Merge pull request #53 from moshejasper/dev

Dev
moshejasper · Mar 21, 2021 · 915a76c · 915a76c
2 parents 8988aa3 + d6e3c90
commit 915a76c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,13 +1,13 @@
 Package: kindisperse
 Title: Simulate and Estimate Close-Kin Dispersal Kernels
-Version: 0.9.0
+Version: 0.9.1
 Authors@R: 
     person(given = "Moshe-Elijah",
            family = "Jasper",
            role = c("aut", "cre"),
            email = "[email protected]",
            comment = c(ORCID = "0000-0003-4541-3223"))
-Description: Functions for simulating and estimating kinship-related dispersal, based
+Description: Functions for simulating and estimating kinship-related dispersal. Based
     on the methods described in M. Jasper, T.L. Schmidt., N.W. Ahmad, S.P. Sinkins & A.A. 
     Hoffmann (2019) <doi:10.1111/1755-0998.13043> "A genomic approach to inferring kinship 
     reveals limited intergenerational dispersal in the yellow fever mosquito".

diff --git a/NAMESPACE b/NAMESPACE
@@ -197,6 +197,7 @@ importFrom(shiny,shinyApp)
 importFrom(shiny,sidebarLayout)
 importFrom(shiny,sidebarPanel)
 importFrom(shiny,sliderInput)
+importFrom(shiny,strong)
 importFrom(shiny,tabPanel)
 importFrom(shiny,tableOutput)
 importFrom(shiny,textInput)

diff --git a/NEWS.md b/NEWS.md
@@ -0,0 +1,80 @@
+# kindisperse 0.9.1
+
+* Added a `NEWS.md` file to track changes to the package.
+* Fixed several display and layout issues in Shiny app
+* Changed parameter of 'elongate' function from 'shape' to 'aspect' to make clear we are manipulating aspect ratios of a rectangular area. 
+
+# kindisperse 0.9.0
+
+* Permutation functions now output mean instead of median
+* Changed all 'dsigma' parameters & references to 'posigma'
+* Changed simulation 'method' parameter input from 'Gamma' to 'gamma'
+* Changed 'lifestage' parameter values from 'larva' to 'immature' and from 'oviposition' to 'ovipositional'
+* Enable package function messages to be suppressed
+* Updated app tutorial and documentation (including vignettes)
+* Updated KinPairSimulation '<-sampledim' method
+* Added Table of Contents to README
+
+# kindisperse 0.8.0
+
+* Added Mentari Court field data for example calculations
+* Added 2d rectangular dimensions to simulate & sample functions
+* Changed the way 'sample_kindist' deals with dimensions
+* Added helper function 'elongate' for dimension handling
+* Changed 'composite' default parameter value from 2 to 1 in function 'axpermute'
+* Changed 'juvsigma' parameter & references to 'initsigma' in line with usage in paper
+* included rgamma function
+* Improved simgraph commands (simgraph_data, simgraph_graph)
+* Cleaned up app
+* Removed unneeded class methods (to_tibble). Fixed kernelshape method
+* Improved package load
+* Updated app interface
+* Updated documentation (CRAN compatibility)
+
+# kindisperse 0.7.0
+
+* Added options to import data from files within app
+* Updated readme, package startup & vignettes
+* Added gamma kernel with shape parameter to simulations
+
+# kindisperse 0.6.0
+
+* Changed 'category' parameter in all functions and classed to 'kinship' parameter
+* Added file writing and reading functions (write_kindata, read_kindata, kinpair_to_tsv, tsv_to_kinpair, kinpair_to_csv, csv_to_kinpair, kinpair_to_tibble)
+* Added appdata interface environment & functions to access it (mount_appdata, unmount_appdata, display_appdata, reset_appdata, retrive_appdata)
+* Enable loading of appdata into app (functions and interface)
+* Improved KinPairSimulation object print function
+
+# kindisperse 0.5.0
+
+* Replaced file-based memory storage with environment storage in app
+* Added 'distances' method for KinPairData & KinPairSimulation classes
+* Added functions to test class membership
+* Updated axial functions to take KinPairData &c classes as input
+* Limit sample size in axial permuation functions under 'std' option
+* Updated class definitions
+* Added class constructor functions
+* Added class import functions
+* Updated dependencies
+
+# kindisperse 0.4.0
+
+* Introduced KinPairData & KinpairSimulation classes
+* Added and updated class methods & documentation
+* Updated app with axial functions
+* Fixed bug in 'axials_decompose' function
+
+# kindisperse 0.3.0
+
+* improved NAMESPACE
+* add axial function
+* document many functions
+
+# kindisperse 0.2.0
+
+* added temp folder & contents to fix app bug
+* removed broken dependencies
+
+# kindisperse 0.1.0 & prior
+
+* initial commit
diff --git a/R/app.R b/R/app.R
@@ -557,31 +557,27 @@ ui <- fluidPage(
                 min = 1, max = 250, value = 50
               ),
 
