diff --git a/man/CohortSchedule.Rd b/man/CohortSchedule.Rd
index 3df7ba75..ce015225 100644
--- a/man/CohortSchedule.Rd
+++ b/man/CohortSchedule.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/RcppR6.R
+% Please edit documentation in r/RcppR6.R
 \name{CohortSchedule}
 \alias{CohortSchedule}
 \title{Schedule of cohort introduction times}
diff --git a/man/Control.Rd b/man/Control.Rd
index 1cbb6f85..2ff69967 100644
--- a/man/Control.Rd
+++ b/man/Control.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/RcppR6.R
+% Please edit documentation in r/RcppR6.R
 \name{Control}
 \alias{Control}
 \title{Control parameters}
diff --git a/man/Disturbance.Rd b/man/Disturbance.Rd
index ee7f6368..0a697bce 100644
--- a/man/Disturbance.Rd
+++ b/man/Disturbance.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/RcppR6.R
+% Please edit documentation in r/RcppR6.R
 \name{Disturbance}
 \alias{Disturbance}
 \title{Disturbance control object}
diff --git a/man/FF16.Rd b/man/FF16.Rd
index f27b62c7..06652ccd 100644
--- a/man/FF16.Rd
+++ b/man/FF16.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ff16.R
+% Please edit documentation in r/ff16.R
 \name{FF16_Individual}
 \alias{FF16_Individual}
 \alias{lcp_whole_plant.Plant<FF16>}
diff --git a/man/FF16_Environment.Rd b/man/FF16_Environment.Rd
index 8ab5ed9e..91cde975 100644
--- a/man/FF16_Environment.Rd
+++ b/man/FF16_Environment.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/RcppR6.R, R/ff16.R, R/ff16r.R
+% Please edit documentation in r/RcppR6.R, r/ff16.R, r/ff16r.R
 \name{FF16_Environment}
 \alias{FF16_Environment}
 \alias{FF16_make_environment}
diff --git a/man/FF16_Strategy.Rd b/man/FF16_Strategy.Rd
index 682e9c2c..04f096c5 100644
--- a/man/FF16_Strategy.Rd
+++ b/man/FF16_Strategy.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/RcppR6.R
+% Please edit documentation in r/RcppR6.R
 \name{FF16_Strategy}
 \alias{FF16_Strategy}
 \title{Strategy parameters}
diff --git a/man/FF16_hyperpar.Rd b/man/FF16_hyperpar.Rd
index 3f4f7f15..71082db8 100644
--- a/man/FF16_hyperpar.Rd
+++ b/man/FF16_hyperpar.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ff16.R
+% Please edit documentation in r/ff16.R
 \name{make_FF16_hyperpar}
 \alias{make_FF16_hyperpar}
 \alias{FF16_hyperpar}
diff --git a/man/FF16r.Rd b/man/FF16r.Rd
index b85b70c1..97a2396d 100644
--- a/man/FF16r.Rd
+++ b/man/FF16r.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ff16r.R
+% Please edit documentation in r/ff16r.R
 \name{FF16r_Individual}
 \alias{FF16r_Individual}
 \alias{lcp_whole_plant.Plant<FF16r>}
diff --git a/man/FF16r_Strategy.Rd b/man/FF16r_Strategy.Rd
index b629e19a..fc85ec07 100644
--- a/man/FF16r_Strategy.Rd
+++ b/man/FF16r_Strategy.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/RcppR6.R
+% Please edit documentation in r/RcppR6.R
 \name{FF16r_Strategy}
 \alias{FF16r_Strategy}
 \title{Strategy parameters}
diff --git a/man/FF16r_hyperpar.Rd b/man/FF16r_hyperpar.Rd
index 6d30090b..b57d73b2 100644
--- a/man/FF16r_hyperpar.Rd
+++ b/man/FF16r_hyperpar.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ff16r.R
+% Please edit documentation in r/ff16r.R
 \name{make_FF16r_hyperpar}
 \alias{make_FF16r_hyperpar}
 \alias{FF16r_hyperpar}
diff --git a/man/Hyperparameter_functions.Rd b/man/Hyperparameter_functions.Rd
index cc85f72f..431d67d8 100644
--- a/man/Hyperparameter_functions.Rd
+++ b/man/Hyperparameter_functions.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/strategy_support.R
+% Please edit documentation in r/strategy_support.R
 \name{make_hyperpar}
 \alias{make_hyperpar}
 \alias{hyperpar}
diff --git a/man/Individual.Rd b/man/Individual.Rd
index 129b05e4..624ccc03 100644
--- a/man/Individual.Rd
+++ b/man/Individual.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/RcppR6.R
