SummaryFigures: SummaryFigures
In R-Burke/SiteSummaryTool: Ecological Site Summaries using Assessment, Inventory, and Monitoring (AIM) and Landscape Monitoring Framework (LMF) data
Description
Usage
Arguments
Details
Author(s)
Examples
View source: R/SummaryFigures.R
Description
Returns a static or interactive (plotly-friendly) ggplot boxplot summarizing cover values of AIM&LMF plots across your ecological site(s) based on summary variables (Growth habit, noxious vs. non-noxious, individual species, ground cover values (total foliar, rock, litter, bare soil), canopy gap size classes, and soil stability values.)
Usage
1
SummaryFigures(SpeciesList, Species_plots_ecosite, EcologicalSiteId, SummaryVar, Interactive)
Arguments
SpeciesList
Official species list. Returned output from function ReadSpeciesList()
Species_plots_ecosite
Combined AIM and LMF species indicator, subset to your ecological site(s). Returned output from Combine_AIM_LMF_Species and SubsetEcologicalSite_Species.
EcologicalSiteId
Full ecological site id, list of ecological sites, or object
SummaryVar
c("GrowthHabitSub", "Noxious", "Species", "GroundCover", "Gap", "SoilStability")
Interactive
logical. If TRUE, boxplot aesthetics will be set up for interactive plotly::ggplotly object. If FALSE, will return static box plot.
Details
If SummaryVar == "GrowthHabitSub", returns a list of plots that must be called on- boxplots are broken up by growth habit. Faceting rows are duration (annual vs. perennial). Y values are percent cover. See example for how to call on plot.
If SummaryVar == "Noxious", faceting rows are noxious and non-noxious. Y values are percent cover.
If SummaryVar == "Species", returns a list of plots that must be called on- boxplots are broken up by GrowthHabitSub, with individual species within each group as faceting row. Y values are percent cover. See example for how to call on plot.
If SummaryVar == "GroundCover", faceting rows are total foliar cover, litter cover, rock cover, and total bare ground cover. Y values are percent cover.
If SummaryVar == "Gap", faceting rows are canopy gap size classes. Y values are percent cover.
If SummaryVar == "SoilStability", faceting rows are soil stability cover class (all, protected by vegetation, and unprotected). Y values are average soil stability class.
Author(s)
Rachel Burke, ecologist/analyst @ Jornada
Examples
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
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
# If Interactive == TRUE & SummaryVar == "GrowthHabitSub"
Boxplots <- SummaryFigures(SpeciesList, Species_plots_ecosite,
EcologicalSiteId, SummaryVar = "GrowthHabitSub",
Interactive = TRUE)
plotly::ggplotly(Boxplots[["Graminoid"]])
# If Interactive == FALSE & SummaryVar == "GrowthHabitSub"
Boxplots <- SummaryFigures(SpeciesList, Species_plots_ecosite,
EcologicalSiteId, SummaryVar = "GrowthHabitSub", Interactive = FALSE)
Boxplots[["Graminoid"]]
# If Interactive == TRUE & SummaryVar == "Noxious"
plotly::ggplotly(SummaryFigures(SpeciesList, Species_plots_ecosite,
EcologicalSiteId,
SummaryVar = "Noxious",
Interactive = TRUE))
## The function is currently defined as
function(SpeciesList, Species_plots_ecosite, EcologicalSiteId,
SummaryVar, Interactive){
#Prep
SpeciesList <- SpeciesList
dplyr::select(Species, ScientificName, CommonName,
Family, SpeciesState,
SynonymOf, UpdatedSpeciesCode)
dplyr::mutate(link = paste("https://plants.sc.egov.usda.gov/core/profile?symbol=", Species, sep = ""))
#Merge with species list so we can hover for scientific name
Species_plots_ecosite <- merge(Species_plots_ecosite , SpeciesList , by = c("Species" , "SpeciesState"))
dplyr::select(Species, ScientificName, CommonName, PrimaryKey,
PlotID, AH_SpeciesCover,
AH_SpeciesCover_n, Hgt_Species_Avg,
Hgt_Species_Avg_n, GrowthHabit, GrowthHabitSub, Duration,
