rename vars to same style

R-Computing-Lab · Sep 8, 2023 · a46d03d · a46d03d
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Showing 15 changed files with 136 additions and 77 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export(PlotPedigree)
 export(SimPed)
 export(allGens)
 export(comp2vech)
@@ -15,8 +14,10 @@ export(ped2com)
 export(ped2fam)
 export(ped2graph)
 export(ped2mit)
+export(plotPedigree)
 export(related_coef)
 export(relatedness)
+export(simulatePedigree)
 export(vech)
 import(kinship2)
 importFrom(stats,runif)
diff --git a/R/famSizeCal.R b/R/famSizeCal.R
@@ -1,5 +1,5 @@
 #' allGens
-#' A function to calculate the number of individuals in each generation. This is a supporting function for \code{SimPed}.
+#' A function to calculate the number of individuals in each generation. This is a supporting function for \code{simulatePedigree}.
 #' @param kpc Number of kids per couple (integer >= 2).
 #' @param Ngen Number of generations (integer >= 1).
 #' @param marR Mating rate (numeric value ranging from 0 to 1).
@@ -27,7 +27,7 @@ allGens <- function(kpc, Ngen, marR) {
 
 
 #' sizeAllGens
-#' An internal supporting function for \code{SimPed}.
+#' An internal supporting function for \code{simulatePedigree}.
 #' @inheritParams allGens
 #' @return Returns a vector including the number of individuals in every generation.
 
@@ -50,7 +50,7 @@ sizeAllGens <- function(kpc, Ngen, marR) {
 
 
 #' famSizeCal
-#' A function to calculate the total number of individuals in a pedigree given parameters. This is a supporting function for function \code{SimPed}
+#' A function to calculate the total number of individuals in a pedigree given parameters. This is a supporting function for function \code{simulatePedigree}
 #' @inheritParams allGens
 #' @return Returns a numeric value indicating the total pedigree size.
 #' @export

diff --git a/R/helper.R b/R/helper.R
@@ -63,3 +63,26 @@ Null <- function(M) {
   }
   return(qr.Q(tmp, complete = TRUE)[, set, drop = FALSE])
 }
+
+#' SimPed (Deprecated)
+#'
+#' This function is a wrapper around the new `simulatePedigree` function.
+#' `SimPed` has been deprecated, and it's advised to use `simulatePedigree` directly.
+#'
+#' @param ... Arguments to be passed to `simulatePedigree`.
+#' @return The same result as calling `simulatePedigree`.
+#' @seealso \code{\link{simulatePedigree}} for the updated function.
+#' @description When calling this function, a warning will be issued about its deprecation.
+#' @keywords deprecated
+#' @examples
+#' \dontrun{
+#' # This is an example of the deprecated function:
+#' SimPed(...)
+#' # It is recommended to use:
+#' simulatePedigree(...)
+#' }
+#' @export
+SimPed <- function(...) {
+  warning("The 'SimPed' function is deprecated. Please use 'simulatePedigree' instead.")
+  simulatePedigree(...)
+}
diff --git a/R/PlotPedigree.R → R/plotPedigree.R b/R/PlotPedigree.R → R/plotPedigree.R
@@ -1,13 +1,13 @@
-#' PlotPedigree
-#' A wrapped function to plot simulated pedigree from function \code{SimPed}. This function require the installation of package \code{kinship2}.
+#' plotPedigree
+#' A wrapped function to plot simulated pedigree from function \code{simulatePedigree}. This function require the installation of package \code{kinship2}.
 #' @import kinship2
-#' @param ped The simulated pedigree data.frame from function \code{SimPed}. Or a pedigree dataframe with the same colnames as the dataframe simulated from function \code{SimPed}.
+#' @param ped The simulated pedigree data.frame from function \code{simulatePedigree}. Or a pedigree dataframe with the same colnames as the dataframe simulated from function \code{simulatePedigree}.
 #' @param cex The font size of the IDs for each individual in the plot.
 #' @inheritParams kinship2::plot.pedigree
 #' @return A plot of the simulated pedigree
 #' @export
 
-PlotPedigree <- function(ped, cex = .5,
+plotPedigree <- function(ped, cex = .5,
                          # optional inputs for the pedigree plot
                          col = 1,
                          symbolsize = 1, branch = 0.6,
@@ -45,4 +45,4 @@ PlotPedigree <- function(ped, cex = .5,
   ))
 }
 
