0.7 dev continued

DESCRIPTION

@@ -33,4 +33,4 @@ License: Apache License (== 2)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr
-Config/roxygen2/version: 8.0.0
+Config/roxygen2/version: 8.1.0

NAMESPACE

@@ -59,71 +59,93 @@ export(das_sight)
 export(das_spcodes_read)
 export(distance_greatcircle)
 export(randpicks_convert)
-importFrom(dplyr,add_row)
-importFrom(dplyr,arrange)
-importFrom(dplyr,between)
-importFrom(dplyr,bind_cols)
-importFrom(dplyr,bind_rows)
-importFrom(dplyr,case_when)
-importFrom(dplyr,desc)
-importFrom(dplyr,distinct)
-importFrom(dplyr,everything)
-importFrom(dplyr,filter)
-importFrom(dplyr,full_join)
-importFrom(dplyr,group_by)
-importFrom(dplyr,if_else)
-importFrom(dplyr,lag)
-importFrom(dplyr,left_join)
-importFrom(dplyr,mutate)
-importFrom(dplyr,n)
-importFrom(dplyr,n_distinct)
-importFrom(dplyr,reframe)
-importFrom(dplyr,right_join)
-importFrom(dplyr,select)
-importFrom(dplyr,slice)
-importFrom(dplyr,starts_with)
-importFrom(dplyr,summarise)
-importFrom(dplyr,ungroup)
-importFrom(lubridate,day)
-importFrom(lubridate,month)
-importFrom(lubridate,tz)
-importFrom(lubridate,year)
+importFrom(dplyr,
+  across,
+  add_row,
+  arrange,
+  between,
+  bind_cols,
+  bind_rows,
+  case_when,
+  desc,
+  distinct,
+  everything,
+  filter,
+  full_join,
+  group_by,
+  if_else,
+  lag,
+  left_join,
+  mutate,
+  n,
+  n_distinct,
+  pull,
+  reframe,
+  right_join,
+  select,
+  slice,
+  starts_with,
+  summarise,
+  ungroup
+)
+importFrom(lubridate,
+  day,
+  month,
+  tz,
+  year
+)
 importFrom(magrittr,"%>%")
 importFrom(methods,setOldClass)
-importFrom(parallel,clusterExport)
-importFrom(parallel,detectCores)
-importFrom(parallel,parLapplyLB)
-importFrom(parallel,stopCluster)
-importFrom(purrr,map_chr)
-importFrom(purrr,pmap)
-importFrom(purrr,pmap_int)
-importFrom(purrr,pmap_lgl)
-importFrom(readr,col_character)
-importFrom(readr,cols)
-importFrom(readr,fwf_cols)
-importFrom(readr,fwf_positions)
-importFrom(readr,read_fwf)
-importFrom(rlang,"!!")
-importFrom(rlang,.data)
-importFrom(sf,st_as_sf)
-importFrom(sf,st_cast)
-importFrom(sf,st_coordinates)
-importFrom(sf,st_geometry)
-importFrom(sf,st_intersection)
-importFrom(sf,st_intersects)
-importFrom(sf,st_linestring)
-importFrom(sf,st_polygon)
-importFrom(sf,st_sf)
-importFrom(sf,st_sfc)
-importFrom(sf,st_wrap_dateline)
-importFrom(stats,na.omit)
-importFrom(stats,runif)
-importFrom(swfscMisc,bearing)
-importFrom(swfscMisc,destination)
-importFrom(swfscMisc,distance)
-importFrom(swfscMisc,setupClusters)
+importFrom(parallel,
+  clusterExport,
+  detectCores,
+  parLapplyLB,
+  stopCluster
+)
+importFrom(purrr,
+  map_chr,
+  pmap,
+  pmap_int,
+  pmap_lgl
+)
+importFrom(readr,
+  col_character,
+  cols,
+  fwf_cols,
+  fwf_positions,
+  read_fwf
+)
+importFrom(rlang,
+  "!!",
+  .data
+)
+importFrom(sf,
+  st_as_sf,
+  st_cast,
+  st_coordinates,
+  st_geometry,
+  st_intersection,
+  st_intersects,
+  st_linestring,
+  st_polygon,
+  st_sf,
+  st_sfc,
+  st_wrap_dateline
+)
+importFrom(stats,
+  na.omit,
+  runif
+)
+importFrom(swfscMisc,
+  bearing,
+  destination,
+  distance,
+  setupClusters
+)
 importFrom(tidyr,pivot_longer)
-importFrom(utils,head)
-importFrom(utils,read.csv)
-importFrom(utils,tail)
-importFrom(utils,write.csv)
+importFrom(utils,
+  head,
+  read.csv,
+  tail,
+  write.csv
+)

NEWS.md

@@ -1,18 +1,28 @@
 # swfscDAS 0.7.0.9000
 
-* Fix bug in `das_process` of incorrect OffsetGMT values, stemming from `as.Date` using 'UTC' tz by default (#16)
+* Fixed bug in `das_process` of incorrect OffsetGMT values, stemming from `as.Date` using 'UTC' tz by default (#16)
+
+* Fixed bug in `das_segdata` to actually only use the last condition value for a segment of length zero (#27)
 
 * Added an exported function `das_spcodes_read` for consistent reading of shipboard SpCode files
 
 * Changed the argument name in `das_check` of the user-provided SpCodes file from `sp.codes` to `sp.codes.file`. Also added a `sp.codes.skip` argument to pass to `das_spcodes_read`
 
