Rm functions out of manuscript and into ManyEcoEvo pkg + pipeline

[egouldo]

See issue egouldo/ManyEcoEvo#29

The following functions are to be moved to software pkg, checking for:

• fn exists, or isn't renamed in ManyEcoEvo
  • if exists, arguments are the same order and name
  • if exists, delete in ManyAnalysts repository
• fn does not exist in ManyEcoEvo:
  • move or copy function into ManyEcoEvo
  • write Roxygen2 documentation with help of GH co-pilot
  • Rebuild package
  • Can or should, application of function be moved to targets pipeline?
    • If so, move into targets pipeline,
      • source tar_make.R
      • Rebuild package
      • Update version number major.
    • If not, Ensure application in either ManyEcoEvo matches argument names, total number and position.

• fit_MA_mv

ManyAnalysts/index.qmd

Lines 2923 to 2931 in 91ca56a

	fit_MA_mv <- function(effects_analysis, Z_colname, VZ_colname, estimate_type){
	Zr <- effects_analysis %>% pull({{Z_colname}})
	VZr <- effects_analysis %>% pull({{VZ_colname}})
	mod <- ManyEcoEvo::fit_metafor_mv(estimate = Zr,
	variance = VZr,
	estimate_type = estimate_type,
	data = effects_analysis)
	return(mod)
	}

ManyAnalysts/supp_mat/SM2_EffectSizeAnalysis.qmd

Lines 721 to 729 in 91ca56a

	fit_MA_mv <- function(effects_analysis, Z_colname, VZ_colname, estimate_type){
	Zr <- effects_analysis %>% pull({{Z_colname}})
	VZr <- effects_analysis %>% pull({{VZ_colname}})
	mod <- ManyEcoEvo::fit_metafor_mv(estimate = Zr,
	variance = VZr,
	estimate_type = estimate_type,
	data = effects_analysis)
	return(mod)
	}

ManyAnalysts/supp_mat/SM3_ExplainingDeviation.qmd

Lines 48 to 61 in 91ca56a

	fit_MA_mv <- function(effects_analysis, Z_colname, VZ_colname, estimate_type){
	Zr <- effects_analysis %>% pull({{Z_colname}})
	VZr <- effects_analysis %>% pull({{VZ_colname}})
	mod <- ManyEcoEvo::fit_metafor_mv(estimate = Zr,
	variance = VZr,
	estimate_type = estimate_type,
	data = effects_analysis)
	return(mod)
	}
	plot_forest <- function(data, intercept = TRUE, MA_mean = TRUE){
	if(MA_mean == FALSE){
	data <- filter(data, study_id != "overall")
	}

• plot_forest
• plot_forest_2 (and what's the difference)?
• consider adding create_model_workflow, could wish to leave in manuscript
• possibly_check_convergence_glm
• plot_model_means_RE
• walk_plot_effects_diversity
• logged Euc analysis

See egould/ManyEcoEvo/

[egouldo]

fit_MA_mv()

• All versions of fit_MA_mv in ManyAnalysts are equal
• Note that fit_MA_mv is a wrapper function around fit_metafor_mv, and calls it explicitly.
• move fun into ManyEcoEvo
• rm from ManyAnalysts

Either:

• update calls in ManyAnalysts with ManyEcoEvo::fit_MA_mv OR
  • move calls into targets pipeline?