Addressing review comments

Author: ZekeMarshall

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: RMAVIS
 Title: Assign Vegetation Survey Data to GB NVC Communities
 Version: 1.0
-Date: 2024-06-16
+Date: 2024-07-02
 Authors@R: c(person(given = "Zeke",
                     family = "Marshall",
                     role = c("aut", "cre"),
@@ -56,7 +56,8 @@ Imports:
   vegan,
   writexl
 Suggests:
-  testthat
+  testthat,
+  tinytex
 URL: https://github.com/NERC-CEH/RMAVIS
 BugReports: https://github.com/NERC-CEH/RMAVIS/issues
 Depends: 

NEWS.md

@@ -1,9 +1,5 @@
----
-title: "Release notes for `RMAVIS`"
-output: html_document
----
 
-# RMAVIS 1.0 (2024-06-16)
+# RMAVIS 1.0 (2024-07-02)
 *   Modifications:
       -   Updating README to include instructions on installing a LaTeX distribution using `{tinytex}`.
       -   Removing Dockerfile and docker-compose.yml as they are currently superfluous.
@@ -13,7 +9,7 @@ output: html_document
           ./inst/app/app.R
 *   New Features:
       -   Adding News section.
-      -   Adding function to run app (`RMAVIS::runApp()`).
+      -   Adding function to run app - `RMAVIS::runApp()`.
       -   Adding contribution guidelines in CONTRIBUTING.md.
 
 # RMAVIS 0.9998 (2024-05-22)

README.Rmd

@@ -57,6 +57,7 @@ To run RMAVIS locally take the following steps.
 2.  Install `RMAVIS` using `remotes::install_github("NERC-CEH/RMAVIS")`
 3.  Run `install.packages("tinytex")` then `tinytex::install_tinytex()` to install a minimal LaTeX distribution.
     This is required to generate a pdf report.
+    Note that this is only required if you do not have a LaTeX distribution already installed.
 4.  From the R terminal run `RMAVIS::runApp()`.
 
 If you wish to use the NVC-matching functions outside of the `RMAVIS` app, 

README.md

@@ -56,7 +56,8 @@ To run RMAVIS locally take the following steps.
 2.  Install `RMAVIS` using `remotes::install_github("NERC-CEH/RMAVIS")`
 3.  Run `install.packages("tinytex")` then `tinytex::install_tinytex()`
     to install a minimal LaTeX distribution. This is required to
-    generate a pdf report.
+    generate a pdf report. Note that this is only required if you do not
+    have a LaTeX distribution already installed.
 4.  From the R terminal run `RMAVIS::runApp()`.
 
 If you wish to use the NVC-matching functions outside of the `RMAVIS`

inst/app/NEWS.md

@@ -1,9 +1,5 @@
----
-title: "Release notes for `RMAVIS`"
-output: html_document
----
 
-# RMAVIS 1.0 (2024-06-16)
+# RMAVIS 1.0 (2024-07-02)
 *   Modifications:
       -   Updating README to include instructions on installing a LaTeX distribution using `{tinytex}`.
       -   Removing Dockerfile and docker-compose.yml as they are currently superfluous.
@@ -13,7 +9,7 @@ output: html_document
           ./inst/app/app.R
 *   New Features:
       -   Adding News section.
-      -   Adding function to run app (`RMAVIS::runApp()`).
+      -   Adding function to run app - `RMAVIS::runApp()`.
       -   Adding contribution guidelines in CONTRIBUTING.md.
 
 # RMAVIS 0.9998 (2024-05-22)

inst/app/README.md

@@ -56,7 +56,8 @@ To run RMAVIS locally take the following steps.
 2.  Install `RMAVIS` using `remotes::install_github("NERC-CEH/RMAVIS")`
 3.  Run `install.packages("tinytex")` then `tinytex::install_tinytex()`
     to install a minimal LaTeX distribution. This is required to
-    generate a pdf report.
+    generate a pdf report. Note that this is only required if you do not
+    have a LaTeX distribution already installed.
 4.  From the R terminal run `RMAVIS::runApp()`.
 
 If you wish to use the NVC-matching functions outside of the `RMAVIS`

inst/app/modules/surveyData_server.R

@@ -158,15 +158,15 @@ surveyData <- function(input, output, session, uploadDataTable, setupData, surve
 
       cover_type <- "dropdown"
       cover_format <- NULL
-      cover_source <- domin_options
+      cover_source <- RMAVIS:::domin_options
       surveyData_reset <- surveyData_long_init |>
         dplyr::mutate(Cover = as.factor("+"))
 
     } else if(coverScale == "braunBlanquet"){
 
       cover_type <- "dropdown"
       cover_format <- NULL
-      cover_source <- braunBlanquet_options
+      cover_source <- RMAVIS:::braunBlanquet_options
       surveyData_reset <- surveyData_long_init |>
         dplyr::mutate(Cover = as.factor("+"))
 
@@ -300,13 +300,13 @@ surveyData <- function(input, output, session, uploadDataTable, setupData, surve
 
         cover_type <- "dropdown"
         cover_format <- NULL
-        cover_source <- domin_options
+        cover_source <- RMAVIS:::domin_options
 
       } else if(coverScale == "braunBlanquet"){
 
         cover_type <- "dropdown"
         cover_format <- NULL
-        cover_source <- braunBlanquet_options
+        cover_source <- RMAVIS:::braunBlanquet_options
 
       }
 
@@ -506,13 +506,13 @@ surveyData <- function(input, output, session, uploadDataTable, setupData, surve
 
       cover_type <- "dropdown"
       cover_format <- NULL
-      cover_source <- domin_options
+      cover_source <- RMAVIS:::domin_options
 
     } else if(coverScale == "braunBlanquet"){
 
       cover_type <- "dropdown"
       cover_format <- NULL
-      cover_source <- braunBlanquet_options
+      cover_source <- RMAVIS:::braunBlanquet_options
 
     }