Merge pull request #139 from dd-harp/dev

Output terms
dd-harp · Dec 1, 2023 · d44d5df · d44d5df
2 parents c0b52fb + 8db706a
commit d44d5df
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Showing 59 changed files with 1,413 additions and 171 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -109,6 +109,38 @@ S3method(check_abiotic,forced)
 S3method(check_abiotic,null)
 S3method(check_civil,forced)
 S3method(check_civil,null)
+S3method(compute_EIR,aqua)
+S3method(compute_EIR,aqua_dde)
+S3method(compute_EIR,cohort)
+S3method(compute_EIR,dde)
+S3method(compute_EIR,human)
+S3method(compute_EIR,mosy)
+S3method(compute_EIR,mosy_dde)
+S3method(compute_EIR,ode)
+S3method(compute_NI,aqua)
+S3method(compute_NI,aqua_dde)
+S3method(compute_NI,cohort)
+S3method(compute_NI,dde)
+S3method(compute_NI,human)
+S3method(compute_NI,mosy)
+S3method(compute_NI,mosy_dde)
+S3method(compute_NI,ode)
+S3method(compute_fqZ,aqua)
+S3method(compute_fqZ,aqua_dde)
+S3method(compute_fqZ,cohort)
+S3method(compute_fqZ,dde)
+S3method(compute_fqZ,human)
+S3method(compute_fqZ,mosy)
+S3method(compute_fqZ,mosy_dde)
+S3method(compute_fqZ,ode)
+S3method(compute_kappa,aqua)
+S3method(compute_kappa,aqua_dde)
+S3method(compute_kappa,cohort)
+S3method(compute_kappa,dde)
+S3method(compute_kappa,human)
+S3method(compute_kappa,mosy)
+S3method(compute_kappa,mosy_dde)
+S3method(compute_kappa,ode)
 S3method(dHdt,numeric)
 S3method(dHdt,static)
 S3method(dLdt,basic)
@@ -283,7 +315,19 @@ export(approx_equal)
 export(checkIt)
 export(check_abiotic)
 export(check_civil)
+export(compute_EIR)
+export(compute_EIR_default)
+export(compute_EIR_i)
+export(compute_NI)
+export(compute_NI_default)
+export(compute_NI_i)
 export(compute_beta)
+export(compute_fqZ)
+export(compute_fqZ_default)
+export(compute_fqZ_i)
+export(compute_kappa)
+export(compute_kappa_default)
+export(compute_kappa_i)
 export(compute_local_frac)
 export(dHdt)
 export(dLdt)

diff --git a/R/aquatic-basic.R b/R/aquatic-basic.R
@@ -113,7 +113,7 @@ make_indices_L.basic <- function(pars) {
 #' @return varslist a [list]
 #' @export
 parse_deout_L.basic <- function(varslist, deout, pars) {
-  varslist$L = deout[,pars$Lpar$Lix+1]
+  varslist$L = deout[,pars$Lpar$L_ix+1]
   return(varslist)
 }