Compute germination indices from a data frame of germination counts recorded at specific time intervals for multiple samples in batch.
germination.indices(
data,
total.seeds.col,
counts.intervals.cols,
intervals,
partial = TRUE,
PeakGermPercent = TRUE,
FirstGermTime = TRUE,
LastGermTime = TRUE,
PeakGermTime = TRUE,
TimeSpreadGerm = TRUE,
t50 = TRUE,
MeanGermTime = TRUE,
VarGermTime = TRUE,
SEGermTime = TRUE,
CVGermTime = TRUE,
MeanGermRate = TRUE,
CVG = TRUE,
VarGermRate = TRUE,
SEGermRate = TRUE,
GermRateRecip = TRUE,
GermSpeed = TRUE,
GermSpeedAccumulated = TRUE,
GermSpeedCorrected = TRUE,
WeightGermPercent = TRUE,
MeanGermPercent = TRUE,
MeanGermNumber = TRUE,
TimsonsIndex = TRUE,
GermRateGeorge = TRUE,
max.int,
GermIndex = TRUE,
EmergenceRateIndex = TRUE,
PeakValue = TRUE,
GermValue = TRUE,
gv.k = 10,
CUGerm = TRUE,
GermSynchrony = TRUE,
GermUncertainty = TRUE
)A data frame with the germination count data. It should possess columns with
Partial or cumulative germination counts per
time interval (to be indicated by the argument counts.intervals.cols
and
Total number of seeds tested (to be indicated by the argument
total.seeds.col).
The name of the column in data with the total
number of seeds tested.
The names of columns in data with the
germination counts (partial or cumulative, as indicated by the argument
partial) per time interval (indicated by the argument
intervals).
The time intervals at which germination counts (in the
columns specified in argument counts.intervals.cols) were recorded.
logical. If TRUE, germination counts in
counts.intervals.cols is considered as partial and if FALSE,
it is considered as cumulative. Default is TRUE.
logical. If TRUE, then the Peak germination
percentage
(Vallance 1950; Roh et al. 2004)
is
computed. Default is TRUE.
logical. If TRUE, the Time of first germination
or Germination time lag (\(t_{0}\))
(Edwards 1932; Czabator 1962; Goloff and Bazzaz 1975; Labouriau 1983; Ranal 1999; Quintanilla et al. 2000)
is computed. Default is TRUE.
logical. If TRUE, the Time of last germination
(\(t_{g}\))
(Edwards 1932; Labouriau 1983; Ranal and de Santana 2006)
.
is computed. Default is TRUE.
logical. If TRUE, the Peak time of germination or
Modal time of germination (Ranal and de Santana 2006)
is computed. Default is TRUE.
logical. If TRUE, the Time spread of germination
(Al-Mudaris 1998; Kader 2005)
or Germination distribution
(Schrader and Graves 2000)
. is computed. Default
is TRUE.
logical. If TRUE, the Median germination time
(\(t_{50}\))
(Coolbear et al. 1984; Farooq et al. 2005)
is computed. Default is TRUE.
logical. If TRUE, the Mean germination time
(\(\overline{T}\)) or Mean length of incubation time
(Edmond and Drapala 1958; Czabator 1962; Ellis and Roberts 1980; Labouriau 1983; Ranal and de Santana 2006)
.
or Sprouting index (\(SI\))
(Smith and Millet 1964)
or Germination
Resistance (\(GR\))
Gordon (1969, 1971)
is computed. Default is TRUE.
logical. If TRUE, the Variance of germination time
(\(s_{T}^{2}\))
(Labouriau 1983; Ranal and de Santana 2006)
is computed. Default is TRUE.
logical. If TRUE, the Standard error of germination
time (\(s_{\overline{T}}\))
(Labouriau 1983; Ranal and de Santana 2006)
.
is computed. Default is TRUE.
logical. If TRUE, the Coefficient of variation of
the germination time (\(CV_{T}\))
(Ranal and de Santana 2006)
is computed. Default is
TRUE.
logical. If TRUE, the Mean germination rate
(\(\overline{V}\))
(Labouriau and Valadares 1976; Labouriau 1983; Ranal and de Santana 2006)
.
is computed. Default is TRUE.
logical. If TRUE, the Coefficient of velocity/rate of
germination or Kotowski's coefficient of velocity (\(CVG\))
(Kotowski 1926; Nichols and Heydecker 1968; Labouriau 1983; Scott et al. 1984; Bewley and Black 1994)
.
is computed. Default is TRUE.
logical. If TRUE, the Variance of germination rate
(\(s_{V}^{2}\))
(Labouriau 1983; Ranal and de Santana 2006)
is
computed. Default is TRUE.