+% Please edit documentation in r/RcppR6.R
 \name{Individual}
 \alias{Individual}
 \title{Individual object}
diff --git a/man/Internals.Rd b/man/Internals.Rd
index e1dee606..83a8a1f9 100644
--- a/man/Internals.Rd
+++ b/man/Internals.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/RcppR6.R
+% Please edit documentation in r/RcppR6.R
 \name{Internals}
 \alias{Internals}
 \title{Internals class holding vectors of states, thier associated rates and auxiliary (aux) state 
diff --git a/man/Interpolator.Rd b/man/Interpolator.Rd
index 23f5d7e2..96cf31cc 100644
--- a/man/Interpolator.Rd
+++ b/man/Interpolator.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/RcppR6.R
+% Please edit documentation in r/RcppR6.R
 \name{Interpolator}
 \alias{Interpolator}
 \title{Spline interpolation}
diff --git a/man/K93.Rd b/man/K93.Rd
index 1d3078f0..40eb1d7a 100644
--- a/man/K93.Rd
+++ b/man/K93.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/k93.R
+% Please edit documentation in r/k93.R
 \name{K93_Individual}
 \alias{K93_Individual}
 \alias{lcp_whole_plant.Individual<K93>}
diff --git a/man/K93_Environment.Rd b/man/K93_Environment.Rd
index 96cd85c9..0ce3d511 100644
--- a/man/K93_Environment.Rd
+++ b/man/K93_Environment.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/RcppR6.R, R/k93.R
+% Please edit documentation in r/RcppR6.R, r/k93.R
 \name{K93_Environment}
 \alias{K93_Environment}
 \alias{K93_make_environment}
diff --git a/man/K93_Strategy.Rd b/man/K93_Strategy.Rd
index 1a532bca..b3d0425f 100644
--- a/man/K93_Strategy.Rd
+++ b/man/K93_Strategy.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/RcppR6.R
+% Please edit documentation in r/RcppR6.R
 \name{K93_Strategy}
 \alias{K93_Strategy}
 \title{Strategy parameters}
diff --git a/man/K93_hyperpar.Rd b/man/K93_hyperpar.Rd
index 8b9ce87e..e5a3cfb7 100644
--- a/man/K93_hyperpar.Rd
+++ b/man/K93_hyperpar.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/k93.R
+% Please edit documentation in r/k93.R
 \name{make_K93_hyperpar}
 \alias{make_K93_hyperpar}
 \alias{K93_hyperpar}
diff --git a/man/OdeControl.Rd b/man/OdeControl.Rd
index a6deed34..4bae484b 100644
--- a/man/OdeControl.Rd
+++ b/man/OdeControl.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/RcppR6.R
+% Please edit documentation in r/RcppR6.R
 \name{OdeControl}
 \alias{OdeControl}
 \title{ODE Control parameters}
diff --git a/man/QK.Rd b/man/QK.Rd
index 69efe8d8..324300b4 100644
--- a/man/QK.Rd
+++ b/man/QK.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/RcppR6.R
+% Please edit documentation in r/RcppR6.R
 \name{QK}
 \alias{QK}
 \title{Gauss-Kronrod Quadrature}
diff --git a/man/assembly_parameters.Rd b/man/assembly_parameters.Rd
index b566d724..72c5ea71 100644
--- a/man/assembly_parameters.Rd
+++ b/man/assembly_parameters.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/scm_support.R
+% Please edit documentation in r/scm_support.R
 \name{assembly_parameters}
 \alias{assembly_parameters}
 \title{Helper function for creating parameter objects}
diff --git a/man/bounds.Rd b/man/bounds.Rd
index fd07c836..93eb879b 100644
--- a/man/bounds.Rd
+++ b/man/bounds.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/fitness_support.R
+% Please edit documentation in r/fitness_support.R
 \name{bounds}
 \alias{bounds}
 \alias{check_bounds}
diff --git a/man/build_schedule.Rd b/man/build_schedule.Rd
index e1ee7d1c..ec18f23a 100644
--- a/man/build_schedule.Rd
+++ b/man/build_schedule.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/build_schedule.R
+% Please edit documentation in r/build_schedule.R
 \name{build_schedule}
 \alias{build_schedule}
 \title{Build Cohort Schedule}
diff --git a/man/carrying_capacity.Rd b/man/carrying_capacity.Rd
index 2b12b521..a50de0b2 100644
--- a/man/carrying_capacity.Rd
