BDI-pathogens · Jan 26, 2021
diff --git a/‎.Rbuildignore
+12-3 b/‎.Rbuildignore
+12-3
diff --git a/‎.gitignore
+10 b/‎.gitignore
+10
diff --git a/‎DESCRIPTION
+2 b/‎DESCRIPTION
+2
diff --git a/‎Makefile
+19-7 b/‎Makefile
+19-7
diff --git a/‎NAMESPACE
+3 b/‎NAMESPACE
+3
diff --git a/‎R/Model.R
+82 b/‎R/Model.R
+82
diff --git a/‎R/Network.R
+2-1 b/‎R/Network.R
+2-1
diff --git a/‎R/Simulation.R
+2 b/‎R/Simulation.R
+2
diff --git a/‎R/VaccineSchedule.R
+76 b/‎R/VaccineSchedule.R
+76
diff --git a/‎R/util.R
+36 b/‎R/util.R
+36
diff --git a/‎README.md
+2 b/‎README.md
+2
diff --git a/‎configure.ac
+13 b/‎configure.ac
+13
diff --git a/‎package-for-CRAN.sh
+18 b/‎package-for-CRAN.sh
+18
diff --git a/‎src/Makevars
-22 b/‎src/Makevars
-22
diff --git a/‎src/Makevars.in
+5 b/‎src/Makevars.in
+5
diff --git a/‎src/Makevars.win
+4-3 b/‎src/Makevars.win
+4-3
diff --git a/‎src/individual.c
+2-2 b/‎src/individual.c
+2-2
diff --git a/‎src/utilities.c
+10 b/‎src/utilities.c
+10
diff --git a/‎src/utilities.h
+1 b/‎src/utilities.h
+1
diff --git a/‎tests/test_R_INSTALL_win.bat
+13 b/‎tests/test_R_INSTALL_win.bat
+13
diff --git a/‎tests/testthat/test-Model.R
+5 b/‎tests/testthat/test-Model.R
+5
diff --git a/‎tests/testthat/test-VaccineSchedule.R
+25 b/‎tests/testthat/test-VaccineSchedule.R
+25
@@ -3,8 +3,8 @@
 # R files
 ^\.Rhistory$
 ^\.RData$
-^.*\.Rproj$
 ^\.Rproj\.user$
+^.*\.Rproj$
 ^.*\.Rcheck$
 
 # R utility scripts
@@ -23,19 +23,28 @@
 ^src\/adapter_covid19$
 ^src\/covid19_wrap\.c$
 
+# Conf files
+^autom4te.cache$
+^config\.log$
+^config\.status$
+^src\/Makevars$
+
 # Build files
-.*\.in$
 ^Makefile$
+^package-for-CRAN\.sh$
 ^OpenABMCovid19.tmp$
 ^OpenABMCovid19_.*\.tar\.gz$
 ^OpenABMCovid19_.*\.tgz$
 ^OpenABMCovid19_.*\.zip$
 
-# Test output
+# Test files
 ^src_test$
 ^data_test$
+^tests\/requirements\.txt$
 ^tests\/src_test$
 ^tests\/data_test$
+^tests\/adapter_covid19$
+^tests\/Dockerfile$
 
 # Misc
 ^\.github$
 
@@ -1,6 +1,13 @@
 # Mac-related files
 .DS_Store
 
+# File associated with configure
+config.log
+config.status
+configure
+src/Makevars
+autom4te.cache/
+
 # File associated with compilation/linking
 src/**/*.o
 src/**/*.exe
@@ -72,6 +79,9 @@ src-x64/
 /man/Parameters.Rd
 /man/SAFE_UPDATE_PARAMS.Rd
 /man/Simulation.Rd
+/man/VaccineSchedule.Rd
+/man/VACCINE_STATUS.Rd
+/man/VACCINE_TYPES.Rd
 
 
 # performance related
 
@@ -24,7 +24,9 @@ Collate:
   Network.R
   Model.R
   Simulation.R
+  VaccineSchedule.R
 Suggests:
     testthat
 RoxygenNote: 7.1.1
 Encoding: UTF-8
+SystemRequirements: GNU GSL
@@ -11,9 +11,20 @@ ifeq ($(OS),Windows_NT)
 # HOME to itself.
 # https://community.rstudio.com/t/rstudio-startup-missing-libpaths/22122/6
 	R_ENV=HOME=
+	UNAME=Windows
 else
 	R_BIN_PKG_EXT=tgz
 	R_ENV=
+	UNAME=$(shell uname -s)
+endif
+
+# The 'in-place' flag is different on macOS (BSD) and Linux/minGW.
+# https://linux.die.net/man/1/sed
+# https://www.freebsd.org/cgi/man.cgi?query=sed&sektion=&n=1
+ifeq ($(UNAME),Darwin)
+	SED_I=sed -i ''
+else
+	SED_I=sed -i
 endif
 
