version 0.7.2

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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: suddengains
 Title: Identify Sudden Gains in Longitudinal Data
-Date: 2023-02-01
-Version: 0.6.1
+Date: 2023-02-27
+Version: 0.7.2
 Authors@R: c(
   person("Milan", "Wiedemann", email = "milan.wiedemann@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1991-282X")),
   person("Graham M", "Thew", role = "aut", comment = c(ORCID = "0000-0003-2851-1315")),
@@ -27,7 +27,7 @@ RoxygenNote: 7.2.3
 VignetteBuilder: knitr
 Language: en-US
 NeedsCompilation: no
-Packaged: 2023-02-01 13:17:16 UTC; milanwiedemann
+Packaged: 2023-02-27 10:16:59 UTC; milanwiedemann
 Author: Milan Wiedemann [aut, cre] (<https://orcid.org/0000-0003-1991-282X>),
   Graham M Thew [aut] (<https://orcid.org/0000-0003-2851-1315>),
   Richard Stott [ctb] (<https://orcid.org/0000-0003-2533-5504>),
@@ -36,4 +36,4 @@ Author: Milan Wiedemann [aut, cre] (<https://orcid.org/0000-0003-1991-282X>),
   Wellcome Trust [fnd]
 Maintainer: Milan Wiedemann <milan.wiedemann@gmail.com>
 Repository: CRAN
-Date/Publication: 2023-02-01 16:20:06 UTC
+Date/Publication: 2023-02-28 08:30:02 UTC
diff --git a/MD5 b/MD5
@@ -1,59 +1,60 @@
-e9546b454619f029c5d12ef36915a935 *DESCRIPTION
+a2d3503e608300372e7653800e586031 *DESCRIPTION
 5aef96d86daa963ee7f4e4f63ff1e7a2 *LICENSE
 45cdd0b6defddae88ed46ec0a303b8ab *NAMESPACE
 112f380ce0b5a0f6f93c0cd26db2d044 *NEWS.md
-9bb945c7e7b16d968b755ddf906edaf8 *R/check_interval.R
-08eb33cfabe439bf2a96a423785fec6e *R/count_intervals.R
+e3674c3d70a6e8fb73f9dd2bb8c1a98d *R/check_interval.R
+b554ac2526ee0c9c319955bfe3b7a1e6 *R/count_intervals.R
 6ee3e0839073213ff3d52f1de19c5715 *R/create_byperson.R
 e062c0e9eb7bfdd4fd94bf40da125631 *R/create_bysg.R
 96a0c76b746ec2a8b0792b1eba6d452f *R/define_crit1_cutoff.R
-17e1f85d4327bc6424d014d9866a73fe *R/describe_sg.R
+5c004ba92bc0197abe7a73f4c19ce708 *R/describe_sg.R
 105e0b20082f9874a685c2eee8c162f2 *R/extract_values.R
 ea2079016c0cff43b81e5dc4b46b03f9 *R/identify_sg.R
 47b90762eb67744d3bfc9ab897a91d8f *R/identify_sl.R
-f583f5b5856f7cb5f2c5fbb04f39f8a8 *R/magrittrpipeoperator.R
+968d2a2963a06a9b0b28cbd9b8e4428a *R/magrittrpipeoperator.R
 434aef93ef042b25f382f74f2fc998d6 *R/plot_sg.R
 228e0e03ffefd59790607eb9c8ef5830 *R/plot_sg_intervals.R
 ebb2ca77c30da10025ed0040b280d9e9 *R/plot_sg_trajectories.R
 7ec62cc314be6630849e584257d3369b *R/rename_sg_vars.R
-2a86f6a260fa4edafb1c8ebce88c094c *R/select_cases.R
+e21075e7640b7855878be8e3d9dddd93 *R/select_cases.R
 007277c2834bb5d3691b1e40b9a55694 *R/sgdata.R
 81cb43764280baed3f9e74de701e63f4 *R/suddengains.R
-3d933b8488d65fa814b0d385986ea3fc *R/write_byperson.R
-28e98f5c82cdeac6ec318d3a184cca8a *R/write_bysg.R
