diff --git a/4.1_JAGS_models/readme.txt b/4.1_JAGS_models/readme.txt index 8f54f4f2..7a47fdd0 100644 --- a/4.1_JAGS_models/readme.txt +++ b/4.1_JAGS_models/readme.txt @@ -6,7 +6,7 @@ Refer to Table 2 and Table S4 of the Lofton et al. 2021 manuscript for descripti AC = null model with autocorrelation term; corresponds to AC model in manuscript -base_DLM = null dynamic linear model; correspond to BaseDLM model in manuscript +base_DLM = null dynamic linear model; correspond to BaseLM model in manuscript GDD = GDD model in manuscript @@ -14,7 +14,7 @@ precip = Precip model in manuscript RW = random walk model with uninformed observation error prior; not presented in manuscript -RW_bias = random walk null model with bias term; correspond to BiasRW in manuscript +RW_bias = random walk null model with bias term; correspond to OffsetRW in manuscript RW_obs = random walk model with informed observation error prior; corresponds to RW model in manuscript diff --git a/5_Model_output/readme.txt b/5_Model_output/readme.txt index 9cf8ddd9..5d3a9255 100644 --- a/5_Model_output/readme.txt +++ b/5_Model_output/readme.txt @@ -17,7 +17,7 @@ There are between 80-120 output files for each Bayesian state-space model, depen The names of the .csv files for each model follow the naming convention below: [model name]_[sources of uncertainty included in hindcast]_[year of hindcast]_[week of year].csv For example, the following file: -AR_det.prediction_2015_1.csv contains the 1-4 week hindcasts generated for weeks 1-4 of the 2015 sampling season for the AR model, with no forms of uncertainty included +AC_det.prediction_2015_1.csv contains the 1-4 week hindcasts generated for weeks 1-4 of the 2015 sampling season for the AC model, with no forms of uncertainty included A second example: GDD_hindcast.IC.Pa.D.P._2016_12.csv contains the 1-4 week hindcasts generated for weeks 12-15 of the 2016 sampling season for the GDD model, and includes initial conditions, parameter, driver, and process uncertainty @@ -46,7 +46,7 @@ There are between 80-120 output files for each Bayesian state-space model, depen The names of the .csv files for each model follow the naming convention below: [model name]_[sources of uncertainty included in hindcast]_[year of hindcast]_[week of year].csv For example, the following file: -AR_det.prediction_2015_1.csv contains the 1-4 week hindcasts generated for weeks 1-4 of the 2015 sampling season for the AR model, with no forms of uncertainty included +AC_det.prediction_2015_1.csv contains the 1-4 week hindcasts generated for weeks 1-4 of the 2015 sampling season for the AC model, with no forms of uncertainty included A second example: GDD_hindcast.IC.Pa.D.P._2016_12.csv contains the 1-4 week hindcasts generated for weeks 12-15 of the 2016 sampling season for the GDD model, and includes initial conditions, parameter, driver, and process uncertainty diff --git a/9_Data_publication/9A_rename_hindcast_files.R b/9_Data_publication/9A_rename_hindcast_files.R index 09425d6b..a703980d 100644 --- a/9_Data_publication/9A_rename_hindcast_files.R +++ b/9_Data_publication/9A_rename_hindcast_files.R @@ -3,6 +3,13 @@ #Date: 25MAY20 library(tidyverse) +#get sampling dates +obs <- read_csv("./00_Data_files/Covariate_analysis_data/HC_Gechinulata_long.csv") %>% + filter(year %in% c(2015:2016)) +dates <- as.character(obs$date) +new_wks <- c("2015-05-14",dates[1:19],"2016-05-19",dates[21:39]) + +#reset working directory setwd("./9_Data_publication/") startingDir <- "./5_Model_output/5.2_Hindcasting/" @@ -10,15 +17,9 @@ startingDir <- "./5_Model_output/5.2_Hindcasting/" #create wks vector wks <- c(paste0("2015_",1:20),paste0("2016_",1:20)) -#get sampling dates -obs <- read_csv("./00_Data_files/Covariate_analysis_data/HC_Gechinulata_long.csv") %>% - filter(year %in% c(2015:2016)) -dates <- as.character(obs$date) -new_wks <- c("2015-05-14",dates[1:19],"2016-05-19",dates[21:39]) - #create vector of model names model_names <- c("RW_obs","RW_bias","AC","base_DLM","wtrtemp_min","wtrtemp_min_lag","wtrtemp_MA7","GDD","wnd_dir_2day_lag","schmidt_max_lag","schmidt_and_wind","temp_and_wind","wind_and_GDD") -new_model_names <- c("RW","BiasRW","AC","BaseDLM","MinWaterTemp","MinWaterTempLag","WaterTempMA","GDD","WindDir","SchmidtLag","SchmidtAndWind","TempAndWind","WindAndGDD") +new_model_names <- c("RW","OffsetRW","AC","BaseLM","MinWaterTemp","MinWaterTempLag","WaterTempMA","GDD","WindDir","SchmidtLag","SchmidtAndWind","TempAndWind","WindAndGDD") for(n in 13:length(model_names)){