 
@@ -48,13 +59,14 @@ SWIG_ROUT = R/$(R_PKGNAME).R
 $(SWIG_COUT): $(SWIG_SRC)
 	swig -r -package $(R_PKGNAME) -Isrc -o $(SWIG_COUT) -outdir R src/covid19.i
 # edit generated C source to mute R check note.
-	sed -i 's/R_registerRoutines/R_useDynamicSymbols(dll,0);R_registerRoutines/' $(SWIG_COUT)
-$(SWIG_ROUT): $(SWIG_COUT)
+	$(SED_I) 's/R_registerRoutines/R_useDynamicSymbols(dll,0);R_registerRoutines/' $(SWIG_COUT)
 # edit generated src lines are cause R check warnings.
-	sed -i 's/.Call("R_SWIG_debug_getCallbackFunctionData"/.Call("R_SWIG_debug_getCallbackFunctionData", PACKAGE="OpenABMCovid19"/' $(SWIG_ROUT)
-	sed -i 's/.Call("R_SWIG_R_pushCallbackFunctionData"/.Call("R_SWIG_R_pushCallbackFunctionData", PACKAGE="OpenABMCovid19"/' $(SWIG_ROUT)
+	$(SED_I) 's/.Call("R_SWIG_debug_getCallbackFunctionData"/.Call("R_SWIG_debug_getCallbackFunctionData", PACKAGE="OpenABMCovid19"/' $(SWIG_ROUT)
+	$(SED_I) 's/.Call("R_SWIG_R_pushCallbackFunctionData"/.Call("R_SWIG_R_pushCallbackFunctionData", PACKAGE="OpenABMCovid19"/' $(SWIG_ROUT)
 # edit generated src that causes errors like: "p_char" is not a defined class
-	sed -i 's/ans <- new("_p_char"/#ans <- new("_p_char"/' $(SWIG_ROUT)
+	$(SED_I) 's/ans <- new("_p_char"/#ans <- new("_p_char"/' $(SWIG_ROUT)
+$(SWIG_ROUT): $(SWIG_COUT)
+
 ALL_OUTPUT += $(SWIG_COUT) $(SWIG_ROUT)
 
 
@@ -171,10 +183,10 @@ Rcheck: $(R_SRC_PKG)
 # Cleaning
 #------------------------------------------------------------------------------
 clean:
-	rm -fr $(ALL_OUTPUT) src/*.o src/*.dll
+	rm -fr $(ALL_OUTPUT) src/*.o src/*.dll src/*.so
 
 dry_clean:
 	@echo '`make clean` will run:'
-	@echo 'rm -fr $(ALL_OUTPUT) src/*.o src/*.dll'
+	@echo 'rm -fr $(ALL_OUTPUT) src/*.o src/*.dll src/*.so'
 
 .PHONY: clean dry_clean Rswig Rman Rbuild Rcheck Rinstall
@@ -14,10 +14,13 @@ export("Environment")
 export("Agent")
 export("Simulation")
 export("COVID19IBM")
+export("VaccineSchedule")
 
 # Enums
 export("AgeGroupEnum")
 export("SAFE_UPDATE_PARAMS")
 export("NETWORK_CONSTRUCTIONS")
+export("VACCINE_TYPES")
+export("VACCINE_STATUS")
 
 useDynLib(OpenABMCovid19, .registration = TRUE)
@@ -20,6 +20,7 @@ SWIG_utils_n_total <- utils_n_total
 SWIG_utils_n_total_age <- utils_n_total_age
 SWIG_utils_n_total_by_day <- utils_n_total_by_day
 SWIG_calculate_R_instanteous <- calculate_R_instanteous
+SWIG_seed_infect_by_idx <- seed_infect_by_idx
 
 #' R6Class Model
 #'
@@ -369,6 +370,28 @@ Model <- R6Class( classname = 'Model', cloneable = FALSE,
       return(Network$new( private$c_model, network_id ))
     },
 
