Package 'plantphysioR'

Title: Fundamental Formulas for Plant Physiology
Description: Functions tailored for scientific and student communities involved in plant science research. Functionalities encompass estimation chlorophyll content according to Arnon (1949) <doi:10.1104/pp.24.1.1>, determination water potential of Polyethylene glycol(PEG)6000 as in Michel and Kaufmann (1973) <doi:10.1104/pp.51.5.914> and functions related to estimation of yield related indices like Abiotic tolerance index as given by Moosavi et al.(2008)<doi:10.22059/JDESERT.2008.27115>, Geometric mean productivity (GMP) by Fernandez (1992) <ISBN:92-9058-081-X>, Golden Mean by Moradi et al.(2012)<doi:10.14207/ejsd.2012.v1n3p543>, HAM by Schneider et al.(1997)<doi:10.2135/cropsci1997.0011183X003700010007x>,MPI and TOL by Hossain etal., (1990)<doi:10.2135/cropsci1990.0011183X003000030030x>, RDI by Fischer et al. (1979)<doi:10.1071/AR9791001>,SSI by Fisher et al.(1978)<doi:10.1071/AR9780897>, STI by Fernandez (1993)<doi:10.22001/wvc.72511>,YSI by Bouslama & Schapaugh (1984)<doi:10.2135/cropsci1984.0011183X002400050026x>, Yield index by Gavuzzi et al.(1997)<doi:10.4141/P96-130>.
Authors: Ramesh Ramasamy [aut, cre] , Rajasekar R [ctb]
Maintainer: Ramesh Ramasamy <[email protected]>
License: GPL (>= 3)
Version: 1.0.0
Built: 2025-02-15 03:23:46 UTC
Source: https://github.com/rameshram96/plantphysior

Help Index

All indices combined

Description

Function to all the indices related to biomass/ yield under different growth conditions

Usage

all_indices(Yp, Ys, Mp, Ms)

Arguments

Yp

Yield under control condition
Ys

Yield under stress condition
Mp

Mean yield of all the genotypes under control condition
Ms

Mean yiels of all the genotyps under Stress condition

Value

Indices Combined

Examples

Mp <- mean(yield_data$Yp)
Ms <- mean(yield_data$Ys)
Yp <- yield_data$Yp
Ys <- yield_data$Ys
all_indices(Yp, Ys, Mp, Ms)

Abiotic Tolerance Index (ATI)

Description

Calculate abiotic tolerance index according to Moosavi et al. (2008)

Usage

ATI(Yp, Ys, Mp, Ms)

Arguments

Yp

Yield under control condition
Ys

Yield under Stress condition
Mp

Mean yield of all the genotypes under stress condition
Ms

Mean yield of all the genotypes under control condition

Value

ATI

References

Moosavi SS, Samadi YB, Naghavi MR, Zali AA, Dashti H, Pourshahbazi A (2008) Introduction of new indices to identify relative drought tolerance and resistance in wheat genotypes. Desert. 12: 165-178.

Examples

ATI(500, 350, 400, 300)

Calculate Polyethylene glycol (PEG) 6000 requirement

Description

Calculate Amount of PEG6000 required to reach desired water potential at given temperature

Usage

calculate_PEG_6000(C, bar)

Arguments

C

Temperature of solution in degree centigrade
bar

Water potential in bars

Value

PEG6000 required

References

Michel, B. E., & Kaufmann, M. R. (1973). The osmotic potential of polyethylene glycol 6000. Plant physiology, 51(5), 914-916.

Examples

calculate_PEG_6000(25, -4)

Total carotenoids content

Description

Calculate total carotenoids using Method by Lichtenthaler (1987)

Usage

caro_total(A470, A663, A646, fresh_weight)

Arguments

A470

Absorbance at 470nm
A663

Absorbance at 663nm
A646

Absorbance at 646nm
fresh_weight

Fresh weight of the sample used in grams

Value

Carotenoids concentration in µg/ml

References

Lichtenthaler, H. K. (1987). Chlorophylls and carotenoids: pigments of photosynthetic biomembranes. In Methods in enzymology (Vol. 148, pp. 350-382). Academic Press.

