Create an Object of Class 'stcs'
stcs.RdThis function creates object of class 'stcs' from a data frame. This is the primary format for long (database style) data sets in the mefa package. The 'stcs' object can be converted into an object of class 'mefa' with the function mefa. The function name 'stcs' refers to first letters of column names of the resulting object: samples, taxa, counts, segments.
Usage
stcs(dframe, expand = FALSE, drop.zero = FALSE, zero.pseudo = "zero.pseudo")
# S3 method for stcs
is(x)
# S3 method for stcs
summary(object, ...)Arguments
- dframe
a data frame with 2-4 columns. If 2 columns are provided, it is assumed that first column contains sample, while second taxa names. If 3 columns are provided, the first two is treated as sample and taxa names, while the third is treated as count if numeric (either integer or non-integer values can be supplied), and segment if character or factor. If 4 columns are provided, those are assumed to be in the samples, taxa, count, segment order.
- expand
logical, whether the object should be (
TRUE) expanded (via the functionrep.data.frame) or not (FALSE, default). If expanded, each rows correspond to one individual observation (value of thecountcolumn is 1) or a zero sample.expand = TRUEworks only with integer values.- drop.zero
logical, whether samples with zero total count should be left out (
TRUE) or not (FALSE, default).- zero.pseudo
character, value in the
taxacolumn that indicates zero samples. If it is a vector of length 2, first element is used for taxa names, second for segment names to indicate zero samples.- x, object
an object of class 'stcs'.
- ...
further arguments passed to the function
stcs.
Details
If the data are in a long (database style) format, the stcs function prepares the ground for the mefa function to make the cross tabulation. But if only a crosstabulated matrix is needed, the table function can be applies as well (in this case be sure to set expand = TRUE, and this is only for integer data), or alternatively see the xtabs or mefaCrosstab functions (these accepts non-integer data). For subsetting, simply use extraction methods available for data frames ([.data.frame).
The summary contains statistics calculated after coercing the object into the class 'mefa'.
Methods for extracting, subsetting are the same as for data frame objects. Plotting 'stcs' objects are discussed elsewhere (see links in 'See also' section).
Value
Returns an object of class 'stcs' with 4 columns. The column names are converted consistently into samp for samples, taxa for taxa names, count for counts and segm for segment names.
