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ChiLiubio / microeco

An R package for data analysis in microbial community ecology
GNU General Public License v3.0
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Betadiversity showing this error #100

Closed panavoorjabir closed 2 years ago

panavoorjabir commented 2 years ago

Show in New WindowClear OutputExpand/Collapse Output Error in install.packages : Updating loaded packages Downloading GitHub repo ChiLiubio/microeco@HEAD

Restarting R session...

Show in New WindowClear OutputExpand/Collapse Output

Attaching package: �microeco�

The following objects are masked by �.GlobalEnv�:

dataset, taxonomy_table_16S

Show in New WindowClear OutputExpand/Collapse Output phyloseq-class experiment-level object otu_table() OTU Table: [ 95 taxa and 16 samples ] sample_data() Sample Data: [ 16 samples by 20 sample variables ] tax_table() Taxonomy Table: [ 95 taxa by 6 taxonomic ranks ] Show in New WindowClear OutputExpand/Collapse Output [1] "data.frame" Show in New WindowClear OutputExpand/Collapse Output

1PM

1FS 1FB 1FM 1PS OTU1 0 0 32147 41 29 OTU2 0 0 55725 90 31 OTU3 69 4349 422 54864 2814 OTU4 0 0 43363 45 1161 OTU5 26 2758 13 10 25 5 rows Show in New WindowClear OutputExpand/Collapse Output Kingdom Phylum Class OTU1 Bacteria Proteobacteria Deltaproteobacteria OTU2 Bacteria Proteobacteria Betaproteobacteria OTU3 Bacteria Proteobacteria Deltaproteobacteria OTU4 Bacteria Proteobacteria Deltaproteobacteria OTU5 Bacteria Proteobacteria Deltaproteobacteria 5 rows Show in New WindowClear OutputExpand/Collapse Output [1] "data.frame" Show in New WindowClear OutputExpand/Collapse Output Type Watermass Level Depth Temperature Salinity DO TOC POC 1FS FL GIW FL_GIW 10 5.31 32.02 7.18 81.43 22.67 5FS FL GIW FL_GIW 10 5.24 31.75 6.57 191.60 18.33 9FS FL GIW FL_GIW 10 3.01 31.87 4.98 81.70 24.71 9FB FL GIW FL_GIW 30 5.08 34.01 4.98 91.57 13.32 1FM FL AIW FL_AIW 75 4.64 34.83 6.87 34.40 11.67 5 rows | 1-10 of 20 columns Show in New WindowClear OutputExpand/Collapse Output [1] "microtable" "R6" Show in New WindowClear OutputExpand/Collapse Output microtable class: sample_table have 16 rows and 20 columns otu_table have 95 rows and 16 columns tax_table have 95 rows and 6 columns phylo_tree have 1147 tips Show in New WindowClear OutputExpand/Collapse Output microtable class: sample_table have 16 rows and 20 columns otu_table have 95 rows and 16 columns tax_table have 95 rows and 6 columns phylo_tree have 95 tips Show in New WindowClear OutputExpand/Collapse Output Total 0 taxa are removed from tax_table ... microtable class: sample_table have 16 rows and 20 columns otu_table have 95 rows and 16 columns tax_table have 95 rows and 6 columns phylo_tree have 95 tips Show in New WindowClear OutputExpand/Collapse Output [1] 157028 317001 Show in New WindowClear OutputExpand/Collapse Output [1] 157028 157028 Show in New WindowClear OutputExpand/Collapse Output The result is stored in object$taxa_abund ... [1] "list" Show in New WindowClear OutputExpand/Collapse Output 'taxa_abund' already exists Show in New WindowClear OutputExpand/Collapse Output The result is stored in object$alpha_diversity ... [1] "data.frame" Show in New WindowClear OutputExpand/Collapse Output 'alpha_diversity' already exists Show in New WindowClear OutputExpand/Collapse Output The result is stored in object$beta_diversity ... No documentation for ‘cal_betadiv’ in specified packages and libraries: you could try ‘??cal_betadiv’ [1] "list" 'beta_diversity' already exists Show in New WindowClear OutputExpand/Collapse Output trans_abund class: abund_data have 23 columns: Taxonomy, Sample, Abundance, Type, Watermass, Level, Depth, Temperature, Salinity, DO, TOC, POC, TPN, DOC, ?13C, ?15N, Cholorophyll-a, Nitrate, Nitrite, CN