diff --git a/DESCRIPTION b/DESCRIPTION
index 61faef7..bad8e18 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: gateR
Type: Package
-Title: Statistical Gating Application for Flow and Mass Cytometry Analysis via Spatial Kernel Density Estimation
-Version: 0.1.1
-Date: 2020-10-29
+Title: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation
+Version: 0.1.2
+Date: 2020-11-05
Authors@R:
c(person(given = "Ian D.",
family = "Buller",
diff --git a/R/gating.R b/R/gating.R
index 76c94b1..9055e6e 100644
--- a/R/gating.R
+++ b/R/gating.R
@@ -233,8 +233,8 @@ gating <- function(dat,
# Go back one gate if current gate has no significant area and produce output of previous gate
if (all(raster::values(Ps)[!is.na(raster::values(Ps))] == 2) | all(is.na(raster::values(Ps)))) {
- cat(paste("\nGate", k, "yeilded no significant", type_cluster, "cluster(s)...",
- "Returning results from previous gate\n",
+ message(paste("Gate", k, "yeilded no significant", type_cluster, "cluster(s)...",
+ "Returning results from previous gate",
sep = " "))
output <- dat[which(dat[ , 1] %in% dat_gate[ , 1]), ]
out_list <- list("obs" = output, "n" = n_out, "gate" = list_gate)
@@ -250,8 +250,8 @@ gating <- function(dat,
pols <- try(maptools::unionSpatialPolygons(out_pol[out_pol$layer == v, ],
IDs = rep(1, length(out_pol[out_pol$layer == v, ]))), silent = TRUE)
if("try-error" %in% class(pols)) {
- cat(paste("Gate", k, "yeilded no significant", type_cluster, "cluster(s)...",
- "Returning results from previous gate\n",
+ message(paste("Gate", k, "yeilded no significant", type_cluster, "cluster(s)...",
+ "Returning results from previous gate",
sep = " "))
output <- dat[which(dat[ , 1] %in% dat_gate[ , 1]), ]
out_list <- list("obs" = output, "n" = n_out, "gate" = list_gate)
@@ -269,7 +269,7 @@ gating <- function(dat,
# Output for the final gate
if (k == n_gate) {
- cat(paste("\nObservations within significant", type_cluster, "cluster(s) of Gate", k, "\n",sep = " "))
+ message(paste("Observations within significant", type_cluster, "cluster(s) of Gate", k, sep = " "))
output <- dat[which(dat[ , 1] %in% dat_gate[ , 1]), ]
n_out[[k + 1]] <- nrow(output)
out_list <- list("obs" = output, "n" = n_out, "gate" = list_gate)
diff --git a/R/lotrrs.R b/R/lotrrs.R
index bb8b424..96459ea 100644
--- a/R/lotrrs.R
+++ b/R/lotrrs.R
@@ -212,14 +212,14 @@ lotrrs <- function(dat,
rm(t0_rr_bd, t1_rr_bd) # conserve memory
if (all(is.na(out$rr$v))) {
- cat("relative risk unable to be estimated")
+ message("relative risk unable to be estimated")
return(out)
}
# Alpha level
if (p_correct == "none") { out$alpha <- alpha }
if (p_correct == "correlated") {
- cat("\nPlease be patient... Calculating correlated Bonferroni correction\n")
+ message("Please be patient... Calculating correlated Bonferroni correction")
alpha_correct <- pval_correct(input = out$lrr, alpha = alpha, nbc = nbc)
out$alpha <- alpha_correct$correlated
}
diff --git a/R/package.R b/R/package.R
index 4899b1b..c4ce1f9 100644
--- a/R/package.R
+++ b/R/package.R
@@ -1,4 +1,4 @@
-#' The gateR Package: Statistical Gating Application for Flow and Mass Cytometry Analysis via Spatial Kernel Density Estimation
+#' The gateR Package: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation
#'
#' Estimates statistically significant fluorescent marker combination values within which one immunologically distinctive group (i.e., disease case) is more associated than another group (i.e., healthy control), successively, using various combinations (i.e., "gates") of fluorescent markers to examine features of cells that may be different between groups.
