From dac3c33692607d71bd3d13ba7d07055f6ced2600 Mon Sep 17 00:00:00 2001
From: brycefrank <bfrank70@gmail.com>
Date: Mon, 20 Nov 2023 20:49:31 -0800
Subject: [PATCH] feat: adding rolim_2019b, closes #37

---
 parameters/dsob_rolim_2019b.csv               | 36 +++++++++++++
 .../p_t/{rolim_2019.R => rolim_2019a.R}       | 15 +++---
 publications/p_t/rolim_2019b.R                | 54 +++++++++++++++++++
 3 files changed, 99 insertions(+), 6 deletions(-)
 create mode 100644 parameters/dsob_rolim_2019b.csv
 rename publications/p_t/{rolim_2019.R => rolim_2019a.R} (80%)
 create mode 100644 publications/p_t/rolim_2019b.R

diff --git a/parameters/dsob_rolim_2019b.csv b/parameters/dsob_rolim_2019b.csv
new file mode 100644
index 0000000..04fc37b
--- /dev/null
+++ b/parameters/dsob_rolim_2019b.csv
@@ -0,0 +1,36 @@
+family,genus,species,pred_fn,A,c,k
+Fabaceae,Amburana,cearensis,H,26.11,344.74,2.32
+Aponyaceae,Aspidosperma,pyricollum,W,53.88,0.7192,0.0348
+Anacardiaceae,Astronium,concinnum,K,23.66,0.8775,3.99
+Anacardiaceae,Astronium,graveolens,G,39.24,1.81,0.03925
+Fabaceae,Barnebydendron,riedelii,K,47.11,0.5434,4.2
+Fabaceae,Bowdichia,virgilioides,H,83.54,42.02,0.8551
+Lecythidaceae,Cariniana,legalis,K,46.4,0.9855,11.38
+Fabaceae,Centrolobium,tomentosum,K,46.43,0.7437,8.3
+Moraceae,Clarisia,racemosa,G,36.23,4.92,0.1038
+Fabaceae,Copaifera,langsdorffii,H,76.46,190.22,1.2478
+Boraginaceae,Cordia,trichotoma,G,41.27,2.15,0.048
+Fabaceae,Dalbergia,nigra,K,61.47,0.4838,3.91
+Fabaceae,Goniorrhachis,marginata,K,49.36,0.5634,5.15
+Bignoniaceae,Handroanthus,serratifolius,K,49.86,0.5405,4.66
+Fabaceae,Hymenaea,courbaril,K,47.67,0.5847,4.08
+Euphorbiaceae,Joannesia,princeps,K,44.59,0.3574,2.32
+Lecythidaceae,Lecythis,pisonis,K,60.82,0.4848,4.774
+Fabaceae,Libidibia,ferrea,K,30.9,0.7867,4.97
+Sapotaceae,Manilkara,longifolia,K,25.25,1.0455,9.59
+Fabaceae,Moldenhawera,papillanthera,H,73.09,104.6,1.059
+Anacardiaceae,Myracrodruon,urundeuva,H,60.42,20.075,0.9038
+Malvaceae,Pachira,endecaphylla,W,29.124,1.3736,0.0413
+Bignoniaceae,Paratecoma,peroba,K,71.15,0.3558,3.8343
+Fabaceae,Parkia,pendula,K,70.98,0.5052,4.61
+Fabaceae,Paubrasilia,echinata,K,40.69,0.6845,6.03
+Fabaceae,Pterocarpus,rohrii,K,81.48,0.4487,4.48
+Malvaceae,Pterygota,brasiliensis,H,89.77,44.28,0.9057
+Fabaceae,Senegalia,polyphylla,K,77.54,0.344,3.935
+Simaroubaceae,Simarouba,amara,G,43.98,2.34,0.0587
+Anacardiaceae,Spondias,venulosa,K,82.59,0.4292,2.97
+Fabaceae,Tachigali,vulgaris,K,90.41,0.5003,5.12
+Combretaceae,Terminalia,mameluco,H,31.74,168.87,1.617
+Fabaceae,Vatairea,heteroptera,K,29.25,0.8561,5.62
+Fabaceae,Vataireopsis,araroba,K,48.59,0.4858,3.54
+Bignoniaceae,Zeyheria,tuberculosa,H,37.62,19.9,1.13823
diff --git a/publications/p_t/rolim_2019.R b/publications/p_t/rolim_2019a.R
similarity index 80%
rename from publications/p_t/rolim_2019.R
rename to publications/p_t/rolim_2019a.R
index dc2f6f2..f3fcbe0 100644
--- a/publications/p_t/rolim_2019.R
+++ b/publications/p_t/rolim_2019a.R
@@ -1,9 +1,12 @@
-rolim_2019 <- Publication(
+rolim_2019a <- Publication(
   citation = RefManageR::BibEntry(
-    key = "rolim_2019",
-    bibtype = "book",
-    title = "Silviculture and Wood Properties of the Native Species of the Atlantic Forest of Brazil",
-    author = "Rolim, Samir and Piotto, Daniel",
+    key = "rolim_2019a",
+    bibtype = "incollection",
+    title = "Biometric Models for Mixed-species Plantation in the North of Espirito Santo, Brazil",
+    author = "Rolim, Samir and Orellano, Enrique and Piotto, Daniel and de Souza Vismara, Edgar",
+    booktitle = "Silviculture and Wood Properties of Native Species of the Atlantic Forest of Brazil",
+    editor = "Rolim, Samir and Piotto, Daniel",
+    pages = "21--29",
     year = 2019
   ),
   descriptors = list(
@@ -91,7 +94,7 @@ table_4_model_5 <- FixedEffectsModel(
   predict_fn = model_5_func
 )
 