Noxious, SG_Group, link)
dplyr::mutate_if(is.numeric, round , digits = 2)
#Get Noxious versus Non in Standard Format
Species_plots_ecosite$Noxious <- gsub("YES" , "Yes", Species_plots_ecosite$Noxious)
Species_plots_ecosite$Noxious <- gsub("NO", "No", Species_plots_ecosite$Noxious)
#Ignoring NAs- make disclosure as this may overestimate cover
#For summarizing across all plots
Species_cover_summary <- Species_plots_ecosite
mutate(Tally = 1)
group_by(Species , GrowthHabit , GrowthHabitSub ,
Duration , Noxious , ScientificName ,
CommonName , SG_Group, link)
summarize(AveragePercentCover = mean(AH_SpeciesCover) ,
StandardDeviation = sd(AH_SpeciesCover),
MinCover = min(AH_SpeciesCover) ,
MaxCover = max(AH_SpeciesCover) , n = sum(Tally))
mutate_if(is.numeric, round , digits = 2)
dplyr::select(Species, ScientificName,
AveragePercentCover, StandardDeviation,
MinCover, MaxCover, n, GrowthHabit,
GrowthHabitSub, Duration,
Noxious, CommonName, SG_Group, link)
##Setting color palette for plot
NoxNonPal_Fill <- c("grey75" , "#D55E00")
NoxNonPal_Dot <- c("grey33" , "#993300")
if(SummaryVar == "GrowthHabitSub"){
if(Interactive){
Plots <- lapply(X = split(Species_plots_ecosite, Species_plots_ecosite[[SummaryVar]] ,
drop = TRUE),
FUN = function(Species_plots_ecosite){
current_plot <- ggplot(Species_plots_ecosite ,
aes(x = SummaryVar ,
y = AH_SpeciesCover,
text = paste("Primary Key: " , PrimaryKey ,
"Plot ID: " , PlotID , "Species: " ,
ScientificName , "Code: " , Species ,
"Percent Cover: " , AH_SpeciesCover ,
"Noxious: " , Noxious , sep = "<br>"))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .2 , size = 1.25 , shape = 21) +
theme_light() +
scale_y_continuous(limits = c(0 , 100)) +
theme(axis.text.y = element_blank() , axis.ticks.y = element_blank() ,
axis.title.y = element_blank() , axis.title.x = element_blank() ,
axis.line.y = element_blank()) + theme(panel.grid.major.y = element_blank() ,
axis.title.y = element_blank()) +
ggtitle(paste0("Percent Cover by Functional Group: " ,
Species_plots_ecosite$SummaryVar,
toString(EcologicalSiteId), sep = " ")) +
coord_flip() + facet_grid(cols = vars(GrowthHabitSub) ,
rows = vars(Duration) ,
switch = "y" ,
scales = "free" , drop = TRUE)
return(current_plot)
})
}
if(!Interactive){
Plots <- lapply(X = split(Species_plots_ecosite, Species_plots_ecosite[[SummaryVar]] , drop = TRUE),
FUN = function(Species_plots_ecosite){
current_plot <- ggplot(Species_plots_ecosite , aes(x = SummaryVar , y = AH_SpeciesCover)) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .2 , size = 1.25, aes(color = Noxious)) +
scale_color_manual(values = NoxNonPal_Dot) +
labs(y = "Percent Cover",
caption = paste("Percent cover in: ", toString(EcologicalSiteId))) +
scale_y_continuous(limits = c(0 , 100)) +
theme_light() +
theme(axis.text.y = element_blank() , axis.ticks.y = element_blank() ,
axis.line.y = element_blank()) + theme(panel.grid.major.y = element_blank() ,
axis.title.y = element_blank()) +
ggtitle(paste("Percent Cover by Functional Group:",
Species_plots_ecosite$SummaryVar,
toString(EcologicalSiteId), sep = " ")) +
coord_flip() + facet_grid(cols = vars(GrowthHabitSub) ,
rows = vars(Duration) , switch = "y" ,
scales = "free" , drop = TRUE)
return(current_plot)
})
}}
if(SummaryVar == "Noxious"){
if(Interactive){
Plots <- Species_plots_ecosite
filter(!is.na(Noxious))
ggplot((aes(x = Noxious , y = AH_SpeciesCover ,
text = paste("Primary Key : " , PrimaryKey,
"Plot ID: " , PlotID ,
"Species: " , ScientificName,
"Code: " , Species,
"Percent Cover: " , AH_SpeciesCover,
"Noxious: " , Noxious ,
sep = "<br>")))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15 , size = 1.25 , shape = 21) +
theme_light() +
scale_y_continuous(limits = c(0 , 100)) +
labs(y = "Percent Cover") +
ggtitle(paste("Percent Cover, Noxious vs. Non-Noxious Species: " ,
toString(EcologicalSiteId))) +