Examples

caro_total(0.7, 0.041, 0.025, 1)

Chlorophyll'a' Concentration by Arnon method

Description

Calculates Chlorophyll a Concentration according to Arnon(1949) method

Usage

chl_a(A663, A645, v, w)

Arguments

A663

Absorbance at 663nm
A645

Absorbance at 645nm
v

Final volume of solvent used in ml
w

Fresh weight of the sample used in grams

Value

Chlorophyll a in mg/g of fresh weight

References

Arnon, D. I. (1949). Copper enzymes in isolated chloroplasts. Polyphenoloxidase in Beta vulgaris. Plant physiology, 24(1), 1. doi:10.1104/pp.24.1.1

Examples

chl_a(0.025, 0.041, 15, 1)

Chlorophyll b concentration

Description

Calculates Chlorophyll b Concentration according to Arnon(1949) method

Usage

chl_b(A645, A663, v, w)

Arguments

A645

Absorbance at 645nm
A663

Absorbance at 663nm
v

Final volume of solvent used in ml
w

Fresh weight of the sample used in grams

Value

Chlorophyll b in mg/g of fresh weight

References

Arnon, D. I. (1949). Copper enzymes in isolated chloroplasts. Polyphenoloxidase in Beta vulgaris. Plant physiology, 24(1), 1. doi:10.1104/pp.24.1.1

Examples

chl_b(0.041, 0.025, 15, 1)

Total chlorophyll (a+b) concentration

Description

Calculate Total chlorophyll (a+b) concentration using method by Arnon (1949)

Usage

chl_total(A645, A663, v, w)

Arguments

A645

Absorbance at 645nm
A663

Absorbance at 663nm
v

Final volume of solvent used in ml
w

Fresh weight of the sample used in grams

Value

Total chlorophyll (a+b) in mg/g of fresh weight

References

Arnon, D. I. (1949). Copper enzymes in isolated chloroplasts. Polyphenoloxidase in Beta vulgaris. Plant physiology, 24(1), 1. doi:10.1104/pp.24.1.1

Examples

chl_total(0.041, 0.025, 15, 1)

Drought resistant index (DRI)

Description

The genotype with high values of this index will be more suitable for drought stress condition

Usage

DRI(Yp, Ys)

Arguments

Yp

Yield under control condition
Ys

Yield under stress condition

Value

DRI

Examples

DRI(500, 350)

Geometric mean productivity (GMP) by Fernandez (1992)

Description

The genotype with high values of this index will be more desirable

Usage

gmp(Yp, Ys)

Arguments

Yp

Yield under control condition
Ys

Yield under stress condition

Value

GMP

References

Fernandez, G. C. (1993). Effective selection criteria for assessing plant stress tolerance.

Examples

gmp(5, 3)

Golden Mean (GM)

Description

Calculates Golden mean value using Moradi et al.,(2012)

Usage

Golden_mean(Yp, Ys)

Arguments

Yp

Yield under control condition
Ys

Yield under stress condition

Value

GM

References

Moradi H, Akbari GA, Khorasani SK, Ramshini HA (2012) Evaluation of drought tolerance in corn (Zea Mays L.) new hybrids with using stress tolerance indices. Eur J Sustain Dev 1. (3): 543-560

Examples

Golden_mean(500, 350)

Harmonic Mean

Description

Harmonic Mean

Usage

HAM(Yp, Ys)

Arguments

Yp

Yield under control condition
Ys

Yield under stress condition

Value

Harmonic mean

References

Schneider, K. A., Rosales‐Serna, R., Ibarra‐Perez, F., Cazares‐Enriquez, B., Acosta‐Gallegos, J. A., Ramirez‐Vallejo, P., ... & Kelly, J. D. (1997). Improving common bean performance under drought stress. Crop science, 37(1), 43-50.

Examples

HAM(500, 350)

Mean productivity Index (MPI)- by Hossain et al., (1990)

Description

The genotype with high values of this index will be more desirable

Usage

mp_index(Yp, Ys)

Arguments

Yp

Yield under control condition
Ys

Yield under stress condition

Value

Mean productivity Index

References

Hossain, A. B. S., Sears, R. G., Cox, T. S., & Paulsen, G. M. (1990). Desiccation tolerance and its relationship to assimilate partitioning in winter wheat. Crop Science, 30(3), 622-627.

Water potential of Polyethylene glycol (PEG) 6000

Description

Calculate the corresponding water potential of PEG6000 when dissolved in 1l of water

Usage

peg_6000(peg, C)

Arguments

peg

Amount PEG600O in grams
C

Temperature of the solution in degree centigrade

Value

Water potential in bars

References

Michel, B. E., & Kaufmann, M. R. (1973). The osmotic potential of polyethylene glycol 6000. Plant physiology, 51(5), 914-916.