The class has its own methods (i.e. is, as.stcs, summary and plot), but also has a data.frame class attribute. Thus other methods that available for data frames are applicable to an object of class 'stcs' (e.g. print, str).
References
S\'olymos P. (2008) mefa: an R package for handling and reporting count data. Community Ecology 9, 125--127.
S\'olymos P. (2009) Processing ecological data in R with the mefa package. Journal of Statistical Software 29(8), 1--28. doi:10.18637/jss.v029.i08
Author
P\'eter S\'olymos, solymos@ualberta.ca
Note
The stcs function nearly equivalent to the sscount function in older (< 2.0) versions of the mefa package.
See also
data.frame, summary.data.frame, str, table
See plot.stcs boxplot.stcs and image.stcs for graphical display options.
See as.stcs for coercion methods.
Examples
## General long format data
x <- data.frame(
sample = paste("Sample", c(1,1,2,2,3,4), sep="."),
species = c(paste("Species", c(1,1,1,2,3), sep="."), "zero.pseudo"),
count = c(1,2,10,3,4,0),
segment = letters[c(6,13,6,13,6,6)])
x
#> sample species count segment
#> 1 Sample.1 Species.1 1 f
#> 2 Sample.1 Species.1 2 m
#> 3 Sample.2 Species.1 10 f
#> 4 Sample.2 Species.2 3 m
#> 5 Sample.3 Species.3 4 f
#> 6 Sample.4 zero.pseudo 0 f
## Long format as stcs
y <- stcs(x)
y
#> samp taxa count segm
#> 1 Sample.1 Species.1 1 f
#> 2 Sample.1 Species.1 2 m
#> 3 Sample.2 Species.1 10 f
#> 4 Sample.2 Species.2 3 m
#> 5 Sample.3 Species.3 4 f
#> 6 Sample.4 zero.pseudo 0 zero.pseudo
## Methods
as.stcs(x)
#> samp taxa count segm
#> 1 Sample.1 Species.1 1 f
#> 2 Sample.1 Species.1 2 m
#> 3 Sample.2 Species.1 10 f
#> 4 Sample.2 Species.2 3 m
#> 5 Sample.3 Species.3 4 f
#> 6 Sample.4 zero.pseudo 0 zero.pseudo
is(y, "stcs")
#> [1] TRUE
is(y, "data.frame")
#> [1] TRUE
## Effects of arguments
stcs(x, expand = TRUE)
#> samp taxa count segm
#> 1 Sample.1 Species.1 1 f
#> 2 Sample.1 Species.1 1 m
#> 3 Sample.1 Species.1 1 m
#> 4 Sample.2 Species.1 1 f
#> 5 Sample.2 Species.1 1 f
#> 6 Sample.2 Species.1 1 f
#> 7 Sample.2 Species.1 1 f
#> 8 Sample.2 Species.1 1 f
#> 9 Sample.2 Species.1 1 f
#> 10 Sample.2 Species.1 1 f
#> 11 Sample.2 Species.1 1 f
#> 12 Sample.2 Species.1 1 f
#> 13 Sample.2 Species.1 1 f
#> 14 Sample.2 Species.2 1 m
#> 15 Sample.2 Species.2 1 m
#> 16 Sample.2 Species.2 1 m
#> 17 Sample.3 Species.3 1 f
#> 18 Sample.3 Species.3 1 f
#> 19 Sample.3 Species.3 1 f
#> 20 Sample.3 Species.3 1 f
#> 21 Sample.4 zero.pseudo 0 zero.pseudo
stcs(x, drop.zero = TRUE)
#> samp taxa count segm
#> 1 Sample.1 Species.1 1 f
#> 2 Sample.1 Species.1 2 m
#> 3 Sample.2 Species.1 10 f
#> 4 Sample.2 Species.2 3 m
#> 5 Sample.3 Species.3 4 f
stcs(x, zero.pseudo = "pseudo.secies")
#> samp taxa count segm
#> 1 Sample.1 Species.1 1 f
#> 2 Sample.1 Species.1 2 m
#> 3 Sample.2 Species.1 10 f
