diff --git a/DESCRIPTION b/DESCRIPTION
index 4a80c7f289a2577accea9503a4d2f35f4a5d6e90..4f6fd761ff7f5374adbe6879029cced62547156b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: GenEst
Title: Generalized Mortality Estimator
-Version: 1.2.1
-Date: 2018-12-18
+Version: 1.2.2
+Date: 2019-02-04
Authors@R: c(
person("Daniel", "Dalthorp", , "ddalthorp@usgs.gov", c("aut", "cre")),
person("Juniper", "Simonis", , "simonis@dapperstats.com", "aut"),
diff --git a/NAMESPACE b/NAMESPACE
index ca9081936ce660c4fee4c9b05e7b76ea5da127de..8259cd810e1b8db17fc45c14ee9559ac4518509b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -335,6 +335,7 @@ importFrom(stats,update.formula)
importFrom(stats,weighted.mean)
importFrom(survival,strata)
importFrom(utils,combn)
+importFrom(utils,globalVariables)
importFrom(utils,packageDescription)
importFrom(utils,read.csv)
importFrom(utils,read.csv2)
diff --git a/R/app_content.R b/R/app_content.R
index e1d624db9b1caf60415b00790aa09bf8c878afee..857735d8e89b99bced10e2af73ea55589c417071 100644
--- a/R/app_content.R
+++ b/R/app_content.R
@@ -323,15 +323,17 @@ disclaimersContent <- function(appType = "base"){
#' @export
#'
disclaimerUSGS <- function(){
- "This software is preliminary or provisional and is subject to revision.
- It is being provided to meet the need for timely best science. The
- software has not received final approval by the U.S. Geological Survey
- (USGS). No warranty, expressed or implied, is made by the USGS or the U.S.
- Government as to the functionality of the software and related material
- nor shall the fact of release constitute any such warranty. The software
- is provided on the condition that neither the USGS nor the U.S. Government
- shall be held liable for any damages resulting from the authorized or
- unauthorized use of the software."
+ "This is an incremental update to GenEst v1.0.0 which was approved for release
+ by the U.S. Geological Survey (USGS) after rigorous review in compliance with
+ US Geological Survey publishing and associated with IP-101457. This update is
+ preliminary or provisional and is subject to revision. It is being provided to
+ meet the need for timely best science. The update has not received final
+ approval by the U.S. Geological Survey (USGS). No warranty, expressed or
+ implied, is made by the USGS or the U.S. Government as to the functionality of
+ the software and related material nor shall the fact of release constitute any
+ such warranty. The software is provided on the condition that neither the USGS
+ nor the U.S. Government shall be held liable for any damages resulting from
+ the authorized or unauthorized use of the software."
# "This software has been approved for release by the U.S. Geological
# Survey (USGS). Although the software has been subjected to rigorous
# review, the USGS reserves the right to update the software as needed
diff --git a/R/app_download_functions.R b/R/app_download_functions.R
index 92c8eeec1a5bbd412081084a6da498db5da4fea4..06baa1731f89955337f5da853a1773cf453de900 100644
--- a/R/app_download_functions.R
+++ b/R/app_download_functions.R
@@ -71,13 +71,11 @@ downloadgFig <- function(rv, sc){
#'
#' @param split logical indicator to use the split or not
#'
-#' @param transpose logical indicator if to transpose the output or not
-#'
#' @return a download handler function
#'
#' @export
#'
-downloadMFig <- function(rv, split = TRUE){#, transpose = FALSE){
+downloadMFig <- function(rv, split = TRUE){
if (split){
downloadHandler(filename = "M_fig.png",
content = function(file){
diff --git a/R/app_ui.R b/R/app_ui.R
index 5124ec364da82e2541bf57cc8d7240e1ad970663..2928b1c261d89905c549dc3d5632eb750a73e08f 100644
--- a/R/app_ui.R
+++ b/R/app_ui.R
@@ -459,24 +459,58 @@ gettingStartedPanel <- function(){
#' @return \code{downloadsPanel}: Help -> Downloads panel.