+    #' @description Infects a new individual from an external source.
+    #' Wrapper for C API \code{seed_infect_by_idx}.
+    #' @param ID The ID of the individual.
+    #' @param strain_multiplier The strain multiplier value, must be a
+    #'   positivate number.
+    #' @param network_id The network ID.
+    #' @return \code{TRUE} on success, \code{FALSE} otherwise.
+    seed_infect_by_idx = function(ID, strain_multiplier = 1, network_id = -1 )
+    {
+      n_total <- private$c_params$n_total
+
+      if (ID < 0 || ID >= n_total) {
+        stop("ID out of range (0<=ID<n_total)")
+      }
+      if (strain_multiplier < 0) {
+        stop("strain_multiplier must be positive")
+      }
+      res <- SWIG_seed_infect_by_idx(private$c_model, ID, strain_multiplier,
+        network_id)
+      return(as.logical(res))
+    },
+
     #' @description Get the list of network IDs
     #' Wrapper for C API \code{get_network_ids}.
     #' @param max_ids The maximum number of IDs to return.
@@ -429,6 +452,65 @@ Model <- R6Class( classname = 'Model', cloneable = FALSE,
       return(as.data.frame(tmp))
     },
 
+    #' @description Vaccinate an individual.
+    #' Wrapper for C API \code{intervention_vaccinate_by_idx}.
+    #' @param ID The ID of the individual (must be \code{0 <= ID <= n_total}).
+    #' @param vaccine_type The type of vaccine, see \code{\link{VACCINE_TYPES}}.
+    #' @param efficacy Probability that the person is successfully vaccinated
+    #'   (must be \code{0 <= efficacy <= 1}).
+    #' @param time_to_protect Delay before it takes effect (in days).
+    #' @param vaccine_protection_period The duration of the vaccine before it
+    #'   wanes.
+    #' @return Logical value, \code{TRUE} if vaccinated \code{FALSE} otherwise.
+    vaccinate_individual = function(
+      ID,
+      vaccine_type = 0,
+      efficacy = 1.0,
+      time_to_protect = 14,
+      vaccine_protection_period = 1000 )
+    {
+      n_total <- private$c_params$n_total
+
+      if (ID < 0 || ID >= n_total) {
+        stop("ID out of range (0<=ID<n_total)")
+      }
+      if (efficacy < 0 || efficacy > 1) {
+        stop("efficacy must be between 0 and 1")
+      }
+      if (time_to_protect < 1) {
+        stop("vaccine must take at least one day to take effect")
+      }
+      if (vaccine_protection_period <= time_to_protect) {
+        stop("vaccine must protect for longer than it takes to by effective")
+      }
+      if (!is.numeric(vaccine_type) || ! vaccine_type %in% VACCINE_TYPES) {
+        stop("vaccine type must be listed in VaccineTypesEnum")
+      }
+
+      res <- intervention_vaccinate_by_idx(private$c_model, ID, vaccine_type,
+        efficacy, time_to_protect, vaccine_protection_period)
+      return(as.logical(res))
+    },
+
+    #' @description Schedule an age-group vaccionation
+    #' Wrapper for C API \code{intervention_vaccinate_age_group}.
+    #' @param schedule An instance of \code{\link{VaccineSchedule}}.
+    #' @return The total number of people vaccinated.
+    vaccinate_schedule = function(schedule)
+    {
+      if (!is.R6(schedule) || !('VaccineSchedule' %in% class(schedule))) {
+        stop("argument VaccineSchedule must be an object of type VaccineSchedule")
+      }
+      return(as.logical(intervention_vaccinate_age_group(
+        private$c_model,
+        schedule$fraction_to_vaccinate,
+        schedule$vaccine_type,
+        schedule$efficacy,
+        schedule$time_to_protect,
+        schedule$vaccine_protection_period,
+        schedule$total_vaccinated)))
+    },
+
     #' @description Delete a network.
     #' Wrapper for C API \code{delete_network}.
     #' @param network The network to delete.
 
