Refactor for code readabilityHEADmain

4 files changed, 15 insertions, 15 deletions

diff --git a/R/saem.R b/R/saem.R
index 45a7f8e9..2a9c2fa5 100644
--- a/R/saem.R
+++ b/R/saem.R
@@ -871,12 +871,12 @@ parms.saem.mmkin <- function(object, ci = FALSE, covariates = NULL, ...)
       # estimates for the corresponding covariate values passed
       # in 'covariates'.
       covariate_centers <- object$covariate_centers
-      centered_covariates <- covariates
+      parm_covariates <- covariates
       if (!is.na(covariate_centers[1])) {
         # If covariates were centered by the saem function, we need to center
         # user specified covariates as well
         for (i in names(covariates)) {
-          centered_covariates[i] <- covariates[i] - object$covariate_centers[i]
+          parm_covariates[i] <- covariates[i] - object$covariate_centers[i]
         }
       }
       est_for_cov <- matrix(NA,
@@ -890,7 +890,7 @@ parms.saem.mmkin <- function(object, ci = FALSE, covariates = NULL, ...)
           beta_degparm_name <- paste0("beta_", covariate,
             "(", deg_parm_name, ")")
           est_for_cov[deg_parm_name, ] <- estimate[deg_parm_name] +
-            centered_covariates[[covariate]] * estimate[beta_degparm_name]
+            parm_covariates[[covariate]] * estimate[beta_degparm_name]
         } else {
           est_for_cov[deg_parm_name, ] <- estimate[deg_parm_name]
         }
diff --git a/log/build.log b/log/build.log
index 37262b29..b2206986 100644
--- a/log/build.log
+++ b/log/build.log
@@ -6,5 +6,5 @@
 * checking for LF line-endings in source and make files and shell scripts
 * checking for empty or unneeded directories
 Removed empty directory ‘mkin/vignettes/web_only’
-* building ‘mkin_1.2.11.tar.gz’
+* building ‘mkin_1.2.10.tar.gz’
 
diff --git a/log/check.log b/log/check.log
index 94fd8095..7f212453 100644
--- a/log/check.log
+++ b/log/check.log
@@ -9,7 +9,7 @@
 * using options ‘--no-tests --as-cran’
 * checking for file ‘mkin/DESCRIPTION’ ... OK
 * checking extension type ... Package
-* this is package ‘mkin’ version ‘1.2.11’
+* this is package ‘mkin’ version ‘1.2.10’
 * package encoding: UTF-8
 * checking CRAN incoming feasibility ... OK
 * checking package namespace information ... OK
@@ -60,7 +60,7 @@
 * checking sizes of PDF files under ‘inst/doc’ ... OK
 * checking installed files from ‘inst/doc’ ... OK
 * checking files in ‘vignettes’ ... OK
-* checking examples ... [13s/13s] OK
+* checking examples ... [12s/12s] OK
 * checking for unstated dependencies in ‘tests’ ... OK
 * checking tests ... SKIPPED
 * checking for unstated dependencies in vignettes ... OK
diff --git a/log/test.log b/log/test.log
index 1b7f5c00..e1726492 100644
--- a/log/test.log
+++ b/log/test.log
@@ -4,29 +4,29 @@
 ✔ |          5 | Analytical solutions for coupled models [1.6s]
 ✔ |          5 | Calculation of Akaike weights
 ✔ |          3 | Export dataset for reading into CAKE
-✔ |          6 | Use of precompiled symbols in mkinpredict [3.6s]
+✔ |          6 | Use of precompiled symbols in mkinpredict [3.7s]
 ✔ |         12 | Confidence intervals and p-values
 ✔ |          1 | Solutions with deSolve
-✔ |      1  12 | Dimethenamid data from 2018 [14.1s]
-✔ |         14 | Error model fitting [2.8s]
+✔ |      1  12 | Dimethenamid data from 2018 [14.0s]
+✔ |         14 | Error model fitting [2.7s]
 ✔ |          5 | Time step normalisation
 ✔ |          4 | Calculation of FOCUS chi2 error levels
 ✔ |         14 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
 ✔ |          4 | Test fitting the decline of metabolites from their maximum
 ✔ |          1 | Fitting the logistic model
 ✔ |         10 | Batch fitting and diagnosing hierarchical kinetic models [20.5s]
-✔ |      2  20 | Nonlinear mixed-effects models [144.7s]
+✔ |      2  20 | Nonlinear mixed-effects models [142.6s]
 ✔ |          3 | Test dataset classes mkinds and mkindsg
 ✔ |         10 | Special cases of mkinfit calls
 ✔ |          3 | mkinfit features
 ✔ |          8 | mkinmod model generation and printing
 ✔ |          4 | Model predictions with mkinpredict
-✔ |         12 | Multistart method for saem.mmkin models [23.7s]
+✔ |         12 | Multistart method for saem.mmkin models [23.8s]
 ✔ |         16 | Evaluations according to 2015 NAFTA guidance [1.5s]
-✔ |          9 | Nonlinear mixed-effects models with nlme [4.3s]
-✔ |         15 | Plotting [4.8s]
+✔ |          9 | Nonlinear mixed-effects models with nlme [4.0s]
+✔ |         15 | Plotting [4.9s]
 ✔ |          4 | Residuals extracted from mkinfit models
-✔ |      1  38 | saemix parent models [35.6s]
+✔ |      1  38 | saemix parent models [36.1s]
 ✔ |          2 | Complex test case from Schaefer et al. (2007) Piacenza paper
 ✔ |         11 | Processing of residue series
 ✔ |         10 | Fitting the SFORB model [1.7s]
@@ -38,7 +38,7 @@
 ✔ |          2 | water-sediment
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 267.4 s
+Duration: 265.7 s
 
 ── Skipped tests (4) ───────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 5 minutes on my new system