theme(axis.title.y = element_blank() , axis.text.y = element_blank() ,
axis.ticks.y = element_blank() , axis.line.y = element_blank() ,
axis.title.x = element_blank()) +
theme(panel.grid.major.y = element_blank() , legend.position = "none") +
coord_flip() +
facet_grid(rows = vars(Noxious) , switch = "y" , scales = "free" ,
drop = TRUE)
return(Plots)
}
if(!Interactive){
Plots <- Species_plots_ecosite
filter(!is.na(Noxious))
ggplot((aes(x = Noxious , y = AH_SpeciesCover))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15 , size = 1.25 , aes(color = Noxious)) +
scale_color_manual(values = NoxNonPal_Dot) +
theme_light() +
scale_y_continuous(limits = c(0 , 100)) +
labs(y = "Percent Cover") +
ggtitle(paste("Percent Cover, Noxious vs. Non-Noxious Species: " ,
toString(EcologicalSiteId))) +
theme(axis.title.y = element_blank() , axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank() ,
panel.grid.major.y = element_blank() ,
legend.position = "none") +
coord_flip() +
facet_grid(rows = vars(Noxious) ,
switch = "y" , scales = "free" , drop = TRUE)
}}
if(SummaryVar == "Species"){
PercentCover <- Species_plots_ecosite
if(Interactive){
Plots <-lapply(X = split(PercentCover, list(PercentCover$GrowthHabitSub , PercentCover$Duration) , drop = TRUE),
FUN = function(PercentCover){
current_plot <- ggplot(PercentCover , aes(x = Species , y = AH_SpeciesCover,
text = paste("PrimaryKey: ", PrimaryKey ,
"Plot ID: " , PlotID , "Species: " ,
ScientificName , "Code: " , Species ,
"Percent Cover: " , AH_SpeciesCover , "Noxious: " ,
Noxious , sep = "<br>"))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15 , size = 1, shape = 21) +
scale_y_continuous(limits = c(0 , 100)) +
theme_light() +
labs(y = "Percent Cover") +
ggtitle(paste("Percent Cover by Species, " ,
PercentCover$GrowthHabitSub,
PercentCover$Duration ,
toString(EcologicalSiteId))) +
theme(axis.title.y = element_blank() ,
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
axis.title.x = element_blank())+
theme(panel.grid.major.y = element_blank() ,
axis.title.y = element_blank()) +
coord_flip() + facet_grid(rows = vars(Species),
scales = "free" , switch = "y", drop = TRUE)
return(current_plot)
})
}
if(!Interactive){
Plots <- lapply(X = split(PercentCover, list(PercentCover$GrowthHabitSub ,
PercentCover$Duration) ,
drop = TRUE),
FUN = function(PercentCover){
current_plot <- ggplot(PercentCover , aes(x = Species , y = AH_SpeciesCover)) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15 , size = 1 , aes(color = Noxious)) +
scale_color_manual(values = NoxNonPal_Dot) + scale_y_continuous(limits = c(0 , 100)) +
theme_light() +
labs(y = "Percent Cover") +
ggtitle(paste("Percent Cover by Species, " ,
PercentCover$GrowthHabitSub ,
PercentCover$Duration ,
toString(EcologicalSiteId))) +
theme(axis.title.y = element_blank()) +
coord_flip() + facet_grid(cols = vars(GrowthHabitSub) , rows = vars(Duration) ,
switch = "y" , scales = "free" , drop = TRUE)
return(current_plot)
})
}
}
if(SummaryVar == "GroundCover"){
#Prep
#BareSoilCover
#TotalFoliarCover
#FH_TotalLitterCover
#FH_RockCover
Ground_Cover_Tall <- EcoSitePlots
dplyr::select(PlotID, PrimaryKey, BareSoilCover ,
TotalFoliarCover , FH_TotalLitterCover ,
FH_RockCover)
gather(key = Indicator , value = Percent,
BareSoilCover:FH_RockCover)
if(Interactive){
Plots <- Ground_Cover_Tall
ggplot((aes(x = Indicator , y = Percent ,
text = paste("PlotID: " , PlotID ,
"PrimaryKey: " , PrimaryKey ,
"Indicator: " , Indicator ,
"Percent Cover: " , Percent ,
sep = "<br>" )))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15 , shape = 21) +
theme_light() +
scale_y_continuous(limits = c(0 , 100)) +
labs(y = "Ground Cover (
theme(axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank() ,
axis.title.x = element_blank() ,
axis.title.y = element_blank()) +
coord_flip() + facet_grid(rows = vars(Indicator) ,
