Merge pull request #16 from trackyverse/build-functions

Build functions

Author: mhpob

.Rbuildignore

@@ -2,6 +2,7 @@
 ^\.Rproj\.user$
 ^vignettes/precompile\.R$
 ^vignettes/_Estimate_COA_vignette\.Rmd$
+^vignettes/_ps_estimate_coa_vignette\.Rmd$
 ^LICENSE\.md$
 ^\.github$
 ^Dockerfile$
@@ -11,4 +12,6 @@
 ^pkgdown$
 ^CNAME$
 ^air\.toml$
-^src/StanExports_*
+^src/StanExports_*
+^[.]?air[.]toml$
+^\.vscode$

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: TelemetrySpace
-Version: 1.3.1
+Version: 1.3.2
 Title: Spatial point process and random field models for electronic tagging data
 Description: A collection of tools to fit spatial models to several types of telemetry data. Models are provided to account for the detection process when estimating individual centers of activity from acoustic telemetry data and to incorporate data from stationary test transmitters when available. Bayesian versions of models are fitted using Stan (http://mc-stan.org/). Maximum likelihood versions are fitted using Template Model Builder (https://kaskr.github.io/adcomp/index.html).
 Authors@R: c(
@@ -16,11 +16,13 @@ Depends:
 Imports: 
     cli,
     dplyr,
+    lubridate,
     methods,
     RcppParallel (>= 5.0.1),
     rlang,
     rstan (>= 2.18.1),
     rstantools (>= 2.4.0),
+    sf,
     stats
 Suggests: 
     ggplot2,
@@ -49,3 +51,4 @@ Roxygen: list(markdown = TRUE)
 URL: https://telemetryspace.trackyverse.org, https://github.com/trackyverse/TelemetrySpace
 BugReports: https://github.com/trackyverse/TelemetrySpace/issues
 Config/roxygen2/version: 8.0.0
+RoxygenNote: 8.0.0

NAMESPACE

@@ -3,6 +3,15 @@
 export(COA_Standard)
 export(COA_TagInt)
 export(COA_TimeVarying)
+export(build_aeqd)
+export(build_bbox)
+export(build_counts)
+export(build_init)
+export(build_ntrans)
+export(build_pixel_grid)
+export(build_rec_coords)
+export(build_time_bin)
+export(build_tstep)
 export(distf)
 import(Rcpp)
 import(methods)

NEWS.md

@@ -1,4 +1,7 @@
 # TelemetrySpace 1.3
+## 1.3.2
+- `build_*()` functions have been added which streamlines the data processing prior to the models ([PR #16](https://github.com/trackyverse/TelemetrySpace/pull/16)). Unit tests have been written for these functions and a small vignette which will need to be further development has been initially made.  
+
 ## 1.3.1
   - Code refactor ([PR #13](https://github.com/trackyverse/TelemetrySpace/pull/13)): leverage [Stan's "Includes" framework](https://mc-stan.org/docs/reference-manual/includes.html) to reduce redundant code across files.
 

R/COA_Tag_Integrated.R

@@ -66,11 +66,6 @@ COA_TagInt <- function(
   exp_len <- expected_lengths(recX = recX, recY = recY, ntest_len = ntest)
 
   validate_standata(standata, exp_len)
-  # set rstan options
-  rstan::rstan_options(auto_write = TRUE)
-  # set coores - this probably should be an argument
-  options(mc.cores = parallel::detectCores())
-
   # fit model
   if (decay == "gaussian") {
     fit_model <- rstan::sampling(

R/COA_TimeVarying.R

@@ -54,11 +54,6 @@ COA_TimeVarying <- function(
 
   validate_standata(standata, exp_len)
 
-  # set rstan options
-  rstan::rstan_options(auto_write = TRUE)
-  # set coores - this probably should be an argument
-  options(mc.cores = parallel::detectCores())
-
   # fit model
   if (decay == "gaussian") {
     fit_model <- rstan::sampling(

R/COA_standard.R

@@ -55,11 +55,6 @@ COA_Standard <- function(
 
   validate_standata(standata, exp_len)
 
-  # set rstan options
-  rstan::rstan_options(auto_write = TRUE)
-  # set coores - this probably should be an argument
-  options(mc.cores = parallel::detectCores())
-
   # fit model
   if (decay == "gaussian") {
     fit_model <- rstan::sampling(