logical. If TRUE, the Standard error of germination
rate (\(s_{\overline{V}}\))
(Labouriau 1983; Ranal and de Santana 2006)
is
computed. Default is TRUE.
logical. If TRUE, the Germination rate as
reciprocal of median time (\(v_{50}\))
(Went 1957; Labouriau 1983; Ranal and de Santana 2006)
is computed.
logical. If TRUE, the Speed of germination or
Germination rate index or Index of velocity of germination or Germination
index or Emergence rate index
(Throneberry and Smith 1955; Maguire 1962; Allan et al. 1962; Kendrick and Frankland 1969; Bouton et al. 1976; AOSA 1983; Khandakar and Bradbeer 1983; Bradbeer 1988; Wardle et al. 1991)
considering both counts and percentages is computed.
logical. If TRUE, the Speed of accumulated
germination
(Bradbeer 1988; Wardle et al. 1991; Haugland and Brandsaeter 1996; de Santana and Ranal 2004)
considering both counts and percentages is computed.
logical. If TRUE, the Corrected speed of
germination or Corrected germination rate index and the Corrected speed of
accumulated germination
(Evetts and Burnside 1972)
is computed.
logical. If TRUE, the Weighted germination
percentage \(WGP\) or Weighted germination index \(WGI\)
(Reddy 1978; Reddy et al. 1985)
is
computed.
logical. If TRUE, the Mean/average germination
percentage per unit time (\(\overline{GP}\))
(Czabator 1962)
is computed.
logical. If TRUE, the Number of seeds germinated
per unit time (\(\overline{N}\))
(Khamassi et al. 2013)
is computed.
logical. If TRUE, the Timson's index or Timson's
germination velocity index
(Grose and Zimmer 1958; Timson 1965; Brown and Mayer 1988; Baskin and Baskin 1998)
and it's modifications by Labouriau
(Ranal and de Santana 2006)
and
(Khan and Ungar 1984)
is computed.
logical. If TRUE, the George's index
George (1961)
is computed.
The maximum interval value up to which Timson's index/George's germination rate is to be computed.
logical. If TRUE, the Germination index according to
Melville et al. (1980)
and its modification by
de Santana and Ranal (2004)
(Ranal and de Santana 2006)
are computed.
logical. If TRUE, the Emergence rate index
or Germination rate index are computed according to
Shmueli and Goldberg (1971) and it's modification by de Santana and Ranal (2004) (Ranal and de Santana 2006) ;
Bilbro and Wanjura (1982) ; and
Fakorede and Ayoola (1980) , Fakorede and Ojo (1981) , and Fakorede and Agbana (1983) .
logical. If TRUE, the Peak value (\(PV\)) or
Emergence Energy (\(EE\))
(Czabator 1962; Bonner 1967)
is computed.
logical. If TRUE, the Germination value
(Czabator 1962; Djavanshir and Pourbeik 1976)
and its modification considering duration from start of test instead of
from onset of germination
(Brown and Mayer 1988)
is computed.
The k Constant for computation of germination value. Default is 10.
logical. If TRUE, the Coefficient of uniformity of
germination (CUG)
(Heydecker 1972; Bewley and Black 1994)
is
computed.
logical. If TRUE, the Synchrony of germination
(\(Z\) index)
(Primack 1985; Ranal and de Santana 2006)
is
computed.
logical. If TRUE, the Synchronization index
(\(\overline{E}\)) or Uncertainty of the germination process
(\(U\)) or Informational entropy (\(H\))
(Shannon 1948; Labouriau and Valadares 1976; Labouriau 1983)
is computed.
A data frame with the original data along with the various single-value germination indices specified in the function arguments.