switch = "y" ,
scales = "free_y" , drop = TRUE)
}
if(!Interactive){
Plots <- Ground_Cover_Tall
ggplot((aes(x = Indicator , y = Percent))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15) +
theme_light() +
scale_y_continuous(limits = c(0 , 100)) +
labs(y = "Ground Cover (
theme(axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank()) +
coord_flip() + facet_grid(rows = vars(Indicator) ,
switch = "y" ,
scales = "free_y" , drop = TRUE)
}
}
if(SummaryVar == "Gap"){
Gap <- EcoSitePlots
GapCover_25_50 , GapCover_51_100 ,
GapCover_101_200 , GapCover_200_plus ,
GapCover_25_plus)
gather(key = Gap_Class_cm ,
value = Percent , GapCover_25_50:GapCover_25_plus)
mutate_if(is.numeric , round, digits = 2)
#Plot prep
if(Interactive){
Plots <- ggplot(data = Gap , aes(x = Gap_Class_cm , y = Percent ,
text = paste("PlotID: " , PlotID ,
"PrimaryKey: ", PrimaryKey ,
"Gap Class (cm): " , Gap_Class_cm,
"Percent Cover: " , Percent ,
sep = "<br>"))) +
geom_boxplot() + coord_flip() +
geom_jitter(width = 0.1 , shape = 21) +
theme_light() +
theme(axis.title.x = element_blank() ,
axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.title.y = element_blank() ,
axis.line.y = element_blank(),
panel.grid.major.y = element_blank()) +
facet_grid(rows = vars(Gap_Class_cm) , switch = "y" ,
scales = "free_y" , drop = TRUE)
}
if(!Interactive){
Plots <- ggplot(data = Gap , aes(x = Gap_Class_cm , y = Percent)) +
labs(y = "Percent Cover" , x = "Gap Size Class (cm)",
caption = paste("Percent cover of canopy gap in: ",
toString(EcologicalSiteId))) +
geom_boxplot() +
coord_flip() +
geom_jitter(width = 0.1) +
theme_light() +
theme(axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank(),
panel.grid.major.y = element_blank()) +
facet_grid(rows = vars(Gap_Class_cm) , switch = "y" ,
scales = "free_y" , drop = TRUE)
}
}
if(SummaryVar == "SoilStability"){
soil_labels <- c("SoilStability_All" = "All" , "SoilStability_Protected" = "Protected" ,
"SoilStability_Unprotected" = "Unprotected")
SoilStability <- EcoSitePlots
SoilStability_All ,
SoilStability_Protected ,
SoilStability_Unprotected)
gather(key = Veg , value = Rating ,
SoilStability_All:SoilStability_Unprotected)
mutate_if(is.numeric, round, digits = 2)
if(Interactive){
Plots <- ggplot(data = SoilStability ,
aes(x = Veg , y = Rating ,
text = paste("Primary Key: " , PrimaryKey,
"Plot ID: " , PlotID ,
"Rating: " , Rating ,
sep = "<br>"))) +
geom_boxplot() +
coord_flip() +
geom_jitter(width = 0.1 , shape = 21) +
theme_light() +
theme(axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank(),
panel.grid.major.y = element_blank(),
axis.title = element_blank()) +
facet_grid(rows = vars(Veg) , switch = "y" ,
scales = "free_y" , drop = TRUE ,
labeller = as_labeller(soil_labels))
}
if(!Interactive){
Plots <- ggplot(data = SoilStability ,
aes(x = Veg , y = Rating)) +
labs(x = "Vegetation cover class" ,
y = "Soil Stability Rating",
caption = paste("Soil stability ratings in: ",
toString(EcologicalSiteId))) +
geom_boxplot() + coord_flip() + geom_jitter(width = 0.1) +
theme_light() +
theme(axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank(),
panel.grid.major.y = element_blank()) +
facet_grid(rows = vars(Veg) ,
switch = "y" ,
scales = "free_y" ,
drop = TRUE ,
labeller = as_labeller(soil_labels))
}
}
return(Plots)
}
R-Burke/SiteSummaryTool documentation built on Oct. 15, 2020, 8:21 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Details Author(s) Examples
View source: R/SummaryFigures.R
Description
Returns a static or interactive (plotly-friendly) ggplot boxplot summarizing cover values of AIM&LMF plots across your ecological site(s) based on summary variables (Growth habit, noxious vs. non-noxious, individual species, ground cover values (total foliar, rock, litter, bare soil), canopy gap size classes, and soil stability values.)
