Merge pull request #85 from guiastrennec/master

Summary and get_prm fixes
UUPharmacometrics · Jan 3, 2018 · ea9c3ed · ea9c3ed
2 parents 420e09c + 3df3da3
commit ea9c3ed
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Showing 4 changed files with 8 additions and 3 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -5,7 +5,9 @@
 * Fixed bug in `summary()` where missing estimation method was reported if NM code written as METH=... instead of METHOD=...
 * Fixed bug where labels in `prm_table()`, `get_prm()` were missing with a commented row in $THETA, $OMEGA or $SIGMA
 * Fixed bug in `prm_table()`, `get_prm()` where only `NA` would be reported when missing the -1000000006 record in the .ext file (i.e. NM <7.3)
+* Prevented negative RSE in `prm_table()` and `get_prm()`
 * Improved description of the `prm_table()` output
+* Fixed bug in `summary()` with non numeric covariance step time
 * Fixed bug in `ind_plots()` where the aesthetics would get mixed up if the variable names were changed
 * Small fixes to vignettes, documentations and website
 

diff --git a/R/summarise_nm_model.R b/R/summarise_nm_model.R
@@ -317,7 +317,7 @@ sum_runtime <- function(model, software) {
   if (software == 'nonmem') {
     x <- model %>% 
       dplyr::filter(.$subroutine == 'lst') %>% 
-      dplyr::filter(stringr::str_detect(.$code, stringr::fixed('Elapsed estimation time')))
+      dplyr::filter(stringr::str_detect(.$code, 'Elapsed estimation\\s+time'))
 
     if (nrow(x) == 0) return(sum_tpl('runtime', 'na'))
 
@@ -336,7 +336,7 @@ sum_covtime <- function(model, software) {
   if (software == 'nonmem') {
     x <- model %>% 
       dplyr::filter(.$subroutine == 'lst') %>% 
-      dplyr::filter(stringr::str_detect(.$code, stringr::fixed('Elapsed covariance time')))
+      dplyr::filter(stringr::str_detect(.$code, 'Elapsed covariance\\s+time in seconds:\\s+\\d'))
 
     if (nrow(x) == 0) return(sum_tpl('covtime', 'na'))
 

diff --git a/R/xpdb_access.R b/R/xpdb_access.R
@@ -396,7 +396,7 @@ get_prm <- function(xpdb,
                                               stringr::str_detect(.$name, 'SIGMA') ~ 'sig'),
                       number = stringr::str_replace_all(.$name, '[^\\d,]+', ''),
                       se     = ifelse(.$fixed, NA_real_, as.numeric(.$se)),
-                      rse    = ifelse(.$fixed, NA_real_, as.numeric(.$rse))) %>%
+                      rse    = ifelse(.$fixed, NA_real_, abs(as.numeric(.$rse)))) %>%
         tidyr::separate(col = 'number', into = c('m', 'n'), sep = ',', fill = 'right') %>% 
         dplyr::mutate(diagonal = dplyr::if_else(.$m == .$n, TRUE, FALSE)) %>% 
         dplyr::rename_(.dots = list(value = 'mean')) %>% 

diff --git a/tests/testthat/test-model-summary.R b/tests/testthat/test-model-summary.R
@@ -71,6 +71,9 @@ test_that('summary default summary is returned for missing information', {
   expect_equal(sum_out(sum_subroutine(model2, software)), c('subroutine', 'na'))
   expect_equal(sum_out(sum_runtime(model2, software)), c('runtime', 'na'))
   expect_equal(sum_out(sum_covtime(model2, software)), c('covtime', 'na'))
+  expect_equal(sum_out(sum_covtime(model = dplyr::data_frame(problem = 1L, level = 1L, subroutine = 'lst', 
+                                                             code = 'Elapsed covariance time in seconds: ********', 
+                                                             comment = ''), software), 1), c('covtime', 'na'))
   expect_equal(sum_out(sum_term(model2, software)), c('term', 'na'))
   expect_equal(sum_out(sum_warnings(model2, software)), c('warnings', 'na'))
   expect_equal(sum_out(sum_errors(model2, software)), c('errors', 'na'))