emm_pip: emm_pip
In lycium0605/SHfunction: SH custom functions

emm_pip

R Documentation

emm_pip

Description

Pipeline for running emmreml

Usage

emm_pip(
  ge_meta,
  sci,
  agi,
  dsi,
  dsi_sum,
  type = "wt_avg",
  res,
  rel,
  sex = "F",
  fix_var = c("age", "rank"),
  change_var = c("eigen_wt", paste0(c("SCI", "AGI", "DSI", "SumBond"), "_F"),
    paste0(c("SCI", "AGI", "DSI", "SumBond"), "_M")),
  lps_name = "treatment",
  numcore = 3,
  sname = "sname",
  outputdir,
  emm_prefix,
  x_axis_size = 20
)

Arguments

`ge_meta`	should contain sname,dart_date,treatment,group,sex,rank,age
`sci`	sci input from Ramboseli::sci
`agi`	agi input from Ramboseli::agi
`dsi`	dsi_pop input from Ramboseli::dsi_pop
`dsi_sum`	dsi_pop_sumamry input from Ramboseli::dsi_pop_summary
`type`	"wt_avg"(default),"dir_avg", or "grp_only". calculating weighted average by days_present across group, direct average, or keep only the group observed on the darting date
`res`	full GE residual dataframe
`rel`	full K matrix
`sex`	The sex to look at, "F" (default) or "M"
`fix_var`	The variables to be included in every emmreml model, defaut to c("age","rank")
`change_var`	The variables to be added with replacement to the basic model. Default to all SR.
`lps_name`	The colname indicating LPS/NULL in ge_meta, default to treatment
`numcore`	The number of core to be used for EMMREML, default to 3
`sname`	The colname indicaiting sname, default to sname, could be sname.x
`outputdir`	The folder to store output, end with /
`emm_prefix`	The prefix for emmresult RDS and p histogram png
`x_axis_size`	The font size of x axis of p histogram, default to 20