Usage
1 | SummaryFigures(SpeciesList, Species_plots_ecosite, EcologicalSiteId, SummaryVar, Interactive)
|
Arguments
SpeciesList |
Official species list. Returned output from function ReadSpeciesList() |
Species_plots_ecosite |
Combined AIM and LMF species indicator, subset to your ecological site(s). Returned output from Combine_AIM_LMF_Species and SubsetEcologicalSite_Species. |
EcologicalSiteId |
Full ecological site id, list of ecological sites, or object |
SummaryVar |
c("GrowthHabitSub", "Noxious", "Species", "GroundCover", "Gap", "SoilStability") |
Interactive |
logical. If TRUE, boxplot aesthetics will be set up for interactive plotly::ggplotly object. If FALSE, will return static box plot. |
Details
If SummaryVar == "GrowthHabitSub", returns a list of plots that must be called on- boxplots are broken up by growth habit. Faceting rows are duration (annual vs. perennial). Y values are percent cover. See example for how to call on plot. If SummaryVar == "Noxious", faceting rows are noxious and non-noxious. Y values are percent cover. If SummaryVar == "Species", returns a list of plots that must be called on- boxplots are broken up by GrowthHabitSub, with individual species within each group as faceting row. Y values are percent cover. See example for how to call on plot. If SummaryVar == "GroundCover", faceting rows are total foliar cover, litter cover, rock cover, and total bare ground cover. Y values are percent cover. If SummaryVar == "Gap", faceting rows are canopy gap size classes. Y values are percent cover. If SummaryVar == "SoilStability", faceting rows are soil stability cover class (all, protected by vegetation, and unprotected). Y values are average soil stability class.
Author(s)
Rachel Burke, ecologist/analyst @ Jornada
Examples
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 | # If Interactive == TRUE & SummaryVar == "GrowthHabitSub"
Boxplots <- SummaryFigures(SpeciesList, Species_plots_ecosite,
EcologicalSiteId, SummaryVar = "GrowthHabitSub",
Interactive = TRUE)
plotly::ggplotly(Boxplots[["Graminoid"]])
# If Interactive == FALSE & SummaryVar == "GrowthHabitSub"
Boxplots <- SummaryFigures(SpeciesList, Species_plots_ecosite,
EcologicalSiteId, SummaryVar = "GrowthHabitSub", Interactive = FALSE)
Boxplots[["Graminoid"]]
# If Interactive == TRUE & SummaryVar == "Noxious"
plotly::ggplotly(SummaryFigures(SpeciesList, Species_plots_ecosite,
EcologicalSiteId,
SummaryVar = "Noxious",
Interactive = TRUE))
## The function is currently defined as
function(SpeciesList, Species_plots_ecosite, EcologicalSiteId,
SummaryVar, Interactive){
#Prep
SpeciesList <- SpeciesList
dplyr::select(Species, ScientificName, CommonName,
Family, SpeciesState,
SynonymOf, UpdatedSpeciesCode)
dplyr::mutate(link = paste("https://plants.sc.egov.usda.gov/core/profile?symbol=", Species, sep = ""))
#Merge with species list so we can hover for scientific name
Species_plots_ecosite <- merge(Species_plots_ecosite , SpeciesList , by = c("Species" , "SpeciesState"))
dplyr::select(Species, ScientificName, CommonName, PrimaryKey,
PlotID, AH_SpeciesCover,
AH_SpeciesCover_n, Hgt_Species_Avg,
Hgt_Species_Avg_n, GrowthHabit, GrowthHabitSub, Duration,
Noxious, SG_Group, link)
dplyr::mutate_if(is.numeric, round , digits = 2)
#Get Noxious versus Non in Standard Format
Species_plots_ecosite$Noxious <- gsub("YES" , "Yes", Species_plots_ecosite$Noxious)
Species_plots_ecosite$Noxious <- gsub("NO", "No", Species_plots_ecosite$Noxious)
#Ignoring NAs- make disclosure as this may overestimate cover
#For summarizing across all plots