#> 4 Sample.2 Species.2 3 m
#> 5 Sample.3 Species.3 4 f
#> 6 Sample.4 pseudo.secies 0 pseudo.secies
## Input options
stcs(x[,1:2])
#> samp taxa count segm
#> 1 Sample.1 Species.1 1 undefined
#> 2 Sample.1 Species.1 1 undefined
#> 3 Sample.2 Species.1 1 undefined
#> 4 Sample.2 Species.2 1 undefined
#> 5 Sample.3 Species.3 1 undefined
#> 6 Sample.4 zero.pseudo 1 undefined
stcs(x[,1:3])
#> samp taxa count segm
#> 1 Sample.1 Species.1 1 undefined
#> 2 Sample.1 Species.1 2 undefined
#> 3 Sample.2 Species.1 10 undefined
#> 4 Sample.2 Species.2 3 undefined
#> 5 Sample.3 Species.3 4 undefined
#> 6 Sample.4 zero.pseudo 0 zero.pseudo
stcs(x[,c(1:2,4)])
#> samp taxa count segm
#> 1 Sample.1 Species.1 1 f
#> 2 Sample.1 Species.1 1 m
#> 3 Sample.2 Species.1 1 f
#> 4 Sample.2 Species.2 1 m
#> 5 Sample.3 Species.3 1 f
#> 6 Sample.4 zero.pseudo 1 f
## The Dolina dataset
data(dol.count)
dol <- stcs(dol.count)
dol
#> samp taxa count segm
#> 1 DQ1 amin 2 fresh
#> 2 DQ1 amin 2 broken
#> 3 DQ1 ctri 2 fresh
#> 4 DQ1 dper 2 fresh
#> 5 DQ1 estr 1 fresh
#> 6 DQ1 vidi 2 broken
#> 7 DQ1 vidi 7 fresh
#> 8 DQ2 amin 1 broken
#> 9 DQ2 amin 3 fresh
#> 10 DQ2 apur 1 broken
#> 11 DQ2 ctri 7 broken
#> 12 DQ2 ctri 13 fresh
#> 13 DQ2 dper 1 fresh
#> 14 DQ2 dper 1 broken
#> 15 DQ2 druf 1 fresh
#> 16 DQ2 druf 1 broken
#> 17 DQ2 ppyg 1 broken
#> 18 DQ2 vidi 4 broken
#> 19 DQ2 vidi 5 fresh
#> 20 DQ3 amin 1 broken
#> 21 DQ3 amin 2 fresh
#> 22 DQ3 apur 1 fresh
#> 23 DQ3 hobv 3 broken
#> 24 DQ3 vidi 2 broken
#> 25 DT1 amin 1 fresh
#> 26 DT1 bcan 1 broken
#> 27 DT1 dper 1 fresh
#> 28 DT1 estr 1 broken
#> 29 DT1 hobv 1 fresh
#> 30 DT1 mbor 5 fresh
#> 31 DT1 pvic 1 fresh
#> 32 DT2 amin 1 fresh
#> 33 DT2 amin 1 fresh
#> 34 DT2 apur 1 fresh
#> 35 DT2 bbip 1 fresh
#> 36 DT2 clam 2 fresh
#> 37 DT2 dper 1 fresh
#> 38 DT2 druf 1 fresh
#> 39 DT2 estr 1 broken
#> 40 DT2 hobv 1 fresh
#> 41 DT2 tuni 1 fresh
#> 42 DT2 vidi 2 fresh
#> 43 DT3 amin 1 fresh
#> 44 DT3 amin 2 fresh
#> 45 DT3 bbip 1 broken
#> 46 DT3 hobv 1 fresh
#> 47 DT3 hobv 1 broken
#> 48 DT3 hobv 4 fresh
#> 49 DT3 pvic 1 fresh
#> 50 DT3 vidi 2 fresh
#> 51 LQ1 aacu 1 fresh
#> 52 LQ1 amin 1 broken
#> 53 LQ1 amin 2 fresh
#> 54 LQ1 dper 1 broken
#> 55 LQ1 ffau 1 broken
#> 56 LQ1 ppyg 13 fresh
#> 57 LQ1 ppyg 15 broken
#> 58 LQ2 aacu 1 fresh
#> 59 LQ2 amin 1 broken
#> 60 LQ2 dper 1 fresh
#> 61 LQ2 ppyg 5 fresh
#> 62 LQ2 ppyg 8 broken
#> 63 LQ2 pvic 1 broken
#> 64 LQ3 amin 2 broken
#> 65 LQ3 apur 1 fresh
#> 66 LQ3 bbip 1 broken
#> 67 LQ3 ccer 1 broken
#> 68 LQ3 dper 1 fresh
#> 69 LQ3 dper 1 broken
#> 70 LQ3 dper 2 fresh
#> 71 LQ3 dper 3 fresh
#> 72 LQ3 ppyg 1 fresh
#> 73 LQ3 ppyg 10 fresh
#> 74 LQ3 ppyg 16 broken
#> 75 LQ3 ppyg 17 broken
#> 76 LQ3 ppyg 25 fresh