+++ b/man/carrying_capacity.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/fitness.R
+% Please edit documentation in r/fitness.R
 \name{carrying_capacity}
 \alias{carrying_capacity}
 \title{Carrying Capacity}
diff --git a/man/check_inviable.Rd b/man/check_inviable.Rd
index 153a2952..a99fa2a3 100644
--- a/man/check_inviable.Rd
+++ b/man/check_inviable.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/equilibrium.R
+% Please edit documentation in r/equilibrium.R
 \name{check_inviable}
 \alias{check_inviable}
 \title{Check low-abundance strategies for viability}
diff --git a/man/clamp_domain.Rd b/man/clamp_domain.Rd
index aeaddc40..6c91f46b 100644
--- a/man/clamp_domain.Rd
+++ b/man/clamp_domain.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/util.R
+% Please edit documentation in r/util.R
 \name{clamp_domain}
 \alias{clamp_domain}
 \title{Clamp function to domain}
diff --git a/man/cohort_schedule_times_default.Rd b/man/cohort_schedule_times_default.Rd
index 80acf5b7..8022f10d 100644
--- a/man/cohort_schedule_times_default.Rd
+++ b/man/cohort_schedule_times_default.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/RcppExports.R
+% Please edit documentation in r/RcppExports.R
 \name{cohort_schedule_times_default}
 \alias{cohort_schedule_times_default}
 \title{Generate Default Cohort Introduction Times}
diff --git a/man/equilibrium_seed_rain.Rd b/man/equilibrium_seed_rain.Rd
index 4597e135..004fe9c4 100644
--- a/man/equilibrium_seed_rain.Rd
+++ b/man/equilibrium_seed_rain.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/equilibrium.R
+% Please edit documentation in r/equilibrium.R
 \name{equilibrium_seed_rain}
 \alias{equilibrium_seed_rain}
 \title{Run system to seed rain equilibrium}
diff --git a/man/equilibrium_verbose.Rd b/man/equilibrium_verbose.Rd
index 91d85892..b80c1a80 100644
--- a/man/equilibrium_verbose.Rd
+++ b/man/equilibrium_verbose.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/scm_support.R
+% Please edit documentation in r/scm_support.R
 \name{equilibrium_verbose}
 \alias{equilibrium_verbose}
 \alias{equilibrium_quiet}
diff --git a/man/expand_parameters.Rd b/man/expand_parameters.Rd
index 3562b970..41f704cd 100644
--- a/man/expand_parameters.Rd
+++ b/man/expand_parameters.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/util_model.R
+% Please edit documentation in r/util_model.R
 \name{expand_parameters}
 \alias{expand_parameters}
 \title{Expand Parameters to include mutants}
diff --git a/man/fast_control.Rd b/man/fast_control.Rd
index 1ddf2ab5..92939b4a 100644
--- a/man/fast_control.Rd
+++ b/man/fast_control.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/scm_support.R
+% Please edit documentation in r/scm_support.R
 \name{fast_control}
 \alias{fast_control}
 \title{Fast Control Defaults}
diff --git a/man/fitness_landscape.Rd b/man/fitness_landscape.Rd
index bd4eff78..fa52474e 100644
--- a/man/fitness_landscape.Rd
+++ b/man/fitness_landscape.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/fitness.R
+% Please edit documentation in r/fitness.R
 \name{fitness_landscape}
 \alias{fitness_landscape}
 \title{Fitness Landscape}
diff --git a/man/grow_plant_to_size.Rd b/man/grow_plant_to_size.Rd
index 0f41bf0a..4c88d7ed 100644
--- a/man/grow_plant_to_size.Rd
+++ b/man/grow_plant_to_size.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plant.R
+% Please edit documentation in r/plant.R
 \name{grow_plant_to_size}
 \alias{grow_plant_to_size}
 \alias{grow_plant_to_height}
diff --git a/man/grow_plant_to_time.Rd b/man/grow_plant_to_time.Rd
index 80d345cc..3b049f42 100644
--- a/man/grow_plant_to_time.Rd
+++ b/man/grow_plant_to_time.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plant.R
+% Please edit documentation in r/plant.R
 \name{grow_plant_to_time}