ratio, Phosphate, NP ratio, Silicate abund_data have 240 rows Filtered taxa names: Desulfuromonadales, Desulfobacterales, Burkholderiales, Rhizobiales, Nitrosomonadales, UCYN-A, Desulfovibrionales, Alteromonadales, Oceanospirillales, Vibrionales Show in New WindowClear OutputExpand/Collapse Output Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale. R Console Show in New WindowClear OutputExpand/Collapse Output Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale. R Console Show in New WindowClear OutputExpand/Collapse Output Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale. R Console Show in New WindowClear OutputExpand/Collapse Output trans_abund class: abund_data have 23 columns: Taxonomy, Sample, Abundance, Type, Watermass, Level, Depth, Temperature, Salinity, DO, TOC, POC, TPN, DOC, ?13C, ?15N, Cholorophyll-a, Nitrate, Nitrite, CN ratio, Phosphate, NP ratio, Silicate abund_data have 272 rows Filtered taxa names: Desulfuromonadaceae, Desulfobulbaceae, Burkholderiaceae, Bradyrhizobiaceae, Gallionellaceae, UCYN-A, Desulfovibrionaceae, Alteromonadaceae, Oceanospirillaceae, Vibrionaceae Show in New WindowClear OutputExpand/Collapse Output Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale. R Console Show in New WindowClear OutputExpand/Collapse Output Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale. R Console Show in New WindowClear OutputExpand/Collapse Output Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale. R Console Show in New WindowClear OutputExpand/Collapse Output trans_abund class: abund_data have 23 columns: Taxonomy, Sample, Abundance, Type, Watermass, Level, Depth, Temperature, Salinity, DO, TOC, POC, TPN, DOC, ?13C, ?15N, Cholorophyll-a, Nitrate, Nitrite, CN ratio, Phosphate, NP ratio, Silicate abund_data have 208 rows Filtered taxa names: Ralstonia, UCYN-A, Desulfuromonas, Desulfovibrio, Rhodopseudomonas, Desulfobulbus, Desulfocapsa, Vibrio diazotrophicus, Methanospirillum, Methylobacter Show in New WindowClear OutputExpand/Collapse Output Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale. R Console Show in New WindowClear OutputExpand/Collapse Output Level column is used to calculate mean abundance ... R Console Show in New WindowClear OutputExpand/Collapse Output Level column is used to calculate mean abundance ... R Console Show in New WindowClear OutputExpand/Collapse Output Level column is used to calculate mean abundance ... R Console Warning `spread_()` was deprecated in tidyr 1.2.0. Please use `spread()` instead. The `.dots` argument of `group_by()` is deprecated as of dplyr 1.0.0. Show in New WindowClear OutputExpand/Collapse Output Level column is used to calculate mean abundance ... R Console Show in New WindowClear OutputExpand/Collapse Output Show in New WindowClear OutputExpand/Collapse Output Show in New WindowClear OutputExpand/Collapse Output Warning Transformation introduced infinite values in discrete y-axis Show in New WindowClear OutputExpand/Collapse Output Level column is used to calculate mean abundance ... R Console Show in New WindowClear OutputExpand/Collapse Output The result is stored in object$venn_table and object$venn_count_abund ... R Console Show in New WindowClear OutputExpand/Collapse Output The result is stored in object$venn_table and object$venn_count_abund ... R Console Show in New WindowClear OutputExpand/Collapse Output The result is stored in object$venn_table and object$venn_count_abund ... R Console Show in New WindowClear OutputExpand/Collapse Output [1] "list" Show in New WindowClear OutputExpand/Collapse Output Error: attempt to apply non-function Show in New WindowClear OutputExpand/Collapse Output Error: attempt