tweaking documentation and small bits of code to get rid of notes at …

…r cmd check

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: EloOptimized
 Title: Optimized Elo Rating Method for Obtaining Dominance Ranks
-Version: 0.3.1.9000
-Date: 2023-05-08
+Version: 0.3.1.9999
+Date: 2024-05-21
 Authors@R: c(
     person("Joseph", "Feldblum", email = "jtf9@duke.edu", role = c("aut", "cre")),
     person("Steffen", "Foerster", email = "sf2041@gmail.com", role = c("aut")),
@@ -13,11 +13,12 @@ Depends:
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Imports: dplyr,
     reshape2,
     BAMMtools,
     magrittr,
+    methods,
     lubridate,
     rlang
 URL: https://github.com/jtfeld/EloOptimized

NAMESPACE

@@ -8,6 +8,7 @@ export(eloratingopt)
 import(BAMMtools)
 import(reshape2)
 importFrom(magrittr,"%>%")
+importFrom(methods,is)
 importFrom(rlang,.data)
 importFrom(stats,approx)
 importFrom(stats,ave)

NEWS.md

@@ -1,11 +1,15 @@
-# EloOptimized 0.3.1.9000 (unreleased)
+# EloOptimized 0.3.1.9999
+
+* Mostly a maintenance release to resubmit package to CRAN
 
 * Added a step to check that agon_data are in chronological order, and throw a warning if not.
 
 * Fixed checks for ubuntu and Mac
 
 * Added new and improved informative errors to eloratingopt() that tell you which individuals are filtered out for not having >= 1 win and 1 loss, and which individuals have interactions outside of their presence window.
 
+* Tweaked documentation formatting and code for converting date columns to comply with R CMD check
+
 # EloOptimized 0.3.1
 
 * Mostly a maintenance update

R/eloratingfixed.R

@@ -37,9 +37,9 @@
 #'   this help file:
 #'   
 #' @return Returns a list with six elements: 
-#' \itemize{
+#' \describe{
 #'  \item{\strong{elo}}{ Data frame with all IDs and dates they were present, with the following columns:}
-#'    \itemize{
+#'    \describe{
 #'      \item{Date}{: Dates of study period}
 #'      \item{Individual}{: the names of each ranked individual, for each date they were present}
 #'      \item{Elo}{: fitted Elo scores for each individual on each day}
@@ -74,6 +74,7 @@
 #' @importFrom stats approx ave optim reshape
 #' @importFrom utils read.csv write.csv
 #' @importFrom rlang .data
+#' @importFrom methods is
 #' @import reshape2
 #' @import BAMMtools
 #' @importFrom magrittr "%>%"
@@ -106,9 +107,10 @@ eloratingfixed <- function(agon_data, pres_data, k = 100, init_elo = 1000,
     stop("can't have same ID win and lose in one interaction")
   }
 
-  if(class(ago$Date) != "Date"){
-    ago$Date = lubridate::mdy(ago$Date)
-  }
+  # if(class(ago$Date) != "Date"){
+  #   ago$Date = lubridate::mdy(ago$Date)
+  # }
+  if(!is(ago$Date, "Date")) ago$Date = lubridate::mdy(ago$Date)
 
   if(any(ago$Date < dplyr::lag(x = ago$Date, 
                                n = 1, 
@@ -140,10 +142,12 @@ eloratingfixed <- function(agon_data, pres_data, k = 100, init_elo = 1000,
     if(!all(names(presence) %in% c("id", "start_date", "end_date"))){
       stop("colnames in presence data should be 'id', 'start_date', 'end_date' (not case sensitive)")
     }
-    if(class(presence$start_date) != "Date"){
-      presence$start_date = lubridate::mdy(presence$start_date)}
-    if(class(presence$end_date) != "Date"){
-      presence$end_date = lubridate::mdy(presence$end_date)}
+    # if(class(presence$start_date) != "Date"){
+    #   presence$start_date = lubridate::mdy(presence$start_date)}
+    if(!is(presence$start_date, "Date")) presence$start_date = lubridate::mdy(presence$start_date)
+    # if(class(presence$end_date) != "Date"){
+    #   presence$end_date = lubridate::mdy(presence$end_date)}
+    if(!is(presence$end_date, "Date")) presence$end_date = lubridate::mdy(presence$end_date)
 
     presence$id = as.character(presence$id)
 

R/eloratingopt.R

@@ -39,9 +39,9 @@
 #'   
 #' 
 #' @return Returns a list with five or six elements (depending on input): 
-#' \itemize{
+#' \describe{
 #'  \item{\strong{elo}}{ Data frame with all IDs and dates they were present, with the following columns:}
-#'    \itemize{
+#'    \describe{
 #'      \item{Date}{: Dates of study period}
 #'      \item{Individual}{: the names of each ranked individual, for each date they were present}
 #'      \item{Elo}{: fitted Elo scores for each individual on each day}
@@ -76,6 +76,7 @@
 #' @importFrom stats approx ave optim reshape
 #' @importFrom utils read.csv write.csv
 #' @importFrom rlang .data
+#' @importFrom methods is
 #' @import reshape2
 #' @import BAMMtools
 #' @importFrom magrittr "%>%"
@@ -107,9 +108,10 @@ eloratingopt <- function(agon_data, pres_data, fit_init_elo = FALSE, outputfile
     stop("can't have same ID win and lose in one interaction")
   }
 
-  if(class(ago$Date) != "Date"){
-    ago$Date = lubridate::mdy(ago$Date)
-  }
+  # if(class(ago$Date) != "Date"){
+  #   ago$Date = lubridate::mdy(ago$Date)
+  # }
+  if(!is(ago$Date, "Date")) ago$Date = lubridate::mdy(ago$Date)
 
   if(any(ago$Date < dplyr::lag(x = ago$Date, 
                                n = 1, 
@@ -141,10 +143,12 @@ eloratingopt <- function(agon_data, pres_data, fit_init_elo = FALSE, outputfile
     if(!all(names(presence) %in% c("id", "start_date", "end_date"))){
       stop("colnames in presence data should be 'id', 'start_date', 'end_date' (not case sensitive)")
     }
-    if(class(presence$start_date) != "Date"){
-      presence$start_date = lubridate::mdy(presence$start_date)}
-    if(class(presence$end_date) != "Date"){
-      presence$end_date = lubridate::mdy(presence$end_date)}
+    # if(class(presence$start_date) != "Date"){
+    #   presence$start_date = lubridate::mdy(presence$start_date)}
+    if(!is(presence$start_date, "Date")) presence$start_date = lubridate::mdy(presence$start_date)
+    # if(class(presence$end_date) != "Date"){
+    #   presence$end_date = lubridate::mdy(presence$end_date)}
+    if(!is(presence$end_date, "Date")) presence$end_date = lubridate::mdy(presence$end_date)
 
     presence$id = as.character(presence$id)