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This function is a wrapper around the different functions for
computation of single-value germination indices in
germinationmetrics
(PeakGermPercent,
FirstGermTime,
LastGermTime,
PeakGermTime,
TimeSpreadGerm,
t50,
MeanGermTime,
VarGermTime,
SEGermTime,
CVGermTime,
MeanGermRate,
CVG,
VarGermRate,
SEGermRate,
GermRateRecip,
GermSpeed,
GermSpeedAccumulated,
GermSpeedCorrected,
WeightGermPercent,
MeanGermPercent,
MeanGermPercent,
TimsonsIndex,
GermRateGeorge,
GermIndex,
EmergenceRateIndex,
GermValue,
PeakValue,
CUGerm,
GermSynchrony,
GermUncertainty)
# \donttest{
data(gcdata)
counts.per.intervals <- c("Day01", "Day02", "Day03", "Day04", "Day05",
"Day06", "Day07", "Day08", "Day09", "Day10",
"Day11", "Day12", "Day13", "Day14")
germination.indices(gcdata, total.seeds.col = "Total Seeds",
counts.intervals.cols = counts.per.intervals,
intervals = 1:14, partial = TRUE, max.int = 5)
#> Genotype Rep Day01 Day02 Day03 Day04 Day05 Day06 Day07 Day08 Day09 Day10
#> 1 G1 1 0 0 0 0 4 17 10 7 1 0
#> 2 G2 1 0 0 0 1 3 15 13 6 2 1
#> 3 G3 1 0 0 0 2 3 18 9 8 2 1
#> 4 G4 1 0 0 0 0 4 19 12 6 2 1
#> 5 G5 1 0 0 0 0 5 20 12 8 1 0
#> 6 G1 2 0 0 0 0 3 21 11 7 1 1
#> 7 G2 2 0 0 0 0 4 18 11 7 1 0
#> 8 G3 2 0 0 0 1 3 14 12 6 2 1
#> 9 G4 2 0 0 0 1 3 19 10 8 1 1
#> 10 G5 2 0 0 0 0 4 18 13 6 2 1
#> 11 G1 3 0 0 0 0 5 21 11 8 1 0
#> 12 G2 3 0 0 0 0 3 20 10 7 1 1
#> 13 G3 3 0 0 0 0 4 19 12 8 1 1
#> 14 G4 3 0 0 0 0 3 21 11 6 1 0
#> 15 G5 3 0 0 0 0 4 17 10 8 1 1
#> Day11 Day12 Day13 Day14 Total Seeds GermPercent PeakGermPercent
#> 1 1 0 0 0 50 80.00000 34.00000
#> 2 0 1 0 0 51 82.35294 29.41176
#> 3 1 1 0 0 48 93.75000 37.50000
#> 4 1 1 0 0 51 90.19608 37.25490
#> 5 0 1 1 0 50 96.00000 40.00000
#> 6 1 1 0 0 49 93.87755 42.85714
#> 7 1 0 0 0 48 87.50000 37.50000
#> 8 0 1 0 0 47 85.10638 29.78723
#> 9 1 1 0 0 52 86.53846 36.53846
#> 10 0 1 0 0 50 90.00000 36.00000
#> 11 0 1 1 0 51 94.11765 41.17647
#> 12 1 1 0 0 51 86.27451 39.21569
#> 13 0 1 1 0 49 95.91837 38.77551
#> 14 1 1 0 0 48 91.66667 43.75000
#> 15 1 0 0 0 48 87.50000 35.41667
#> FirstGermTime LastGermTime PeakGermTime TimeSpreadGerm t50_Coolbear
#> 1 5 11 6 6 5.970588
#> 2 4 12 6 8 6.192308
#> 3 4 12 6 8 6.000000
#> 4 5 12 6 7 6.041667
#> 5 5 13 6 8 5.975000
#> 6 5 12 6 7 5.976190
#> 7 5 11 6 6 5.972222
#> 8 4 12 6 8 6.208333
#> 9 4 12 6 8 6.000000
#> 10 5 12 6 7 6.076923
#> 11 5 13 6 8 5.928571
#> 12 5 12 6 7 5.975000
#> 13 5 13 6 8 6.083333
#> 14 5 12 6 7 5.928571
#> 15 5 11 6 6 6.050000
#> t50_Farooq MeanGermTime VarGermTime SEGermTime CVGermTime MeanGermRate
#> 1 5.941176 6.700000 1.446154 0.1901416 0.1794868 0.1492537
#> 2 6.153846 6.857143 2.027875 0.2197333 0.2076717 0.1458333
#> 3 5.972222 6.866667 2.572727 0.2391061 0.2335882 0.1456311
#> 4 6.000000 6.891304 2.187923 0.2180907 0.2146419 0.1451104
#> 5 5.950000 6.812500 2.368351 0.2221275 0.2259002 0.1467890
#> 6 5.952381 6.869565 2.071498 0.2122088 0.2095140 0.1455696
#> 7 5.944444 6.690476 1.389663 0.1818989 0.1761967 0.1494662
#> 8 6.166667 6.875000 2.112179 0.2297923 0.2113940 0.1454545