@@ -12,7 +12,7 @@ Network <- R6Class( classname = 'Network', cloneable = FALSE,
   private = list( id = NULL ),
 
   public = list(
-    #' @field External pointer, reference to \code{network} C struct.
+    #' @field c_network External pointer, reference to \code{network} C struct.
     c_network = NULL,
 
     #' @param c_model External pointer, reference to \code{model} C struct.
@@ -76,6 +76,7 @@ Network <- R6Class( classname = 'Network', cloneable = FALSE,
     },
 
     #' @description Wrapper for C API \code{update_daily_fraction}.
+    #' @param daily_fraction New fraction value; a value vetween 0 and 1.
     #' @return \code{TRUE} on success, \code{FALSE} on failure.
     update_daily_fraction = function(daily_fraction) {
       res <- SWIG_update_daily_fraction( self$c_network, daily_fraction )
 
@@ -191,6 +191,8 @@ Simulation <- R6Class( classname = 'Simulation', cloneable = FALSE,
 
     #' @description Collect model results at each step;
     #' fixme action is not currently stored
+    #' @param state The state to collect results from.
+    #' @param action Currently unused.
     collect_results = function(state, action) {
       # Save results to a named vector
       for (i in 1:length(state)) {
 
@@ -0,0 +1,76 @@
+SWIG_update_daily_fraction = update_daily_fraction
+
+#' R6Class VaccineSchedule
+#'
+#' @description
+#' VaccineSchedule object has information an age-group vaccination plan.
+#'
+VaccineSchedule <- R6Class( classname = 'VaccineSchedule', cloneable = FALSE,
+
+  public = list(
+    #' @field fraction_to_vaccinate Get the vaccination fractions per age-group.
+    fraction_to_vaccinate = NULL,
+
+    #' @field total_vaccinated The total number of vaccinations per age-group.
+    total_vaccinated = NULL,
+
+    #' @field vaccine_type The type of vaccine, see \code{\link{VACCINE_TYPES}}.
+    vaccine_type    = NULL,
+
+    #' @field efficacy Probability that the person is successfully vaccinated
+    #'   (must be \code{0 <= efficacy <= 1}).
+    efficacy        = NULL,
+
+    #' @field time_to_protect Delay before it takes effect (in days).
+    time_to_protect = NULL,
+
+    #' @field vaccine_protection_period The duration of the vaccine before it
+    #'   wanes.
+    vaccine_protection_period = NULL,
+
+    #' @param frac_0_9 Fraction of age group 0-9.
+    #' @param frac_10_19 Fraction of age group 10-19.
+    #' @param frac_20_29 Fraction of age group 20-29.
+    #' @param frac_30_39 Fraction of age group 30-39.
+    #' @param frac_40_49 Fraction of age group 40-49.
+    #' @param frac_50_59 Fraction of age group 50-59.
+    #' @param frac_60_69 Fraction of age group 60-69.
+    #' @param frac_70_79 Fraction of age group 70-79.
+    #' @param frac_80 Fraction of age group >80.
+    #' @param vaccine_type The type of vaccine, see \code{\link{VACCINE_TYPES}}.
+    #' @param efficacy Probability that the person is successfully vaccinated
+    #'   (must be \code{0 <= efficacy <= 1}).
+    #' @param time_to_protect Delay before it takes effect (in days).
+    #' @param vaccine_protection_period The duration of the vaccine before it
+    #'   wanes.
+    initialize = function(
+      frac_0_9   = 0,
+      frac_10_19 = 0,
+      frac_20_29 = 0,
+      frac_30_39 = 0,
+      frac_40_49 = 0,
+      frac_50_59 = 0,
+      frac_60_69 = 0,
+      frac_70_79 = 0,
+      frac_80    = 0,
+      vaccine_type    = 0,
+      efficacy        = 1.0,
+      time_to_protect = 15,
+      vaccine_protection_period = 365 )
+    {
+      fractions <- c(frac_0_9, frac_10_19, frac_20_29, frac_30_39, frac_40_49,
+                     frac_50_59, frac_60_69, frac_70_79, frac_80)
+      n <- length(AgeGroupEnum)
+      if (n != length(fractions)) {
+        stop("length(AgeGroupEnum) doesn't match VaccineSchedule's age groups")
+      }
+
+      self$fraction_to_vaccinate     <- fractions
+      self$total_vaccinated          <- as.integer(rep(0,n))
+      self$vaccine_type              <- vaccine_type
+      self$efficacy                  <- efficacy
+      self$time_to_protect           <- time_to_protect
+      self$vaccine_protection_period <- vaccine_protection_period
+    }
+  )
+)
@@ -184,6 +184,42 @@ NETWORK_CONSTRUCTIONS <- c(
   'RANDOM'         = 4
 )
 