#'
#' @export
-#'
+ #'
downloadsPanel<- function(){
- tabPanel("Example Data",
+ if (.Platform$OS.type == "windows"){
+ tabPanel("Example Data",
mainPanel(
- column(10, offset = 0,
- br(),
- h3("Example data sets"),
- br(),
- dataDownloadWidget("RP"),
- dataDownloadWidget("RPbat"),
- dataDownloadWidget("cleared"),
- dataDownloadWidget("powerTower"),
- dataDownloadWidget("PV"),
- dataDownloadWidget("trough"),
- dataDownloadWidget("mock")
+ column(10, offset = 0,
+ br(),
+ h3("Example data sets"),
+ br(),
+ dataDownloadWidget("RP"),
+ dataDownloadWidget("RPbat"),
+ dataDownloadWidget("cleared"),
+ dataDownloadWidget("powerTower"),
+ dataDownloadWidget("PV"),
+ dataDownloadWidget("trough"),
+ dataDownloadWidget("mock"),
+ br(), br(),
+ h5("NOTE: If you are having trouble downloading the example data sets..."),
+ br(),
+ h5("Downloading the zip files in Windows relies on a zip program being
+ in the Windows path statement. If no such program is present, the download
+ will not be successful. However, the examples data sets can be directly
+ loaded into the app by clicking \"Load Data\" and then viewed under the
+ \"Data Input\" tab and analyzed under the \"Analyses\" tab. Templates for
+ formatting the data are also included in the appendices in the User Guide.
+ If you need the .csv's for some other purpose, you can download them via
+ the command line in R. For example, enter
+ write.csv(\"mock$SE\", file = \"NameOfFileToCreate.csv\", row.names = FALSE)
+ to download the SE file for the 'mock' data set. For more information
+ about downloadable example data files, enter ?GenEst from the R command
+ line.")
+ )
+ )
)
- )
- )
+ } else {
+ tabPanel("Example Data",
+ mainPanel(
+ column(10, offset = 0,
+ br(),
+ h3("Example data sets"),
+ br(),
+ dataDownloadWidget("RP"),
+ dataDownloadWidget("RPbat"),
+ dataDownloadWidget("cleared"),
+ dataDownloadWidget("powerTower"),
+ dataDownloadWidget("PV"),
+ dataDownloadWidget("trough"),
+ dataDownloadWidget("mock")
+ )
+ )
+ )
+ }
}
#' @rdname GenEstUI
diff --git a/R/app_update_rv.R b/R/app_update_rv.R
index 00cfa040f88edccecef8685e641969488cde3270..9d21f1a1c02871380a2631c7d5255fd2123e9791 100644
--- a/R/app_update_rv.R
+++ b/R/app_update_rv.R
@@ -110,6 +110,7 @@ update_rv <- function(eventName, rv, input){
rv$sizeCol <- NULL
}
+
if (eventName == "file_SE_clear"){
toNULL <- c("data_SE", "filename_SE", "colNames_SE", "colNames_SE_preds",
"colNames_SE_preds0", "colNames_SE_obs", "colNames_SE_obs0",
@@ -352,7 +353,7 @@ update_rv <- function(eventName, rv, input){
if (max(rv$SStemp)%%rv$SStemp[2] == 0){
rv$SS <- list("span" = max(rv$SStemp), "I" = rv$SStemp[2])
} else {
- rv$SS <- list("span" = SStmp[2] * length(rv$SStemp), "I" = rv$SStemp[2])
+ rv$SS <- list("span" = rv$SStemp[2] * length(rv$SStemp), "I" = rv$SStemp[2])
}
} else {
rv$SS <- NULL
@@ -531,6 +532,7 @@ update_rv <- function(eventName, rv, input){
rv$CL <- input$CL
rv$sizeCol <- input$class
+
rv$mods_SE <- suppressWarnings(
pkmSize(formula_p = rv$formula_p,
formula_k = rv$formula_k, data = rv$data_SE,
@@ -891,7 +893,6 @@ update_rv <- function(eventName, rv, input){
rv$SEmodToUse <- gsub("~ constant", "~ 1", rv$SEmodToUse)
rv$CPmodToUse <- gsub("~ constant", "~ 1", rv$CPmodToUse)
-
rv$models_SE <- tryCatch(
trimSetSize(rv$mods_SE, rv$SEmodToUse),
error = function(x){NULL}
@@ -1011,6 +1012,5 @@ update_rv <- function(eventName, rv, input){
rv$Msplit <- transposeSplits(rv$Msplit)
}
}
-
return(rv)
}
\ No newline at end of file
diff --git a/R/detection_probability_functions.R b/R/detection_probability_functions.R
