0.0 1.0 0.3750000
clump4 8 10 0.1 0.8 0.4375000
even 1 10 0.9 0.1 0.5625000
random 3 10 0.7 0.3 0.5208333
pd_alt_rand_mean pd_alt_rand_sd pd_alt_obs_z pd_alt_obs_c_upper
clump1 0.5520833 0.06750772 -3.2403703 0
clump2a 0.4812500 0.08698592 -1.4609643 0
clump2b 0.4833333 0.10101720 -1.0724246 2
clump4 0.5208333 0.08157875 -1.0215078 2
even 0.4916667 0.09430136 0.7511380 9
random 0.4562500 0.13939145 0.4633235 7
pd_alt_obs_c_lower pd_alt_obs_q pd_alt_obs_p_upper pd_alt_obs_p_lower
clump1 10 10 0.0 1.0
clump2a 10 10 0.0 1.0
clump2b 8 10 0.2 0.8
clump4 8 10 0.2 0.8
even 1 10 0.9 0.1
random 3 10 0.7 0.3
rpd_obs rpd_rand_mean rpd_rand_sd rpd_obs_z rpd_obs_c_upper
clump1 0.9056604 0.9801306 0.03418566 -2.1784051 0
clump2a 0.9056604 0.9553943 0.04922881 -1.0102603 1
clump2b 0.9056604 0.9889415 0.06711588 -1.2408552 1
clump4 0.9487871 0.9681869 0.04110090 -0.4720052 4
even 1.0062893 0.9796788 0.04214566 0.6313947 5
random 0.9781132 0.9677022 0.04286896 0.2428560 6
rpd_obs_c_lower rpd_obs_q rpd_obs_p_upper rpd_obs_p_lower pe_obs
clump1 10 10 0.0 1.0 0.1333333
clump2a 7 10 0.1 0.7 0.1081761
clump2b 8 10 0.1 0.8 0.1286164
clump4 6 10 0.4 0.6 0.1411950
even 4 10 0.5 0.4 0.2506289
random 4 10 0.6 0.4 0.2380503
pe_rand_mean pe_rand_sd pe_obs_z pe_obs_c_upper pe_obs_c_lower
clump1 0.1791509 0.02725248 -1.6812272 1 9
clump2a 0.1520126 0.04640687 -0.9446117 3 7
clump2b 0.1592453 0.04203294 -0.7286887 3 7
clump4 0.1587421 0.03853247 -0.4553866 4 6
even 0.1582390 0.04329376 2.1340241 9 1
random 0.1416667 0.05971076 1.6141755 9 1
pe_obs_q pe_obs_p_upper pe_obs_p_lower pe_alt_obs pe_alt_rand_mean
clump1 10 0.1 0.9 0.1472222 0.1797917
clump2a 10 0.3 0.7 0.1194444 0.1511806
clump2b 10 0.3 0.7 0.1420139 0.1588542
clump4 10 0.4 0.6 0.1454861 0.1595139
even 10 0.9 0.1 0.2246528 0.1577431
random 10 0.9 0.1 0.2211806 0.1470833
pe_alt_rand_sd pe_alt_obs_z pe_alt_obs_c_upper pe_alt_obs_c_lower
clump1 0.02393557 -1.3607134 1 9
clump2a 0.04123464 -0.7696468 3 7
clump2b 0.04999551 -0.3368358 3 7
clump4 0.03548174 -0.3953520 5 5
even 0.03637172 1.8396085 9 1
random 0.06502801 1.1394663 8 2
pe_alt_obs_q pe_alt_obs_p_upper pe_alt_obs_p_lower rpe_obs
clump1 10 0.1 0.9 0.9056604
clump2a 10 0.3 0.7 0.9056604
clump2b 10 0.3 0.7 0.9056604
clump4 10 0.5 0.5 0.9705048
even 10 0.9 0.1 1.1156280
random 10 0.8 0.2 1.0762714
rpe_rand_mean rpe_rand_sd rpe_obs_z rpe_obs_c_upper rpe_obs_c_lower
clump1 0.9955043 0.06343205 -1.416381 0 10