-# PlotPedigree(SimPed(kpc = 2, Ngen = 6, marR = .8))
+# plotPedigree(simulatePedigree(kpc = 2, Ngen = 6, marR = .8))
diff --git a/R/SimPed.R → R/simulatePedigree.R b/R/SimPed.R → R/simulatePedigree.R
@@ -25,7 +25,7 @@
 #' }
 #' @export
 
-SimPed <- function(kpc = 3,
+simulatePedigree <- function(kpc = 3,
                    Ngen = 4,
                    sexR = .5,
                    marR = 2 / 3,

diff --git a/man/PlotPedigree.Rd b/man/PlotPedigree.Rd
diff --git a/man/SimPed.Rd b/man/SimPed.Rd
diff --git a/man/allGens.Rd b/man/allGens.Rd
diff --git a/man/famSizeCal.Rd b/man/famSizeCal.Rd
diff --git a/man/hazard.Rd b/man/hazard.Rd
diff --git a/man/simulatePedigree.Rd b/man/simulatePedigree.Rd
diff --git a/man/sizeAllGens.Rd b/man/sizeAllGens.Rd
diff --git a/tests/testthat/test-pedigreesim.R b/tests/testthat/test-pedigreesim.R
@@ -1,6 +1,6 @@
 test_that("simulated pedigree generates expected data structure", {
   set.seed(5)
-  results <- SimPed(kpc = 4, Ngen = 4, sexR = .5, marR = .7)
+  results <- simulatePedigree(kpc = 4, Ngen = 4, sexR = .5, marR = .7)
 
   expect_equal(length(results$ID), 57)
   expect_equal(length(results), 7)

diff --git a/vignettes/vignette_pedigree.Rmd b/vignettes/vignette_pedigree.Rmd
@@ -38,7 +38,7 @@ For example, a pedigree that follows these conditions: There are a total of four
 
 ```{r}
 set.seed(5)
-Ped <- SimPed(kpc = 4, Ngen = 4, sexR = .5, marR = .7)
+Ped <- simulatePedigree(kpc = 4, Ngen = 4, sexR = .5, marR = .7)
 
 summary(Ped)
 ```
@@ -54,15 +54,15 @@ The columns represents the individual's family ID, the individual's personal ID,
 ## Plotting Pedigree
 
 
-Pedigrees are visual diagrams that represent family relationships across generations. They are commonly used in genetics to trace the inheritance of specific traits or conditions. This vignette will guide you through visualizing simulated pedigrees using the `PlotPedigree` function. This function is a wrapper function for Kinship2's base R plotting.
+Pedigrees are visual diagrams that represent family relationships across generations. They are commonly used in genetics to trace the inheritance of specific traits or conditions. This vignette will guide you through visualizing simulated pedigrees using the `plotPedigree` function. This function is a wrapper function for Kinship2's base R plotting.
 
 ### Single Pedigree Visualization
 
-To visualize a single simulated pedigree, use the `PlotPedigree()` function.
+To visualize a single simulated pedigree, use the `plotPedigree()` function.
 
 ```{r,fig.width=8,fig.height=6}
 # Plot the simulated pedigree
-PlotPedigree(Ped)
+plotPedigree(Ped)
 ```
 
 
@@ -75,19 +75,19 @@ If you wish to compare different pedigrees side by side, you can plot them toget
 
 ```{r,fig.width=8, fig.height=6}
 # Simulate a family with 3 generations
-df_ped_3 <- SimPed(Ngen = 3)
+df_ped_3 <- simulatePedigree(Ngen = 3)
 
 # Simulate a family with 4 generations
-df_ped_4 <- SimPed(Ngen = 4)
+df_ped_4 <- simulatePedigree(Ngen = 4)
 
 # Set up plotting parameters for side-by-side display
 par(mfrow = c(1, 2))
 
 # Plot the 3-generation pedigree
-PlotPedigree(df_ped_3, width = 3)
+plotPedigree(df_ped_3, width = 3)
 
 # Plot the 4-generation pedigree
-PlotPedigree(df_ped_4, width = 1)
+plotPedigree(df_ped_4, width = 1)
 ```   
 
 By examining the side-by-side plots, you can contrast and analyze the structures of different families, tracing the inheritance of specific traits or conditions if needed.