Species_cover_summary <- Species_plots_ecosite
mutate(Tally = 1)
group_by(Species , GrowthHabit , GrowthHabitSub ,
Duration , Noxious , ScientificName ,
CommonName , SG_Group, link)
summarize(AveragePercentCover = mean(AH_SpeciesCover) ,
StandardDeviation = sd(AH_SpeciesCover),
MinCover = min(AH_SpeciesCover) ,
MaxCover = max(AH_SpeciesCover) , n = sum(Tally))
mutate_if(is.numeric, round , digits = 2)
dplyr::select(Species, ScientificName,
AveragePercentCover, StandardDeviation,
MinCover, MaxCover, n, GrowthHabit,
GrowthHabitSub, Duration,
Noxious, CommonName, SG_Group, link)
##Setting color palette for plot
NoxNonPal_Fill <- c("grey75" , "#D55E00")
NoxNonPal_Dot <- c("grey33" , "#993300")
if(SummaryVar == "GrowthHabitSub"){
if(Interactive){
Plots <- lapply(X = split(Species_plots_ecosite, Species_plots_ecosite[[SummaryVar]] ,
drop = TRUE),
FUN = function(Species_plots_ecosite){
current_plot <- ggplot(Species_plots_ecosite ,
aes(x = SummaryVar ,
y = AH_SpeciesCover,
text = paste("Primary Key: " , PrimaryKey ,
"Plot ID: " , PlotID , "Species: " ,
ScientificName , "Code: " , Species ,
"Percent Cover: " , AH_SpeciesCover ,
"Noxious: " , Noxious , sep = "<br>"))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .2 , size = 1.25 , shape = 21) +
theme_light() +
scale_y_continuous(limits = c(0 , 100)) +
theme(axis.text.y = element_blank() , axis.ticks.y = element_blank() ,
axis.title.y = element_blank() , axis.title.x = element_blank() ,
axis.line.y = element_blank()) + theme(panel.grid.major.y = element_blank() ,
axis.title.y = element_blank()) +
ggtitle(paste0("Percent Cover by Functional Group: " ,
Species_plots_ecosite$SummaryVar,
toString(EcologicalSiteId), sep = " ")) +
coord_flip() + facet_grid(cols = vars(GrowthHabitSub) ,
rows = vars(Duration) ,
switch = "y" ,
scales = "free" , drop = TRUE)
return(current_plot)
})
}
if(!Interactive){
Plots <- lapply(X = split(Species_plots_ecosite, Species_plots_ecosite[[SummaryVar]] , drop = TRUE),
FUN = function(Species_plots_ecosite){
current_plot <- ggplot(Species_plots_ecosite , aes(x = SummaryVar , y = AH_SpeciesCover)) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .2 , size = 1.25, aes(color = Noxious)) +
scale_color_manual(values = NoxNonPal_Dot) +
labs(y = "Percent Cover",
caption = paste("Percent cover in: ", toString(EcologicalSiteId))) +
scale_y_continuous(limits = c(0 , 100)) +
theme_light() +
theme(axis.text.y = element_blank() , axis.ticks.y = element_blank() ,
axis.line.y = element_blank()) + theme(panel.grid.major.y = element_blank() ,
axis.title.y = element_blank()) +
ggtitle(paste("Percent Cover by Functional Group:",
Species_plots_ecosite$SummaryVar,
toString(EcologicalSiteId), sep = " ")) +
coord_flip() + facet_grid(cols = vars(GrowthHabitSub) ,
rows = vars(Duration) , switch = "y" ,
scales = "free" , drop = TRUE)
return(current_plot)
})
}}
if(SummaryVar == "Noxious"){
if(Interactive){
Plots <- Species_plots_ecosite
filter(!is.na(Noxious))
ggplot((aes(x = Noxious , y = AH_SpeciesCover ,
text = paste("Primary Key : " , PrimaryKey,
"Plot ID: " , PlotID ,
"Species: " , ScientificName,
"Code: " , Species,
"Percent Cover: " , AH_SpeciesCover,
"Noxious: " , Noxious ,
sep = "<br>")))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15 , size = 1.25 , shape = 21) +
theme_light() +
scale_y_continuous(limits = c(0 , 100)) +
labs(y = "Percent Cover") +
ggtitle(paste("Percent Cover, Noxious vs. Non-Noxious Species: " ,
toString(EcologicalSiteId))) +
theme(axis.title.y = element_blank() , axis.text.y = element_blank() ,
axis.ticks.y = element_blank() , axis.line.y = element_blank() ,
