diff --git a/src/model_fitting/abundance_model.R b/src/model_fitting/abundance_model.R index 9ccafdc7b3e7e50abfb3b160f0995b75300fa42b..8a19785ab7552228815f4ad636f36375021fb480 100644 --- a/src/model_fitting/abundance_model.R +++ b/src/model_fitting/abundance_model.R @@ -338,8 +338,8 @@ if (!is.na(exclude_rand)){ ids_to_exclude <- sample(predictors_obs$id, size = nrow(predictors_obs)/100 * exclude_rand_perc, replace = FALSE) - predictors_excluded <- predictors_obs[predictors_obs$bin_id %in% ids_to_exclude, ] - predictors_obs <- predictors_obs[!predictors_obs$bin_id %in% ids_to_exclude, ] + predictors_excluded <- predictors_obs[predictors_obs$id %in% ids_to_exclude, ] + predictors_obs <- predictors_obs[!predictors_obs$id %in% ids_to_exclude, ] nr_excluded <- nrow(predictors_excluded) } @@ -388,8 +388,6 @@ m_terms <- c("1", "I(rain_dry^2)") -save.image(file.path(outdir, paste0("image_before_model_", exclude_rand, ".RData"))) - # save model_terms here model_terms <- names(glm.nb(as.formula(paste("nr_nests~", paste(m_terms, collapse = "+"), @@ -516,7 +514,7 @@ results_res <- foreach(i = 1:nrow(all_model_terms), predictors_excluded_pred <- predictors_excluded predictors_excluded_pred$offset_term <- 0 prediction_transect_excluded <- predict.glm(res, - newdata = predictors_excluded, + newdata = predictors_excluded_pred, type = "response") cross_lm = lm(log(predictors_excluded$ou_dens+ 1) ~ log(prediction_transect_excluded + 1)) @@ -573,8 +571,8 @@ write.csv(summary_mean_coefficients, Sys.Date(), ".csv"))) -save.image(file.path(outdir, paste0("abundance_model_fitting_", - name_suffix, - Sys.Date(), ".RData"))) +#save.image(file.path(outdir, paste0("abundance_model_fitting_", +# name_suffix, +# Sys.Date(), ".RData"))) print(paste("Finished model_fitting script, at", Sys.time())) diff --git a/src/pipeline/submit_pipeline_model.sh b/src/pipeline/submit_pipeline_model.sh index a861045e9c28d2e4a5eefb6ff22e7301f5412b31..b21e587566e55c8ccb410b6675bbf7a4ae66e9e6 100644 --- a/src/pipeline/submit_pipeline_model.sh +++ b/src/pipeline/submit_pipeline_model.sh @@ -6,9 +6,9 @@ # here somehow write the prefix depending on what we are testing -JOB_NAME_PREFIX=ppln_ae75m_50_ac +JOB_NAME_PREFIX=ppln_ae150m_50 -INPUT_PATH='/work/voigtma/ppln_ae75m_50_fixing-2017-02-28T18-00-52' +INPUT_PATH='/data/idiv_kuehl/maria_data/pipeline' NAME=$JOB_NAME_PREFIX-$(date +%FT%H-%M-%S) # FIX THIS @@ -27,7 +27,7 @@ QSUB="qsub -terse -v OUTPUT_PATH=$OUTPUT_PATH -o /work/$USER/$NAME.log -j y" -N ${JOB_NAME_PREFIX}_fitting \ $HOME/orangutan_density_distribution/src/model_fitting/submit_abundance_model_ac_term.sh \ -i $INPUT_PATH \ - --ESW-aerial 0.075 \ + --ESW-aerial 0.15 \ --include-aerial \ --stability) @@ -38,5 +38,6 @@ QSUB="qsub -terse -v OUTPUT_PATH=$OUTPUT_PATH -o /work/$USER/$NAME.log -j y" -hold_jid $MODEL_JOB_ID_FITTING \ -t 1999:2015 \ $HOME/orangutan_density_distribution/src/prediction/submit_abundance_pred.sh \ - -i $INPUT_PATH ) + -i $INPUT_PATH \ + --focal-change-predictor NA)