get.data: Query SHiNeMaS and return the datasets

In priviere/shinemas2R_deprecated: An R package to visualize outputs from the data base Seed History and Network Management System (SHiNeMaS)

Description

get.data queries SHiNeMaS and returns the data-sets.

Usage

get.data(db_user = "pierre", db_host = "127.0.0.1",
  db_name = "shinemas_tuto", db_password = "pierre",
  query.type = "person", filter.on = NULL, germplasm.in = NULL,
  germplasm.out = NULL, germplasm.type.in = NULL,
  germplasm.type.out = NULL, year.in = NULL, year.out = NULL,
  project.in = NULL, project.out = NULL, person.in = NULL,
  person.out = NULL, seed.lot.in = NULL, seed.lot.out = NULL,
  relation.in = NULL, reproduction.type.in = NULL, variable.in = NULL,
  data.type = NULL, network.info = TRUE, Mdist = FALSE,
  fill.diffusion.gap = FALSE, mixrep_to_repro = TRUE)

Arguments

db_user	user name of SHiNeMaS
db_host	IP address of the computer where SHiNeMaS is. If local host db_host = "127.0.0.1"
db_name	name of the data base
db_password	your password to login. If no password is needed, put ""
query.type	Type of query, which will create a data set. There are eight types: "network": network relations between seed-lots. All filters are possible. "cross": seed-lots used to give a cross: father, grandfather, mother, grandmother and cross. All filters are possible except variable.in, relation.in, seed.lots.in, seed.lots.out and reproduction.type.in. raw information on levels and variables contained in SHiNeMaS : "species" "variable" "person" "year" "project" "seed.lot" "selection.person": persons that performed intra-varietal mass selection "reproduction.type" "germplasm.type" "germplasm" data with variable on specific seed-lots : "data-classic": default dataframe. "data-S": selection differential for a given year. "data-SR": seed-lots pairs of selection differential for year n-1 and response to selection for year n. "data-mixture-1": seed-lots used in a mixture "methods": information related to the methods used for each variable in SHiNeMaS with its description and units Filters can be applied on variables. Possible filter is variable.in. "person.info": information regarding persons stored in SHiNeMaS. Possible filters are person.in and person.out. "grandfather": information on son, father and grandfather. All filters are possible except relation.in and variable.in.
filter.on	This argument is needed if you want to use filters. It chooses on which seed-lots the filters are applied: "son", "father" or "father-son". Filter.on is not used for data.type = "seed-lots", query.type = "methods" and query.type = "person.info"
germplasm.in	Filter: vector with germplasms to keep. By default, all the germplasms are in.
germplasm.out	Filter: vector with germplasms to discard. By default, no germplasm is out.
germplasm.type.in	Filter: vector with germplasms to keep. By default, all the germplasm types are in.
germplasm.type.out	Filter: vector with germplasms to discard. By default, no germplasm type is out.
year.in	Filter: vector with years to keep. By default, all the years are in.
year.out	Filter: vector with years to discard. By default, no year is out.
project.in	Filter: vector of projects to keep. By default, all the projects are in.
project.out	Filter: vector of projects to discard. By default, no project is out.
person.in	Filter: vector of persons to keep. By default, all the persons are in.
person.out	Filter: vector of persons to discard. By default, no person is out.
seed.lot.in	Filter: vector of seed-lots to keep. By default, all the seed-lots are in.
seed.lot.out	Filter: vector of seed-lots to discard. By default, no seed-lot is out.
relation.in	Filter on a relation to keep: "reproduction", "mixture", "selection" or "diffusion". By default, all relations are in.
reproduction.type.in	Filter on reproduction types
variable.in	Filter: vector with variables to keep. If NULL, all variables in SHiNeMaS are displayed.
data.type	For queries in "data-". Type of data: "relation" for data linked to relation between seed lots and "seed-lots" for data linked to seed lots
network.info	For query.type = "network". If TRUE, aggregates information on relations and seed-lots on the network and return it in the results.
Mdist	For query.type = "network". If TRUE, computes the Mdist matrix and return it in the results. See details.
fill.diffusion.gap	For query.type = "network", create a network with no gaps between seed-lots (as long as there is information!)
mixrep_to_repro	For query.type = "network", tranform the mixtures of replications into reproductions, i.e. the network keeps only 'real' mixtures (i.e. different germplasm for father and son) and correct the information regarding what have been harvested and sown after as the mixture disappear. TRUE by default.

Details

• Queries "cross"

  The data frame returned has a column "expe" which corresponds to an id of the set of seed-lots used in the cross

• Queries "S"

  The data frame returned has a column "expe" which corresponds to an id of one selection differential

• Queries "SR"

  The data frame returned has a column "expe" which corresponds to an id of one selection differential and the corresponding response to selection

  The query "data-SR" takes into account when selection has been done to get a seed lot, that this seed lot has been merged and then has been sown. It is the case when selection has been carried out in a replication that has been merged afterwards. Even if this case should not arrise, it might happen.

• Query "network"

  The Mdist square matrix can be compared to a differentiation distance. It can be put in relation with genetic Fst for example. Note that a value of 1 means a distance between

  • a seed-lot that has been diffused to location A without beeing sown and harvested on location B and

  • a seed-lot that has been diffused to location B and beeing sown and harvested on location B

• Correlated data or not

  Note that for data linked to seed-lots, all the data are correlated as there is one measure for a given seed-lot. Therefore the element of the list for non correlated data is always NULL.

  For data linked to relations, as it can be linked to individual within a seed-lot, data may be correlated (data taken on the same individual) or not.

Value

The function returns a list with

• data according to the query type.

  1. For network it returns a list with

     • the network object with information on:

       • vertex: year, person, germplasm, germplasm.type, sex

       • edges: relation type, number of generations on a given location + confidence of the information, number of generations since the information is known + confidence of the information

     • the network.query dataframe coming from the query

     • the network.info matrix with information on relations in the network. The possible information are:

       • reproduction: "sow", "harvest", "harvest-sow"

       • selection: "selection"

       • mixture: "mixture_real" (for 'real' mixture i.e. seed-lots of different germplasm), "mixture_rep" (for mixture of replication i.e. seed-lots of identical germplasm)

       • diffusion: "give", "receive", "give-receive"

     • the Mdist square matrix with the number of reproductions that separate two seed-lots since their last common diffusion.

  2. For raw information on levels and variables present in SHiNeMaS it returns a vector

  3. For data with variables on specific seed-lots it returns a list with

     • a data frame with the data set

     • a list with data set with individuals that are correlated for a set of variables

     • the description of methods used for each variable with its description and units

• information to connect to SHiNeMaS

Author(s)

Pierre Riviere for R code and Yannick de Oliveira for SQL code

See Also

encrypt.data, translate.data,, format.data, get.ggplot, get.table

Examples

# See the vignette

priviere/shinemas2R_deprecated documentation built on May 8, 2019, 1:21 p.m.