-2b3972cee1ad77cc487122c74f3ea32f *R/zzz.R
-fd6cf4ad348faf8ae92937d5ab852a67 *README.md
+c9750c7b2e915b4924e72e9e8d88e752 *R/write_byperson.R
+22d70025743ef91f6a47fdb1a325af38 *R/write_bysg.R
+24e5b0398c8ccb1e1b098c441005e066 *R/zzz.R
+6d426b084bbd3075c5fbe2ec47e2ec5c *README.md
 ea124a494ad7922985532ad3b308e4d5 *build/partial.rdb
 ffbc5e0e4b4d33b9c8ab590990824146 *build/vignette.rds
 1aae8c00122076a7afbf638c5fffe83e *data/sgdata.RData
 abfd6092c9e0e0d6c6f39457778b7215 *data/sgdata_bad.RData
 d1902cbeeff54ed0ac9d5252b6ddad88 *inst/CITATION
 6b88cd47b56e7d497d071295ee812d69 *inst/doc/shinygains.Rmd
-b7f0395423217cf64b165a4df2134e16 *inst/doc/shinygains.html
+2d93d3c1c0ded2e4c3b3d0a167767c49 *inst/doc/shinygains.html
 8355fa5c97a76e94f814272d11471a17 *inst/doc/suddengains-tutorial.R
 9760c07f72897bce63f76c6b6a7d1c0b *inst/doc/suddengains-tutorial.Rmd
-026dee4f6763d61c08c0020a3c53a3dc *inst/doc/suddengains-tutorial.html
-ad035fd438e226557efa72d404a3266f *man/check_interval.Rd
+d4749da77fa30637920a7a83c903428b *inst/doc/suddengains-tutorial.html
+a8517e58e06cb1b8b974a4db70ff045f *man/check_interval.Rd
 8ab622c2774dd46d68838ca0feb7182a *man/count_intervals.Rd
 31e50d24fadf54a7e31c0bd91b476378 *man/create_byperson.Rd
 3995788126a9a44e2ecaeba33ebdffb7 *man/create_bysg.Rd
 ba12f2a88df0d6d695d9c11a3d0e9eef *man/define_crit1_cutoff.Rd
 eb4f231ab7b1b359f8e6976642d100d3 *man/describe_sg.Rd
 fc27a73033eaa958111140db3ab99781 *man/extract_values.Rd
 e021cab4345411df921275a6afd55d2f *man/figures/README-unnamed-chunk-4-1.png
-716bf0efb8c476abd85f5d6bf3ee001a *man/figures/README-unnamed-chunk-5-1.png
+e021cab4345411df921275a6afd55d2f *man/figures/README-unnamed-chunk-5-1.png
+52a7b7f00e3f642e0a669d1c253928fe *man/figures/README-unnamed-chunk-6-1.png
 16400914ac362830ec7af5117d226951 *man/identify_sg.Rd
 8db2094dd5c798f035b59478fba29421 *man/identify_sl.Rd
-df34053394040e7ed49c0c49fc239a67 *man/pipe.Rd
+5107f59d340da71c34aed24e8f6f35f3 *man/pipe.Rd
 c6a2c63380b4ff14e13d2c8fb7cc0855 *man/plot_sg.Rd
 a336895ec821d484c88a75f55dc28a91 *man/plot_sg_intervals.Rd
 53bb0dd86e9fba9d76c737bd7d5136a7 *man/plot_sg_trajectories.Rd
 8a528de9d7364d691383a5e2285be409 *man/rename_sg_vars.Rd
 042982de74cbde374ab27ed5aec9a5b9 *man/select_cases.Rd
 cf8ed303d439f690179b7cc846d23299 *man/sgdata.Rd
 978347c9735884f2a4a1cc6e74138700 *man/sgdata_bad.Rd
-ad6ca9d03b837a3bc6f89e0e590658a0 *man/write_byperson.Rd
-7e1d79004f1ec682aaee15289f6aa5c6 *man/write_bysg.Rd
+fad92c3651d12678e6529f903827b670 *man/write_byperson.Rd
+c050561707a9c301988871d2c58e12ca *man/write_bysg.Rd
 99f6992a246e4719f00e69e8e7196bfe *vignettes/r-references.bib
 b10d7f33763f284d4831a1730fc3f130 *vignettes/references.bib
 6b88cd47b56e7d497d071295ee812d69 *vignettes/shinygains.Rmd

