biomass: Biomass estimative
In ThaiseRF/forImage: Foraminiferal Image Analysis and Test Measurement

Description Usage Arguments Details Value Author(s) References See Also Examples

The function estimates biomass through biovolume data and applies different cell density values as conversion methods. See details ‘Details’:

1	biomass(biovolume, method = "michaels")

biovolume

numeric value, object or data.frame with cell living volume values.

method

The methods of conversion from biovolume to biomass are listed below, default is 'michaels':

'saidova' : adopted cell density of 1.027 g/cm3;
'strathmann' : measured cell density of 0.110 pgC[org]/um3;
'turley' : estimated cell density of 0.132 pgC[org]/um3;
'putt' : estimated cell density of 0.140 pgC[org]/um3;
'gerlach' : adopted cell density of 1.13 g/cm3 wet mass, assuming 10 percent as living organic carbon;
'michaels' : calculated cell density of 0.089 pgC[org]/um3.

For biomass estimates based on biovolume is usual the application of a cell density value, to retrieve the amount of organic carbon in the organism. The function made available distinct options of conversion factor which are based in several authors. These factors have been applied to a wide diversity of nano, micro, and macro-organisms, some applied to foraminifera and other nearby groups.

An 'data.frame' or numeric object, consisting of calculated biomass in ugC[org]/ind.

Thaise R. Freitas thaisericardo.freitas@gmail.com

Saidova, K. (1966). The biomass and quantitative distribution of live foraminifera in the Kurile-Kamchatka trench area. DOKLADY AKAD. NAUK SSSR, 174(1), 216–217.
Strathmann, R. (1967). Estimating the Organic Carbon Content of Phytoplankton from Cell Volume or Plasma Volume. Limnology and Oceanography, 12, 411–418. doi:10.4319/lo.1967.12.3.0411
Turley, C., Newell, R., & Robins, D. (1986). Survival Strategies of 2 Small Marine Ciliates and Their Role in Regulating Bacterial Community Structure Under Experimental Conditions. Marine Ecology Progress Series, 33(1), 59–70. doi:10.3354/meps033059
Putt, M., & Stoecker, D. K. (1989). An experimentally determined carbon : volume ratio for marine ‘oligotrichous’ ciliates from estuarine and coastal waters. Limnology and Oceanography, 34(6), 1097–1103. doi:10.4319/lo.1989.34.6.1097
Gerlach, S. A., Hahn, A., & Schrage, M. (1985). Size spectra of benthic biomass and metabolism . Marine Ecology Progress Series, 26, 161–173. doi:10.3354/meps026161
Michaels, A. F., Caron, D. A., Swanberg, N. R., Howse, F. A., & Michaels, C. M. (1995). Planktonic sarcodines (Acantaria, Radiolaria, Foraminifera) in surface waters near Bermuda: abundance, biomass and vertical flux. Journal of Plankton Research, 17(0), 131–163. doi:10.1093/plankt/17.1.131

bio.volume, volume.total

#Ammonia biomass calculation
data(ammonia)

#calculate test volume and biovolume
df <- bio.volume(data = ammonia, genus = "ammonia")
df

#calculate individual biomass with choosen method
res <- biomass(df, method = 'michaels')
res