From 85505257c28e9535c65597ec626c9c00dfe73e1a Mon Sep 17 00:00:00 2001
From: Patricia Kaye Dumandan <46734193+patdumandan@users.noreply.github.com>
Date: Thu, 19 Oct 2023 14:11:17 -0400
Subject: [PATCH 1/3] Update README.md

---
 README.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 0d6c00e..64e47c9 100644
--- a/README.md
+++ b/README.md
@@ -1,13 +1,13 @@
 # Portal-Forecast-Swap
-repo for Portal forecasting group project assessing the effects of biotic conditions on forecasts
+repo for the manuscript:  Transferability of ecological forecasting models to novel biotic conditions in a long-term experimental study
 
 ## **Files:**
 
-**LTcompare_functions.R**: functions used for analyses  
+**model-transfer-functions.R**: source code for functions used in the analyses 
 
-**PB_LTcomparison.R and PP_LTcomparison.R**: species-specific analyses scripts  
+**PB-model-transfer.R and PP-model-transfer.R**: species-specific analyses scripts  
 
-**results_viz.R and results-viz-PB.R**: species-specific data and results visualization scripts  
+**figures.R**: visualization scripts   
 
 **supplementary-stuff.R**: additional analyses scripts  
 

From 93cae6423ecdfea569e912c2b132234a56f080ed Mon Sep 17 00:00:00 2001
From: Patricia Kaye Dumandan <46734193+patdumandan@users.noreply.github.com>
Date: Fri, 20 Oct 2023 12:02:00 -0400
Subject: [PATCH 2/3] remove unused scripts

---
 multiple_comparisons.R | 82 ------------------------------------------
 1 file changed, 82 deletions(-)
 delete mode 100644 multiple_comparisons.R

