From c8a661a40e7638f3117501ebb167df6b7337707c Mon Sep 17 00:00:00 2001
From: Liang Zhang <psychelzh@outlook.com>
Date: Sun, 6 Oct 2024 14:40:01 +0800
Subject: [PATCH 1/5] Add issue links in NEWS

---
 NEWS.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index a1ecabd..0b91d92 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,8 +2,8 @@
 
 ## New features
 
-* Added `summary()` method to summarize the results of the CPM analysis.
-* Added `tidy()` method to tidy the results of the CPM analysis.
+* Added `summary()` method to summarize the results of the CPM analysis (#8).
+* Added `tidy()` method to tidy the results of the CPM analysis (#10).
 * Support `na_action` argument in `cpm()` function to handle missing values in the input data (#2).
 
 ## Enhancements

From 6267a62a6deec4ae1d6a41b1d0628559ed51bd88 Mon Sep 17 00:00:00 2001
From: Liang Zhang <psychelzh@outlook.com>
Date: Sun, 6 Oct 2024 14:48:03 +0800
Subject: [PATCH 2/5] Fix check notes

---
 R/cpm.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/cpm.R b/R/cpm.R
index f8142b8..f84fb4f 100644
--- a/R/cpm.R
+++ b/R/cpm.R
@@ -133,10 +133,10 @@ cpm <- function(conmat, behav, ...,
     exclude = Reduce(
       function(x, y) intersect(x, y),
       list(
-        which(complete.cases(conmat)),
-        which(complete.cases(behav)),
+        which(stats::complete.cases(conmat)),
+        which(stats::complete.cases(behav)),
         if (!is.null(confounds)) {
-          which(complete.cases(confounds))
+          which(stats::complete.cases(confounds))
         } else {
           seq_along(behav)
         }
@@ -225,7 +225,7 @@ print.cpm <- function(x, ...) {
   cat("  Call: ")
   print(x$call)
   cat(sprintf("  Number of observations: %d\n", length(x$real)))
-  cat(sprintf("    Complete cases: %d\n", sum(complete.cases(x$pred))))
+  cat(sprintf("    Complete cases: %d\n", sum(stats::complete.cases(x$pred))))
   if (!is.null(x$edges)) {
     cat(sprintf("  Number of edges: %d\n", dim(x$edges)[1]))
   } else {

From 315788a02e2b3754382b7db69f186c51dbed714f Mon Sep 17 00:00:00 2001
From: Liang Zhang <psychelzh@outlook.com>
Date: Sun, 6 Oct 2024 14:53:31 +0800
Subject: [PATCH 3/5] Update link anchor

---
 R/tidy.R        | 2 +-
 man/tidy.cpm.Rd | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/tidy.R b/R/tidy.R
index dfccb24..29f447b 100644
--- a/R/tidy.R
+++ b/R/tidy.R
@@ -7,7 +7,7 @@ generics::tidy
 #' @param x A `cpm` object.
 #' @param ... Additional arguments passed to `summary()`.
 #' @param component A character vector indicating the component to tidy.
-#' @return A [tibble][tibble-package] with columns storing parameters of the
+#' @return A [tibble][tibble::tibble-package] with columns storing parameters of the
 #'   [cpm()] object and further columns depending on the `component` argument:
 #'
 #'   For `component = "performance"`:
diff --git a/man/tidy.cpm.Rd b/man/tidy.cpm.Rd
index 4cfdff0..eb4e0c8 100644
--- a/man/tidy.cpm.Rd
+++ b/man/tidy.cpm.Rd
@@ -14,7 +14,7 @@
 \item{component}{A character vector indicating the component to tidy.}
 }
 \value{
-A \link[=tibble-package]{tibble} with columns storing parameters of the
+A \link[tibble:tibble-package]{tibble} with columns storing parameters of the
 \code{\link[=cpm]{cpm()}} object and further columns depending on the \code{component} argument:
 
 For \code{component = "performance"}:

From 392c4e9ce92aa7839e28f681d658712afda45ace Mon Sep 17 00:00:00 2001
From: Liang Zhang <psychelzh@outlook.com>
Date: Sun, 6 Oct 2024 14:58:09 +0800
Subject: [PATCH 4/5] Update cran comments

---
 cran-comments.md | 14 +-------------
 1 file changed, 1 insertion(+), 13 deletions(-)

diff --git a/cran-comments.md b/cran-comments.md
index d6a0fba..b21fce6 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,15 +1,3 @@
 ## R CMD check results
 
-0 errors | 0 warnings | 1 note
-
-* This is a new release.
-
-The NOTE is as follows:
-
-```
-❯ checking for non-standard things in the check directory ... NOTE
-  Found the following files/directories:
-    ''NULL''
-```
-
-As noted in [this issue](https://github.com/r-hub/rhub/issues/560), this is a known issue with the `rhub` package and can be safely ignored.
+Use `devtools::check_win_devel()` shows no errors, warnings and notes.

From 9853375200efe8dfc100c10bdcf1ae4046ab3314 Mon Sep 17 00:00:00 2001
From: Liang Zhang <psychelzh@outlook.com>
Date: Sun, 6 Oct 2024 15:00:43 +0800
Subject: [PATCH 5/5] Increment version number to 0.1.0

---
 DESCRIPTION | 2 +-
 NEWS.md     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 2a96c41..9465145 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: cpmr
 Title: Connectome Predictive Modelling in R
-Version: 0.0.9.9000
+Version: 0.1.0
 Authors@R:
     person("Liang", "Zhang", , "psychelzh@outlook.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-9041-1150"))
diff --git a/NEWS.md b/NEWS.md
index 0b91d92..4c84c38 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# cpmr (development version)
+# cpmr 0.1.0
 
 ## New features