#> 77 LQ3 pvic 1 broken
#> 78 LT1 zero.pseudo 0 zero.pseudo
#> 79 LT2 amin 1 fresh
#> 80 LT2 pvic 1 broken
#> 81 LT3 amin 1 fresh
#> 82 LT3 amin 1 fresh
#> 83 LT3 amin 3 fresh
#> 84 LT3 dper 1 fresh
#> 85 LT3 pinc 1 fresh
#> 86 LT3 pvic 1 fresh
#> 87 LT3 tuni 1 fresh
#> 88 LT3 tuni 1 broken
#> 89 RQ1 amin 1 fresh
#> 90 RQ1 amin 1 fresh
#> 91 RQ1 amin 1 broken
#> 92 RQ1 ccer 1 broken
#> 93 RQ1 clam 1 fresh
#> 94 RQ1 cort 1 fresh
#> 95 RQ1 dper 1 fresh
#> 96 RQ1 dper 1 fresh
#> 97 RQ1 dper 1 broken
#> 98 RQ1 ffau 1 broken
#> 99 RQ1 ffau 1 broken
#> 100 RQ1 hobv 1 fresh
#> 101 RQ1 hobv 1 fresh
#> 102 RQ1 ogla 1 broken
#> 103 RQ1 ppyg 1 fresh
#> 104 RQ1 ppyg 1 fresh
#> 105 RQ1 ppyg 1 broken
#> 106 RQ1 ppyg 2 fresh
#> 107 RQ1 vidi 1 fresh
#> 108 RQ1 vidi 1 broken
#> 109 RQ1 vidi 1 broken
#> 110 RQ1 vidi 1 broken
#> 111 RQ2 amin 1 fresh
#> 112 RQ2 amin 6 fresh
#> 113 RQ2 bbip 1 fresh
#> 114 RQ2 bbip 1 fresh
#> 115 RQ2 bbip 1 broken
#> 116 RQ2 bbip 1 broken
#> 117 RQ2 ctri 1 fresh
#> 118 RQ2 ctri 1 broken
#> 119 RQ2 ctri 2 broken
#> 120 RQ2 ctri 3 fresh
#> 121 RQ2 dbre 1 broken
#> 122 RQ2 dper 1 fresh
#> 123 RQ2 dper 1 fresh
#> 124 RQ2 dper 1 broken
#> 125 RQ2 dper 1 broken
#> 126 RQ2 dper 2 fresh
#> 127 RQ2 estr 3 fresh
#> 128 RQ2 ffau 1 fresh
#> 129 RQ2 ffau 1 broken
#> 130 RQ2 hobv 9 fresh
#> 131 RQ2 mobs 2 fresh
#> 132 RQ2 odol 4 broken
#> 133 RQ2 odol 9 fresh
#> 134 RQ2 ogla 1 broken
#> 135 RQ2 ogla 2 fresh
#> 136 RQ2 ppyg 9 broken
#> 137 RQ2 ppyg 19 fresh
#> 138 RQ2 pvic 1 broken
#> 139 RQ2 tuni 2 fresh
#> 140 RQ2 vcos 2 fresh
#> 141 RQ2 vidi 1 fresh
#> 142 RQ2 vidi 3 fresh
#> 143 RQ2 vidi 3 fresh
#> 144 RQ3 aacu 2 broken
#> 145 RQ3 amin 2 broken
#> 146 RQ3 amin 3 fresh
#> 147 RQ3 amin 4 fresh
#> 148 RQ3 amin 4 broken
#> 149 RQ3 bbip 1 broken
#> 150 RQ3 ctri 1 fresh
#> 151 RQ3 ctri 2 broken
#> 152 RQ3 ctri 7 fresh
#> 153 RQ3 dbre 1 fresh
#> 154 RQ3 dbre 2 fresh
#> 155 RQ3 dper 1 fresh
#> 156 RQ3 dper 1 broken
#> 157 RQ3 dper 2 fresh
#> 158 RQ3 dper 2 broken
#> 159 RQ3 eful 1 fresh
#> 160 RQ3 eful 1 broken
#> 161 RQ3 ffau 1 broken
#> 162 RQ3 ffau 1 broken
#> 163 RQ3 hobv 1 fresh
#> 164 RQ3 hobv 1 broken
#> 165 RQ3 mobs 1 broken
#> 166 RQ3 ppyg 1 fresh
#> 167 RQ3 ppyg 1 broken
#> 168 RQ3 ppyg 3 fresh
#> 169 RQ3 ppyg 4 broken
#> 170 RQ3 pvic 1 broken
#> 171 RQ3 vidi 1 fresh
#> 172 RQ3 vidi 1 broken
#> 173 RQ3 vidi 1 broken
#> 174 RQ3 vidi 2 broken
#> 175 RQ3 vidi 6 fresh
#> 176 RT1 amin 1 fresh
#> 177 RT1 amin 3 broken
#> 178 RT1 bbip 3 broken
#> 179 RT1 ccer 1 fresh
#> 180 RT1 ccer 1 broken
#> 181 RT1 cort 1 broken
#> 182 RT1 dper 1 fresh
#> 183 RT1 ffau 2 fresh
#> 184 RT1 ffau 5 broken
#> 185 RT1 hobv 1 fresh
#> 186 RT1 hobv 7 broken
#> 187 RT1 iiso 6 broken