#'
diff --git a/R/rrs.R b/R/rrs.R
index 469dbae..02748a3 100644
--- a/R/rrs.R
+++ b/R/rrs.R
@@ -140,7 +140,7 @@ rrs <- function(dat,
...)))
if (all(is.na(out$rr$v))) {
- cat("relative risk unable to be estimated")
+ message("relative risk unable to be estimated")
return(out)
}
@@ -150,7 +150,7 @@ rrs <- function(dat,
# Alpha level
if (p_correct == "none") { out$alpha <- alpha }
if (p_correct == "correlated") {
- cat("\nPlease be patient... Calculating correlated Bonferroni correction\n")
+ message("Please be patient... Calculating correlated Bonferroni correction")
alpha_correct <- pval_correct(input = out$lrr, alpha = alpha, nbc = nbc)
out$alpha <- alpha_correct$correlated
}
diff --git a/cran-comments.md b/cran-comments.md
index 7a945b7..693cb0d 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,9 +1,8 @@
-## This is the first resubmission
+## This is the second resubmission
-* Actions taken regarding feedback from CRAN teams' auto-check service
- * Reduced overall checktime by changing example in gating() by changing from \donttest{} to if (interactive()) {}
- * Reduced overall checktime by streamlining the number of "[it] works" tests in testthat for gating(), lotrrs(), and rrs()
- * Note about "Possibly mis-spelled words in DESCRIPTION" can be safely ignored
+* Actions taken regarding feedback from Gregor Seyer:
+ * Reduced the length of the title to less than 65 characters
+ * Replaced cat() with message() in gating(), lotrrs(), and rrs() functions to allow for suppressable information messages
## Test environments
* local OS X install, R 3.6.3
@@ -27,9 +26,9 @@ There was 1 NOTE:
0 errors | 0 warnings | 0 notes
* Duration
- * local OS X install, R 3.6.3: 97 seconds
- * win-builder, devel: 584 seconds (under 10 minutes)
- * win-builder, oldrelease: 530 seconds
- * win-builder, release: 620 seconds
+ * local OS X install, R 3.6.3: 99 seconds
+ * win-builder, devel: 341 seconds
+ * win-builder, oldrelease: 282 seconds
+ * win-builder, release: 330 seconds
## Submitted by Maintainer
diff --git a/man/gateR-package.Rd b/man/gateR-package.Rd
index e36daac..d44e3ba 100644
--- a/man/gateR-package.Rd
+++ b/man/gateR-package.Rd
@@ -4,7 +4,7 @@
\name{gateR-package}
\alias{gateR-package}
\alias{gateR}
-\title{The gateR Package: Statistical Gating Application for Flow and Mass Cytometry Analysis via Spatial Kernel Density Estimation}
+\title{The gateR Package: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation}
\description{
Estimates statistically significant fluorescent marker combination values within which one immunologically distinctive group (i.e., disease case) is more associated than another group (i.e., healthy control), successively, using various combinations (i.e., "gates") of fluorescent markers to examine features of cells that may be different between groups.
}
diff --git a/vignettes/vignette.Rmd b/vignettes/vignette.Rmd
index 34c9ffa..4d3a8cb 100644
--- a/vignettes/vignette.Rmd
+++ b/vignettes/vignette.Rmd
@@ -1,10 +1,10 @@
---
-title: "gateR: Statistical Gating Application for Flow and Mass Cytometry Analysis via Spatial Kernel Density Estimation"
+title: "gateR: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation"
author: 'Ian D. Buller, Ph.D., M.A. (Github: @idblr)'
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
- %\VignetteIndexEntry{gateR: Statistical Gating Application for Flow and Mass Cytometry Analysis via Spatial Kernel Density Estimation}
+ %\VignetteIndexEntry{gateR: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation}
%\VignetteEngine{R.rsp::asis}
%\VignetteEncoding{UTF-8}
---
diff --git a/vignettes/vignette.html b/vignettes/vignette.html
index 9ad13ce..ccbb5a1 100644
--- a/vignettes/vignette.html
+++ b/vignettes/vignette.html
@@ -12,9 +12,9 @@
-
+
-gateR: Statistical Gating Application for Flow and Mass Cytometry Analysis via Spatial Kernel Density Estimation
+gateR: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation