forked from microbiome/microbiome
-
Notifications
You must be signed in to change notification settings - Fork 0
/
NAMESPACE
213 lines (212 loc) · 5.49 KB
/
NAMESPACE
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
# Generated by roxygen2: do not edit by hand
export(abundances)
export(add_besthit)
export(add_refseq)
export(aggregate_rare)
export(aggregate_taxa)
export(alpha)
export(associate)
export(baseline)
export(bimodality)
export(boxplot_abundance)
export(boxplot_alpha)
export(collapse_replicates)
export(combine_otu_tax)
export(core)
export(core_abundance)
export(core_members)
export(coverage)
export(default_colors)
export(divergence)
export(diversity)
export(dominance)
export(dominant)
export(evenness)
export(gktau)
export(group_age)
export(group_bmi)
export(heat)
export(hotplot)
export(inequality)
export(intermediate_stability)
export(is_compositional)
export(log_modulo_skewness)
export(low_abundance)
export(map_levels)
export(merge_taxa2)
export(meta)
export(multimodality)
export(neat)
export(neatsort)
export(otu_tibble)
export(overlap)
export(plot_atlas)
export(plot_composition)
export(plot_core)
export(plot_density)
export(plot_frequencies)
export(plot_landscape)
export(plot_regression)
export(plot_taxa_prevalence)
export(plot_tipping)
export(potential_analysis)
export(prevalence)
export(psmelt2)
export(quiet)
export(rare)
export(rare_abundance)
export(rare_members)
export(rarity)
export(read_biom2phyloseq)
export(read_csv2phyloseq)
export(read_mothur2phyloseq)
export(read_phyloseq)
export(readcount)
export(remove_samples)
export(remove_taxa)
export(richness)
export(sample_tibble)
export(spreadplot)
export(summarize_phyloseq)
export(tax_tibble)
export(taxa)
export(time_normalize)
export(time_sort)
export(timesplit)
export(top)
export(top_taxa)
export(transform)
importFrom(Biostrings,DNAStringSet)
importFrom(Rtsne,Rtsne)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,do)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_jitter)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_linerange)
importFrom(ggplot2,geom_path)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_polygon)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,position_jitter)
importFrom(ggplot2,scale_alpha_continuous)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_colour_gradient2)
importFrom(ggplot2,scale_fill_gradient)
importFrom(ggplot2,scale_fill_gradientn)
importFrom(ggplot2,scale_size)
importFrom(ggplot2,scale_size_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_discrete)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,stat_density2d)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_set)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(phyloseq,"otu_table<-")
importFrom(phyloseq,"sample_data<-")
importFrom(phyloseq,"tax_table<-")
importFrom(phyloseq,"taxa_are_rows<-")
importFrom(phyloseq,"taxa_names<-")
importFrom(phyloseq,distance)
importFrom(phyloseq,estimate_richness)
importFrom(phyloseq,get_taxa)
importFrom(phyloseq,get_variable)
importFrom(phyloseq,import_biom)
importFrom(phyloseq,merge_phyloseq)
importFrom(phyloseq,merge_taxa)
importFrom(phyloseq,nsamples)
importFrom(phyloseq,ntaxa)
importFrom(phyloseq,ordinate)
importFrom(phyloseq,otu_table)
importFrom(phyloseq,parse_taxonomy_default)
importFrom(phyloseq,phyloseq)
importFrom(phyloseq,prune_samples)
importFrom(phyloseq,prune_taxa)
importFrom(phyloseq,psmelt)
importFrom(phyloseq,rank_names)
importFrom(phyloseq,sample_data)
importFrom(phyloseq,sample_names)
importFrom(phyloseq,sample_sums)
importFrom(phyloseq,tax_glom)
importFrom(phyloseq,tax_table)
importFrom(phyloseq,taxa_are_rows)
importFrom(phyloseq,taxa_names)
importFrom(phyloseq,taxa_sums)
importFrom(reshape2,melt)
importFrom(scales,percent)
importFrom(stats,aggregate)
importFrom(stats,as.dist)
importFrom(stats,coef)
importFrom(stats,cor)
importFrom(stats,cor.test)
importFrom(stats,density)
importFrom(stats,dist)
importFrom(stats,dnorm)
importFrom(stats,frequency)
importFrom(stats,hclust)
importFrom(stats,kernel)
importFrom(stats,lm)
importFrom(stats,loess)
importFrom(stats,loess.control)
importFrom(stats,median)
importFrom(stats,na.fail)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,pnorm)
importFrom(stats,predict)
importFrom(stats,princomp)
importFrom(stats,quantile)
importFrom(stats,rnorm)
importFrom(stats,sd)
importFrom(stats,time)
importFrom(tibble,data_frame)
importFrom(tidyr,separate)
importFrom(utils,capture.output)
importFrom(utils,flush.console)
importFrom(utils,head)
importFrom(utils,read.csv)
importFrom(utils,read.table)
importFrom(utils,tail)
importFrom(utils,write.csv)
importFrom(vegan,decostand)
importFrom(vegan,fisher.alpha)
importFrom(vegan,metaMDS)
importFrom(vegan,scores)
importFrom(vegan,vegdist)
importFrom(vegan,wascores)