Skip to content

Commit 77a69d1

Browse files
aravind-jaravind-j
committed
Fix bugs in examples
1 parent 720df74 commit 77a69d1

2 files changed

Lines changed: 136 additions & 136 deletions

File tree

‎R/allocate.diversity.R‎

Lines changed: 68 additions & 68 deletions
Original file line numberDiff line numberDiff line change
@@ -132,118 +132,118 @@
132132
#' #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
133133
#'
134134
#' ## Shannon-Weaver Diversity Index
135-
#' dist_out_shannon1 <-
135+
#' div_out_shannon1 <-
136136
#' allocate.diversity(data = data, names = "genotypes",
137137
#' group = "Cluster",
138138
#' qualitative = traits,
139139
#' method = "div",
140140
#' div.index = "shannon", metric = "pooled",
141141
#' size = 0.2)
142-
#' dist_out_shannon1
142+
#' div_out_shannon1
143143
#'
144-
#' dist_out_shannon2 <-
144+
#' div_out_shannon2 <-
145145
#' allocate.diversity(data = data, names = "genotypes",
146146
#' group = "Cluster",
147147
#' qualitative = traits,
148148
#' method = "div",
149149
#' div.index = "shannon", metric = "mean",
150150
#' size = 0.2)
151-
#' dist_out_shannon2
151+
#' div_out_shannon2
152152
#'
153153
#' ## Gini-Simpson Index
154-
#' dist_out_simpson1 <-
154+
#' div_out_simpson1 <-
155155
#' allocate.diversity(data = data, names = "genotypes",
156156
#' group = "Cluster",
157157
#' qualitative = traits,
158158
#' method = "div",
159159
#' div.index = "simpson", metric = "pooled",
160160
#' size = 0.2)
161-
#' dist_out_simpson1
161+
#' div_out_simpson1
162162
#'
163-
#' dist_out_simpson2 <-
163+
#' div_out_simpson2 <-
164164
#' allocate.diversity(data = data, names = "genotypes",
165165
#' group = "Cluster",
166166
#' qualitative = traits,
167167
#' method = "div",
168168
#' div.index = "simpson", metric = "mean",
169169
#' size = 0.2)
170-
#' dist_out_simpson2
170+
#' div_out_simpson2
171171
#'
172172
#' ## McIntosh Diversity Index
173-
#' dist_out_mcintosh1 <-
173+
#' div_out_mcintosh1 <-
174174
#' allocate.diversity(data = data, names = "genotypes",
175175
#' group = "Cluster",
176176
#' qualitative = traits,
177177
#' method = "div",
178178
#' div.index = "mcintosh", metric = "pooled",
179179
#' size = 0.2)
180-
#' dist_out_mcintosh1
180+
#' div_out_mcintosh1
181181
#'
182-
#' dist_out_mcintosh2 <-
182+
#' div_out_mcintosh2 <-
183183
#' allocate.diversity(data = data, names = "genotypes",
184184
#' group = "Cluster",
185185
#' qualitative = traits,
186186
#' method = "div",
187187
#' div.index = "mcintosh", metric = "mean",
188188
#' size = 0.2)
189-
#' dist_out_mcintosh2
189+
#' div_out_mcintosh2
190190
#'
191191
#' ## Richness
192-
#' dist_out_richness1 <-
192+
#' div_out_richness1 <-
193193
#' allocate.diversity(data = data, names = "genotypes",
194194
#' group = "Cluster",
195195
#' qualitative = traits,
196196
#' method = "div",
197-
#' div.index = richness, metric = "pooled",
197+
#' div.index = "richness", metric = "pooled",
198198
#' size = 0.2)
199-
#' dist_out_richness1
199+
#' div_out_richness1
200200
#'
201-
#' dist_out_richness2 <-
201+
#' div_out_richness2 <-
202202
#' allocate.diversity(data = data, names = "genotypes",
203203
#' group = "Cluster",
204204
#' qualitative = traits,
205205
#' method = "div",
206-
#' div.fun = richness, metric = "mean",
206+
#' div.index = "richness", metric = "mean",
207207
#' size = 0.2)
208-
#' dist_out_richness2
208+
#' div_out_richness2
209209
#'
210210
#' ## Brillouin Diversity Index
211-
#' dist_out_brillouin1 <-
211+
#' div_out_brillouin1 <-
212212
#' allocate.diversity(data = data, names = "genotypes",
213213
#' group = "Cluster",
214214
#' qualitative = traits,
215215
#' method = "div",
216216
#' div.fun = div_fun_brillouin, metric = "pooled",
217217
#' size = 0.2)
218-
#' dist_out_brillouin1
218+
#' div_out_brillouin1
219219
#'
220-
#' dist_out_brillouin2 <-
220+
#' div_out_brillouin2 <-
221221
#' allocate.diversity(data = data, names = "genotypes",
222222
#' group = "Cluster",
223223
#' qualitative = traits,
224224
#' method = "div",
225225
#' div.fun = div_fun_brillouin, metric = "mean",
226226
#' size = 0.2)
227-
#' dist_out_brillouin2
227+
#' div_out_brillouin2
228228