+* Added 'SwellDir' (Event V, Data 3) and 'WindDir' (Event W, Data 4) to the output of `das_process` (#21)
+
+* Changed behavior of `das_effort` when the `seg0.drop` argument is `TRUE`. Now, for segments with distance traveled <=0.1 km, either a) they are dropped if they have no associated sighting events are dropped, or b) if they have associated sightings they are kept and given a distance of 0.1km. This behavior matches historical SWFSC segment chopping logic (#22)
+
+* Added optional argument `gs.sp.min1` to `das_sight`, to allow the user to choose to set the minimum value for all non-NA species group size values to 1. This functionality is important for  group size calibration efforts. Users can also specify this argument in `das_effort`, where it is passed to `das_sight` when creating the sightinfo data frame (#26)
+
+* Added 'Trackline' (Event R, Data 3)to the output of `das_process` (#10)
+
 * Moved example data files to an 'extdata' folder within 'inst'
 
-* Update link to NOAA Tech Memo describing DAS data; now (https://repository.library.noaa.gov/view/noaa/3174)[https://repository.library.noaa.gov/view/noaa/3174](#17)
+* Update link to NOAA Tech Memo describing DAS data; now [https://repository.library.noaa.gov/view/noaa/3174](#17)
 
-* Update roxygen to use markdown, fix documentation issues related to upgrade to roxygen2 v8.0
+* Update roxygen to use markdown, fix documentation issues related to upgrade to roxygen2 v8
 
-* Added the SpCodes.dat file from [`CruzPlot`](https://github.com/SWFSC/CruzPlot) to 'inst' to have available as a default
+* Added the SpCodes.dat file (from [`CruzPlot`](https://github.com/SWFSC/CruzPlot)) to 'inst' to have available as a default
 
 
 # swfscDAS 0.6.4

R/as_das_df.R

@@ -38,7 +38,9 @@ as_das_df.data.frame <- function(x) {
     SpdKt = "numeric",
     Bft = "numeric",
     SwellHght = "numeric",
+    SwellDir  = "numeric",
     WindSpdKt = "numeric",
+    WindDir   = "numeric",
     RainFog = "numeric",
     HorizSun = "numeric",
     VertSun = "numeric",

R/das_check.R

@@ -43,11 +43,14 @@
 #'   Echo sounder             \tab B             \tab Data4          \tab Must be one of Y, N, y, n, or NA (blank)                                  \cr
 #'   Effort type              \tab R             \tab Data1          \tab Must be one of F, N, S, or NA (blank)                                     \cr
 #'   ESW sides                \tab R             \tab Data2          \tab Effective strip width; must be one of F, H, or NA (blank)                 \cr
+#'   Trackline number         \tab R             \tab Data3          \tab Trackline number, represented as a character                              \cr
 #'   Course                   \tab N             \tab Data1          \tab Can be converted to a numeric value                                       \cr
 #'   Speed                    \tab N             \tab Data2          \tab Can be converted to a numeric value                                       \cr
 #'   Beaufort                 \tab V             \tab Data1          \tab Must be a whole number between 0 and 9                                    \cr
 #'   Swell height             \tab V             \tab Data2          \tab Can be converted to a numeric value                                       \cr
+#'   Swell direction          \tab V             \tab Data3          \tab Can be converted to a numeric value                                       \cr
 #'   Wind speed               \tab V             \tab Data5          \tab Can be converted to a numeric value                                       \cr
+#'   Wind direction           \tab W             \tab Data4          \tab Can be converted to a numeric value                                       \cr
 #'   Rain or fog              \tab W             \tab Data1          \tab Must be between 0 and 5 and either a whole number or have decimal value .5\cr
 #'   Horizontal sun           \tab W             \tab Data2          \tab Must be a whole number between 0 and 12                                   \cr
 #'   Vertical sun             \tab W             \tab Data3          \tab Must be a whole number between 0 and 12                                   \cr
@@ -336,7 +339,7 @@ das_check <- function(
   txt.e.na <- "E events should only have data in the Data1 column"
 
   # R events
-  idx.r.na <- .check_isna(x, c("R"), paste0("Data", 3:9))
+  idx.r.na <- .check_isna(x, c("R"), paste0("Data", 4:9))
   txt.r.na <- "R events should only have data in the Data1-2 columns"
 
   # N events
@@ -413,10 +416,18 @@ das_check <- function(
   idx.v.2 <- .check_numeric(x, "V", "Data2")
   txt.v.2 <- "Swell height (Data2 of V events) cannot be converted to a numeric"
 
+  # Swell direction
+  idx.v.2 <- .check_numeric(x, "V", "Data3")
+  txt.v.2 <- "Swell direction (Data3 of V events) cannot be converted to a numeric"
+
   # Wind speed
   idx.v.5 <- .check_numeric(x, "V", "Data5")
   txt.v.5 <- "Wind speed (Data5 of V events) cannot be converted to a numeric"
 
+  # Wind direction
+  idx.v.5 <- .check_numeric(x, "W", "Data4")
+  txt.v.5 <- "Wind direction (Data4 of W events) cannot be converted to a numeric"
+
   # RainFog
   rf.acc <- c(seq(0, 5, by = 0.5), sprintf("%02d", 1:5), NA)
   idx.w.1 <- .check_character(x, "W", "Data1", rf.acc)

R/das_class.R

@@ -83,7 +83,9 @@ NULL
 #'     SpdKt     \tab "numeric"\cr
 #'     Bft       \tab "numeric"\cr
 #'     SwellHght \tab "numeric"\cr
+#'     SwellDir  \tab "numeric"\cr
 #'     WindSpdKt \tab "numeric"\cr
+#'     WindDir   \tab "numeric"\cr
 #'     RainFog   \tab "numeric"\cr
 #'     HorizSun  \tab "numeric"\cr
 #'     VertSun   \tab "numeric"\cr