#> 9 5.973684 6.866667 2.300000 0.2260777 0.2208604 0.1456311
#> 10 6.038462 6.822222 1.831313 0.2017321 0.1983606 0.1465798
#> 11 5.904762 6.791667 2.381206 0.2227295 0.2272072 0.1472393
#> 12 5.950000 6.886364 2.149577 0.2210295 0.2129053 0.1452145
#> 13 6.041667 6.936170 2.539315 0.2324392 0.2297410 0.1441718
#> 14 5.904762 6.772727 1.900634 0.2078370 0.2035568 0.1476510
#> 15 6.000000 6.809524 1.670151 0.1994129 0.1897847 0.1468531
#> VarGermRate SEGermRate CVG GermRateRecip_Coolbear
#> 1 0.0007176543 0.004235724 14.92537 0.1674877
#> 2 0.0009172090 0.004673148 14.58333 0.1614907
#> 3 0.0011572039 0.005071059 14.56311 0.1666667
#> 4 0.0009701218 0.004592342 14.51104 0.1655172
#> 5 0.0010995627 0.004786184 14.67890 0.1673640
#> 6 0.0009301809 0.004496813 14.55696 0.1673307
#> 7 0.0006935558 0.004063648 14.94662 0.1674419
#> 8 0.0009454531 0.004861721 14.54545 0.1610738
#> 9 0.0010345321 0.004794747 14.56311 0.1666667
#> 10 0.0008453940 0.004334343 14.65798 0.1645570
#> 11 0.0011191581 0.004828643 14.72393 0.1686747
#> 12 0.0009558577 0.004660905 14.52145 0.1673640
#> 13 0.0010970785 0.004831366 14.41718 0.1643836
#> 14 0.0009033254 0.004531018 14.76510 0.1686747
#> 15 0.0007767634 0.004300508 14.68531 0.1652893
#> GermRateRecip_Farooq GermSpeed_Count GermSpeed_Percent
#> 1 0.1683168 6.138925 12.27785
#> 2 0.1625000 6.362698 12.47588
#> 3 0.1674419 6.882179 14.33787
#> 4 0.1666667 6.927417 13.58317
#> 5 0.1680672 7.318987 14.63797
#> 6 0.1680000 6.931782 14.14649
#> 7 0.1682243 6.448449 13.43427
#> 8 0.1621622 6.053175 12.87909
#> 9 0.1674009 6.830592 13.13575
#> 10 0.1656051 6.812698 13.62540
#> 11 0.1693548 7.342796 14.39764
#> 12 0.1680672 6.622258 12.98482
#> 13 0.1655172 7.052320 14.39249
#> 14 0.1693548 6.706782 13.97246
#> 15 0.1666667 6.363925 13.25818
#> GermSpeedAccumulated_Count GermSpeedAccumulated_Percent
#> 1 34.61567 69.23134
#> 2 35.54058 69.68741
#> 3 38.29725 79.78594
#> 4 38.68453 75.85202
#> 5 41.00786 82.01571
#> 6 38.77620 79.13509
#> 7 36.38546 75.80304
#> 8 33.77079 71.85275
#> 9 38.11511 73.29829
#> 10 38.19527 76.39054
#> 11 41.17452 80.73436
#> 12 37.00640 72.56158
#> 13 39.29399 80.19182
#> 14 37.69490 78.53103
#> 15 35.69697 74.36868
#> GermSpeedCorrected_Normal GermSpeedCorrected_Accumulated WeightGermPercent
#> 1 0.1534731 0.8653917 47.42857
#> 2 0.1514928 0.8462043 47.89916
#> 3 0.1529373 0.8510501 54.46429
#> 4 0.1505960 0.8409680 52.24090
#> 5 0.1524789 0.8543303 56.14286
#> 6 0.1506909 0.8429608 54.51895
#> 7 0.1535345 0.8663205 51.93452
#> 8 0.1513294 0.8442698 49.39210
#> 9 0.1517909 0.8470024 50.27473
#> 10 0.1513933 0.8487837 52.57143
#> 11 0.1529749 0.8578026 55.18207
#> 12 0.1505059 0.8410547 50.00000
#> 13 0.1500494 0.8360424 55.24781
#> 14 0.1524269 0.8567022 53.86905
#> 15 0.1515220 0.8499278 51.19048
#> MeanGermPercent MeanGermNumber TimsonsIndex TimsonsIndex_Labouriau
#> 1 5.714286 2.857143 8.000000 1.00
#> 2 5.882353 3.000000 9.803922 1.25
#> 3 6.696429 3.214286 14.583333 1.40
#> 4 6.442577 3.285714 7.843137 1.00
#> 5 6.857143 3.428571 10.000000 1.00
#> 6 6.705539 3.285714 6.122449 1.00
