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FishRatioR:

Calculate the ratio and logarithmic value of species contained in several genus of a family to all species in this family

install.packages("FishRatioR")

or 

devtools::install_github("benben-miao/FishRatioR")

library(FishRatioR)

1.Example data view and usage

data("famgenspe")

famgenspe

Family	Genus	Species
Myxinidae	Eptatretus	3
Chimaeridae	Chimaera	1
Chimaeridae	Hydrolagus	1
Scyliorhinidae	Apristurus	2
Scyliorhinidae	Atelomycterus	1
Scyliorhinidae	Cephaloscyllium	3
Scyliorhinidae	Galeus	1
Scyliorhinidae	Halaelurus	1
Scyliorhinidae	Parmaturus	1

2. Calculate Ratio values

Formula: Ratio = (N_species_in_genus) / (N_species_in_family)

ratio <- calc_ratio(famgenspe = famgenspe)

ratio

Family	Genus	Species	Ratios
Chimaeridae	Chimaera	1	0.5
Chimaeridae	Hydrolagus	1	0.5
Myxinidae	Eptatretus	3	1
Scyliorhinidae	Apristurus	2	0.222222222222222
Scyliorhinidae	Atelomycterus	1	0.111111111111111
Scyliorhinidae	Cephaloscyllium	3	0.333333333333333
Scyliorhinidae	Galeus	1	0.111111111111111
Scyliorhinidae	Halaelurus	1	0.111111111111111
Scyliorhinidae	Parmaturus	1	0.111111111111111

3. Calculate Ln(Ratio) values

Formula: Ln(Ratio) = Ln((N_species_in_genus) / (N_species_in_family))

ln_ratio <- calc_ln_ratio(famgenspe = famgenspe)

ln_ratio

Family	Genus	Species	LnRatio
Chimaeridae	Chimaera	1	-0.693147180559945
Chimaeridae	Hydrolagus	1	-0.693147180559945
Myxinidae	Eptatretus	3	0
Scyliorhinidae	Apristurus	2	-1.50407739677627
Scyliorhinidae	Atelomycterus	1	-2.19722457733622
Scyliorhinidae	Cephaloscyllium	3	-1.09861228866811
Scyliorhinidae	Galeus	1	-2.19722457733622
Scyliorhinidae	Halaelurus	1	-2.19722457733622
Scyliorhinidae	Parmaturus	1	-2.19722457733622

4. Calculate Ratio(-Ln(Ratio)) values

Formula: NegMulRatio = Ratio * (-Ln((N_species_in_genus) / (N_species_in_family)))

mul_ratio <- calc_mul_ratio(famgenspe = famgenspe)

mul_ratio

Family	Genus	Species	NegMulRatio
Chimaeridae	Chimaera	1	0.346573590279973
Chimaeridae	Hydrolagus	1	0.346573590279973
Myxinidae	Eptatretus	3	0
Scyliorhinidae	Apristurus	2	0.334239421505839
Scyliorhinidae	Atelomycterus	1	0.244136064148469
Scyliorhinidae	Cephaloscyllium	3	0.366204096222703
Scyliorhinidae	Galeus	1	0.244136064148469
Scyliorhinidae	Halaelurus	1	0.244136064148469
Scyliorhinidae	Parmaturus	1	0.244136064148469

5. Calculate all values based one step

Formula: Ratio = (N_species_in_genus) / (N_species_in_family), Ln(Ratio) = Ln((N_species_in_genus) / (N_species_in_family)), NegMulRatio = Ratio * (-Ln((N_species_in_genus) / (N_species_in_family)))

all_ratio <- calc_all(famgenspe = famgenspe)

all_ratio

Family	Genus	Species	Ratios	LnRatio	NegMulRatio
Chimaeridae	Chimaera	1	0.5	-0.693147180559945	0.346573590279973
Chimaeridae	Hydrolagus	1	0.5	-0.693147180559945	0.346573590279973
Myxinidae	Eptatretus	3	1	0	0
Scyliorhinidae	Apristurus	2	0.222222222222222	-1.50407739677627	0.334239421505839
Scyliorhinidae	Atelomycterus	1	0.111111111111111	-2.19722457733622	0.244136064148469
Scyliorhinidae	Cephaloscyllium	3	0.333333333333333	-1.09861228866811	0.366204096222703
Scyliorhinidae	Galeus	1	0.111111111111111	-2.19722457733622	0.244136064148469
Scyliorhinidae	Halaelurus	1	0.111111111111111	-2.19722457733622	0.244136064148469
Scyliorhinidae	Parmaturus	1	0.111111111111111	-2.19722457733622	0.244136064148469

6. FishRatioR for Python

FishRatio PYPI Code: https://github.com/benben-miao/FishRatio

FishRatio PYPI: https://pypi.org/project/fishratio

pip install fishratio
  
fishratio --help
Usage: fishratio [OPTIONS]

     Description:

     Calculate the ratio and logarithmic value of species contained in
     several genus of a family to all species in this family.

     Examples:

     1. Get options and parameters help:

     FishRatio --help

     2. Sample command with all default parameters:

     FishRatio --input input.xlsx     or

     FishRatio --input input.xlsx --ratio true --ln_ratio true --neg_ratio
     true --output output.xlsx

     3. Only calculate (species number of genus) / (species number of
     family):

     FishRatio --input input.xlsx --ratio true --ln_ratio false --neg_ratio
     false --output output.xlsx

Options:
  --input TEXT        Full name (path + name + extension) of input file.
                      default="input.xlsx"

  --ratio BOOLEAN     Formula: (species number of genus) / (species number of
                      family) ratio value. default=True

  --ln_ratio BOOLEAN  Formula: Log(e)(ratio value). default=True
  --neg_mul BOOLEAN   Formula: -(ratio x Log(e)(ratio value)). default=True
  --output TEXT       Full name (path + name + extension) of output file.
                      default="output.xlsx"

  --help              Show this message and exit.