clonecorrect: Remove potential bias caused by cloned genotypes in genind or...
In poppr: Genetic Analysis of Populations with Mixed Reproduction

Description Usage Arguments Details Value Author(s) Examples

This function removes any duplicated multilocus genotypes from any specified population strata.

1	clonecorrect(pop, strata = 1, combine = FALSE, keep = 1)

`pop`	a `genind`, `genclone`, or `snpclone` object
`strata`	a hierarchical formula or numeric vector. This will define the columns of the data frame in the strata slot to use.
`combine`	`logical`. When set to TRUE, the strata will be combined to create a new population for the clone-corrected genind or genclone object.
`keep`	`integer`. When `combine` is set to `FALSE`, you can use this flag to choose the levels of your population strata. For example: if your clone correction strata is set to "Pop", "Subpop", and "Year", and you want to analyze your populations with respect to year, you can set `keep = c(1,3)`.

This function will clone correct based on the stratification provided. To clone correct indiscriminately of population structure, set strata = NA.

a clone corrected genclone, snpclone, or genind object.

Zhian N. Kamvar

# LOAD A. euteiches data set
data(Aeut)

# Redefine it as a genclone object
Aeut <- as.genclone(Aeut)
strata(Aeut) <- other(Aeut)$population_hierarchy[-1]

# Check the number of multilocus genotypes
mlg(Aeut)
popNames(Aeut)

# Clone correct at the population level.
Aeut.pop <- clonecorrect(Aeut, strata =  ~Pop)
mlg(Aeut.pop)
popNames(Aeut.pop)

## Not run: 
# Clone correct at the subpopulation level with respect to population and
# combine.
Aeut.subpop <- clonecorrect(Aeut, strata = ~Pop/Subpop, combine=TRUE)
mlg(Aeut.subpop)
popNames(Aeut.subpop)

# Do the same, but set to the population level.
Aeut.subpop2 <- clonecorrect(Aeut, strata = ~Pop/Subpop, keep=1)
mlg(Aeut.subpop2)
popNames(Aeut.subpop2)

# LOAD H3N2 dataset
data(H3N2)

strata(H3N2) <- other(H3N2)$x

# Extract only the individuals located in China
country <- clonecorrect(H3N2, strata =  ~country)

# How many isolates did we have from China before clone correction?
sum(strata(H3N2, ~country) == "China") # 155

# How many unique isolates from China after clone correction?
sum(strata(country, ~country) == "China") # 79

# Something a little more complicated. (This could take a few minutes on
# slower computers)

# setting the hierarchy to be Country > Year > Month  
c.y.m <- clonecorrect(H3N2, strata =  ~year/month/country)

# How many isolates in the original data set?
nInd(H3N2) # 1903

# How many after we clone corrected for country, year, and month?
nInd(c.y.m) # 1190

## End(Not run)

Loading required package: adegenet
Loading required package: ade4
Registered S3 method overwritten by 'spdep':
  method   from
  plot.mst ape 

   /// adegenet 2.1.3 is loaded ////////////

   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature requests: adegenetIssues()


Registered S3 method overwritten by 'pegas':
  method      from
  print.amova ade4
This is poppr version 2.8.6. To get started, type package?poppr
OMP parallel support: available
#############################
# Number of Individuals:  187 
# Number of MLG:  119 
#############################
[1] 119
[1] "Athena"     "Mt. Vernon"
#############################
# Number of Individuals:  120 
# Number of MLG:  119 
#############################
[1] 119
[1] "Athena"     "Mt. Vernon"
#############################
# Number of Individuals:  141 
# Number of MLG:  119 
#############################
[1] 119
 [1] "Athena_1"     "Athena_2"     "Athena_3"     "Athena_4"     "Athena_5"    
 [6] "Athena_6"     "Athena_7"     "Athena_8"     "Athena_9"     "Athena_10"   
[11] "Mt. Vernon_1" "Mt. Vernon_2" "Mt. Vernon_3" "Mt. Vernon_4" "Mt. Vernon_5"
[16] "Mt. Vernon_6" "Mt. Vernon_7" "Mt. Vernon_8"
#############################
# Number of Individuals:  141 
# Number of MLG:  119 
#############################
[1] 119
[1] "Athena"     "Mt. Vernon"
[1] 155
[1] 79
[1] 1903
[1] 1190