clump2a 0.9992278 0.09063131 -1.032396 3 7
clump2b 1.0238019 0.11633329 -1.015543 3 7
clump4 0.9925977 0.05399095 -0.409196 4 6
even 0.9980011 0.06350954 1.852114 10 0
random 0.9703781 0.04810763 2.201176 10 0
rpe_obs_q rpe_obs_p_upper rpe_obs_p_lower
clump1 10 0.0 1.0
clump2a 10 0.3 0.7
clump2b 10 0.3 0.7
clump4 10 0.4 0.6
even 10 1.0 0.0
random 10 1.0 0.0
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Output is formatted as expected
Code
cpr_rand_test(phylocom$comm, phylocom$phy, null_model = "swap", n_reps = 10,
quiet = TRUE)
Output
pd_obs pd_rand_mean pd_rand_sd pd_obs_z pd_obs_c_upper
clump1 0.3018868 0.4584906 0.03563325 -4.3948781 0
clump2a 0.3207547 0.4641509 0.04464966 -3.2115862 0
clump2b 0.3396226 0.4830189 0.02976644 -4.8173793 0
clump4 0.4150943 0.4509434 0.04398021 -0.8151179 0
even 0.5660377 0.4679245 0.02142061 4.5803177 10
random 0.5094340 0.4716981 0.03444796 1.0954451 8
pd_obs_c_lower pd_obs_q pd_obs_p_upper pd_obs_p_lower pd_alt_obs
clump1 10 10 0.0 1.0 0.3333333
clump2a 10 10 0.0 1.0 0.3541667
clump2b 10 10 0.0 1.0 0.3750000
clump4 7 10 0.0 0.7 0.4375000
even 0 10 1.0 0.0 0.5625000
random 2 10 0.8 0.2 0.5208333
pd_alt_rand_mean pd_alt_rand_sd pd_alt_obs_z pd_alt_obs_c_upper
clump1 0.4833333 0.03074437 -4.8789427 0
clump2a 0.4833333 0.03227486 -4.0020828 0
clump2b 0.5104167 0.02820847 -4.8005681 0
clump4 0.4729167 0.03113404 -1.1375543 0
even 0.5000000 0.02196026 2.8460499 10
random 0.4979167 0.02680592 0.8549108 8
pd_alt_obs_c_lower pd_alt_obs_q pd_alt_obs_p_upper pd_alt_obs_p_lower
clump1 10 10 0.0 1.0
clump2a 10 10 0.0 1.0
clump2b 10 10 0.0 1.0
clump4 8 10 0.0 0.8
even 0 10 1.0 0.0
random 1 10 0.8 0.1
rpd_obs rpd_rand_mean rpd_rand_sd rpd_obs_z rpd_obs_c_upper
clump1 0.9056604 0.9480594 0.02889592 -1.46730000 0
clump2a 0.9056604 0.9590221 0.03945354 -1.35252111 0
clump2b 0.9056604 0.9462078 0.02127311 -1.90604245 0
clump4 0.9487871 0.9523440 0.04174814 -0.08519907 5
even 1.0062893 0.9359165 0.01603741 4.38804158 10
random 0.9781132 0.9469540 0.03698009 0.84259495 7
rpd_obs_c_lower rpd_obs_q rpd_obs_p_upper rpd_obs_p_lower pe_obs
clump1 10 10 0.0 1.0 0.1333333
clump2a 8 10 0.0 0.8 0.1081761
clump2b 10 10 0.0 1.0 0.1286164
clump4 3 10 0.5 0.3 0.1411950
even 0 10 1.0 0.0 0.2506289
random 3 10 0.7 0.3 0.2380503
pe_rand_mean pe_rand_sd pe_obs_z pe_obs_c_upper pe_obs_c_lower
clump1 0.1677358 0.02224209 -1.5467304 1 9
clump2a 0.1696541 0.02480060 -2.4788908 0 10
clump2b 0.1716981 0.02340134 -1.8409958 0 10
