metagMisc
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Published
20 hours ago •
vmikk
vmikk
Error in if (class(dis) %in% "phylo") { : the condition has length > 1
My Code:
# Merge seq and tree
OTU <- otu_table(species_otu_table, taxa_are_rows = TRUE)
physeq <- phyloseq(OTU, otu_tree)
# Count
phy_SES <- phyloseq_phylo_ses(
physeq,
measures = c("PD", "MPD", "VPD"),
null_model = "richness",
package = "picante",
abundance_weighted = FALSE,
nsim = 1000,
swapiter = 1000,
)
Error information:
SES analysis started at 10:06:44
Error in if (class(dis) %in% "phylo") { : the condition has length > 1
I can used this function to calculate "PD" and "MPD", But not "VPD" parameter.
> phy_SES <- phyloseq_phylo_ses(
+ physeq,
+ measures = c("PD", "MPD"),
+ null_model = "richness",
+ package = "picante",
+ abundance_weighted = FALSE,
+ nsim = 1000,
+ swapiter = 1000,
+ )
SES analysis started at 10:12:25
..Randomizing data with 'richness' algorithm
|===================================================================================================| 100%
..Estimating phylogenetic diversity for the randomized data
|===================================================================================================| 100%
..Estimating effect size
..Done
Analysis finished at 10:12:37
I guess the "VPD" calculate got wrong.
Show "OTU" content:
> OTU
OTU Table: [17 taxa and 32 samples]
taxa are rows
LYG1 LYG2 LYG3 LYG4 LYG5 LYG6 LYG7 LYG8 LYG9 LYG10 LYG11 LYG12 LYG13 LYG14
Amblychaeturichthys_hexanema 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Chaeturichthys_stigmatias 7509 13980 5698 36438 2463 31835 2985 4479 8514 11374 13725 3886 43904 44243
Coilia_nasus 0 0 0 0 0 0 0 0 0 31 0 33 0 0
Collichthys_lucidus 1339 119 70 71 189 3421 2064 3032 1273 6879 2141 2081 0 0
Ctenotrypauchen_chinensis 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Cynoglossus_joyneri 10944 442 3136 5513 4444 4426 4067 1640 1909 2166 5682 1345 5810 4196
Engraulis_japonicus 2882 274 201 19840 530 921 5837 8303 18928 6489 28 502 21 402
Hexagrammos_otakii 69 12 0 12 37 718 7 453 1152 38 14 2264 1089 1808
Konosirus_punctatus 40 0 0 15 0 0 0 0 0 0 18 1280 3551 19
Larimichthys_polyactis 1002 0 0 0 704 53 12 15 13 14 27 1198 0 0
Liparis_tanakae 1026 105 0 0 52 577 0 0 1304 9149 1754 0 275 1161
Lophius_litulon 901 7363 1295 132 45 803 33 1578 222 62 8 1222 1402 823
Odontamblyopus_lacepedii 0 0 0 0 0 0 0 0 0 0 0 0 53 508
Pholis_fangi 971 35 1865 68 3233 235 6094 2609 12732 188 1050 2014 747 387
Scomber_japonicus 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Setipinna_taty 106 0 16 53 63 14 767 1903 1574 23 3796 25 8 0
Thryssa_kammalensis 603 11153 880 41 1014 2611 4213 24 2874 3058 3038 4066 22 2424
LYG15 LYG16 ZH1 ZH2 ZH3 ZH4 ZH5 ZH6 ZH7 ZH8 ZH9 ZH12 ZH13 ZH15 ZH16
Amblychaeturichthys_hexanema 47 28 0 0 0 0 0 0 0 0 0 0 0 0 0
Chaeturichthys_stigmatias 32321 27175 1160 9 8 0 0 0 0 2529 0 36 0 256 0
Coilia_nasus 0 0 0 0 0 0 0 0 0 0 1853 246 7 0 105
Collichthys_lucidus 58 40 0 0 0 0 0 0 9 0 0 0 540 587 9
Ctenotrypauchen_chinensis 0 0 0 0 0 0 1148 0 0 864 0 14 0 270 1479
Cynoglossus_joyneri 5682 5531 0 0 0 0 0 0 0 0 0 0 0 0 0
Engraulis_japonicus 2395 3425 6344 4096 949 2462 187 2594 2363 7442 4109 269 2084 448 128
Hexagrammos_otakii 7 70 0 0 0 0 0 0 0 0 0 0 0 0 0
Konosirus_punctatus 923 4595 0 0 0 0 0 0 0 0 0 0 0 0 0
Larimichthys_polyactis 0 19 0 0 0 0 0 0 0 0 0 0 0 0 0
Liparis_tanakae 44 0 662 67 10 24 13 0 6061 1400 1229 11768 20 465 0
Lophius_litulon 11 48 0 0 0 0 0 0 0 0 0 0 0 0 0
Odontamblyopus_lacepedii 568 19 0 0 0 0 0 0 0 0 0 0 0 0 0
Pholis_fangi 3256 101 0 0 0 0 0 0 351 0 0 0 0 8 0
Scomber_japonicus 0 0 0 0 0 3093 0 13 0 0 0 0 0 0 0
Setipinna_taty 828 1910 0 0 0 0 0 0 0 0 0 0 0 0 0
Thryssa_kammalensis 4896 152 0 0 0 0 0 0 0 0 0 0 0 0 0
ZH17 ZH18 ZH19
Amblychaeturichthys_hexanema 0 0 0
Chaeturichthys_stigmatias 6 0 21
Coilia_nasus 24 12 0
Collichthys_lucidus 0 0 7
Ctenotrypauchen_chinensis 14 12 0
Cynoglossus_joyneri 0 0 0
Engraulis_japonicus 16132 10753 7846
Hexagrammos_otakii 0 0 0
Konosirus_punctatus 0 0 0
Larimichthys_polyactis 0 0 0
Liparis_tanakae 26 1209 2092
Lophius_litulon 0 0 0
Odontamblyopus_lacepedii 0 0 0
Pholis_fangi 0 0 1956
Scomber_japonicus 0 0 0
Setipinna_taty 0 0 0
Thryssa_kammalensis 0 0 0
Show "otu_tree" content:
> otu_tree
Phylogenetic tree with 17 tips and 15 internal nodes.
Tip labels:
Amblychaeturichthys_hexanema, Chaeturichthys_stigmatias, Ctenotrypauchen_chinensis, Odontamblyopus_lacepedii, Hexagrammos_otakii, Pholis_fangi, ...
Unrooted; includes branch lengths.
How can I fix this error? Many Thanks!
Hello Ming,
Thank you for reporting the issue.
I've fixed the problem (closed via 5e9c680). Please pull the latest version of metagMisc.
It works on a test dataset:
library(phyloseq)
library(metagMisc)
data("GlobalPatterns")
res <- phyloseq_phylo_ses(
physeq = GlobalPatterns,
measures = c("PD", "MPD", "VPD"),
null_model = "richness",
package = "picante",
abundance_weighted = FALSE,
nsim = 5,
swapiter = 5
)
Unfortunately, multi-threading is not implemented yet for the diversity estimation for the randomized datasets, so it may take a while to run.