diff --git a/R/check_interval.R b/R/check_interval.R
@@ -47,7 +47,7 @@
 #'                sg_crit3_alpha = .01,
 #'                identify = "sg")
 #'
-#' # Check intervall for sudden gain using only third criterion
+#' # Check interval for sudden gain using only third criterion
 #' # Some missing data, alpha = 0.01
 #' check_interval(pre_values = c(NA,31,33),
 #'                post_values = c(5, NA, 7),
@@ -57,7 +57,7 @@
 #'                sg_crit3_alpha = .01,
 #'                identify = "sg")
 #'
-#' # Check intervall for sudden loss using all three criteria
+#' # Check interval for sudden loss using all three criteria
 #' # Some missing data, alpha = 0.05
 #' check_interval(pre_values = c(5, NA, 7),
 #'                post_values = c(16, 12, 14),

diff --git a/R/count_intervals.R b/R/count_intervals.R
@@ -25,7 +25,7 @@
 count_intervals <- function(data, id_var_name, sg_var_list, identify_sg_1to2 = FALSE) {
 
   # First, run identify_sg() function to identify sudden gains and store results
-  data_sg <- suppressMessages(suddengains::identify_sg(data = data,
+  data_sg <- suppressWarnings(suppressMessages(suddengains::identify_sg(data = data,
                                                        # Set this to 1 as it doesnt matter for counting, between session intervals
                                                        # I just need to know where all three criteria can be applied
                                                        sg_crit1_cutoff = 1,
@@ -34,7 +34,7 @@ count_intervals <- function(data, id_var_name, sg_var_list, identify_sg_1to2 = F
                                                        id_var_name = id_var_name,
                                                        sg_var_list = sg_var_list,
                                                        identify_sg_1to2 = identify_sg_1to2
-  ))
+  )))
 
   total_between_sess_intervals <- (base::length(sg_var_list) - 1) * base::nrow(data)
 

diff --git a/R/describe_sg.R b/R/describe_sg.R
@@ -92,5 +92,5 @@ describe_sg <- function(data, sg_data_structure = c("bysg", "byperson")) {
     }
 
     # Return descriptives
-    print(results)
+    results
 }
diff --git a/R/magrittrpipeoperator.R b/R/magrittrpipeoperator.R
@@ -4,6 +4,7 @@
 #' @rdname pipe
 #' @keywords internal
 #' @export
+#' @return Pipe operator %>% from magrittr
 #' @importFrom magrittr %>%
 #' @usage lhs \%>\% rhs
 NULL
diff --git a/R/select_cases.R b/R/select_cases.R
@@ -66,7 +66,7 @@ select_cases <- function(data, id_var_name, sg_var_list, method = c("pattern", "
 
     # Select variables and arrange by id
     data_select <- data %>%
-      dplyr::select(id_var_name, sg_var_list) %>%
+      dplyr::select(dplyr::all_of(id_var_name), dplyr::all_of(sg_var_list)) %>%
       dplyr::arrange(!! rlang::sym(id_var_name))
 
     method <- match.arg(method)
@@ -79,20 +79,20 @@ select_cases <- function(data, id_var_name, sg_var_list, method = c("pattern", "
       data_pattern <- !is.na(data_select[ , 2:(length(sg_var_list) + 1)])
 
       # Get list of IDs
-      id_list <- dplyr::select(data_select, id_var_name)
+      id_list <- dplyr::select(data_select, dplyr::all_of(id_var_name))
 
       # Combine IDs with data pattern
       data_pattern <- base::cbind(id_list, data_pattern)
 
       data_out <- data_pattern %>%
           tibble::as_tibble() %>%
-          tidyr::unite("pattern", sg_var_list, sep = " ") %>%
+          tidyr::unite("pattern", dplyr::all_of(sg_var_list), sep = " ") %>%
           dplyr::mutate(sg_pattern_1 = stringr::str_detect(pattern, "TRUE TRUE TRUE TRUE"),
                sg_pattern_2 = stringr::str_detect(pattern, "TRUE TRUE TRUE FALSE TRUE"),
                sg_pattern_3 = stringr::str_detect(pattern, "TRUE FALSE TRUE TRUE TRUE"),
                sg_pattern_4 = stringr::str_detect(pattern, "TRUE FALSE TRUE TRUE FALSE TRUE"),
                sg_select = dplyr::if_else(condition = (sg_pattern_1 == TRUE | sg_pattern_2 == TRUE | sg_pattern_3 == TRUE | sg_pattern_4 == TRUE), TRUE, FALSE)) %>%
-          dplyr::select(id_var_name, sg_select)
+          dplyr::select(dplyr::all_of(id_var_name), sg_select)
 