-              h5("Site dimensions"),
-
-              column(width = 4,
+              strong("Site dimensions (n x n)"),
 
               numericInput(
                 inputId = "sim_simple_dimx",
-                label = "(n x n)",
+                label = "",
                 min = 25, max = 1000, value = 1000
-              )),
-
-              column(width = 4,
-                     hr(),
-                     checkboxInput(
-                       inputId = "sim_simple_bothdims",
-                       label = h5("link dimensions"),
-                       value = TRUE
-                     )
               ),
 
-              column(width = 4,
-                     numericInput(
-                       inputId = "sim_simple_dimy",
-                       label = "",
-                       min = 25, max = 1000, value = 1000
-                     )
+              conditionalPanel(
+                condition = "input.sim_simple_bothdims == false",
+                numericInput(
+                 inputId = "sim_simple_dimy",
+                 label = "",
+                 min = 25, max = 1000, value = 1000
+                )
+              ),
+
+              checkboxInput(
+                inputId = "sim_simple_bothdims",
+                label = h5("square site"),
+                value = TRUE
               ),
 
               selectInput(
@@ -686,31 +682,27 @@ ui <- fluidPage(
                 min = 1, max = 250, value = 50
               ),
 
-              h5("Site dimensions"),
-
-              column(width = 4,
+              strong("Site dimensions (n x n)"),
 
-                     numericInput(
-                       inputId = "sim_composite_dimx",
-                       label = "(n x n)",
-                       min = 25, max = 1000, value = 1000
-                     )),
+              numericInput(
+                inputId = "sim_composite_dimx",
+                label = "",
+                min = 25, max = 1000, value = 1000
+              ),
 
-              column(width = 4,
-                     hr(),
-                     checkboxInput(
-                       inputId = "sim_composite_bothdims",
-                       label = h5("link dimensions"),
-                       value = TRUE
-                     )
+              conditionalPanel(
+                condition = "input.sim_composite_bothdims == false",
+                numericInput(
+                  inputId = "sim_composite_dimy",
+                  label = "",
+                  min = 25, max = 1000, value = 1000
+                )
               ),
 
-              column(width = 4,
-                     numericInput(
-                       inputId = "sim_composite_dimy",
-                       label = "",
-                       min = 25, max = 1000, value = 1000
-                     )
+              checkboxInput(
+                inputId = "sim_composite_bothdims",
+                label = h5("square site"),
+                value = TRUE
               ),
 
               selectInput(
@@ -882,33 +874,28 @@ ui <- fluidPage(
 
           conditionalPanel(
             condition = "input.samp_checkbox.includes('use_samp_dims')",
-            h5("choose trap dimensions"),
-
-            column(width = 5,
-
-                   numericInput(
-                     inputId = "samp_dimx",
-                     label = "(n x n)",
-                     min = 25, max = 1000, value = 1000
-                   )),
-
-            column(width = 2,
-                   hr(),
-                   checkboxInput(
-                     inputId = "samp_bothdims",
-                     label = h5("link"),
-                     value = TRUE
-                   )
+            strong("Choose site dimensions (n x n)"),
+
+            numericInput(
+              inputId = "samp_dimx",
+              label = "",
+              min = 25, max = 1000, value = 1000
             ),
 
-            column(width = 5,
-                   numericInput(
-                     inputId = "samp_dimy",
-                     label = "",
-                     min = 25, max = 1000, value = 1000
-                   )
-            )
-          ),
+            conditionalPanel(
+              condition = "input.samp_bothdims == false",
+              numericInput(
+                inputId = "samp_dimy",
+                label = "",
+                min = 25, max = 1000, value = 1000
+              )
+            ),
+
+            checkboxInput(
+              inputId = "samp_bothdims",
+              label = h5("square site"),
+              value = TRUE
+            )),
 
           conditionalPanel(
             condition = "input.samp_checkbox.includes('use_samp_spacing')",
@@ -1912,7 +1899,7 @@ server <- function(input, output, session) {
 
   output$est_smp_ci_table <- renderTable({
     # est_smp_ci()
-    tibble("Lower" = est_smp_ci()[1], "Median" = est_smp_ci()[2], "Upper" = est_smp_ci()[3])
+    tibble("Lower" = est_smp_ci()[1], "Mean" = est_smp_ci()[2], "Upper" = est_smp_ci()[3])
     # tibble("a" = 1, "b" = 2, "c" = 3)
   })
 
