rename config.writer package to flepiconfig

HopkinsIDD · Mar 8, 2024 · 45e5d18 · 45e5d18
1 parent d9d8ce0
commit 45e5d18
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Showing 19 changed files with 20 additions and 20 deletions.
diff --git a/build/renv/renv.lock b/build/renv/renv.lock
@@ -421,12 +421,12 @@
       "Hash": "2ba81b120c1655ab696c935ef33ea716",
       "Requirements": []
     },
-    "config.writer": {
-      "Package": "config.writer",
+    "flepiconfig": {
+      "Package": "flepiconfig",
       "Version": "1.0.0",
       "Source": "Local",
       "RemoteType": "local",
-      "RemoteUrl": "~/pkgs/config.writer/",
+      "RemoteUrl": "~/pkgs/flepiconfig/",
       "Hash": "6926b00e7a264696bc5b5ec3147bdd6e",
       "Requirements": [
         "MMWRweek",

diff --git a/flepimop/R_packages/config.writer/tests/testthat.R b/flepimop/R_packages/config.writer/tests/testthat.R
diff --git a/flepimop/R_packages/flepicommon/R/DataUtils.R b/flepimop/R_packages/flepicommon/R/DataUtils.R
@@ -13,7 +13,7 @@
 ##'
 ##' @return a data frame with columns for state USPS, county subpop and population
 ##' @examples
-##' geodata <- load_geodata_file(filename = system.file("extdata", "geodata_territories_2019_statelevel.csv", package = "config.writer"))
+##' geodata <- load_geodata_file(filename = system.file("extdata", "geodata_territories_2019_statelevel.csv", package = "flepiconfig"))
 ##' geodata
 ##'
 ##' @export

diff --git a/...imop/R_packages/config.writer/DESCRIPTION → flepimop/R_packages/flepiconfig/DESCRIPTION b/...imop/R_packages/config.writer/DESCRIPTION → flepimop/R_packages/flepiconfig/DESCRIPTION
@@ -1,4 +1,4 @@
-Package: config.writer
+Package: flepiconfig
 Title: Config creator for flepiMoP 
 Version: 3.0.0
 Imports:

diff --git a/flepimop/R_packages/config.writer/NAMESPACE → flepimop/R_packages/flepiconfig/NAMESPACE b/flepimop/R_packages/config.writer/NAMESPACE → flepimop/R_packages/flepiconfig/NAMESPACE
diff --git a/...ages/config.writer/R/create_config_data.R → ...ckages/flepiconfig/R/create_config_data.R b/...ages/config.writer/R/create_config_data.R → ...ckages/flepiconfig/R/create_config_data.R
@@ -681,7 +681,7 @@ set_variant_params <- function(b117_only = FALSE, variant_path, variant_path_2 =
     } else {
         # we can get rid of this B117 part eventually
         if (b117_only) {
-            variant_data <- config.writer::generate_variant_b117(variant_path = variant_path,
+            variant_data <- flepiconfig::generate_variant_b117(variant_path = variant_path,
                                                                  sim_start_date = sim_start_date, sim_end_date = sim_end_date,
                                                                  variant_lb = variant_lb, variant_effect = variant_effect,
                                                                  month_shift = month_shift) %>% dplyr::mutate(subpop = "all",

diff --git a/...ckages/config.writer/R/process_npi_list.R → ...packages/flepiconfig/R/process_npi_list.R b/...ckages/config.writer/R/process_npi_list.R → ...packages/flepiconfig/R/process_npi_list.R
@@ -109,8 +109,8 @@ npi_recode_scenario_mult <- function(data){
 #' @export
 #'
 #' @examples
-#' geodata <- load_geodata_file(filename = system.file("extdata", "geodata_territories_2019_statelevel.csv", package = "config.writer"))
-#' npi_dat <- process_npi_shub(intervention_path = system.file("extdata", "intervention_data.csv", package = "config.writer"), geodata)
+#' geodata <- load_geodata_file(filename = system.file("extdata", "geodata_territories_2019_statelevel.csv", package = "flepiconfig"))
+#' npi_dat <- process_npi_shub(intervention_path = system.file("extdata", "intervention_data.csv", package = "flepiconfig"), geodata)
 #'
 #' npi_dat
 process_npi_usa <- function (intervention_path,
@@ -215,7 +215,7 @@ process_npi_ca <- function(intervention_path,
 #' @return
 #' @examples
 #'
-#' variant <- generate_variant_b117(variant_path = system.file("extdata", "strain_replace_mmwr.csv", package = "config.writer"))
+#' variant <- generate_variant_b117(variant_path = system.file("extdata", "strain_replace_mmwr.csv", package = "flepiconfig"))
 #' variant
 #'
 #' @export
@@ -301,8 +301,8 @@ generate_variant_b117 <- function(variant_path,
 #'
 #' @examples
 #'
-#' variant <- generate_multiple_variants(variant_path_1 = system.file("extdata", "B117-fits.csv", package = "config.writer"),
-#'                                       variant_path_2 = system.file("extdata", "B617-fits.csv", package = "config.writer"))
+#' variant <- generate_multiple_variants(variant_path_1 = system.file("extdata", "B117-fits.csv", package = "flepiconfig"),
+#'                                       variant_path_2 = system.file("extdata", "B617-fits.csv", package = "flepiconfig"))
 #' variant
 #'
 generate_multiple_variants <- function(variant_path_1,
@@ -399,8 +399,8 @@ generate_multiple_variants <- function(variant_path_1,
 #'
 #' @examples
 #'
-#' variant <- generate_multiple_variants(variant_path_1 = system.file("extdata", "B117-fits.csv", package = "config.writer"),
-#'                                       variant_path_2 = system.file("extdata", "B617-fits.csv", package = "config.writer"))
+#' variant <- generate_multiple_variants(variant_path_1 = system.file("extdata", "B117-fits.csv", package = "flepiconfig"),
+#'                                       variant_path_2 = system.file("extdata", "B617-fits.csv", package = "flepiconfig"))
 #' variant
 #'
 generate_multiple_variants_state <- function(variant_path_1,
@@ -520,8 +520,8 @@ generate_multiple_variants_state <- function(variant_path_1,
 #'
 #' @examples
 #'
-#' variant <- generate_multiple_variants(variant_path_1 = system.file("extdata", "B117-fits.csv", package = "config.writer"),
-#'                                       variant_path_2 = system.file("extdata", "B617-fits.csv", package = "config.writer"))
+#' variant <- generate_multiple_variants(variant_path_1 = system.file("extdata", "B117-fits.csv", package = "flepiconfig"),
+#'                                       variant_path_2 = system.file("extdata", "B617-fits.csv", package = "flepiconfig"))
 #' variant
 #'
 generate_compartment_variant <- function(variant_path = "../COVID19_USA/data/variant/variant_props_long.csv",