axis.title.x = element_blank()) +
theme(panel.grid.major.y = element_blank() , legend.position = "none") +
coord_flip() +
facet_grid(rows = vars(Noxious) , switch = "y" , scales = "free" ,
drop = TRUE)
return(Plots)
}
if(!Interactive){
Plots <- Species_plots_ecosite
filter(!is.na(Noxious))
ggplot((aes(x = Noxious , y = AH_SpeciesCover))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15 , size = 1.25 , aes(color = Noxious)) +
scale_color_manual(values = NoxNonPal_Dot) +
theme_light() +
scale_y_continuous(limits = c(0 , 100)) +
labs(y = "Percent Cover") +
ggtitle(paste("Percent Cover, Noxious vs. Non-Noxious Species: " ,
toString(EcologicalSiteId))) +
theme(axis.title.y = element_blank() , axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank() ,
panel.grid.major.y = element_blank() ,
legend.position = "none") +
coord_flip() +
facet_grid(rows = vars(Noxious) ,
switch = "y" , scales = "free" , drop = TRUE)
}}
if(SummaryVar == "Species"){
PercentCover <- Species_plots_ecosite
if(Interactive){
Plots <-lapply(X = split(PercentCover, list(PercentCover$GrowthHabitSub , PercentCover$Duration) , drop = TRUE),
FUN = function(PercentCover){
current_plot <- ggplot(PercentCover , aes(x = Species , y = AH_SpeciesCover,
text = paste("PrimaryKey: ", PrimaryKey ,
"Plot ID: " , PlotID , "Species: " ,
ScientificName , "Code: " , Species ,
"Percent Cover: " , AH_SpeciesCover , "Noxious: " ,
Noxious , sep = "<br>"))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15 , size = 1, shape = 21) +
scale_y_continuous(limits = c(0 , 100)) +
theme_light() +
labs(y = "Percent Cover") +
ggtitle(paste("Percent Cover by Species, " ,
PercentCover$GrowthHabitSub,
PercentCover$Duration ,
toString(EcologicalSiteId))) +
theme(axis.title.y = element_blank() ,
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
axis.title.x = element_blank())+
theme(panel.grid.major.y = element_blank() ,
axis.title.y = element_blank()) +
coord_flip() + facet_grid(rows = vars(Species),
scales = "free" , switch = "y", drop = TRUE)
return(current_plot)
})
}
if(!Interactive){
Plots <- lapply(X = split(PercentCover, list(PercentCover$GrowthHabitSub ,
PercentCover$Duration) ,
drop = TRUE),
FUN = function(PercentCover){
current_plot <- ggplot(PercentCover , aes(x = Species , y = AH_SpeciesCover)) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15 , size = 1 , aes(color = Noxious)) +
scale_color_manual(values = NoxNonPal_Dot) + scale_y_continuous(limits = c(0 , 100)) +
theme_light() +
labs(y = "Percent Cover") +
ggtitle(paste("Percent Cover by Species, " ,
PercentCover$GrowthHabitSub ,
PercentCover$Duration ,
toString(EcologicalSiteId))) +
theme(axis.title.y = element_blank()) +
coord_flip() + facet_grid(cols = vars(GrowthHabitSub) , rows = vars(Duration) ,
switch = "y" , scales = "free" , drop = TRUE)
return(current_plot)
})
}
}
if(SummaryVar == "GroundCover"){
#Prep
#BareSoilCover
#TotalFoliarCover
#FH_TotalLitterCover
#FH_RockCover
Ground_Cover_Tall <- EcoSitePlots
dplyr::select(PlotID, PrimaryKey, BareSoilCover ,
TotalFoliarCover , FH_TotalLitterCover ,
FH_RockCover)
gather(key = Indicator , value = Percent,
BareSoilCover:FH_RockCover)
if(Interactive){
Plots <- Ground_Cover_Tall
ggplot((aes(x = Indicator , y = Percent ,
text = paste("PlotID: " , PlotID ,
"PrimaryKey: " , PrimaryKey ,
"Indicator: " , Indicator ,
"Percent Cover: " , Percent ,
sep = "<br>" )))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15 , shape = 21) +
theme_light() +
scale_y_continuous(limits = c(0 , 100)) +
labs(y = "Ground Cover (