to apply non-function Show in New WindowClear OutputExpand/Collapse Output The transformed diversity data is stored in object$alpha_data ... The group statistics are stored in object$alpha_stat ... cannot compute exact p-value with tiescannot compute exact p-value with tiescannot compute exact p-value with tiescannot compute exact p-value with tiesThe result is stored in object$res_alpha_diff ... R Console Type Measure N Mean FL Observed 8 44.2500000 FL Chao1 8 45.0416667 FL ACE 8 44.6959880 FL Shannon 8 2.2549072 FL Simpson 8 0.8318603 FL InvSimpson 8 7.0817658 FL Fisher 8 4.2093690 FL Coverage 8 0.9999936 PA Observed 8 50.7500000 PA Chao1 8 51.1250000 1-10 of 16 rows | 1-4 of 6 columns data.frame 16 x 6 Groups Measure FL vs PA Observed FL vs PA Chao1 FL vs PA ACE FL vs PA Shannon FL vs PA Simpson FL vs PA InvSimpson FL vs PA Fisher FL vs PA Coverage 8 rows | 1-2 of 6 columns data.frame 8 x 6 Groups Measure Test_method p.value p.adjust Significance FL vs PA Observed Wilcoxon Rank Sum Test 0.1028000 0.3476819 FL vs PA Chao1 Wilcoxon Rank Sum Test 0.1889374 0.3778749 FL vs PA ACE Wilcoxon Rank Sum Test 0.1303807 0.3476819 FL vs PA Shannon Wilcoxon Rank Sum Test 0.7984460 1.0000000 FL vs PA Simpson Wilcoxon Rank Sum Test 1.0000000 1.0000000 FL vs PA InvSimpson Wilcoxon Rank Sum Test 1.0000000 1.0000000 FL vs PA Fisher Wilcoxon Rank Sum Test 0.1028000 0.3476819 FL vs PA Coverage Wilcoxon Rank Sum Test 0.6571172 1.0000000 8 rows Show in New WindowClear OutputExpand/Collapse Output Show in New WindowClear OutputExpand/Collapse Output The transformed diversity data is stored in object$alpha_data ... The group statistics are stored in object$alpha_stat ... cannot compute exact p-value with tiescannot compute exact p-value with tiescannot compute exact p-value with tiescannot compute exact p-value with tiesThe result is stored in object$res_alpha_diff ... R Console Watermass Measure N Mean AIW Observed 8 43.3750000 AIW Chao1 8 44.2291667 AIW ACE 8 43.9286191 AIW Shannon 8 1.9642496 AIW Simpson 8 0.7806630 AIW InvSimpson 8 5.1356593 AIW Fisher 8 4.1173908 AIW Coverage 8 0.9999912 GIW Observed 8 51.6250000 GIW Chao1 8 51.9375000 1-10 of 16 rows | 1-4 of 6 columns data.frame 16 x 6 Groups Measure GIW vs AIW Observed GIW vs AIW Chao1 GIW vs AIW ACE GIW vs AIW Shannon GIW vs AIW Simpson GIW vs AIW InvSimpson GIW vs AIW Fisher GIW vs AIW Coverage 8 rows | 1-2 of 6 columns data.frame 8 x 6 Groups Measure Test_method p.value p.adjust GIW vs AIW Observed Wilcoxon Rank Sum Test 0.04552021 0.08660969 GIW vs AIW Chao1 Wilcoxon Rank Sum Test 0.08289641 0.09473875 GIW vs AIW ACE Wilcoxon Rank Sum Test 0.06495726 0.08660969 GIW vs AIW Shannon Wilcoxon Rank Sum Test 0.04988345 0.08660969 GIW vs AIW Simpson Wilcoxon Rank Sum Test 0.06495726 0.08660969 GIW vs AIW InvSimpson Wilcoxon Rank Sum Test 0.06495726 0.08660969 GIW vs AIW Fisher Wilcoxon Rank Sum Test 0.04552021 0.08660969 GIW vs AIW Coverage Wilcoxon Rank Sum Test 0.29176627 0.29176627 8 rows | 1-5 of 6 columns Show in New WindowClear OutputExpand/Collapse Output Show in New WindowClear OutputExpand/Collapse Output Registered S3 methods overwritten by 'klaR': method from predict.rda vegan print.rda vegan plot.rda vegan The result is stored in object$res_alpha_diff ... R Console Observed Chao1 ACE Shannon Simpson GIW a a a a a AIW b a b b a 2 rows | 1-6 of 8 columns data.frame 2 x 8 Observed Chao1 ACE Shannon Simpson InvSimpson Fisher Coverage GIW a a a a a a a a AIW b a b b a b b a 2 rows Show in New WindowClear OutputExpand/Collapse Output Show in New WindowClear OutputExpand/Collapse Output Error in initialize(...) : unused argument (ordination = "NMDS")
ChiLiubio commented 2 years ago

I am confused about how can I repeat your error.