#> 7 6.250000 3.000000 8.333333 1.00
#> 8 6.079027 2.857143 10.638298 1.25
#> 9 6.181319 3.214286 9.615385 1.25
#> 10 6.428571 3.214286 8.000000 1.00
#> 11 6.722689 3.428571 9.803922 1.00
#> 12 6.162465 3.142857 5.882353 1.00
#> 13 6.851312 3.357143 8.163265 1.00
#> 14 6.547619 3.142857 6.250000 1.00
#> 15 6.250000 3.000000 8.333333 1.00
#> TimsonsIndex_KhanUngar GermRateGeorge GermIndex GermIndex_mod
#> 1 0.5714286 4 5.840000 7.300000
#> 2 0.7002801 5 5.882353 7.142857
#> 3 1.0416667 7 6.687500 7.133333
#> 4 0.5602241 4 6.411765 7.108696
#> 5 0.7142857 5 6.900000 7.187500
#> 6 0.4373178 3 6.693878 7.130435
#> 7 0.5952381 4 6.395833 7.309524
#> 8 0.7598784 5 6.063830 7.125000
#> 9 0.6868132 5 6.173077 7.133333
#> 10 0.5714286 4 6.460000 7.177778
#> 11 0.7002801 5 6.784314 7.208333
#> 12 0.4201681 3 6.137255 7.113636
#> 13 0.5830904 4 6.775510 7.063830
#> 14 0.4464286 3 6.625000 7.227273
#> 15 0.5952381 4 6.291667 7.190476
#> EmergenceRateIndex_SG EmergenceRateIndex_SG_mod
#> 1 292 7.300000
#> 2 300 7.142857
#> 3 321 7.133333
#> 4 327 7.108696
#> 5 345 7.187500
#> 6 328 7.130435
#> 7 307 7.309524
#> 8 285 7.125000
#> 9 321 7.133333
#> 10 323 7.177778
#> 11 346 7.208333
#> 12 313 7.113636
#> 13 332 7.063830
#> 14 318 7.227273
#> 15 302 7.190476
#> EmergenceRateIndex_BilbroWanjura EmergenceRateIndex_Fakorede PeakValue
#> 1 5.970149 8.375000 9.500000
#> 2 6.125000 8.326531 9.313725
#> 3 6.553398 7.324444 10.416667
#> 4 6.675079 7.640359 10.049020
#> 5 7.045872 7.096354 11.250000
#> 6 6.696203 7.317580 10.714286
#> 7 6.277580 7.646259 10.416667
#> 8 5.818182 8.078125 9.574468
#> 9 6.553398 7.934815 9.855769
#> 10 6.596091 7.580247 10.250000
#> 11 7.067485 7.216146 11.029412
#> 12 6.389439 7.981921 9.803922
#> 13 6.776074 7.231326 10.969388
#> 14 6.496644 7.388430 10.677083
#> 15 6.167832 7.782313 10.156250
#> GermValue_Czabator GermValue_DP GermValue_Czabator_mod GermValue_DP_mod
#> 1 54.28571 57.93890 54.28571 39.56076
#> 2 54.78662 52.58713 54.78662 40.99260
#> 3 69.75446 68.62289 69.75446 53.42809
#> 4 64.74158 70.43331 64.74158 48.86825
#> 5 77.14286 80.16914 77.14286 56.23935
#> 6 71.84506 76.51983 71.84506 53.06435
#> 7 65.10417 69.41325 65.10417 47.37690
#> 8 58.20345 56.00669 58.20345 43.67948
#> 9 60.92165 58.13477 60.92165 45.30801
#> 10 65.89286 70.91875 65.89286 49.10820
#> 11 74.14731 77.39782 74.14731 54.27520
#> 12 60.41632 64.44988 60.41632 44.71582
#> 13 75.15470 78.16335 75.15470 54.94192
#> 14 69.90947 74.40140 69.90947 51.41913
#> 15 63.47656 67.62031 63.47656 46.48043
#> CUGerm GermSynchrony GermUncertainty
#> 1 0.7092199 0.2666667 2.062987
#> 2 0.5051546 0.2346109 2.321514
#> 3 0.3975265 0.2242424 2.462012
#> 4 0.4672113 0.2502415 2.279215
#> 5 0.4312184 0.2606383 2.146051
#> 6 0.4934701 0.2792271 2.160545
#> 7 0.7371500 0.2729384 2.040796
#> 8 0.4855842 0.2256410 2.357249
#> 9 0.4446640 0.2494949 2.321080
#> 10 0.5584666 0.2555556 2.187983
#> 11 0.4288905 0.2686170 2.128670
#> 12 0.4760266 0.2737844 2.185245
#> 13 0.4023679 0.2506938 2.241181
#> 14 0.5383760 0.2991543 2.037680
#> 15 0.6133519 0.2497096 2.185028
# }