Merge pull request #654 from metrumresearchgroup/release/1.9.0

Prepare for 1.9.0 Release
metrumresearchgroup · Feb 7, 2024 · 5c3b0d4 · 5c3b0d4
2 parents 01b4ff5 + eadc261
commit 5c3b0d4
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Showing 7 changed files with 35 additions and 13 deletions.
diff --git a/.drone.yml b/.drone.yml
@@ -34,8 +34,8 @@ steps:
   image: 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.0:latest
   commands:
   - R -s -e 'devtools::install_deps(upgrade = '"'"'never'"'"')'
-    # this can be removed once nmrec 0.3.0.8001 is available on MPN
-  - git clone --branch 0.3.0.8001 --depth 1 https://github.com/metrumresearchgroup/nmrec.git /tmp/nmrec
+    # this can be removed once nmrec 0.4.0 is available on MPN
+  - git clone --branch 0.4.0 --depth 1 https://github.com/metrumresearchgroup/nmrec.git /tmp/nmrec
   - R -s -e 'devtools::install("/tmp/nmrec", upgrade = "never")'
   - R -s -e 'devtools::check(env_vars = c("BBI_EXE_PATH" = "/ephemeral/bbi", "NOT_CRAN" = "true"))'
   environment:
@@ -50,8 +50,8 @@ steps:
   image: 906087756158.dkr.ecr.us-east-1.amazonaws.com/r-dev-ci-mpn-4.1:latest
   commands:
   - R -s -e 'devtools::install_deps(upgrade = '"'"'never'"'"')'
-    # this can be removed once nmrec 0.3.0.8001 is available on MPN
-  - git clone --branch 0.3.0.8001 --depth 1 https://github.com/metrumresearchgroup/nmrec.git /tmp/nmrec
+    # this can be removed once nmrec 0.4.0 is available on MPN
+  - git clone --branch 0.4.0 --depth 1 https://github.com/metrumresearchgroup/nmrec.git /tmp/nmrec
   - R -s -e 'devtools::install("/tmp/nmrec", upgrade = "never")'
   - R -s -e 'devtools::check(env_vars = c("BBI_EXE_PATH" = "/ephemeral/bbi", "NOT_CRAN" = "true"))'
   environment:
@@ -107,7 +107,7 @@ steps:
   commands:
   - R -s -e 'devtools::install_deps(upgrade = '"'"'never'"'"')'
   # nmrec isn't available until the 2023-09-19 snapshot.
-  - git clone --branch 0.3.0.8001 --depth 1 https://github.com/metrumresearchgroup/nmrec.git /tmp/nmrec
+  - git clone --branch 0.4.0 --depth 1 https://github.com/metrumresearchgroup/nmrec.git /tmp/nmrec
   - R -s -e 'devtools::install("/tmp/nmrec", upgrade = "never")'
   - R -s -e 'devtools::check(env_vars = c("BBI_EXE_PATH" = "/ephemeral/bbi", "NOT_CRAN" = "true"))'
   environment:

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: bbr
 Title: R package for bbi
-Version: 1.8.1
+Version: 1.9.0
 Authors@R: 
     c(person(given = "Seth",
              family = "Green",

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,25 @@
+# bbr 1.9.0
+
+## New features and changes
+
+* New `initial_estimates()` function for extracting and formatting initial
+  parameter estimates from a `NONMEM` control stream file. (#646)
+
+* New `tweak_initial_estimates()` function for tweaking or 'jittering' initial
+  parameter estimates. Only `$THETA` records are supported for now. (#646)
+
+## Bugs addressed
+
+* With the latest `data.table` release (1.15.0), `param_estimates_batch()`
+  failed for an edge case due to a change in the header detection heuristics.
+  `param_estimates_batch()` now tells `data.table::fread()` to expect a header.
+  (#648)
+
+* When passed `.recurse = TRUE`, `run_log()`, `config_log()`, and
+  `summary_log()` included nested models, which was not by design. Any models
+  under another model's output directory are considered an implementation
+  detail. (#643, #644, #645)
+
 # bbr 1.8.1
 
 ## Bugs addressed

diff --git a/R/initial-estimates.R b/R/initial-estimates.R
@@ -90,7 +90,7 @@ initial_estimates <- function(.mod, flag_fixed = FALSE){
 #' @noRd
 get_initial_est <- function(.mod, flag_fixed = FALSE){
 
-  test_nmrec_version(.min_version = "0.3.0.8001")
+  test_nmrec_version(.min_version = "0.4.0")
   check_model_object(.mod, "bbi_nonmem_model")
 
 

diff --git a/R/tweak-initial-estimates.R b/R/tweak-initial-estimates.R
@@ -54,7 +54,7 @@ tweak_initial_estimates <- function(
 ){
 
   # Assertions
-  test_nmrec_version(.min_version = "0.3.0.8001")
+  test_nmrec_version(.min_version = "0.4.0")
   check_model_object(.mod, "bbi_nonmem_model")
   checkmate::assert_true(all(tweak %in% BBR_ESTIMATES_INHERIT))
 

diff --git a/tests/testthat/test-initial-estimates.R b/tests/testthat/test-initial-estimates.R
@@ -13,7 +13,7 @@ describe("initial_estimates", {
   })
 
   it("get_theta_inits", {
-    skip_if_old_nmrec("0.3.0.8001")
+    skip_if_old_nmrec("0.4.0")
     ctl <- nmrec::read_ctl(get_model_path(MOD1))
     theta_inits <- get_theta_inits(ctl, mark_flags = "fix")
 
@@ -25,7 +25,7 @@ describe("initial_estimates", {
   })
 
   it("fmt_record_num", {
-    skip_if_old_nmrec("0.3.0.8001")
+    skip_if_old_nmrec("0.4.0")
     ctl <- nmrec::read_ctl(get_model_path(MOD1))
 
     # Test THETA
@@ -61,7 +61,7 @@ describe("initial_estimates", {
   })
 
   it("initial_estimates: integration", {
-    skip_if_old_nmrec("0.3.0.8001")
+    skip_if_old_nmrec("0.4.0")
     mod_c <- read_model(file.path(MODEL_DIR_X, "1001"))
     initial_est_df <- initial_estimates(mod_c, flag_fixed = TRUE)
     initial_est <- get_initial_est(mod_c, flag_fixed = TRUE)
@@ -87,7 +87,7 @@ describe("initial_estimates", {
   })
 
   it("initial_estimates: SAME blocks", {
-    skip_if_old_nmrec("0.3.0.8001")
+    skip_if_old_nmrec("0.4.0")
     mod_c <- read_model(file.path(MODEL_DIR_X, "acop-iov"))
     initial_est_df <- initial_estimates(mod_c, flag_fixed = TRUE)
     initial_est <- get_initial_est(mod_c, flag_fixed = TRUE)

diff --git a/tests/testthat/test-tweak-initial-estimates.R b/tests/testthat/test-tweak-initial-estimates.R
@@ -7,7 +7,7 @@
 # of the bounds.
 
 describe("tweak_initial_estimates", {
-  skip_if_old_nmrec("0.3.0.8001")
+  skip_if_old_nmrec("0.4.0")
 
   it("base case - tweaking initial value works", {
     test_case <- list(