Examples

peg_6000(20, 25)

Relative Drought Index (RDI)

Description

Calculates relative drought index according to Fisher and Wood (1979)

Usage

R_drought_index(Yp, Ys, Mp, Ms)

Arguments

Yp

Yield under control condition
Ys

Yield under stress condition
Mp

Mean Yield of all the genotypes under control Condition
Ms

Mean Yield of all the genotypes under stress Condition

Value

RDI

References

Fischer RA, Wood JT (1979) Drought resistance in spring wheat cultivars III. Yield association with morphological traits. Aust J Agr Res. 30: 1001-1020

Examples

R_drought_index(500, 350, 400, 300)

Stress susceptibility index (SSI) by Fischer and Maurer (1978)

Description

The genotype with high SSI < 1 are more resistant to drought stress conditions

Usage

ss_index(Yp, Ys, Ms, Mp)

Arguments

Yp

Yield under control condition
Ys

Yield under Stress condition
Ms

Mean yield of all the genotypes under control condition
Mp

Mean yield of all the genotypes under stress condition

Value

SSI

References

Fischer, R. A., & Maurer, R. (1978). Drought resistance in spring wheat cultivars. I. Grain yield responses. Australian Journal of Agricultural Research, 29(5), 897-912.

Examples

ss_index(500, 350, 450, 370)

Calculate Stress tolerance index (STI) suggested by Fernandez (1992)

Description

The genotype with high STI values will be tolerant to drought

Usage

st_index(Yp, Ys)

Arguments

Yp

Yield under control condition
Ys

Yield under stress condition

Value

STI

References

Fernandez, G. C. (1993). Effective selection criteria for assessing plant stress tolerance.

Examples

st_index(500, 350)

Tolerance index -TOL by Hossain et al., (1990)

Description

Higher the TOL value indicates the genotype is tolerant to stress

Usage

tol_index(Yp, Ys)

Arguments

Yp

Yield under control condition
Ys

Yield under stress condition

Value

TOL

References

Hossain, A. B. S., Sears, R. G., Cox, T. S., & Paulsen, G. M. (1990). Desiccation tolerance and its relationship to assimilate partitioning in winter wheat. Crop Science, 30(3), 622-627.

Examples

tol_index(500, 350)

Yield index (YI)

Description

Yield index (YI)

Usage

Y_index(Ys, Ms)

Arguments

Ys

Yield under stress condition
Ms

Mean Yield of all the genotypes under stress Condition

Value

Yield Index

References

Gavuzzi, P., Rizza, F., Palumbo, M., Campanile, R. G., Ricciardi, G. L., & Borghi, B. (1997). Evaluation of field and laboratory predictors of drought and heat tolerance in winter cereals. Canadian journal of plant science, 77(4), 523-531.

Examples

Y_index(500, 300)

Example data

Description

Yield data of rice in kg/ha under two different growth conditions

Usage

yield_data

Format

A data frame with 50 rows and 3 variables:

Genotype

character Genotype

Yp

integer Yield under control condition

Ys

integer Yield under drought condition

Source

Simulated data, no external source were used

References

No external reference

Yield Reduction

Description

Claculate percent yield reduction over control

Usage

yield_reduction(Yp, Ys)

Arguments

Yp

Yield under control condition
Ys

Yield under stress condition

Value

YR

Examples

yield_reduction(500, 350)

Yield reduction ratio (YR)

Description

lesser the YR value more stable under stress conditions

Usage

YR_ratio(Yp, Ys)

Arguments

Yp

Yield under control condition
Ys

Yield under stress condition

Value

YR

Examples

YR_ratio(500, 350)

Yield reduction index or Yield Stability Index (YSI)

Description

Higer YSI value depicts that particular genotype is stable under both normal and stressed conditions

Usage

YSI(Yp, Ys)

Arguments

Yp

Yield under control condition
Ys

Yield under stress condition

Value

YSI

References

Bouslama, M., & Schapaugh Jr, W. T. (1984). Stress tolerance in soybeans. I. Evaluation of three screening techniques for heat and drought tolerance 1. Crop science, 24(5), 933-937.

Examples

YSI(500, 350)