clump4 0.1632704 0.03027039 -0.7292761 1 9
even 0.1693711 0.03068082 2.6484902 10 0
random 0.1582704 0.02963402 2.6921723 10 0
pe_obs_q pe_obs_p_upper pe_obs_p_lower pe_alt_obs pe_alt_rand_mean
clump1 10 0.1 0.9 0.1472222 0.1671528
clump2a 10 0.0 1.0 0.1194444 0.1651042
clump2b 10 0.0 1.0 0.1420139 0.1743056
clump4 10 0.1 0.9 0.1454861 0.1604861
even 10 1.0 0.0 0.2246528 0.1741667
random 10 1.0 0.0 0.2211806 0.1587847
pe_alt_rand_sd pe_alt_obs_z pe_alt_obs_c_upper pe_alt_obs_c_lower
clump1 0.01482223 -1.3446397 1 9
clump2a 0.02123409 -2.1503028 0 10
clump2b 0.01631082 -1.9797693 0 10
clump4 0.01795720 -0.8353193 1 9
even 0.02709530 1.8632792 10 0
random 0.02576632 2.4216047 10 0
pe_alt_obs_q pe_alt_obs_p_upper pe_alt_obs_p_lower rpe_obs
clump1 10 0.1 0.9 0.9056604
clump2a 10 0.0 1.0 0.9056604
clump2b 10 0.0 1.0 0.9056604
clump4 10 0.1 0.9 0.9705048
even 10 1.0 0.0 1.1156280
random 10 1.0 0.0 1.0762714
rpe_rand_mean rpe_rand_sd rpe_obs_z rpe_obs_c_upper rpe_obs_c_lower
clump1 1.0019661 0.08572047 -1.1234857 1 9
clump2a 1.0300549 0.10965468 -1.1344201 0 8
clump2b 0.9825458 0.05753612 -1.3362985 1 9
clump4 1.0156585 0.12320378 -0.3664962 6 4
even 0.9692653 0.04299290 3.4043453 10 0
random 0.9978245 0.10380152 0.7557401 8 2
rpe_obs_q rpe_obs_p_upper rpe_obs_p_lower
clump1 10 0.1 0.9
clump2a 10 0.0 0.8
clump2b 10 0.1 0.9
clump4 10 0.6 0.4
even 10 1.0 0.0
random 10 0.8 0.2
Custom randomization algorithms work
Code
cpr_rand_test(phylocom$comm, phylocom$phy, cs_object, n_reps = 10, quiet = TRUE)
Output
pd_obs pd_rand_mean pd_rand_sd pd_obs_z pd_obs_c_upper
clump1 0.3018868 0.5415094 0.07118319 -3.3662813 0
clump2a 0.3207547 0.4603774 0.08903315 -1.5682096 0
clump2b 0.3396226 0.4735849 0.08027188 -1.6688568 0
clump4 0.4150943 0.5037736 0.07957901 -1.1143547 1
even 0.5660377 0.4811321 0.09423474 0.9010017 9
random 0.5094340 0.4396226 0.12674165 0.5508159 7
pd_obs_c_lower pd_obs_q pd_obs_p_upper pd_obs_p_lower pd_alt_obs
clump1 10 10 0.0 1.0 0.3333333
clump2a 10 10 0.0 1.0 0.3541667
clump2b 10 10 0.0 1.0 0.3750000
clump4 8 10 0.1 0.8 0.4375000
even 1 10 0.9 0.1 0.5625000
random 3 10 0.7 0.3 0.5208333
pd_alt_rand_mean pd_alt_rand_sd pd_alt_obs_z pd_alt_obs_c_upper
clump1 0.5520833 0.06750772 -3.2403703 0
clump2a 0.4812500 0.08698592 -1.4609643 0
clump2b 0.4833333 0.10101720 -1.0724246 2
clump4 0.5208333 0.08157875 -1.0215078 2
even 0.4916667 0.09430136 0.7511380 9
random 0.4562500 0.13939145 0.4633235 7