diff --git a/...p/R_packages/config.writer/R/yaml_utils.R → ...mop/R_packages/flepiconfig/R/yaml_utils.R b/...p/R_packages/config.writer/R/yaml_utils.R → ...mop/R_packages/flepiconfig/R/yaml_utils.R
@@ -1081,7 +1081,7 @@ print_seir <- function(integration_method = "rk4",
                        ifelse(use_descriptions & !(is.na(seir_dat$description[i]) |
                                                        is.null(seir_dat$description[i]) | seir_dat$description[i] == ""),
                               paste0("# ", seir_dat$transition[i], " - ", seir_dat$description[i], "\n"), ""),
-                       config.writer::seir_chunk(resume_modifier = resume_modifier,
+                       flepiconfig::seir_chunk(resume_modifier = resume_modifier,
                                                  SEIR_source = strsplit(seir_dat$SEIR_source[i], ",")[[1]],
                                                  SEIR_dest = strsplit(seir_dat$SEIR_dest[i], ",")[[1]],
                                                  vaccine_compartments_source = strsplit(seir_dat$vaccine_compartments_source[i], ",")[[1]],

diff --git a/flepimop/R_packages/flepiconfig/tests/testthat.R b/flepimop/R_packages/flepiconfig/tests/testthat.R
@@ -0,0 +1,4 @@
+library(testthat)
+library(flepiconfig)
+
+# test_check("flepiconfig")
diff --git a/.../config.writer/tests/testthat/geodata.csv → ...es/flepiconfig/tests/testthat/geodata.csv b/.../config.writer/tests/testthat/geodata.csv → ...es/flepiconfig/tests/testthat/geodata.csv
diff --git a/...ig.writer/tests/testthat/intervention.csv → ...epiconfig/tests/testthat/intervention.csv b/...ig.writer/tests/testthat/intervention.csv → ...epiconfig/tests/testthat/intervention.csv
diff --git a/...fig.writer/tests/testthat/outcome_adj.csv → ...lepiconfig/tests/testthat/outcome_adj.csv b/...fig.writer/tests/testthat/outcome_adj.csv → ...lepiconfig/tests/testthat/outcome_adj.csv
diff --git a/.../testthat/processed_intervention_data.csv → .../testthat/processed_intervention_data.csv b/.../testthat/processed_intervention_data.csv → .../testthat/processed_intervention_data.csv
diff --git a/...g.writer/tests/testthat/sample_config.yml → ...piconfig/tests/testthat/sample_config.yml b/...g.writer/tests/testthat/sample_config.yml → ...piconfig/tests/testthat/sample_config.yml
diff --git a/...nfig.writer/tests/testthat/test-gen_npi.R → ...flepiconfig/tests/testthat/test-gen_npi.R b/...nfig.writer/tests/testthat/test-gen_npi.R → ...flepiconfig/tests/testthat/test-gen_npi.R
diff --git a/...writer/tests/testthat/test-print_config.R → ...config/tests/testthat/test-print_config.R b/...writer/tests/testthat/test-print_config.R → ...config/tests/testthat/test-print_config.R
diff --git a/...nfig.writer/tests/testthat/vacc_rates.csv → ...flepiconfig/tests/testthat/vacc_rates.csv b/...nfig.writer/tests/testthat/vacc_rates.csv → ...flepiconfig/tests/testthat/vacc_rates.csv
diff --git a/...onfig.writer/tests/testthat/var1_fits.csv → .../flepiconfig/tests/testthat/var1_fits.csv b/...onfig.writer/tests/testthat/var1_fits.csv → .../flepiconfig/tests/testthat/var1_fits.csv
diff --git a/...onfig.writer/tests/testthat/var2_fits.csv → .../flepiconfig/tests/testthat/var2_fits.csv b/...onfig.writer/tests/testthat/var2_fits.csv → .../flepiconfig/tests/testthat/var2_fits.csv