diff --git a/multiple_comparisons.R b/multiple_comparisons.R
deleted file mode 100644
index 186129e..0000000
--- a/multiple_comparisons.R
+++ /dev/null
@@ -1,82 +0,0 @@
-#MULTIPLE COMPARISONS TEST####
-
-#get p-value####
-
-#calculate pvalue following: https://www.bmj.com/content/343/bmj.d2304 
-
-get_pvalue=function(model) {
-
-  coef_est=tscount::se(model)$est
-  coef_ci_u=tscount::se(model)$ci[,"upper"]
-  coef_ci_l=tscount::se(model)$ci[,"lower"]
-  
-  coef_se= (coef_ci_u - coef_ci_l)/ (2*1.96)
-  
-  coef_z=coef_est/coef_se
-  
-  coef_P = list(round(exp(-0.717 * coef_z - 0.416* ((coef_z)^2)), digits=4))
-  
-}
-
-#add column of pvalues
-
-PBcontrol_dat$pvalue=map(PBcontrol_dat$model, get_pvalue)
-PBexclosure_dat$pvalue=map(PBexclosure_dat$model, get_pvalue)
-
-#select pvalues for each parameter
-
-pbcont_int_pval=PBcontrol_dat$pvalue%>%map(unlist)%>%map_dbl(1)
-pbcont_b1_pval=PBcontrol_dat$pvalue%>%map(unlist)%>%map_dbl(2)
-pbcont_b12_pval=PBcontrol_dat$pvalue%>%map(unlist)%>%map_dbl(3)
-pbcont_temp_pval=PBcontrol_dat$pvalue%>%map(unlist)%>%map_dbl(4)
-pbcont_wprec_pval=PBcontrol_dat$pvalue%>%map(unlist)%>%map_dbl(5)
-pbcont_cprec_pval=PBcontrol_dat$pvalue%>%map(unlist)%>%map_dbl(6)
-
-pbexcl_int_pval=PBexclosure_dat$pvalue%>%map(unlist)%>%map_dbl(1)
-pbexcl_b1_pval=PBexclosure_dat$pvalue%>%map(unlist)%>%map_dbl(2)
-pbexcl_b12_pval=PBexclosure_dat$pvalue%>%map(unlist)%>%map_dbl(3)
-pbexcl_temp_pval=PBexclosure_dat$pvalue%>%map(unlist)%>%map_dbl(4)
-pbexcl_wprec_pval=PBexclosure_dat$pvalue%>%map(unlist)%>%map_dbl(5)
-pbexcl_cprec_pval=PBexclosure_dat$pvalue%>%map(unlist)%>%map_dbl(6)
-
-#combine dataframes
-
-pbint_pval=cbind(pbcont_int_pval, pbexcl_int_pval)%>%as.data.frame%>%
-  rename("control"="pbcont_int_pval", "removal"="pbexcl_int_pval")%>%
-  pivot_longer(cols=c(1:2),names_to="treatment", values_to = "raw_pvalue")
-
-pbb1_pval=cbind(pbcont_b1_pval, pbexcl_b1_pval)%>%as.data.frame%>%
-  rename("control"="pbcont_b1_pval", "removal"="pbexcl_b1_pval")%>%
-  pivot_longer(cols=c(1:2),names_to="treatment", values_to = "raw_pvalue")
-
-pbb12_pval=cbind(pbcont_b12_pval, pbexcl_b12_pval)%>%as.data.frame%>%
-  rename("control"="pbcont_b12_pval", "removal"="pbexcl_b12_pval")%>%
-  pivot_longer(cols=c(1:2),names_to="treatment", values_to = "raw_pvalue")
-
-pbtemp_pval=cbind(pbcont_temp_pval, pbexcl_temp_pval)%>%as.data.frame%>%
-  rename("control"="pbcont_temp_pval", "removal"="pbexcl_temp_pval")%>%
-  pivot_longer(cols=c(1:2),names_to="treatment", values_to = "raw_pvalue")
-
-pbwarmprec_pval=cbind(pbcont_wprec_pval, pbexcl_wprec_pval)%>%as.data.frame%>%
-  rename("control"="pbcont_wprec_pval", "removal"="pbexcl_wprec_pval")%>%
-  pivot_longer(cols=c(1:2),names_to="treatment", values_to = "raw_pvalue")
-
-pbcoolprec_pval=cbind(pbcont_cprec_pval, pbexcl_cprec_pval)%>%as.data.frame%>%
-  rename("control"="pbcont_cprec_pval", "removal"="pbexcl_cprec_pval")%>%
-  pivot_longer(cols=c(1:2),names_to="treatment", values_to = "raw_pvalue")
-
-#pairwise t-test####
-pairwise.t.test(pbint_pval$raw_pvalue, pbint_pval$treatment, p.adjust.method="fdr") # <0.05
-pairwise.t.test(pbb1_pval$raw_pvalue, pbb1_pval$treatment, p.adjust.method="fdr") #0.32
-pairwise.t.test(pbb12_pval$raw_pvalue, pbb12_pval$treatment, p.adjust.method="fdr") #0.009
-pairwise.t.test(pbtemp_pval$raw_pvalue, pbtemp_pval$treatment, p.adjust.method="fdr") #0.004
-pairwise.t.test(pbwarmprec_pval$raw_pvalue, pbwarmprec_pval$treatment, p.adjust.method="fdr") #0.32
-pairwise.t.test(pbcoolprec_pval$raw_pvalue, pbcoolprec_pval$treatment, p.adjust.method="fdr")  #<0.05
-
-#add adjusted p-values (FDR)####
-pbint_pval$FDR=p.adjust(pbint_pval$raw_pvalue, method="fdr")
-pbb1_pval$FDR=p.adjust(pbb1_pval$raw_pvalue, method="fdr")
-pbb12_pval$FDR=p.adjust(pbb12_pval$raw_pvalue, method="fdr")
-pbtemp_pval$FDR=p.adjust(pbtemp_pval$raw_pvalue, method="fdr")
-pbwarmprec_pval$FDR=p.adjust(pbwarmprec_pval$raw_pvalue, method="fdr")
-pbcoolprec_pval$FDR=p.adjust(pbcoolprec_pval$raw_pvalue, method="fdr")

From 13d1ec7f3dd555d302ae6b26aa6c8ace5f1b39a4 Mon Sep 17 00:00:00 2001
From: Patricia Kaye Dumandan <46734193+patdumandan@users.noreply.github.com>
Date: Sat, 28 Oct 2023 09:36:28 -0400
Subject: [PATCH 3/3] Update README.md

---
 README.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 64e47c9..3e77807 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,7 @@
 # Portal-Forecast-Swap
-repo for the manuscript:  Transferability of ecological forecasting models to novel biotic conditions in a long-term experimental study
+[![DOI](https://zenodo.org/badge/596188870.svg)](https://zenodo.org/doi/10.5281/zenodo.10050034)
+
+repo for the analyses scripts used in the manuscript titled: Transferability of ecological forecasting models to novel biotic conditions in a long-term experimental study
 
 ## **Files:**