ecopop: Creating a new ecopop object

In EcoGenetics: Management and Exploratory Analysis of Spatial Data in Landscape Genetics

Description

Creating a new ecopop object

Usage

ecopop(
  XY = data.frame(),
  P = data.frame(),
  AF = data.frame(),
  E = data.frame(),
  S = data.frame(),
  C = data.frame(),
  pop_names_column = 1L,
  ploidy,
  type = c("codominant", "dominant"),
  order.df = FALSE,
  allele_data = c("counts", "frequencies"),
  lock.rows = TRUE
)

Arguments

XY	Data frame with n rows (populations) and m columns (coordinates).
P	Data frame with n rows (populations), and m columns (phenotypic variables).
AF	Data of class: "matrix", with n rows (populations) and m columns (allele counts). The ploidy and the type (codominant, dominant) of the data, must be passed with the arguments "ploidy" and "type" for consistency with other methods of the package.
E	Data frame with n rows (populations), and n columns (environmental variables).
S	Vector (factor) with n items (population hierarchical levels).
C	Data frame with n rows (populations), and m columns (custom variables).
pop_names_column	Column with the population in the slot S that represents used to create the name of the object. Dafault is the first column.
ploidy	Ploidy of the AF data frame.
type	Marker type: "codominant" or "dominant".
order.df	Order populations of data frames by row? (all data frames with a same row order). Defalut FALSE. The row names of all the data frames must be ordered. In this case, the use of data frames with row names in different order will return an error. In both cases, the program set the content of the S slots as the reference names of the object using the row names of the first non-empty data frame found in the following order: XY, P, AF, E, C. This attribute is used as reference to order rows when order.df = TRUE.
allele_data	format for allele data output (slot AF). Can be "counts" or "frequencies".
lock.rows	Turn on row names check. Data frames require indentical individuals in rows. Default TRUE.

Details

This is a generic function for creation of ecopop objects. Missing data should be coded as "NA".

ACCESS TO THE SLOTS. MODIFICATION OF ecopop OBJECTS

The content of the slots can be extracted with the corresponding accessors ecoslot.XY, ecoslot.P, ecoslot.AF, ecoslot.E and ecoslot.C. Accessors can be also used to assign data to the slots. The correct use of ecopop objects requires the implementation of accessors, as they ensure the checking and pre-processing of the data. The use of accessors allows to modify or fill the slots of ecopop objects, without the need of creating a new object each time. See help("EcoGenetics accessors") for a detailed description and examples about ecopop accessors.

OTHER SLOT ACCESS METHODS FOR ECOPOP OBJECTS

The use of brackets is defined for ecopop objects:

- Single bracket: the single bracket ("[") is used to subset all the ecopop data frames (P, G, E, S, AF and C) by row, at once. The notation for an object is eco[from:to], where eco is any ecopop object, and from: to is the row range. For example: my_ecopop[1:10] , subsets the object my_ecopop from row 1 to row 10, for all the data frames at once.

- Double square brackets: the double square brackets are symbolic abbreviations of the accessors (i.e., it is a call to the corresponding accessor). The usage is: my_ecopop[["X"]], where X is a slot: my_ecopop[["P"]], my_ecopop[["AF"]], my_ecopop[["E"]], my_ecopop[["S"]] and my_ecopop[["C"]]. Double square brackets can be used in get/set mode. See Examples below and in help("EcoGenetics accessors").

ABOUT THE CONSTRUCTION OF NEW ECOPOP OBJECTS

In most cases, a new ecopop object is created from an ecogen object, using the function ecogen2ecopop. A new ecopop object can also be directly constructed in two different ways. First, a new object can be created, incorporating all the information in one step with the constructor. Second, the data can be added to each slot, using the corresponding accessor or, in an equivalent way, with double brackets notation ("[[").

LOCKED AND UNLOCKED OBJECTS #' Starting from version 1.2.1.5, ecogen and ecopop objects can be "locked" (default) or "unlocked". A "locked" object must have identical number of rows and row names in all the input data frames (or a rule must be provided to construct the row names in case of ecogen objects, with valid.names or set.names arguments). An unlocked objects allows to have a free number of rows in each table, and row names do not need to coincide among tables. See examples below.

Author(s)

Leandro Roser [e-mail]

Examples

## Not run: 

data(eco.test)

## Three ways to construct an ecopop object 

## 1) ecogen to ecopop
my_ecopop <- ecogen2ecopop(eco, hier = "pop")

# extracting tables with accessors (double brackets notation)
XY_pop <- my_ecopop[["XY"]]
P_pop <- my_ecopop[["P"]]
AF_pop <- my_ecopop[["AF"]]
E_pop <- my_ecopop[["E"]]
S_pop <- my_ecopop[["S"]]

## 2) Creating a new ecopop object
my_ecopop2 <- ecopop(XY = XY_pop, P = XY_pop, AF = AF_pop, E = E_pop, 
                     S = S_pop,
                     ploidy = 2, type = "codominant")

## 3) From an empty object
# new empty object
my_ecopop3 <- ecopop(ploidy = 2, type = "codominant")

set slots, using as example the data generated above

my_ecopop3[["XY"]] <- XY_pop # The first assignments initializes the S slot
                            # with the row names of the data frame used (XY)
my_ecopop3[["P"]] <- P_pop
my_ecopop3[["AF", ploidy = 2]] <- AF_pop
my_ecopop3[["E"]] <- E_pop
my_ecopop3[["S"]] <- S_pop

## Subsetting by rows:
my_ecopop3[1:10]
#--------------------------------
# Locked and unlocked objects 
#--------------------------------

is.locked(my_ecopop) # check if object is locked
my_ecopop[["P"]] <- rbind(my_ecopop[["P"]], my_ecopop[["P"]]) # invalid in locked object

my_ecopop_unlocked <- eco.unlock(my_ecopop) #unlocked object
my_ecopop_unlocked[["P"]]<-rbind(my_ecopop[["P"]], my_ecopop[["P"]])  # valid now

new_locked <- eco.lock(my_ecopop_unlocked) # invalid
my_ecopop_unlocked[["P"]]<- my_ecopop[["P"]]
new_locked <- eco.lock(my_ecopop_unlocked) # valid now









## End(Not run)

EcoGenetics documentation built on July 8, 2020, 5:46 p.m.