index 8eec602e91389be8875e85f00e8d895443fb57c2..4d501c261ee308f9a5782ca7995285e9be5b9544 100644
--- a/R/detection_probability_functions.R
+++ b/R/detection_probability_functions.R
@@ -985,7 +985,7 @@ prepSS <- function(data_SS, SSdate = NULL, preds = NULL){
stop(paste(SSdate, "is not properly formatted as dates"))
}
}
- # extract units
+ # extract (potential) units (i.e. cols w/ 0-1 data)
unitNames <- NULL
preds <- SSdate
for (coli in colnames(data_SS)){
@@ -1022,6 +1022,7 @@ prepSS <- function(data_SS, SSdate = NULL, preds = NULL){
}
ans$searches_unit <- t(as.matrix(data_SS[, unitNames]))
ans$unit <- unitNames
+ rownames(ans$searches_unit) <- ans$unit
ans$SSdate <- SSdate
class(ans) <- c("prepSS", "list")
return(ans)
diff --git a/R/mortality_functions.R b/R/mortality_functions.R
index a983ecbea2f10dcd04c1d9ab2aab2e71515ccc66..283b69043814d8675e6b4bfd5014ddf2c689f6ec 100644
--- a/R/mortality_functions.R
+++ b/R/mortality_functions.R
@@ -1,4 +1,4 @@
-#' @title Estimate mortality
+#' @title Estimate mortality
#'
#' @description Given given fitted Searcher Efficiency and Carcass
#' Persistence models; Search Schedule, Density Weighted Proportion,
@@ -128,7 +128,7 @@ estM <- function(data_CO, data_SS, data_DWP, frac = 1,
n <- length(gDf)
Mhat[-c_out,] <- ((cbinom::rcbinom(n, 1/gDf, gDf)) - (Ecbinom(gDf) - 1))/gDf
}
- out <- list(Mhat = Mhat, Aj = est$Aj, ghat = est$ghat, Xtot = nrow(data_CO))
+ out <- list(Mhat = Mhat, Aj = est$Aj, ghat = est$ghat, DWP = DWP, Xtot = nrow(data_CO))
class(out) <- c("estM", "list")
return(out)
}
diff --git a/REVISIONS.txt b/REVISIONS.txt
index 1bd4c23400ace62fa3641619cf479eb9cd63df50..9b07b93d534e7a4d514de09a5870fce879a50ea8 100644
--- a/REVISIONS.txt
+++ b/REVISIONS.txt
@@ -1,5 +1,24 @@
Revision log
+2019.02.04
+v1.2.2
+
+* added a note for Windows users about downloading example data sets.
+
+* with data sets with only 1 unit, prepSS was not properly assigning unit
+names to rows of searches_unit array. This caused an error in prepSS and its
+dependencies (estM and estg), which was expressed in the error message:
+"no 'dimnames' attribute for array”. This has been corrected.
+
+* corrected the download button for figures showing transposed mortality
+splits (previously, the untransposed figs were downloaded)
+
+* corrected an error in calculating average SS under certain conditions,
+the error affected default values in a convenience funtion and had
+zero potential for producing erroneous or misleading results but would
+require users to enter specific values into a input box for which reasonable
+default values should have been made available.
+
2018.12.09
v1.2.1
diff --git a/code.json b/code.json
index d985bc5e3e23bfc8393975eff129ce54789d9e20..6acc3bd06076c89c49576144f05ebe6dcf34e3ae 100644
--- a/code.json
+++ b/code.json
@@ -3,7 +3,7 @@
"Name": "GenEst",
"organization": "U.S. Geological Survey",
"description": "R package for estimating bird and bat fatalities at wind and solar power facilities",
- "version": "1.2.1",
+ "version": "1.2.2",
"status": "Release Candidate",
"permissions": {
@@ -44,7 +44,7 @@
},
"date": {
- "metadataLastUpdated": "2018-12-18"
+ "metadataLastUpdated": "2019-02-04"
}
} }
}
diff --git a/man/downloadMFig.Rd b/man/downloadMFig.Rd
index f009abec48039b0e4e1e71f9c53db708a23d44ff..891b8558e60d4ca04ba5442a1f6f010ee188dadb 100644
--- a/man/downloadMFig.Rd
+++ b/man/downloadMFig.Rd
@@ -10,8 +10,6 @@ downloadMFig(rv, split = TRUE)
\item{rv}{the reactive values list}
\item{split}{logical indicator to use the split or not}
-
-\item{transpose}{logical indicator if to transpose the output or not}
}
\value{
a download handler function