theme(axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank() ,
axis.title.x = element_blank() ,
axis.title.y = element_blank()) +
coord_flip() + facet_grid(rows = vars(Indicator) ,
switch = "y" ,
scales = "free_y" , drop = TRUE)
}
if(!Interactive){
Plots <- Ground_Cover_Tall
ggplot((aes(x = Indicator , y = Percent))) +
geom_boxplot(width = .6 , outlier.shape = NA) +
geom_jitter(width = .15) +
theme_light() +
scale_y_continuous(limits = c(0 , 100)) +
labs(y = "Ground Cover (
theme(axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank()) +
coord_flip() + facet_grid(rows = vars(Indicator) ,
switch = "y" ,
scales = "free_y" , drop = TRUE)
}
}
if(SummaryVar == "Gap"){
Gap <- EcoSitePlots
GapCover_25_50 , GapCover_51_100 ,
GapCover_101_200 , GapCover_200_plus ,
GapCover_25_plus)
gather(key = Gap_Class_cm ,
value = Percent , GapCover_25_50:GapCover_25_plus)
mutate_if(is.numeric , round, digits = 2)
#Plot prep
if(Interactive){
Plots <- ggplot(data = Gap , aes(x = Gap_Class_cm , y = Percent ,
text = paste("PlotID: " , PlotID ,
"PrimaryKey: ", PrimaryKey ,
"Gap Class (cm): " , Gap_Class_cm,
"Percent Cover: " , Percent ,
sep = "<br>"))) +
geom_boxplot() + coord_flip() +
geom_jitter(width = 0.1 , shape = 21) +
theme_light() +
theme(axis.title.x = element_blank() ,
axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.title.y = element_blank() ,
axis.line.y = element_blank(),
panel.grid.major.y = element_blank()) +
facet_grid(rows = vars(Gap_Class_cm) , switch = "y" ,
scales = "free_y" , drop = TRUE)
}
if(!Interactive){
Plots <- ggplot(data = Gap , aes(x = Gap_Class_cm , y = Percent)) +
labs(y = "Percent Cover" , x = "Gap Size Class (cm)",
caption = paste("Percent cover of canopy gap in: ",
toString(EcologicalSiteId))) +
geom_boxplot() +
coord_flip() +
geom_jitter(width = 0.1) +
theme_light() +
theme(axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank(),
panel.grid.major.y = element_blank()) +
facet_grid(rows = vars(Gap_Class_cm) , switch = "y" ,
scales = "free_y" , drop = TRUE)
}
}
if(SummaryVar == "SoilStability"){
soil_labels <- c("SoilStability_All" = "All" , "SoilStability_Protected" = "Protected" ,
"SoilStability_Unprotected" = "Unprotected")
SoilStability <- EcoSitePlots
SoilStability_All ,
SoilStability_Protected ,
SoilStability_Unprotected)
gather(key = Veg , value = Rating ,
SoilStability_All:SoilStability_Unprotected)
mutate_if(is.numeric, round, digits = 2)
if(Interactive){
Plots <- ggplot(data = SoilStability ,
aes(x = Veg , y = Rating ,
text = paste("Primary Key: " , PrimaryKey,
"Plot ID: " , PlotID ,
"Rating: " , Rating ,
sep = "<br>"))) +
geom_boxplot() +
coord_flip() +
geom_jitter(width = 0.1 , shape = 21) +
theme_light() +
theme(axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank(),
panel.grid.major.y = element_blank(),
axis.title = element_blank()) +
facet_grid(rows = vars(Veg) , switch = "y" ,
scales = "free_y" , drop = TRUE ,
labeller = as_labeller(soil_labels))
}
if(!Interactive){
Plots <- ggplot(data = SoilStability ,
aes(x = Veg , y = Rating)) +
labs(x = "Vegetation cover class" ,
y = "Soil Stability Rating",
caption = paste("Soil stability ratings in: ",
toString(EcologicalSiteId))) +
geom_boxplot() + coord_flip() + geom_jitter(width = 0.1) +
theme_light() +
theme(axis.text.y = element_blank() ,
axis.ticks.y = element_blank() ,
axis.line.y = element_blank(),
panel.grid.major.y = element_blank()) +
facet_grid(rows = vars(Veg) ,
switch = "y" ,
scales = "free_y" ,
drop = TRUE ,
labeller = as_labeller(soil_labels))
}
}
return(Plots)
}
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.