#'
229229
#' ## Margalef's richness Index
230-
#' dist_out_margalef1 <-
230+
#' div_out_margalef1 <-
231231
#' allocate.diversity(data = data, names = "genotypes",
232232
#' group = "Cluster",
233233
#' qualitative = traits,
234234
#' method = "div",
235235
#' div.fun = div_fun_margalef, metric = "pooled",
236236
#' size = 0.2)
237-
#' dist_out_margalef1
237+
#' div_out_margalef1
238238
#'
239-
#' dist_out_margalef2 <-
239+
#' div_out_margalef2 <-
240240
#' allocate.diversity(data = data, names = "genotypes",
241241
#' group = "Cluster",
242242
#' qualitative = traits,
243243
#' method = "div",
244244
#' div.fun = div_fun_margalef, metric = "mean",
245245
#' size = 0.2)
246-
#' dist_out_margalef2
246+
#' div_out_margalef2
247247
#'
248248
#'
249249
#' #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -308,61 +308,61 @@
308308
#' dist_prop_out_mcintosh2
309309
#'
310310
#' ## Richness
311-
#' dist_out_richness1 <-
311+
#' div_out_richness1 <-
312312
#' allocate.diversity(data = data, names = "genotypes",
313313
#' group = "Cluster",
314314
#' qualitative = traits,
315315
#' method = "div.log",
316-
#' div.index = richness, metric = "pooled",
316+
#' div.index = "richness", metric = "pooled",
317317
#' size = 0.2)
318-
#' dist_out_richness1
318+
#' div_out_richness1
319319
#'
320-
#' dist_out_richness2 <-
320+
#' div_out_richness2 <-
321321
#' allocate.diversity(data = data, names = "genotypes",
322322
#' group = "Cluster",
323323
#' qualitative = traits,
324324
#' method = "div.log",
325-
#' div.fun = richness, metric = "mean",
325+
#' div.index = "richness", metric = "mean",
326326
#' size = 0.2)
327-
#' dist_out_richness2
327+
#' div_out_richness2
328328
#'
329329
#' ## Brillouin Diversity Index
330-
#' dist_out_brillouin1 <-
330+
#' div_out_brillouin1 <-
331331
#' allocate.diversity(data = data, names = "genotypes",
332332
#' group = "Cluster",
333333
#' qualitative = traits,
334334
#' method = "div.prop",
335335
#' div.fun = div_fun_brillouin, metric = "pooled",
336336
#' size = 0.2)
337-
#' dist_out_brillouin1
337+
#' div_out_brillouin1
338338
#'
339-
#' dist_out_brillouin2 <-
339+
#' div_out_brillouin2 <-
340340
#' allocate.diversity(data = data, names = "genotypes",
341341
#' group = "Cluster",
342342
#' qualitative = traits,
343343
#' method = "div.prop",
344344
#' div.fun = div_fun_brillouin, metric = "mean",
345345
#' size = 0.2)
346-
#' dist_out_brillouin2
346+
#' div_out_brillouin2
347347
#'
348348
#' ## Margalef's richness Index
349-
#' dist_out_margalef1 <-
349+
#' div_out_margalef1 <-
350350
#' allocate.diversity(data = data, names = "genotypes",
351351
#' group = "Cluster",
352352
#' qualitative = traits,
353353
#' method = "div.prop",
354354
#' div.fun = div_fun_margalef, metric = "pooled",
355355
#' size = 0.2)
356-
#' dist_out_margalef1
356+
#' div_out_margalef1
357357
#'
358-
#' dist_out_margalef2 <-
358+
#' div_out_margalef2 <-
359359
#' allocate.diversity(data = data, names = "genotypes",
360360
#' group = "Cluster",
361361
#' qualitative = traits,
362362
#' method = "div.prop",
363363
#' div.fun = div_fun_margalef, metric = "mean",
364364
#' size = 0.2)
365-
#' dist_out_margalef2
365+
#' div_out_margalef2
366366
#'
367367
#' #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
368368
#' # Diversity allocation & Logarithmic
@@ -426,61 +426,61 @@
426426
#' dist_log_out_mcintosh2
427427
#'
428428
#' ## Richness
429-
#' dist_out_richness1 <-
429+
#' div_out_richness1 <-
430430
#' allocate.diversity(data = data, names = "genotypes",
431431
#' group = "Cluster",
432432
#' qualitative = traits,
433433
#' method = "div.log",
434-
#' div.index = richness, metric = "pooled",
434+
#' div.index = "richness", metric = "pooled",
435435
#' size = 0.2)
436-
#' dist_out_richness1
436+
#' div_out_richness1
437437
#'
438-
#' dist_out_richness2 <-
438+
#' div_out_richness2 <-
439439
#' allocate.diversity(data = data, names = "genotypes",
440440
#' group = "Cluster",
441441
#' qualitative = traits,
442442
#' method = "div.log",
443-
#' div.fun = richness, metric = "mean",
443+
#' div.index = "richness", metric = "mean",
444444
#' size = 0.2)
445-
#' dist_out_richness2