       } else if (method == "min_sess") {
 
@@ -110,7 +110,7 @@ select_cases <- function(data, id_var_name, sg_var_list, method = c("pattern", "
 
       data_out <- data_select %>%
           dplyr::mutate(sg_select = dplyr::if_else(nvalid >= min_sess_num, TRUE, FALSE)) %>%
-          dplyr::select(id_var_name, sg_select)
+          dplyr::select(dplyr::all_of(id_var_name), sg_select)
       }
 
     if (return_id_lgl == TRUE) {

diff --git a/R/write_byperson.R b/R/write_byperson.R
@@ -39,6 +39,7 @@
 #' @param stata_version Numeric, specifying STATA version number.
 #' @references Tang, T. Z., & DeRubeis, R. J. (1999). Sudden gains and critical sessions in cognitive-behavioral therapy for depression. Journal of Consulting and Clinical Psychology, 67(6), 894–904. \doi{10.1037/0022-006X.67.6.894}.
 #' @export
+#' @return A csv file containing a wide data set with one row per case (\code{id_var_name}) in \code{data}.
 #' @examples
 #' # Adjust "path" argument before running
 #' # Create character string name for temporary "byperson.csv" file

diff --git a/R/write_bysg.R b/R/write_bysg.R
@@ -36,6 +36,7 @@
 #' @param stata_version Numeric, specifying STATA version number.
 #' @references Tang, T. Z., & DeRubeis, R. J. (1999). Sudden gains and critical sessions in cognitive-behavioral therapy for depression. Journal of Consulting and Clinical Psychology, 67(6), 894–904. \doi{10.1037/0022-006X.67.6.894}.
 #' @export
+#' @return A csv file containing a wide data set with one row per sudden gain/loss.
 #' @importFrom rlang :=
 #' @examples # Adjust "path" argument before running
 #' # Create character string name for temporary "bysg.csv" file

diff --git a/R/zzz.R b/R/zzz.R
@@ -5,10 +5,9 @@
                         fields = "Version")
 
     startup_msg <- function() {
-        cli::cli_h1(paste0("This is ", pkgname, " ", version))
-        cli::cli_alert_info(paste0("Please report any issues or ideas at:"))
-        cli::cli_alert_info("https://github.com/milanwiedemann/suddengains/issues")
-        invisible()
+        packageStartupMessage("This is ", pkgname, " ", version)
+        packageStartupMessage("Please report any issues or ideas at:")
+        packageStartupMessage("https://github.com/milanwiedemann/suddengains/issues")
     }
 
     packageStartupMessage(startup_msg())

diff --git a/README.md b/README.md
@@ -1,12 +1,12 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# suddengains
+# suddengains: Identify Sudden Gains in Longitudinal Data
 
 <!-- badges: start -->
+
 [![licence](https://img.shields.io/badge/Licence-MIT-brightgreen.svg)](https://choosealicense.com/licenses/mit/)
 [![CRANstatus](https://www.r-pkg.org/badges/version/suddengains)](https://cran.r-project.org/package=suddengains)
-[![](https://cranlogs.r-pkg.org/badges/grand-total/suddengains/)](https://cran.r-project.org/package=suddengains/)
 <!-- badges: end -->
 
 Sudden gains are large and stable improvements in an outcome variable
@@ -93,7 +93,19 @@ A detailed illustration of all functions can be found in the vignette on
 [CRAN](https://CRAN.R-project.org/package=suddengains/). Note that the
 vignette is only available in R when you install the package from CRAN.
 
-## Examples
+## How to use `suddengains`
+
+Here are a few examples how to use the `suddengains` package.
+
+``` r
+# Load the package
+library(suddengains)
+#> 
+#> ── This is suddengains 0.7.0 ───────────────────────────────────────────────────
+#> ℹ Please report any issues or ideas at:
+#> ℹ https://github.com/milanwiedemann/suddengains/issues
+#> 
+```
 
 Below are some examples illustrating the suddengains package. More
 details can be found in the
@@ -177,7 +189,7 @@ plot_sg(data = bysg,
 #> Warning: Removed 10 rows containing non-finite values (`stat_summary()`).
 ```
 
-<img src="man/figures/README-unnamed-chunk-4-1.png" width="50%" />
+<img src="man/figures/README-unnamed-chunk-5-1.png" width="50%" />
 
 ``` r
 # Visualise trajectories for a selection of individual cases
@@ -205,4 +217,4 @@ plot_sg_trajectories(data = sgdata,
 #> Warning: Removed 3 rows containing missing values (`geom_label_repel()`).
 ```
 
-<img src="man/figures/README-unnamed-chunk-5-1.png" width="80%" />
+<img src="man/figures/README-unnamed-chunk-6-1.png" width="80%" />
diff --git a/inst/doc/shinygains.html b/inst/doc/shinygains.html