 \alias{grow_plant_to_time}
 \title{Grow a plant}
diff --git a/man/lcp_whole_plant.Rd b/man/lcp_whole_plant.Rd
index ef728220..55f44850 100644
--- a/man/lcp_whole_plant.Rd
+++ b/man/lcp_whole_plant.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plant.R
+% Please edit documentation in r/plant.R
 \name{lcp_whole_plant}
 \alias{lcp_whole_plant}
 \title{Whole plant light compensation point}
diff --git a/man/make_patch.Rd b/man/make_patch.Rd
index 22394f68..de658d2e 100644
--- a/man/make_patch.Rd
+++ b/man/make_patch.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/scm_support.R
+% Please edit documentation in r/scm_support.R
 \name{make_patch}
 \alias{make_patch}
 \alias{scm_state}
diff --git a/man/make_reference_plant.Rd b/man/make_reference_plant.Rd
index c97dec84..e404aecd 100644
--- a/man/make_reference_plant.Rd
+++ b/man/make_reference_plant.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/reference_plant.R
+% Please edit documentation in r/reference_plant.R
 \name{make_reference_plant}
 \alias{make_reference_plant}
 \title{Reference Growth Model}
diff --git a/man/make_reference_plant_FF16.Rd b/man/make_reference_plant_FF16.Rd
index 098f6d6f..43830bde 100644
--- a/man/make_reference_plant_FF16.Rd
+++ b/man/make_reference_plant_FF16.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/reference_plant.R
+% Please edit documentation in r/reference_plant.R
 \name{make_reference_plant_FF16}
 \alias{make_reference_plant_FF16}
 \title{Reference Growth Model}
diff --git a/man/make_scm_integrate.Rd b/man/make_scm_integrate.Rd
index b779baa1..63d3cd02 100644
--- a/man/make_scm_integrate.Rd
+++ b/man/make_scm_integrate.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/scm_support.R
+% Please edit documentation in r/scm_support.R
 \name{make_scm_integrate}
 \alias{make_scm_integrate}
 \title{Integrate SCM variables}
diff --git a/man/make_transparent.Rd b/man/make_transparent.Rd
index 75e315ac..ba6d02d3 100644
--- a/man/make_transparent.Rd
+++ b/man/make_transparent.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/util.R
+% Please edit documentation in r/util.R
 \name{make_transparent}
 \alias{make_transparent}
 \title{Make colours transparent}
diff --git a/man/max_fitness.Rd b/man/max_fitness.Rd
index ce0a46ec..70bf378f 100644
--- a/man/max_fitness.Rd
+++ b/man/max_fitness.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/fitness_trait_space.R
+% Please edit documentation in r/fitness_trait_space.R
 \name{max_fitness}
 \alias{max_fitness}
 \title{Find point of maximum fitness within some range.}
diff --git a/man/max_growth_rate.Rd b/man/max_growth_rate.Rd
index a8ea8fbe..6eedf7c4 100644
--- a/man/max_growth_rate.Rd
+++ b/man/max_growth_rate.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/fitness.R
+% Please edit documentation in r/fitness.R
 \name{max_growth_rate}
 \alias{max_growth_rate}
 \title{Compute Max Growth Rate}
diff --git a/man/nlsolve.Rd b/man/nlsolve.Rd
index 0bc1bdce..1f62e77f 100644
--- a/man/nlsolve.Rd
+++ b/man/nlsolve.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/util_solve.R
+% Please edit documentation in r/util_solve.R
 \name{nlsolve}
 \alias{nlsolve}
 \title{Thin wrapper around nleqslv and dfsane}
diff --git a/man/plant_log_console.Rd b/man/plant_log_console.Rd
index 846360a6..b22a7cff 100644
--- a/man/plant_log_console.Rd
+++ b/man/plant_log_console.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/logging.R
+% Please edit documentation in r/logging.R
 \name{plant_log_console}
 \alias{plant_log_console}
 \title{Activate logging with loggr}
diff --git a/man/rbind_list.Rd b/man/rbind_list.Rd
index fcfb25ab..f5153e88 100644
--- a/man/rbind_list.Rd
+++ b/man/rbind_list.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/util.R
+% Please edit documentation in r/util.R