-rolim_2019 <- rolim_2019 %>%
+rolim_2019a <- rolim_2019a %>%
   add_model(table_2_naslund_hst) %>%
   add_model(table_2_logistic_hsm) %>%
   add_model(table_3_schumacher_hall_vs) %>%
diff --git a/publications/p_t/rolim_2019b.R b/publications/p_t/rolim_2019b.R
new file mode 100644
index 0000000..5c264ba
--- /dev/null
+++ b/publications/p_t/rolim_2019b.R
@@ -0,0 +1,54 @@
+rolim_2019b <- Publication(
+  citation = RefManageR::BibEntry(
+    key = "rolim_2019b",
+    bibtype = "incollection",
+    title = "Diameter Growth Models for 35 Atlantic Forest Tree Species in Silvicultural Trials in the North of Espirito Santo, Brazil",
+    author = "Rolim, Samir and Piotto, Daniel and Orellana, Enrique",
+    booktitle = "Silviculture and Wood Properties of Native Species of the Atlantic Forest of Brazil",
+    editor = "Rolim, Samir and Piotto, Daniel",
+    pages = "31--44",
+    year = 2019
+  ),
+  descriptors = list(
+    country = "BR",
+    region = "BR-ES"
+  )
+)
+
+dia_gro_funcs <- list(
+  H = function(att) {
+    A * (1 + c * exp(-k * log(att)))^-1
+  },
+  W = function(att) {
+    A * (1 - exp(-k * att^c))
+  },
+  K = function(att) {
+    A * exp(-k * att^(-c))
+  },
+  G = function(att) {
+    A * exp(-c * exp(-k * att))
+  }
+)
+
+params <- load_parameter_frame("dsob_rolim_2019b") %>%
+  aggregate_taxa()
+
+pred_fns <- unique(params$pred_fn)
+
+for(pred_fn_name in pred_fns) {
+  func <- dia_gro_funcs[[pred_fn]]
+
+  set <- FixedEffectsSet(
+    response = list(
+      dsob = units::as_units("cm")
+    ),
+    covariates = list(
+      att = units::as_units("years")
+    ),
+    predict_fn = func,
+    parameter_names = c("A", "k", "c"),
+    model_specifications = params %>% dplyr::filter(pred_fn == pred_fn_name)
+  )
+
+  rolim_2019b <- rolim_2019b %>% add_set(set)
+}
\ No newline at end of file