pd_alt_obs_c_lower pd_alt_obs_q pd_alt_obs_p_upper pd_alt_obs_p_lower
clump1 10 10 0.0 1.0
clump2a 10 10 0.0 1.0
clump2b 8 10 0.2 0.8
clump4 8 10 0.2 0.8
even 1 10 0.9 0.1
random 3 10 0.7 0.3
rpd_obs rpd_rand_mean rpd_rand_sd rpd_obs_z rpd_obs_c_upper
clump1 0.9056604 0.9801306 0.03418566 -2.1784051 0
clump2a 0.9056604 0.9553943 0.04922881 -1.0102603 1
clump2b 0.9056604 0.9889415 0.06711588 -1.2408552 1
clump4 0.9487871 0.9681869 0.04110090 -0.4720052 4
even 1.0062893 0.9796788 0.04214566 0.6313947 5
random 0.9781132 0.9677022 0.04286896 0.2428560 6
rpd_obs_c_lower rpd_obs_q rpd_obs_p_upper rpd_obs_p_lower pe_obs
clump1 10 10 0.0 1.0 0.1333333
clump2a 7 10 0.1 0.7 0.1081761
clump2b 8 10 0.1 0.8 0.1286164
clump4 6 10 0.4 0.6 0.1411950
even 4 10 0.5 0.4 0.2506289
random 4 10 0.6 0.4 0.2380503
pe_rand_mean pe_rand_sd pe_obs_z pe_obs_c_upper pe_obs_c_lower
clump1 0.1791509 0.02725248 -1.6812272 1 9
clump2a 0.1520126 0.04640687 -0.9446117 3 7
clump2b 0.1592453 0.04203294 -0.7286887 3 7
clump4 0.1587421 0.03853247 -0.4553866 4 6
even 0.1582390 0.04329376 2.1340241 9 1
random 0.1416667 0.05971076 1.6141755 9 1
pe_obs_q pe_obs_p_upper pe_obs_p_lower pe_alt_obs pe_alt_rand_mean
clump1 10 0.1 0.9 0.1472222 0.1797917
clump2a 10 0.3 0.7 0.1194444 0.1511806
clump2b 10 0.3 0.7 0.1420139 0.1588542
clump4 10 0.4 0.6 0.1454861 0.1595139
even 10 0.9 0.1 0.2246528 0.1577431
random 10 0.9 0.1 0.2211806 0.1470833
pe_alt_rand_sd pe_alt_obs_z pe_alt_obs_c_upper pe_alt_obs_c_lower
clump1 0.02393557 -1.3607134 1 9
clump2a 0.04123464 -0.7696468 3 7
clump2b 0.04999551 -0.3368358 3 7
clump4 0.03548174 -0.3953520 5 5
even 0.03637172 1.8396085 9 1
random 0.06502801 1.1394663 8 2
pe_alt_obs_q pe_alt_obs_p_upper pe_alt_obs_p_lower rpe_obs
clump1 10 0.1 0.9 0.9056604
clump2a 10 0.3 0.7 0.9056604
clump2b 10 0.3 0.7 0.9056604
clump4 10 0.5 0.5 0.9705048
even 10 0.9 0.1 1.1156280
random 10 0.8 0.2 1.0762714
rpe_rand_mean rpe_rand_sd rpe_obs_z rpe_obs_c_upper rpe_obs_c_lower
clump1 0.9955043 0.06343205 -1.416381 0 10
clump2a 0.9992278 0.09063131 -1.032396 3 7
clump2b 1.0238019 0.11633329 -1.015543 3 7
clump4 0.9925977 0.05399095 -0.409196 4 6
even 0.9980011 0.06350954 1.852114 10 0
random 0.9703781 0.04810763 2.201176 10 0
rpe_obs_q rpe_obs_p_upper rpe_obs_p_lower
clump1 10 0.0 1.0
clump2a 10 0.3 0.7
clump2b 10 0.3 0.7
clump4 10 0.4 0.6
even 10 1.0 0.0
random 10 1.0 0.0
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