+#' Vaccine types
+#' @description
+#' List of vaccine types.
+#' Wrapper for \code{enum VACCINE_TYPES} (in \emph{constant.h}).
+#' \itemize{
+#'   \item{FULL} Wrapper for C enum \code{VACCINE_TYPE_FULL}
+#'   \item{SYMPTOM} Wrapper for C enum \code{VACCINE_TYPE_SYMPTOM}
+#' }
+VACCINE_TYPES <- c(
+  'FULL'    = 0,
+  'SYMPTOM' = 1
+)
+
+#' Vaccine status
+#' @description
+#' List of vaccines statuses.
+#' Wrapper for \code{enum VACCINE_STATUS} (in \emph{constant.h}).
+#' \itemize{
+#'   \item{NO_VACCINE} Wrapper for C enum
+#'     \code{NO_VACCINE}
+#'   \item{VACCINE_NO_PROTECTION} Wrapper for C enum
+#'     \code{VACCINE_NO_PROTECTION}
+#'   \item{VACCINE_PROTECTED_FULLY} Wrapper for C enum
+#'     \code{VACCINE_PROTECTED_FULLY}
+#'   \item{VACCINE_PROTECTED_SYMPTOMS} Wrapper for C enum
+#'     \code{VACCINE_PROTECTED_SYMPTOMS}
+#'   \item{VACCINE_WANED} Wrapper for C enum
+#'     \code{VACCINE_WANED}
+#' }
+VACCINE_STATUS <- c(
+  'NO_VACCINE'                 = 0,
+  'VACCINE_NO_PROTECTION'      = 1,
+  'VACCINE_PROTECTED_FULLY'    = 2,
+  'VACCINE_PROTECTED_SYMPTOMS' = 3,
+  'VACCINE_WANED'              = 4
+)
 
 
 get_base_param_from_enum <- function(param) {
 
@@ -132,3 +132,5 @@ If you're building on Windows, there are additional tools that are needed to bui
 - Download precompiled 32 and 64 bits libraries of GSL (installed in C:\gsl).
 - Install Rtools (in C:\Rtools).
 - Install make & SWIG via Cygwin64 (to run `make Rswig`).
+
+You can use the batch script *tests/test_R_INSTALL_win.bat* to build the source package.
@@ -0,0 +1,13 @@
+AC_INIT([OpenABMCovid19], 0.3)
+
+AC_PATH_PROG([GSL_CONFIG], [gsl-config])
+if test "${GSL_CONFIG}" != ""; then
+    GSL_CFLAGS=`${GSL_CONFIG} --cflags`
+    GSL_LIBS=`${GSL_CONFIG} --libs`
+    AC_SUBST(GSL_CFLAGS)
+    AC_SUBST(GSL_LIBS)
+    AC_OUTPUT(src/Makevars)
+else
+    AC_MSG_ERROR(['gsl-config not found, GNU GSL required'])
+fi
+
@@ -0,0 +1,18 @@
+#!/bin/sh
+# Initialize all generated files and run `R CMD build`.
+#
+
+# src/Makefile confuses Roxygen. Remove it temporarily.
+if [[ `git status --porcelain src/Makefile` ]]; then
+    echo 'src/Makefile has uncommitted changes. Aborting.' > /dev/stderr
+    exit 1
+else
+    rm src/Makefile
+fi
+
+autoconf
+make Rswig
+R -e 'devtools::document()'
+R CMD build .
+
+git checkout src/Makefile
@@ -0,0 +1,5 @@
+GSL_CFLAGS=@GSL_CFLAGS@
+GSL_LIBS=@GSL_LIBS@
+
+PKG_CFLAGS=$(GSL_CFLAGS) -DBUILD_RPKG
+PKG_LIBS=$(GSL_LIBS) -lm
@@ -1,3 +1,4 @@
-# Build flags for 'R CMD INSTALL'
-PKG_LIBS=   -LC:/gsl$(R_ARCH)/lib -l:libgsl.a -l:libgslcblas.a -lm
-PKG_CFLAGS= -IC:/gsl$(R_ARCH)/include -DBUILD_RPKG
+# To comply with CRAN's build-infrastructure, environment variable LIB_GSL
+# should point to a Windows GNU GSL install.
+PKG_CFLAGS= -I$(LIB_GSL)/include -DBUILD_RPKG
+PKG_LIBS=-L$(LIB_GSL)/lib -lgsl -lgslcblas -lm
@@ -468,7 +468,7 @@ void print_individual( model *model, long idx)
         if( idx >= model->params->n_total )
         {
             printf("idx higher than n_total; individual does not exist");
-            fflush(stdout);
+            fflush_stdout();
             return;
         }
 
