Merge branch 'improve-codefactor' into cran-prep

wleoncio · Oct 4, 2024 · 05d8014 · 05d8014
2 parents e142cfa + 818fcb0
commit 05d8014
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: smms
 Title: Semi-Markov Multi-State Models for Interval Censored Data
-Version: 1.0.0.9001
+Version: 1.0.0.9002
 Date: 2024-03-12
 Authors@R:
     c(

diff --git a/R/sm_msm_likelihood_func.R b/R/sm_msm_likelihood_func.R
@@ -419,7 +419,7 @@ finding_limits <- function(timepoints,form_type,edge_mats,absorbing_states,abs_e
     #id_na <- which(is.na(m_times) & substr(names(m_times),2,2)%in%unobs_states)
     id_na <- which(is.na(m_times))
     if (length(id_na)>0){
-      for (j in length(id_na):1){  ## CHECK
+      for (j in rev(seq_along(id_na))){  ## CHECK
         m_times[id_na[j]] <- m_times[id_na[j]+1]
       }
     }

diff --git a/R/sm_msm_optim_func.R b/R/sm_msm_optim_func.R
@@ -686,7 +686,7 @@ transition_prob_delta = function(trans_ji, time_t,time_v, param, graph, xval = N
           })
 
         }else if (length(lower)>2){
-          integrand2 <- integrand # TODO: placeholder. check if this is correct (probably isn't)
+          integrand2 <- change_integrand(integrand) # introduced on 8ed1f77bb85b2ec323645c7f7e3e72a1fdfd1f2d
           n_deriv[j,] = pracma::grad(cubint,x0=param,integrand=integrand2,lower = lower,upper = upper, tmax=tmax,xval=xval)
         }
       }