445+
#' div_out_richness2
446446
#'
447447
#' ## Brillouin Diversity Index
448-
#' dist_out_brillouin1 <-
448+
#' div_out_brillouin1 <-
449449
#' allocate.diversity(data = data, names = "genotypes",
450450
#' group = "Cluster",
451451
#' qualitative = traits,
452452
#' method = "div.log",
453453
#' div.fun = div_fun_brillouin, metric = "pooled",
454454
#' size = 0.2)
455-
#' dist_out_brillouin1
455+
#' div_out_brillouin1
456456
#'
457-
#' dist_out_brillouin2 <-
457+
#' div_out_brillouin2 <-
458458
#' allocate.diversity(data = data, names = "genotypes",
459459
#' group = "Cluster",
460460
#' qualitative = traits,
461461
#' method = "div.log",
462462
#' div.fun = div_fun_brillouin, metric = "mean",
463463
#' size = 0.2)
464-
#' dist_out_brillouin2
464+
#' div_out_brillouin2
465465
#'
466466
#' ## Margalef's richness Index
467-
#' dist_out_margalef1 <-
467+
#' div_out_margalef1 <-
468468
#' allocate.diversity(data = data, names = "genotypes",
469469
#' group = "Cluster",
470470
#' qualitative = traits,
471471
#' method = "div.log",
472472
#' div.fun = div_fun_margalef, metric = "pooled",
473473
#' size = 0.2)
474-
#' dist_out_margalef1
474+
#' div_out_margalef1
475475
#'
476-
#' dist_out_margalef2 <-
476+
#' div_out_margalef2 <-
477477
#' allocate.diversity(data = data, names = "genotypes",
478478
#' group = "Cluster",
479479
#' qualitative = traits,
480480
#' method = "div.log",
481481
#' div.fun = div_fun_margalef, metric = "mean",
482482
#' size = 0.2)
483-
#' dist_out_margalef2
483+
#' div_out_margalef2
484484
#'
485485
#' #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486486
#' # Diversity allocation & Square root
@@ -544,61 +544,61 @@
544544
#' dist_sqrt_out_mcintosh2
545545
#'
546546
#' ## Richness
547-
#' dist_out_richness1 <-
547+
#' div_out_richness1 <-
548548
#' allocate.diversity(data = data, names = "genotypes",
549549
#' group = "Cluster",
550550
#' qualitative = traits,
551551
#' method = "div.sqrt",
552-
#' div.index = richness, metric = "pooled",
552+
#' div.index = "richness", metric = "pooled",
553553
#' size = 0.2)
554-
#' dist_out_richness1
554+
#' div_out_richness1
555555
#'
556-
#' dist_out_richness2 <-
556+
#' div_out_richness2 <-
557557
#' allocate.diversity(data = data, names = "genotypes",
558558
#' group = "Cluster",
559559
#' qualitative = traits,
560560
#' method = "div.sqrt",
561-
#' div.fun = richness, metric = "mean",
561+
#' div.index = "richness", metric = "mean",
562562
#' size = 0.2)
563-
#' dist_out_richness2
563+
#' div_out_richness2
564564
#'
565565
#' ## Brillouin Diversity Index
566-
#' dist_out_brillouin1 <-
566+
#' div_out_brillouin1 <-
567567
#' allocate.diversity(data = data, names = "genotypes",
568568
#' group = "Cluster",
569569
#' qualitative = traits,
570570
#' method = "div.sqrt",
571571
#' div.fun = div_fun_brillouin, metric = "pooled",
572572
#' size = 0.2)
573-
#' dist_out_brillouin1
573+
#' div_out_brillouin1
574574
#'
575-
#' dist_out_brillouin2 <-
575+
#' div_out_brillouin2 <-
576576
#' allocate.diversity(data = data, names = "genotypes",
577577
#' group = "Cluster",
578578
#' qualitative = traits,
579579
#' method = "div.sqrt",
580580
#' div.fun = div_fun_brillouin, metric = "mean",
581581
#' size = 0.2)
582-
#' dist_out_brillouin2
582+
#' div_out_brillouin2
583583
#'
584584
#' ## Margalef's richness Index
585-
#' dist_out_margalef1 <-
585+
#' div_out_margalef1 <-
586586
#' allocate.diversity(data = data, names = "genotypes",
587587
#' group = "Cluster",
588588
#' qualitative = traits,
589589
#' method = "div.sqrt",
590590
#' div.fun = div_fun_margalef, metric = "pooled",
591591
#' size = 0.2)
592-
#' dist_out_margalef1
592+
#' div_out_margalef1
593593
#'
594-
#' dist_out_margalef2 <-
594+
#' div_out_margalef2 <-
595595
#' allocate.diversity(data = data, names = "genotypes",
596596
#' group = "Cluster",
597597
#' qualitative = traits,
598598
#' method = "div.sqrt",
599599
#' div.fun = div_fun_margalef, metric = "mean",
600600
#' size = 0.2)
601-
#' dist_out_margalef2
601+
#' div_out_margalef2
602602
#'
603603
allocate.diversity <- function(data, names, group,
604604
qualitative,

0 commit comments

Comments
 (0)