@@ -500,5 +500,5 @@ void print_individual( model *model, long idx)
         }else{
             printf("indiv->index_trace_token: non-NULL\n");
         }
-	fflush(stdout);
+	fflush_stdout();
 }
@@ -85,7 +85,17 @@ void print_exit( char *s, ... )
 void print_now( char *s )
 {
     printf_w("%s\n", s );
+    fflush_stdout();
+}
+
+/*****************************************************************************************
+*  Name:		fflush_stdout
+******************************************************************************************/
+void fflush_stdout()
+{
+#ifndef BUILD_RPKG /* Referencing `stdout` can raise a NOTE with `R CMD check` */
     fflush(stdout);
+#endif
 }
 
 /*****************************************************************************************
 
@@ -39,6 +39,7 @@
 int printf_w( const char*, ... ) _AF_PRINTF(1,2);
 void print_now( char* );
 void print_exit( char*, ... ) _AF_PRINTF(1,2);
+void fflush_stdout();
 void gamma_draw_list( int*, int, double, double );
 void bernoulli_draw_list( int*, int, double );
 void geometric_max_draw_list( int*, int, double, int );
 
@@ -0,0 +1,13 @@
+
+@echo off
+
+REM Add R-3.6.3 and Rtools35
+set PATH=C:\Rtools\bin;C:\Program Files\R\R-3.6.3\bin\x64;%PATH%
+
+REM Set LIB_GSL (64-bit); gcc needs forward-slashes
+set LIB_GSL=C:/gsl/x64
+
+REM Build the source package
+mkdir OpenABMCovid19.tmp
+R CMD INSTALL --library=OpenABMCovid19.tmp --no-multiarch --build ^
+  OpenABMCovid19_*.tar.gz
@@ -314,4 +314,9 @@ test_that("Model::baseline_params", {
   results_expected$R_inst_05 <- c(-1 ,-1 ,-1)
   results_expected$R_inst_95 <- c(-1 ,-1 ,-1)
   expect_equal(sim$results, results_expected)
+
+  # test infections / vaccinations.
+  expect_true(m$seed_infect_by_idx(0))
+  expect_true(m$vaccinate_individual(2))
+  expect_false(m$vaccinate_schedule(VaccineSchedule$new()))
 })
@@ -0,0 +1,25 @@
+library(R6)
+
+test_that("VaccineSchedule initialization", {
+  v <- VaccineSchedule$new(
+      frac_0_9        = 0.0,
+      frac_10_19      = 0.1,
+      frac_20_29      = 0.2,
+      frac_30_39      = 0.3,
+      frac_40_49      = 0.4,
+      frac_50_59      = 0.5,
+      frac_60_69      = 0.6,
+      frac_70_79      = 0.7,
+      frac_80         = 0.8,
+      vaccine_type    = 0,
+      efficacy        = 1.0,
+      time_to_protect = 15,
+      vaccine_protection_period = 365 )
+
+  expect_equal(v$fraction_to_vaccinate, seq(0, 0.8, 0.1))
+  expect_equal(v$total_vaccinated, rep(0,9))
+  expect_equal(v$vaccine_type, 0)
+  expect_equal(v$efficacy, 1)
+  expect_equal(v$time_to_protect, 15)
+  expect_equal(v$vaccine_protection_period, 365)
+})
Original file line number	Diff line number	Diff line change
`@@ -468,7 +468,7 @@ void print_individual( model *model, long idx)`
`468`	`468`	`if( idx >= model->params->n_total )`
`469`	`469`	`{`
`470`	`470`	`printf("idx higher than n_total; individual does not exist");`
`471`		`- fflush(stdout);`
	`471`	`+ fflush_stdout();`
`472`	`472`	`return;`
`473`	`473`	`}`
`474`	`474`
`@@ -500,5 +500,5 @@ void print_individual( model *model, long idx)`
`500`	`500`	`}else{`
`501`	`501`	`printf("indiv->index_trace_token: non-NULL\n");`
`502`	`502`	`}`
`503`		`- fflush(stdout);`
	`503`	`+ fflush_stdout();`
`504`	`504`	`}`