 \name{rbind_list}
 \alias{rbind_list}
 \alias{cbind_list}
diff --git a/man/run_plant_benchmarks.Rd b/man/run_plant_benchmarks.Rd
index c7734b0f..2344c2b3 100644
--- a/man/run_plant_benchmarks.Rd
+++ b/man/run_plant_benchmarks.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/benchmark.R
+% Please edit documentation in r/benchmark.R
 \name{run_plant_benchmarks}
 \alias{run_plant_benchmarks}
 \title{Check performance on current system using package bench}
diff --git a/man/run_scm.Rd b/man/run_scm.Rd
index be4e5a5a..23d3d5cd 100644
--- a/man/run_scm.Rd
+++ b/man/run_scm.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/scm_support.R
+% Please edit documentation in r/scm_support.R
 \name{run_scm}
 \alias{run_scm}
 \title{Run SCM}
diff --git a/man/run_scm_collect.Rd b/man/run_scm_collect.Rd
index 245cac49..3f3ed730 100644
--- a/man/run_scm_collect.Rd
+++ b/man/run_scm_collect.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/scm_support.R
+% Please edit documentation in r/scm_support.R
 \name{run_scm_collect}
 \alias{run_scm_collect}
 \title{Run the SCM, Collecting Output}
diff --git a/man/run_stochastic_collect.Rd b/man/run_stochastic_collect.Rd
index 11fca65f..d9f77cc7 100644
--- a/man/run_stochastic_collect.Rd
+++ b/man/run_stochastic_collect.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/stochastic.R
+% Please edit documentation in r/stochastic.R
 \name{run_stochastic_collect}
 \alias{run_stochastic_collect}
 \title{Run a stochastic patch, Collecting Output}
diff --git a/man/scm_base_parameters.Rd b/man/scm_base_parameters.Rd
index e09a84fc..1e10473c 100644
--- a/man/scm_base_parameters.Rd
+++ b/man/scm_base_parameters.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/scm_support.R
+% Please edit documentation in r/scm_support.R
 \name{scm_base_parameters}
 \alias{scm_base_parameters}
 \title{Sensible, fast (ish) SCM parameters}
diff --git a/man/seq_log.Rd b/man/seq_log.Rd
index 53bd1bf8..ed584133 100644
--- a/man/seq_log.Rd
+++ b/man/seq_log.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/util.R
+% Please edit documentation in r/util.R
 \name{seq_log}
 \alias{seq_log}
 \alias{seq_log_range}
diff --git a/man/splinefun_log.Rd b/man/splinefun_log.Rd
index 550e8783..65cf33c1 100644
--- a/man/splinefun_log.Rd
+++ b/man/splinefun_log.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/util.R
+% Please edit documentation in r/util.R
 \name{splinefun_log}
 \alias{splinefun_log}
 \alias{splinefun_loglog}
diff --git a/man/strategy_list.Rd b/man/strategy_list.Rd
index a2234a90..9677807e 100644
--- a/man/strategy_list.Rd
+++ b/man/strategy_list.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/util_model.R
+% Please edit documentation in r/util_model.R
 \name{strategy_list}
 \alias{strategy_list}
 \alias{strategy_default}
diff --git a/man/trait_matrix.Rd b/man/trait_matrix.Rd
index 203e3747..9ca2d1cb 100644
--- a/man/trait_matrix.Rd
+++ b/man/trait_matrix.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/util_model.R
+% Please edit documentation in r/util_model.R
 \name{trait_matrix}
 \alias{trait_matrix}
 \title{Create trait matrix}
diff --git a/man/validate.Rd b/man/validate.Rd
index 8ee8fa05..db04e6be 100644
--- a/man/validate.Rd
+++ b/man/validate.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/util.R
+% Please edit documentation in r/util.R
 \name{validate}
 \alias{validate}
 \title{Validate an object}
diff --git a/man/viable_fitness.Rd b/man/viable_fitness.Rd
index 2c10d3ae..a0e69d0e 100644
--- a/man/viable_fitness.Rd
+++ b/man/viable_fitness.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/fitness_trait_space.R
+% Please edit documentation in r/fitness_trait_space.R
 \name{viable_fitness}
 \alias{viable_fitness}
 \title{Compute Region of Positive Fitnes}