#> 188 RT1 pinc 1 fresh
#> 189 RT1 pinc 2 broken
#> 190 RT1 pvic 1 fresh
#> 191 RT1 pvic 3 broken
#> 192 RT1 tuni 1 fresh
#> 193 RT1 tuni 4 broken
#> 194 RT2 amin 1 broken
#> 195 RT2 apur 2 broken
#> 196 RT2 bbip 1 fresh
#> 197 RT2 bbip 2 broken
#> 198 RT2 bcan 1 broken
#> 199 RT2 cort 1 broken
#> 200 RT2 ctri 1 fresh
#> 201 RT2 dper 1 fresh
#> 202 RT2 dper 1 fresh
#> 203 RT2 estr 1 fresh
#> 204 RT2 estr 3 broken
#> 205 RT2 ffau 1 fresh
#> 206 RT2 ffau 5 broken
#> 207 RT2 ffau 6 broken
#> 208 RT2 hobv 1 broken
#> 209 RT2 iiso 4 broken
#> 210 RT2 iiso 4 broken
#> 211 RT2 pinc 1 fresh
#> 212 RT2 pinc 1 broken
#> 213 RT2 pinc 3 broken
#> 214 RT2 pvic 1 broken
#> 215 RT2 tuni 1 fresh
#> 216 RT2 tuni 2 broken
#> 217 RT2 vidi 1 fresh
#> 218 RT2 vidi 1 broken
#> 219 RT3 amin 1 broken
#> 220 RT3 amin 4 fresh
#> 221 RT3 apur 1 broken
#> 222 RT3 bbip 5 fresh
#> 223 RT3 clam 1 broken
#> 224 RT3 ffau 1 fresh
#> 225 RT3 ffau 2 fresh
#> 226 RT3 ffau 3 broken
#> 227 RT3 hobv 1 fresh
#> 228 RT3 hobv 1 broken
#> 229 RT3 hobv 2 fresh
#> 230 RT3 iiso 1 fresh
#> 231 RT3 pinc 3 broken
#> 232 RT3 pvic 1 fresh
#> 233 RT3 pvic 2 broken
#> 234 RT3 tuni 1 broken
#> 235 WQ1 amin 1 fresh
#> 236 WQ1 amin 1 fresh
#> 237 WQ1 amin 1 broken
#> 238 WQ1 bbip 1 broken
#> 239 WQ1 bcan 1 broken
#> 240 WQ1 cort 1 broken
#> 241 WQ1 cort 2 broken
#> 242 WQ1 iiso 1 fresh
#> 243 WQ1 iiso 1 fresh
#> 244 WQ1 pinc 1 fresh
#> 245 WQ1 pinc 1 fresh
#> 246 WQ1 ppyg 1 broken
#> 247 WQ1 ppyg 2 broken
#> 248 WQ1 ppyg 4 fresh
#> 249 WQ1 ppyg 7 fresh
#> 250 WQ1 ppyg 17 broken
#> 251 WQ1 pvic 1 broken
#> 252 WQ1 vidi 1 fresh
#> 253 WQ1 vidi 1 fresh
#> 254 WQ1 vidi 1 broken
#> 255 WQ1 vidi 1 broken
#> 256 WQ2 amin 1 fresh
#> 257 WQ2 amin 1 broken
#> 258 WQ2 amin 2 broken
#> 259 WQ2 bbip 1 broken
#> 260 WQ2 ccer 1 fresh
#> 261 WQ2 dper 1 fresh
#> 262 WQ2 dper 1 broken
#> 263 WQ2 dper 2 fresh
#> 264 WQ2 dper 4 broken
#> 265 WQ2 dper 12 fresh
#> 266 WQ2 estr 2 broken
#> 267 WQ2 mobs 2 broken
#> 268 WQ2 pinc 1 fresh
#> 269 WQ2 ppyg 3 broken
#> 270 WQ2 ppyg 5 fresh
#> 271 WQ2 ppyg 22 fresh
#> 272 WQ2 ppyg 26 broken
#> 273 WQ2 pvic 1 fresh
#> 274 WQ2 tuni 2 fresh
#> 275 WQ3 amin 3 broken
#> 276 WQ3 amin 7 fresh
#> 277 WQ3 bbip 1 broken
#> 278 WQ3 bbip 2 fresh
#> 279 WQ3 estr 1 broken
#> 280 WQ3 ffau 2 broken
#> 281 WQ3 pinc 1 fresh
#> 282 WQ3 ppyg 2 broken
#> 283 WQ3 ppyg 3 fresh
#> 284 WQ3 vicr 1 fresh
#> 285 WQ3 vidi 1 broken
#> 286 WT1 amin 1 broken
#> 287 WT1 cort 1 fresh
#> 288 WT1 estr 1 broken
#> 289 WT1 ffau 1 fresh
#> 290 WT1 tuni 1 fresh
#> 291 WT2 amin 2 fresh
#> 292 WT2 apur 1 fresh
#> 293 WT2 bbip 1 broken
#> 294 WT2 dper 2 fresh
#> 295 WT3 amin 4 broken
#> 296 WT3 ffau 1 broken
#> 297 WT3 vidi 1 fresh
plot(dol)