@@ -1962,7 +1949,7 @@ server <- function(input, output, session) {
 
   output$est_std_ci_table <- renderTable({
     # est_smp_ci()
-    tibble("Lower" = est_std_ci()[1], "Median" = est_std_ci()[2], "Upper" = est_std_ci()[3])
+    tibble("Lower" = est_std_ci()[1], "Mean" = est_std_ci()[2], "Upper" = est_std_ci()[3])
     # tibble("a" = 1, "b" = 2, "c" = 3)
   })
 

diff --git a/R/kindisperse-package.R b/R/kindisperse-package.R
@@ -19,7 +19,7 @@
 #' @importFrom shiny column conditionalPanel fluidPage fluidRow mainPanel navbarPage sidebarLayout sidebarPanel tabPanel titlePanel shinyApp downloadButton
 #' @importFrom shiny actionButton checkboxGroupInput checkboxInput fileInput numericInput radioButtons selectInput sliderInput downloadHandler
 #' @importFrom shiny eventReactive observeEvent reactive updateNumericInput updateSelectInput
-#' @importFrom shiny h1 h2 h3 h4 h5 h6 hr icon p
+#' @importFrom shiny h1 h2 h3 h4 h5 h6 hr icon p strong
 #' @importFrom shiny plotOutput renderPlot renderTable renderText tableOutput textOutput renderPrint textInput
 #' @importFrom shinythemes shinytheme
 #' @importFrom stats quantile rexp rnorm runif rweibull rgamma

diff --git a/R/sample_kindist.R b/R/sample_kindist.R
@@ -104,18 +104,18 @@ sample_kindist <- function(kindist, upper = NULL, lower = NULL, spacing = NULL,
 
 # additional comment
 
-#' Change the shape of a rectangle while preserving area
+#' Change the shape (aspect ratio) of a rectangle while preserving area
 #'
-#' @param dims  Original rectangle dimensions - either single number (length of side of square) or length 2 numeric vector (lenghts of sides x and y of rectangle)
-#' @param shape Ratio of side lengths x & y in the new rectangle
+#' @param dims  Original rectangle dimensions - either single number (length of side of square) or length 2 numeric vector (lengths of sides x and y of rectangle)
+#' @param aspect Aspect ratio of side lengths x & y (i.e. x/y) in the new rectangle
 #'
 #' @return Returns a numeric vector containing the side lengths c(x, y) of a transformed rectangle with preserved area
 #' @export
 #'
 #' @examples
 #' elongate(10, 100)
 #' elongate(c(5, 125), 4)
-elongate <- function(dims, shape = 1){
+elongate <- function(dims, aspect = 1){
   if (length(dims) > 2){
     stop("'dims' cannot have length > 2")
   }
@@ -127,7 +127,7 @@ elongate <- function(dims, shape = 1){
   }
 
   # calculate dimensions
-  xdim <- sqrt(area / shape)
+  xdim <- sqrt(area * aspect)
   ydim <- area / xdim
 
   return(c(xdim, ydim))
@@ -136,7 +136,7 @@ elongate <- function(dims, shape = 1){
 #' Change the dimensions of a KinPairSimulation Object and shift kinpairs so at least one individual is within the area
 #'
 #' @param kindist   \code{KinPairSimulation} - \code{KinPairSimulation} Class Object
-#' @param dims      New site dimensions - either single number (length of side of square) or length 2 vector (lenghts of sides x and y of rectangle)
+#' @param dims      New site dimensions - either single number (length of side of square) or length 2 vector (lengths of sides x and y of rectangle)
 #'
 #' @return returns a rebased object of class \code{KinPairSimulation} with adjusted simulation dimensions
 #' @export

diff --git a/README.Rmd b/README.Rmd
@@ -1,5 +1,5 @@
 ---
-title: "KINDISPERSE 0.9.0"
+title: "KINDISPERSE 0.9.1"
 output:
   github_document:
     toc: true